[PR PATCH] [BETA] sagemath: update to 10.5.beta2

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* [PR PATCH] [BETA] sagemath: update to 10.5.beta2
@ 2024-08-18 17:54 tornaria
  2024-08-20 20:57 ` [PR PATCH] [Updated] " tornaria
                   ` (11 more replies)
  0 siblings, 12 replies; 13+ messages in thread
From: tornaria @ 2024-08-18 17:54 UTC (permalink / raw)
  To: ml

[-- Attachment #1: Type: text/plain, Size: 1460 bytes --]

There is a new pull request by tornaria against master on the void-packages repository

https://github.com/tornaria/void-packages sagemath
https://github.com/void-linux/void-packages/pull/51902

[BETA] sagemath: update to 10.5.beta2
<!-- Uncomment relevant sections and delete options which are not applicable -->

 - python3-Cython: alternative fix for 6122
 - python3-gmpy2: update to 2.2.1.
 - python3-cypari2: update to 2.2.0.
 - python3-sympy: update to 1.13.2.
 - sagemath: enable all cython warnings

#### Testing the changes
- I tested the changes in this PR: **YES**

@dkwo

<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->

<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
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and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
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<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
  - aarch64-musl
  - armv7l
  - armv6l-musl
-->


A patch file from https://github.com/void-linux/void-packages/pull/51902.patch is attached

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-sagemath-51902.patch --]
[-- Type: text/x-diff, Size: 47392 bytes --]

From e958571efef0400689590747a0c00b3b2d8fe4d6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 11 Aug 2024 22:53:42 -0300
Subject: [PATCH 1/6] python3-Cython: alternative fix for 6122

---
 srcpkgs/python3-Cython/patches/fix-regression.patch | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/srcpkgs/python3-Cython/patches/fix-regression.patch b/srcpkgs/python3-Cython/patches/fix-regression.patch
index f2e761608e373b..f5957cfa59c2f5 100644
--- a/srcpkgs/python3-Cython/patches/fix-regression.patch
+++ b/srcpkgs/python3-Cython/patches/fix-regression.patch
@@ -15,3 +15,11 @@ serious regression, e.g. sagemath FTBS with cython 3.0.11
              warning(self.pos,
                      "Implicit noexcept declaration is deprecated."
                      " Function declaration should contain 'noexcept' keyword.",
+@@ -3128,6 +3126,7 @@ class DefNode(FuncDefNode):
+             if scope is None:
+                 scope = cfunc.scope
+             cfunc_type = cfunc.type
++            has_explicit_exc_clause=True
+             if len(self.args) != len(cfunc_type.args) or cfunc_type.has_varargs:
+                 error(self.pos, "wrong number of arguments")
+                 error(cfunc.pos, "previous declaration here")

From d38b90940269d0bb79a258f1e33f93a9963a7136 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sat, 17 Aug 2024 19:56:10 -0300
Subject: [PATCH 2/6] python3-gmpy2: update to 2.2.1.

---
 srcpkgs/python3-gmpy2/template | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/srcpkgs/python3-gmpy2/template b/srcpkgs/python3-gmpy2/template
index 307eed419804a2..44de709067551d 100644
--- a/srcpkgs/python3-gmpy2/template
+++ b/srcpkgs/python3-gmpy2/template
@@ -1,7 +1,6 @@
 # Template file for 'python3-gmpy2'
 pkgname=python3-gmpy2
-# need $version > 2.2.0a1 which we shipped before by necessity
-version=2.2.0r
+version=2.2.1
 revision=1
 build_style=python3-pep517
 hostmakedepends="python3-setuptools python3-wheel"
@@ -14,7 +13,7 @@ license="LGPL-3.0-or-later"
 homepage="https://github.com/aleaxit/gmpy"
 changelog="https://github.com/aleaxit/gmpy/releases"
 distfiles="${PYPI_SITE}/g/gmpy2/gmpy2-${version%r}.tar.gz"
-checksum=e19e62dfeb1e4a57079f0bf51c51dec30633d9fe9e89cb9a083e05e4823afa70
+checksum=e83e07567441b78cb87544910cb3cc4fe94e7da987e93ef7622e76fb96650432
 
 if [ "$XBPS_CHECK_PKGS" = full ]; then
 	# this would cause a build-time circular dependency

From b3f34b57321cc4e7db77f066da49677d1259ff48 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sat, 17 Aug 2024 19:58:47 -0300
Subject: [PATCH 3/6] python3-cypari2: update to 2.2.0.

---
 srcpkgs/python3-cypari2/template | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/srcpkgs/python3-cypari2/template b/srcpkgs/python3-cypari2/template
index 8b7e06abd5aace..2a6b284f2f0ab1 100644
--- a/srcpkgs/python3-cypari2/template
+++ b/srcpkgs/python3-cypari2/template
@@ -1,6 +1,6 @@
 # Template file for 'python3-cypari2'
 pkgname=python3-cypari2
-version=2.1.5
+version=2.2.0
 revision=1
 build_style=python3-pep517
 hostmakedepends="python3-setuptools python3-wheel python3-Cython
@@ -14,7 +14,7 @@ license="GPL-2.0-or-later"
 homepage="https://github.com/sagemath/cypari2"
 changelog="https://github.com/sagemath/cypari2/releases"
 distfiles="https://github.com/sagemath/cypari2/archive/refs/tags/${version}.tar.gz"
-checksum=3cea1051f7cd8832b7907d11c68764e83a430036698a215abae48924a580d7fb
+checksum=08804f8e73859447cd1882d0cdc6d1e62dd813c3f291e8cba4313916e162f7cd
 
 do_check() {
 	# Please do not disable this custom check;

From 4290bd2f3174284fc3a02ccc185d4caec70cee53 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 12:02:20 -0300
Subject: [PATCH 4/6] python3-sympy: update to 1.13.2.

---
 srcpkgs/python3-sympy/template | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/srcpkgs/python3-sympy/template b/srcpkgs/python3-sympy/template
index 07c0547e01b136..64e799d5a2bad3 100644
--- a/srcpkgs/python3-sympy/template
+++ b/srcpkgs/python3-sympy/template
@@ -1,6 +1,6 @@
 # Template file for 'python3-sympy'
 pkgname=python3-sympy
-version=1.13.1
+version=1.13.2
 revision=1
 build_style=python3-pep517
 hostmakedepends="python3-setuptools python3-wheel"
@@ -14,7 +14,7 @@ license="BSD-3-Clause"
 homepage="https://sympy.org/"
 changelog="https://github.com/sympy/sympy/wiki/Release-Notes"
 distfiles="${PYPI_SITE}/s/sympy/sympy-${version}.tar.gz"
-checksum=9cebf7e04ff162015ce31c9c6c9144daa34a93bd082f54fd8f12deca4f47515f
+checksum=401449d84d07be9d0c7a46a64bd54fe097667d5e7181bfe67ec777be9e01cb13
 
 post_install() {
 	vman doc/man/isympy.1

From 88056e2ebc746fc3e522b8cec762f5ee29e608b2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 5 Aug 2024 00:21:23 -0300
Subject: [PATCH 5/6] sagemath: update to 10.5.beta2.

---
 .../sagemath/patches/36641-sympy_1.13.patch   |  22 +-
 .../sagemath/patches/37884-gap_4.13.1.patch   |  28 +-
 .../sagemath/patches/38250-numpy_2.0.patch    | 587 ------------------
 .../sagemath/patches/38344-ecm_7.0.6.patch    |  43 --
 srcpkgs/sagemath/patches/get_patches          |   4 +-
 srcpkgs/sagemath/template                     |   8 +-
 6 files changed, 22 insertions(+), 670 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/38250-numpy_2.0.patch
 delete mode 100644 srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch

diff --git a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
index 625c582cdd41b7..01e859ad023f4d 100644
--- a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
+++ b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
@@ -1,8 +1,5 @@
-diff --git a/build/pkgs/sympy/requirements.txt b/build/pkgs/sympy/requirements.txt
-new file mode 100644
-index 00000000000..3ef8f90b550
 diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py
-index 7e9eab2ff2e..43365cd645e 100644
+index 823a0d14a41..de1c8531814 100644
 --- a/src/sage/doctest/forker.py
 +++ b/src/sage/doctest/forker.py
 @@ -150,14 +150,15 @@ def init_sage(controller=None):
@@ -28,7 +25,7 @@ index 7e9eab2ff2e..43365cd645e 100644
      The displayhook sorts dictionary keys to simplify doctesting of
      dictionary output::
 diff --git a/src/sage/functions/hypergeometric.py b/src/sage/functions/hypergeometric.py
-index 010c61febe0..bbccbd20032 100644
+index ade7836b310..eb5c6665c0d 100644
 --- a/src/sage/functions/hypergeometric.py
 +++ b/src/sage/functions/hypergeometric.py
 @@ -124,7 +124,7 @@
@@ -40,21 +37,8 @@ index 010c61febe0..bbccbd20032 100644
      sage: hypergeometric((5, 4), (4, 4), 3)._mathematica_init_()                        # needs sage.symbolic
      'HypergeometricPFQ[{5,4},{4,4},3]'
  
-diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx
-index a92fe241355..f62311423be 100644
---- a/src/sage/symbolic/expression.pyx
-+++ b/src/sage/symbolic/expression.pyx
-@@ -1167,7 +1167,7 @@ cdef class Expression(Expression_abc):
-             sage: unicode_art(SR(13 - I))
-             13 - ⅈ
-             sage: unicode_art(SR(1.3 - I))
--            1.3 - ⅈ
-+            1.3 - 1.0⋅ⅈ
-             sage: unicode_art(cos(I))
-             cosh(1)
- 
 diff --git a/src/sage/typeset/ascii_art.py b/src/sage/typeset/ascii_art.py
-index 28024405d27..458fa8724a3 100644
+index 83d92af8959..e470e2bd88d 100644
 --- a/src/sage/typeset/ascii_art.py
 +++ b/src/sage/typeset/ascii_art.py
 @@ -44,11 +44,12 @@
diff --git a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
index 1550d47e2436c6..321e0a94487da3 100644
--- a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
+++ b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
@@ -1,21 +1,21 @@
 diff --git a/src/sage/algebras/fusion_rings/fusion_double.py b/src/sage/algebras/fusion_rings/fusion_double.py
-index 7ce086f70d0..954513572c3 100644
+index 71277561331..3b681d75d3b 100644
 --- a/src/sage/algebras/fusion_rings/fusion_double.py
 +++ b/src/sage/algebras/fusion_rings/fusion_double.py
 @@ -133,7 +133,7 @@ class FusionDouble(CombinatorialFreeModule):
          sage: G = SmallPermutationGroup(16,9)
-         sage: F = FusionDouble(G, prefix="b",inject_variables=True)
+         sage: F = FusionDouble(G, prefix='b', inject_variables=True)
          sage: b13^2 # long time (4s)
 -        b0 + b2 + b4 + b15 + b16 + b17 + b18 + b24 + b26 + b27
 +        b0 + b3 + b4
- 
      """
      @staticmethod
+     def __classcall_private__(cls, G, prefix='s', inject_variables=False):
 diff --git a/src/sage/categories/simplicial_sets.py b/src/sage/categories/simplicial_sets.py
-index e714a4571c4..a2b87a729d1 100644
+index aabd3cdbb4f..14bebdcd080 100644
 --- a/src/sage/categories/simplicial_sets.py
 +++ b/src/sage/categories/simplicial_sets.py
-@@ -593,9 +593,9 @@ def _canonical_twisting_operator(self):
+@@ -591,9 +591,9 @@ def _canonical_twisting_operator(self):
                      sage: X = simplicial_sets.Torus()
                      sage: d = X._canonical_twisting_operator()
                      sage: d
@@ -27,7 +27,7 @@ index e714a4571c4..a2b87a729d1 100644
                      sage: Y = simplicial_sets.RealProjectiveSpace(2)
                      sage: d2 = Y._canonical_twisting_operator()
                      sage: d2
-@@ -677,10 +677,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
+@@ -674,10 +674,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
                      sage: X = simplicial_sets.Torus()
                      sage: C = X.twisted_chain_complex()
                      sage: C.differential(1)
@@ -41,7 +41,7 @@ index e714a4571c4..a2b87a729d1 100644
                      [      -1       -1]
                      sage: C.differential(3)
                      []
-@@ -848,29 +848,29 @@ def twisted_homology(self, n, reduced=False):
+@@ -844,29 +844,29 @@ def twisted_homology(self, n, reduced=False):
                      sage: # needs sage.graphs
                      sage: Y = simplicial_sets.Torus()
                      sage: Y.twisted_homology(1)
@@ -80,10 +80,10 @@ index e714a4571c4..a2b87a729d1 100644
                      [1 0 0 0 0]
                      [0 1 0 0 0]
 diff --git a/src/sage/combinat/matrices/latin.py b/src/sage/combinat/matrices/latin.py
-index 936edcc6ea4..c06a53d9afd 100644
+index e2d818e9480..84e6c4fcc9b 100644
 --- a/src/sage/combinat/matrices/latin.py
 +++ b/src/sage/combinat/matrices/latin.py
-@@ -2453,7 +2453,7 @@ def p3_group_bitrade_generators(p):
+@@ -2444,7 +2444,7 @@ def p3_group_bitrade_generators(p):
      EXAMPLES::
  
          sage: from sage.combinat.matrices.latin import *
@@ -93,7 +93,7 @@ index 936edcc6ea4..c06a53d9afd 100644
           (1,2,3)(4,7,8)(5,6,9),
           (1,9,2)(3,7,4)(5,8,6),
 diff --git a/src/sage/groups/cubic_braid.py b/src/sage/groups/cubic_braid.py
-index 257b400f1c7..36423c756aa 100644
+index 61db70925e1..521289c7578 100644
 --- a/src/sage/groups/cubic_braid.py
 +++ b/src/sage/groups/cubic_braid.py
 @@ -282,7 +282,7 @@ def _richcmp_(self, other, op):
@@ -106,7 +106,7 @@ index 257b400f1c7..36423c756aa 100644
               c1*c0^-1*c1, c0^-1*c1^-1*c0^-1, c0^-1*c1^-1, c1^-1*c0*c1^-1,
               c0*c1^-1*c0^-1, c0^-1*c1, c0^-1*c1*c0, c0*c1^-1, c1*c0^-1,
 diff --git a/src/sage/groups/finitely_presented.py b/src/sage/groups/finitely_presented.py
-index 4bb52ee4efb..85f572fac6c 100644
+index 4ac2faa783b..7016d08381b 100644
 --- a/src/sage/groups/finitely_presented.py
 +++ b/src/sage/groups/finitely_presented.py
 @@ -1344,8 +1344,8 @@ def abelianization_map(self):
@@ -161,10 +161,10 @@ index 4bb52ee4efb..85f572fac6c 100644
              sage: G.characteristic_varieties(groebner=True)
              {0: [-1 + F1, 1 + F1, 1 - F1 + F1^2, 1 + F1 + F1^2], 1: [1 - F1 + F1^2],  2: []}
 diff --git a/src/sage/groups/perm_gps/permgroup_named.py b/src/sage/groups/perm_gps/permgroup_named.py
-index c1f2683907b..d219e104a2c 100644
+index 5c153b93d4c..bd4afad2942 100644
 --- a/src/sage/groups/perm_gps/permgroup_named.py
 +++ b/src/sage/groups/perm_gps/permgroup_named.py
-@@ -3468,16 +3468,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
+@@ -3465,16 +3465,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
          sage: G = SmallPermutationGroup(12,4); G
          Group of order 12 and GAP Id 4 as a permutation group
          sage: G.gens()
@@ -186,7 +186,7 @@ index c1f2683907b..d219e104a2c 100644
          sage: def numgps(n): return ZZ(libgap.NumberSmallGroups(n))
          sage: all(SmallPermutationGroup(n,k).id() == [n,k]
          ....:     for n in [1..64] for k in [1..numgps(n)])
-@@ -3486,11 +3484,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
+@@ -3483,11 +3481,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
          sage: H.is_abelian()
          False
          sage: [H.centralizer(g) for g in H.conjugacy_classes_representatives()]
diff --git a/srcpkgs/sagemath/patches/38250-numpy_2.0.patch b/srcpkgs/sagemath/patches/38250-numpy_2.0.patch
deleted file mode 100644
index e28fd857afcb75..00000000000000
--- a/srcpkgs/sagemath/patches/38250-numpy_2.0.patch
+++ /dev/null
@@ -1,587 +0,0 @@
-diff --git a/src/sage/arith/misc.py b/src/sage/arith/misc.py
-index 28f81d7b798..d184c52bf19 100644
---- a/src/sage/arith/misc.py
-+++ b/src/sage/arith/misc.py
-@@ -2277,7 +2277,7 @@ def power_mod(a, n, m):
- 
-         sage: from numpy import int32                                                   # needs numpy
-         sage: power_mod(int32(2), int32(390), int32(391))                               # needs numpy
--        285
-+        ...285...
-         sage: from gmpy2 import mpz
-         sage: power_mod(mpz(2), mpz(390), mpz(391))
-         mpz(285)
-diff --git a/src/sage/calculus/interpolators.pyx b/src/sage/calculus/interpolators.pyx
-index 221b52369e2..bb0be7bab0c 100644
---- a/src/sage/calculus/interpolators.pyx
-+++ b/src/sage/calculus/interpolators.pyx
-@@ -27,6 +27,9 @@ Development supported by NSF award No. 0702939.
- import numpy as np
- cimport numpy as np
- 
-+if int(np.version.short_version[0]) > 1:
-+    np.set_printoptions(legacy="1.25")
-+
- from math import pi
- cdef double TWOPI = 2*pi
- 
-diff --git a/src/sage/calculus/riemann.pyx b/src/sage/calculus/riemann.pyx
-index 6ec80d89aa7..c09d93c4260 100644
---- a/src/sage/calculus/riemann.pyx
-+++ b/src/sage/calculus/riemann.pyx
-@@ -44,6 +44,9 @@ from sage.calculus.integration import numerical_integral
- import numpy as np
- cimport numpy as np
- 
-+if int(np.version.short_version[0]) > 1:
-+    np.set_printoptions(legacy="1.25")
-+
- from math import pi
- from math import sin
- from math import cos
-diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index b198fed0c0d..b3ebd206cd2 100644
---- a/src/sage/combinat/fully_packed_loop.py
-+++ b/src/sage/combinat/fully_packed_loop.py
-@@ -66,6 +66,9 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
-     r"""
-     TESTS::
- 
-+        sage: import numpy as np
-+        sage: if int(np.version.short_version[0]) > 1:
-+        ....:     np.set_printoptions(legacy="1.25")
-         sage: from sage.combinat.fully_packed_loop import _make_color_list
-         sage: _make_color_list(5)
-         sage: _make_color_list(5, ['blue', 'red'])
-diff --git a/src/sage/env.py b/src/sage/env.py
-index 722649ab3da..abb9b19f9e3 100644
---- a/src/sage/env.py
-+++ b/src/sage/env.py
-@@ -296,7 +296,7 @@ def sage_include_directories(use_sources=False):
-         sage: import sage.env
-         sage: sage.env.sage_include_directories()
-         ['...',
--         '.../numpy/core/include',
-+         '.../numpy/...core/include',
-          '.../include/python...']
- 
-     To check that C/C++ files are correctly found, we verify that we can
-diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
-index e100ba3ee23..2a03bb68f67 100644
---- a/src/sage/functions/special.py
-+++ b/src/sage/functions/special.py
-@@ -217,6 +217,9 @@ class SphericalHarmonic(BuiltinFunction):
-         sage: spherical_harmonic(1, 1, pi/2, pi).n()  # abs tol 1e-14                   # needs sage.symbolic
-         0.345494149471335
-         sage: from scipy.special import sph_harm  # NB: arguments x and y are swapped   # needs scipy
-+        sage: import numpy as np                                                        # needs scipy
-+        sage: if int(np.version.short_version[0]) > 1:                                  # needs scipy
-+        ....:     np.set_printoptions(legacy="1.25")                                    # needs scipy
-         sage: sph_harm(1, 1, pi.n(), (pi/2).n())  # abs tol 1e-14                       # needs scipy sage.symbolic
-         (0.3454941494713355-4.231083042742082e-17j)
- 
-diff --git a/src/sage/graphs/generators/classical_geometries.py b/src/sage/graphs/generators/classical_geometries.py
-index da04362eef3..957f88d2061 100644
---- a/src/sage/graphs/generators/classical_geometries.py
-+++ b/src/sage/graphs/generators/classical_geometries.py
-@@ -1315,7 +1315,7 @@ def CossidentePenttilaGraph(q):
- 
-     from sage.libs.gap.libgap import libgap
-     adj_list = libgap.function_factory("""function(q)
--        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x;
-+        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x, sqo;
-         LoadPackage("grape");
-         G0:=SO(3,q^2);
-         so:=GeneratorsOfGroup(G0);
-diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
-index 063931ae274..0bafbd00564 100644
---- a/src/sage/graphs/generic_graph.py
-+++ b/src/sage/graphs/generic_graph.py
-@@ -18420,6 +18420,9 @@ def shortest_path_all_pairs(self, by_weight=False, algorithm=None,
-                 M = self.adjacency_matrix(vertices=int_to_vertex)
- 
-             # We call the Floyd-Warshall method from SciPy
-+            import numpy  # to ensure numpy 2.0 compatibility
-+            if int(numpy.version.short_version[0]) > 1:
-+                numpy.set_printoptions(legacy="1.25")
-             from numpy import array as np_array
-             from scipy.sparse.csgraph import floyd_warshall
-             dd, pp = floyd_warshall(np_array(M), directed=self.is_directed(),
-diff --git a/src/sage/graphs/graph_generators_pyx.pyx b/src/sage/graphs/graph_generators_pyx.pyx
-index 033e8b22adc..04b20d3229b 100644
---- a/src/sage/graphs/graph_generators_pyx.pyx
-+++ b/src/sage/graphs/graph_generators_pyx.pyx
-@@ -57,7 +57,7 @@ def RandomGNP(n, p, bint directed=False, bint loops=False, seed=None):
- 
-         sage: from numpy import mean                                                    # needs numpy
-         sage: abs(mean([RandomGNP(200, .2).density() for i in range(30)]) - .2) < .001  # needs numpy
--        True
-+        ...True...
-         sage: RandomGNP(150, .2, loops=True)
-         Traceback (most recent call last):
-         ...
-diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
-index a810418389c..c38df5412f0 100644
---- a/src/sage/matrix/matrix1.pyx
-+++ b/src/sage/matrix/matrix1.pyx
-@@ -705,12 +705,15 @@ cdef class Matrix(Matrix0):
-         Type ``numpy.typecodes`` for a list of the possible
-         typecodes::
- 
--            sage: import numpy                                                          # needs numpy
--            sage: sorted(numpy.typecodes.items())                                       # needs numpy
-+            sage: import numpy                            # needs numpy
-+            sage: numpy.typecodes.items()                 # needs numpy # random
-             [('All', '?bhilqpBHILQPefdgFDGSUVOMm'), ('AllFloat', 'efdgFDG'),
--             ('AllInteger', 'bBhHiIlLqQpP'), ('Character', 'c'), ('Complex', 'FDG'),
--             ('Datetime', 'Mm'), ('Float', 'efdg'), ('Integer', 'bhilqp'),
--             ('UnsignedInteger', 'BHILQP')]
-+            ...
-+
-+        For instance, you can see possibilities for real floating point numbers::
-+
-+            sage: numpy.typecodes['Float']                # needs numpy
-+            'efdg'
- 
-         Alternatively, numpy automatically calls this function (via
-         the magic :meth:`__array__` method) to convert Sage matrices
-diff --git a/src/sage/modules/free_module_element.pyx b/src/sage/modules/free_module_element.pyx
-index d71d22ac1f7..b6f297a3510 100644
---- a/src/sage/modules/free_module_element.pyx
-+++ b/src/sage/modules/free_module_element.pyx
-@@ -555,7 +555,11 @@ def vector(arg0, arg1=None, arg2=None, sparse=None, immutable=False):
-         R = None
- 
-     try:
-+        import numpy
-         from numpy import ndarray
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-+
-     except ImportError:
-         pass
-     else:
-@@ -1188,7 +1192,11 @@ cdef class FreeModuleElement(Vector):   # abstract base class
-             over Rational Field to numpy array of type <... 'float'>:
-             setting an array element with a sequence.
-         """
-+        import numpy
-         from numpy import array
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-+
-         try:
-             return array(self, dtype=dtype)
-         except ValueError as e:
-diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index e3d94d1746e..7ae8ca4966f 100644
---- a/src/sage/numerical/optimize.py
-+++ b/src/sage/numerical/optimize.py
-@@ -155,6 +155,10 @@ def find_root(f, a, b, xtol=10e-13, rtol=2.0**-50, maxiter=100, full_output=Fals
-         b = max(s_1, s_2)
- 
-     import scipy.optimize
-+    import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     g = lambda x: float(f(x))
-     brentqRes = scipy.optimize.brentq(g, a, b,
-                                  full_output=full_output, xtol=xtol, rtol=rtol, maxiter=maxiter)
-@@ -288,6 +292,10 @@ def find_local_minimum(f, a, b, tol=1.48e-08, maxfun=500):
-     a = float(a)
-     b = float(b)
-     import scipy.optimize
-+    import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     xmin, fval, iter, funcalls = scipy.optimize.fminbound(f, a, b, full_output=1, xtol=tol, maxfun=maxfun)
-     return fval, xmin
- 
-@@ -376,6 +384,8 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
-         sage: def rosen(x):  # The Rosenbrock function
-         ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
-         sage: import numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:
-+        ....:     numpy.set_printoptions(legacy="1.25")
-         sage: from numpy import zeros
-         sage: def rosen_der(x):
-         ....:    xm = x[1r:-1r]
-@@ -393,6 +403,9 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
-     from sage.structure.element import Expression
-     from sage.ext.fast_callable import fast_callable
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     from scipy import optimize
-     if isinstance(func, Expression):
-         var_list = func.variables()
-@@ -530,6 +543,8 @@ def minimize_constrained(func,cons,x0,gradient=None,algorithm='default', **args)
-     from sage.structure.element import Expression
-     from sage.ext.fast_callable import fast_callable
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-     from scipy import optimize
-     function_type = type(lambda x,y: x+y)
- 
-@@ -652,6 +667,8 @@ def find_fit(data, model, initial_guess=None, parameters=None, variables=None, s
-     ``lmdif`` and ``lmder`` algorithms.
-     """
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
- 
-     if not isinstance(data, numpy.ndarray):
-         try:
-diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index ac1dc79d802..23e2517ca56 100644
---- a/src/sage/plot/arrow.py
-+++ b/src/sage/plot/arrow.py
-@@ -53,6 +53,9 @@ def get_minmax_data(self):
- 
-         EXAMPLES::
- 
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: from sage.plot.arrow import CurveArrow
-             sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
-             ....:                options={})
-diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx
-index f1f2671a803..4d71414e1c2 100644
---- a/src/sage/plot/complex_plot.pyx
-+++ b/src/sage/plot/complex_plot.pyx
-@@ -1282,15 +1282,13 @@ def rgb_to_hls(rgb):
-         raise ValueError("Last dimension of input array must be 3; "
-                          "shape {} was found.".format(rgb.shape))
-     in_shape = rgb.shape
--    rgb = np.array(
--        rgb, copy=False, dtype=np.dtype(float), ndmin=2
--    )
-+    rgb = np.asarray(rgb, dtype=np.dtype(float))
-     rgb_max = rgb.max(-1)
-     rgb_min = rgb.min(-1)
-     l = (rgb_max + rgb_min)/2.0  # lightness
- 
-     hls = np.zeros_like(rgb)
--    delta = rgb.ptp(-1)
-+    delta = np.ptp(rgb, -1)
-     s = np.zeros_like(delta)
- 
-     ipos = delta > 0
-diff --git a/src/sage/plot/graphics.py b/src/sage/plot/graphics.py
-index a84d162cb56..94f5db09d83 100644
---- a/src/sage/plot/graphics.py
-+++ b/src/sage/plot/graphics.py
-@@ -2754,7 +2754,7 @@ def matplotlib(self, filename=None,
-             sage: xmin, xmax = sub.get_xlim()
-             sage: ymin, ymax = sub.get_ylim()
-             sage: xmin > xmax, ymin > ymax
--            (True, True)
-+            (...True..., ...True...)
-         """
-         if not isinstance(ticks, (list, tuple)):
-             ticks = (ticks, None)
-diff --git a/src/sage/plot/histogram.py b/src/sage/plot/histogram.py
-index fa86a44bd0a..a585cacf9cd 100644
---- a/src/sage/plot/histogram.py
-+++ b/src/sage/plot/histogram.py
-@@ -92,6 +92,8 @@ def get_minmax_data(self):
-             {'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.476190476190..., 'ymin': 0}
-         """
-         import numpy
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
- 
-         # Extract these options (if they are not None) and pass them to
-         # histogram()
-diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
-index b583be32317..6be448f1e04 100644
---- a/src/sage/plot/multigraphics.py
-+++ b/src/sage/plot/multigraphics.py
-@@ -784,6 +784,9 @@ def _add_subplot(self, figure, index, **options):
-             True
-             sage: G.position(1)
-             (0.2, 0.3, 0.4, 0.1)
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: ax1.get_position().bounds  # tol 1.0e-13
-             (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
- 
-@@ -1295,6 +1298,9 @@ def position(self, index):
-             sage: g1 = plot(sin(x), (x, -pi, pi))
-             sage: g2 = circle((0,1), 1.)
-             sage: G = graphics_array([g1, g2])
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: G.position(0)  # tol 5.0e-3
-             (0.025045451349937315,
-              0.03415488992713045,
-diff --git a/src/sage/plot/plot3d/implicit_surface.pyx b/src/sage/plot/plot3d/implicit_surface.pyx
-index ce0da48a4e0..f4d5059b620 100644
---- a/src/sage/plot/plot3d/implicit_surface.pyx
-+++ b/src/sage/plot/plot3d/implicit_surface.pyx
-@@ -468,6 +468,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
-             sage: cube_marcher.y_vertices.tolist()
-             [[[<1.0, 0.5, 0.0>, None]], [[None, None]]]
-             sage: cube_marcher.x_vertices.any() # This shouldn't affect the X vertices.
-+            ...
-         """
-         (self.y_vertices, self.y_vertices_swapped) = \
-             (self.y_vertices_swapped, self.y_vertices)
-@@ -574,6 +575,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
-             sage: cube_marcher.x_vertices.tolist()
-             [[None, None], [None, <1.5, 1.0, 1.0>]]
-             sage: cube_marcher.y_vertices.any() or cube_marcher.z_vertices.any() # This shouldn't affect the Y or Z vertices.
-+            ...
-         """
-         cdef bint has_prev = (_prev is not None)
-         cdef bint has_next = (_next is not None)
-diff --git a/src/sage/plot/scatter_plot.py b/src/sage/plot/scatter_plot.py
-index 4ad418f040b..781854d372c 100644
---- a/src/sage/plot/scatter_plot.py
-+++ b/src/sage/plot/scatter_plot.py
-@@ -63,9 +63,9 @@ def get_minmax_data(self):
-             sage: s = scatter_plot([[0,1],[2,4],[3.2,6]])
-             sage: d = s.get_minmax_data()
-             sage: d['xmin']
--            0.0
-+            ...0.0...
-             sage: d['ymin']
--            1.0
-+            ...1.0...
-         """
-         return {'xmin': self.xdata.min(),
-                 'xmax': self.xdata.max(),
-diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index 663d3aee70b..d2cb11088c7 100644
---- a/src/sage/plot/streamline_plot.py
-+++ b/src/sage/plot/streamline_plot.py
-@@ -71,6 +71,9 @@ def get_minmax_data(self):
-         EXAMPLES::
- 
-             sage: x, y = var('x y')
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: d = streamline_plot((.01*x, x+y), (x,10,20), (y,10,20))[0].get_minmax_data()
-             sage: d['xmin']
-             10.0
-diff --git a/src/sage/probability/probability_distribution.pyx b/src/sage/probability/probability_distribution.pyx
-index e2c71af9c25..59ba4a95ab6 100644
---- a/src/sage/probability/probability_distribution.pyx
-+++ b/src/sage/probability/probability_distribution.pyx
-@@ -140,6 +140,9 @@ cdef class ProbabilityDistribution:
-              1.8,
-              2.0]
-         """
-+        import numpy as np
-+        if int(np.version.short_version[0]) > 1:
-+            np.set_printoptions(legacy="1.25")
-         import pylab
-         ell = [float(self.get_random_element()) for _ in range(num_samples)]
-         S = pylab.hist(ell, bins, density=True)
-diff --git a/src/sage/rings/complex_double.pyx b/src/sage/rings/complex_double.pyx
-index c59a2b46d6f..b4dddebb4dc 100644
---- a/src/sage/rings/complex_double.pyx
-+++ b/src/sage/rings/complex_double.pyx
-@@ -2558,10 +2558,10 @@ cdef class ComplexToCDF(Morphism):
- 
-         sage: # needs numpy
-         sage: import numpy
--        sage: f = CDF.coerce_map_from(numpy.complex_)
--        sage: f(numpy.complex_(I))
-+        sage: f = CDF.coerce_map_from(numpy.complex128)
-+        sage: f(numpy.complex128(I))
-         1.0*I
--        sage: f(numpy.complex_(I)).parent()
-+        sage: f(numpy.complex128(I)).parent()
-         Complex Double Field
-     """
-     def __init__(self, R):
-@@ -2578,7 +2578,7 @@ cdef class ComplexToCDF(Morphism):
-         EXAMPLES::
- 
-             sage: import numpy                                                          # needs numpy
--            sage: CDF(numpy.complex_(I))    # indirect doctest                          # needs numpy
-+            sage: CDF(numpy.complex128(I))    # indirect doctest                          # needs numpy
-             1.0*I
-         """
-         cdef ComplexDoubleElement z = <ComplexDoubleElement>ComplexDoubleElement.__new__(ComplexDoubleElement)
-@@ -2592,7 +2592,7 @@ cdef class ComplexToCDF(Morphism):
-         EXAMPLES::
- 
-             sage: import numpy                                                          # needs numpy
--            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex_)            # needs numpy
-+            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex128)          # needs numpy
-             sage: f._repr_type()                                                        # needs numpy
-             'Native'
-         """
-diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index b4a1fa5039b..38c30f7627b 100644
---- a/src/sage/rings/integer.pyx
-+++ b/src/sage/rings/integer.pyx
-@@ -593,6 +593,8 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
-         Test comparisons with numpy types (see :issue:`13386` and :issue:`18076`)::
- 
-             sage: import numpy                                                          # needs numpy
-+            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
-+            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-             sage: numpy.int8('12') == 12                                                # needs numpy
-             True
-             sage: 12 == numpy.int8('12')                                                # needs numpy
-diff --git a/src/sage/rings/polynomial/polynomial_element.pyx b/src/sage/rings/polynomial/polynomial_element.pyx
-index dcf2af7cdf2..c87eccd44f1 100644
---- a/src/sage/rings/polynomial/polynomial_element.pyx
-+++ b/src/sage/rings/polynomial/polynomial_element.pyx
-@@ -8851,7 +8851,7 @@ cdef class Polynomial(CommutativePolynomial):
-                          'you expect.')
- 
-                 import numpy
--                from numpy.linalg.linalg import LinAlgError
-+                from numpy.linalg import LinAlgError
-                 from sage.rings.complex_double import CDF
- 
-                 numpy_dtype = ('complex' if input_complex else 'double')
-diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
-index 95b472e912c..76fbfedab95 100644
---- a/src/sage/rings/real_mpfi.pyx
-+++ b/src/sage/rings/real_mpfi.pyx
-@@ -231,6 +231,8 @@ specified if given a non-interval and an interval::
- TESTS::
- 
-     sage: import numpy                                                                  # needs numpy
-+    sage: if int(numpy.version.short_version[0]) > 1:                                   # needs numpy
-+    ....:     numpy.set_printoptions(legacy="1.25")                                     # needs numpy
-     sage: RIF(2) == numpy.int8('2')                                                     # needs numpy
-     True
-     sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
-diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-index 8f240627e77..70ce616f92f 100644
---- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-+++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-@@ -77,6 +77,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
-@@ -295,6 +297,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((10, 10))
-             sage: data[1:4,1:4] = True
-@@ -317,6 +321,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1,1] = True
-@@ -370,6 +376,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
- 
-             sage: data = np.zeros((20, 20))
-@@ -520,6 +528,8 @@ cdef class PeriodicRegion:
-         TESTS::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1, 1] = True
-diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index b2e6b301bf7..6937f6cb410 100644
---- a/src/sage/stats/basic_stats.py
-+++ b/src/sage/stats/basic_stats.py
-@@ -227,6 +227,8 @@ def std(v, bias=False):
- 
-         sage: # needs numpy
-         sage: import numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:
-+        ....:     numpy.set_printoptions(legacy="1.25")
-         sage: x = numpy.array([1,2,3,4,5])
-         sage: std(x, bias=False)
-         1.5811388300841898
-@@ -304,6 +306,8 @@ def variance(v, bias=False):
-         sage: variance([RIF(1.0103, 1.0103), RIF(2)])
-         0.4897530450000000?
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-         sage: x = numpy.array([1,2,3,4,5])                                              # needs numpy
-         sage: variance(x, bias=False)                                                   # needs numpy
-         2.5
-diff --git a/src/sage/stats/time_series.pyx b/src/sage/stats/time_series.pyx
-index 2e22ec45c69..23adae84fb4 100644
---- a/src/sage/stats/time_series.pyx
-+++ b/src/sage/stats/time_series.pyx
-@@ -1718,6 +1718,8 @@ cdef class TimeSeries:
-         if len(v0) == 1:
-             return v1[0]/v0[0]
-         import numpy
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-         coeffs = numpy.polyfit(v0,v1,1)
-         return coeffs[0]
- 
-diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
-index dfbd5ff82fa..955a256e9b4 100644
---- a/src/sage/structure/coerce.pyx
-+++ b/src/sage/structure/coerce.pyx
-@@ -520,6 +520,8 @@ cdef class CoercionModel:
-     Check that :issue:`8426` is fixed (see also :issue:`18076`)::
- 
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
- 
-         sage: # needs sage.rings.real_mpfr
-         sage: x = polygen(RR)
-diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
-index 2cb2f09c715..cd89ad2a256 100644
---- a/src/sage/symbolic/function.pyx
-+++ b/src/sage/symbolic/function.pyx
-@@ -964,6 +964,9 @@ cdef class BuiltinFunction(Function):
-             mpc(real='0.83373002513114902', imag='-0.98889770576286506')
- 
-             sage: import numpy                                                          # needs numpy
-+            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
-+            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-+
-             sage: sin(numpy.int32(0))                                                   # needs numpy
-             0.0
-             sage: type(_)                                                               # needs numpy
-diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 501b0920898..5b007d9e5fd 100644
---- a/src/sage/symbolic/ring.pyx
-+++ b/src/sage/symbolic/ring.pyx
-@@ -1162,6 +1162,8 @@ cdef class NumpyToSRMorphism(Morphism):
-     We check that :issue:`8949` and :issue:`9769` are fixed (see also :issue:`18076`)::
- 
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-         sage: f(x) = x^2
-         sage: f(numpy.int8('2'))                                                        # needs numpy
-         4
diff --git a/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch b/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch
deleted file mode 100644
index db0ae9030623b6..00000000000000
--- a/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-diff --git a/src/sage/interfaces/ecm.py b/src/sage/interfaces/ecm.py
-index 99287dec718..98011970404 100644
---- a/src/sage/interfaces/ecm.py
-+++ b/src/sage/interfaces/ecm.py
-@@ -508,7 +508,6 @@ def _find_factor(self, n, factor_digits, B1, **kwds):
-         """
-         n = self._validate(n)
-         kwds.setdefault('c', 1000000000)
--        kwds.setdefault('I', 1)
-         if factor_digits is not None:
-             B1 = self.recommended_B1(factor_digits)
-         kwds['one'] = True
-diff --git a/src/sage/libs/libecm.pyx b/src/sage/libs/libecm.pyx
-index 886a9b816e4..83fb7adaf8d 100644
---- a/src/sage/libs/libecm.pyx
-+++ b/src/sage/libs/libecm.pyx
-@@ -149,11 +149,13 @@ def ecmfactor(number, double B1, verbose=False, sigma=0):
-     Some special cases::
- 
-         sage: ecmfactor(1, 100)
--        (True, 1, ...)
-+        Traceback (most recent call last):
-+        ...
-+        ValueError: Input number (1) must be greater than 1
-         sage: ecmfactor(0, 100)
-         Traceback (most recent call last):
-         ...
--        ValueError: Input number (0) must be positive
-+        ValueError: Input number (0) must be greater than 1
-     """
-     cdef mpz_t n, f
-     cdef int res
-@@ -164,8 +166,8 @@ def ecmfactor(number, double B1, verbose=False, sigma=0):
-     sage_int_number = Integer(number)
-     sage_int_sigma = Integer(sigma)
- 
--    if number <= 0:
--        raise ValueError("Input number (%s) must be positive"%number)
-+    if number <= 1:
-+        raise ValueError("Input number (%s) must be greater than 1"%number)
- 
-     if verbose:
-         print("Performing one curve with B1=%1.0f" % B1)
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 28162dff8a38e1..5cab228f286365 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -19,7 +19,7 @@ get_pr() {
 	echo "curl -sL \"$url\" | filterdiff ... > \"$pr-$desc.patch\""
 	if [ -z "$dry" ]; then
 		curl -sL "$url" |
-			filterdiff -p1 -x src/setup.py -x build/* -x src/doc/* |
+			filterdiff -p1 -x src/setup.py -x environment* -x src/environment* -x build/* -x src/doc/* |
 			cat > "$pr-$desc.patch"
 	fi
 }
@@ -29,8 +29,6 @@ cd $(dirname "$0")
 
 get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
-get_pr 38250 "numpy 2.0"
-get_pr 38344 "ecm 7.0.6"
 
 #get_pr 37645 "fix doctest"
 #get_pr 37885 "cython warnings"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index befe33a0188687..f5e1d8c68cfcbe 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,7 +1,7 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.4
-revision=2
+version=10.5.beta2
+revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
 build_style=python3-pep517
@@ -25,14 +25,14 @@ depends="eclib-devel fflas-ffpack flintlib-devel gcc-fortran meson gd-devel
  python3-sympy python3-traitlets sage-data-combinatorial_designs
  python3-conway-polynomials sage-data-elliptic_curves sage-data-graphs
  sage-data-polytopes_db sympow tachyon threejs-sage"
-checkdepends="$depends pythran python3-Sphinx gdb"
+checkdepends="$depends python3-pytest pythran python3-Sphinx gdb"
 short_desc="Open source mathematics software"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=f6579e85f33bd9bb6e9b991bfc4c49dab1e649858ed9ee41c7cec75cb92d4c62
+checksum=0fe0c82dd6959951fc07d55737d270290f64947e183a403ca25709e21b751dee
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From 2b51aeceb934ee0d250e969bbe1d8512a78895fe Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Wed, 14 Aug 2024 00:12:02 -0300
Subject: [PATCH 6/6] sagemath: enable all cython warnings

---
 srcpkgs/sagemath/patches/37885-cython_warnings.patch | 12 ++++++++++++
 srcpkgs/sagemath/patches/get_patches                 |  2 +-
 2 files changed, 13 insertions(+), 1 deletion(-)
 create mode 100644 srcpkgs/sagemath/patches/37885-cython_warnings.patch

diff --git a/srcpkgs/sagemath/patches/37885-cython_warnings.patch b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
new file mode 100644
index 00000000000000..fa4b648cfc1577
--- /dev/null
+++ b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
@@ -0,0 +1,12 @@
+diff --git a/src/sage_setup/command/sage_build_cython.py b/src/sage_setup/command/sage_build_cython.py
+index f4b1357c543..3435c196d49 100644
+--- a/src/sage_setup/command/sage_build_cython.py
++++ b/src/sage_setup/command/sage_build_cython.py
+@@ -226,6 +226,7 @@ def run(self):
+                 compiler_directives=self.cython_directives,
+                 compile_time_env=self.compile_time_env,
+                 create_extension=self.create_extension,
++                show_all_warnings=True,
+                 # Debugging
+                 gdb_debug=self.debug,
+                 output_dir=os.path.join(self.build_lib, "sage"),
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 5cab228f286365..c182576ea553cd 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -31,4 +31,4 @@ get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
 
 #get_pr 37645 "fix doctest"
-#get_pr 37885 "cython warnings"
+get_pr 37885 "cython warnings"

^ permalink raw reply	[flat|nested] 13+ messages in thread

* Re: [PR PATCH] [Updated] [BETA] sagemath: update to 10.5.beta2
  2024-08-18 17:54 [PR PATCH] [BETA] sagemath: update to 10.5.beta2 tornaria
@ 2024-08-20 20:57 ` tornaria
  2024-08-21  1:11 ` tornaria
                   ` (10 subsequent siblings)
  11 siblings, 0 replies; 13+ messages in thread
From: tornaria @ 2024-08-20 20:57 UTC (permalink / raw)
  To: ml

[-- Attachment #1: Type: text/plain, Size: 1465 bytes --]

There is an updated pull request by tornaria against master on the void-packages repository

https://github.com/tornaria/void-packages sagemath
https://github.com/void-linux/void-packages/pull/51902

[BETA] sagemath: update to 10.5.beta2
<!-- Uncomment relevant sections and delete options which are not applicable -->

 - python3-Cython: alternative fix for 6122
 - python3-gmpy2: update to 2.2.1.
 - python3-cypari2: update to 2.2.0.
 - python3-sympy: update to 1.13.2.
 - sagemath: enable all cython warnings

#### Testing the changes
- I tested the changes in this PR: **YES**

@dkwo

<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->

<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration
and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
  - aarch64-musl
  - armv7l
  - armv6l-musl
-->


A patch file from https://github.com/void-linux/void-packages/pull/51902.patch is attached

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-sagemath-51902.patch --]
[-- Type: text/x-diff, Size: 75158 bytes --]

From 416e90f2c36dd4a394daaafb63207dba5203c706 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 11 Aug 2024 22:53:42 -0300
Subject: [PATCH 1/6] python3-Cython: alternative fix for 6122

---
 srcpkgs/python3-Cython/patches/fix-regression.patch | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/srcpkgs/python3-Cython/patches/fix-regression.patch b/srcpkgs/python3-Cython/patches/fix-regression.patch
index f2e761608e373b..f5957cfa59c2f5 100644
--- a/srcpkgs/python3-Cython/patches/fix-regression.patch
+++ b/srcpkgs/python3-Cython/patches/fix-regression.patch
@@ -15,3 +15,11 @@ serious regression, e.g. sagemath FTBS with cython 3.0.11
              warning(self.pos,
                      "Implicit noexcept declaration is deprecated."
                      " Function declaration should contain 'noexcept' keyword.",
+@@ -3128,6 +3126,7 @@ class DefNode(FuncDefNode):
+             if scope is None:
+                 scope = cfunc.scope
+             cfunc_type = cfunc.type
++            has_explicit_exc_clause=True
+             if len(self.args) != len(cfunc_type.args) or cfunc_type.has_varargs:
+                 error(self.pos, "wrong number of arguments")
+                 error(cfunc.pos, "previous declaration here")

From 21b3dad478a94fe98ddd4ca793d16eedf424e199 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 5 Aug 2024 00:21:23 -0300
Subject: [PATCH 2/6] sagemath: update to 10.5.beta2.

---
 .../sagemath/patches/36641-sympy_1.13.patch   |  22 +-
 .../sagemath/patches/37884-gap_4.13.1.patch   |  28 +-
 .../sagemath/patches/38250-numpy_2.0.patch    | 587 ------------------
 .../sagemath/patches/38344-ecm_7.0.6.patch    |  43 --
 srcpkgs/sagemath/patches/get_patches          |   4 +-
 srcpkgs/sagemath/template                     |   8 +-
 6 files changed, 22 insertions(+), 670 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/38250-numpy_2.0.patch
 delete mode 100644 srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch

diff --git a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
index 625c582cdd41b7..01e859ad023f4d 100644
--- a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
+++ b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
@@ -1,8 +1,5 @@
-diff --git a/build/pkgs/sympy/requirements.txt b/build/pkgs/sympy/requirements.txt
-new file mode 100644
-index 00000000000..3ef8f90b550
 diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py
-index 7e9eab2ff2e..43365cd645e 100644
+index 823a0d14a41..de1c8531814 100644
 --- a/src/sage/doctest/forker.py
 +++ b/src/sage/doctest/forker.py
 @@ -150,14 +150,15 @@ def init_sage(controller=None):
@@ -28,7 +25,7 @@ index 7e9eab2ff2e..43365cd645e 100644
      The displayhook sorts dictionary keys to simplify doctesting of
      dictionary output::
 diff --git a/src/sage/functions/hypergeometric.py b/src/sage/functions/hypergeometric.py
-index 010c61febe0..bbccbd20032 100644
+index ade7836b310..eb5c6665c0d 100644
 --- a/src/sage/functions/hypergeometric.py
 +++ b/src/sage/functions/hypergeometric.py
 @@ -124,7 +124,7 @@
@@ -40,21 +37,8 @@ index 010c61febe0..bbccbd20032 100644
      sage: hypergeometric((5, 4), (4, 4), 3)._mathematica_init_()                        # needs sage.symbolic
      'HypergeometricPFQ[{5,4},{4,4},3]'
  
-diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx
-index a92fe241355..f62311423be 100644
---- a/src/sage/symbolic/expression.pyx
-+++ b/src/sage/symbolic/expression.pyx
-@@ -1167,7 +1167,7 @@ cdef class Expression(Expression_abc):
-             sage: unicode_art(SR(13 - I))
-             13 - ⅈ
-             sage: unicode_art(SR(1.3 - I))
--            1.3 - ⅈ
-+            1.3 - 1.0⋅ⅈ
-             sage: unicode_art(cos(I))
-             cosh(1)
- 
 diff --git a/src/sage/typeset/ascii_art.py b/src/sage/typeset/ascii_art.py
-index 28024405d27..458fa8724a3 100644
+index 83d92af8959..e470e2bd88d 100644
 --- a/src/sage/typeset/ascii_art.py
 +++ b/src/sage/typeset/ascii_art.py
 @@ -44,11 +44,12 @@
diff --git a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
index 1550d47e2436c6..321e0a94487da3 100644
--- a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
+++ b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
@@ -1,21 +1,21 @@
 diff --git a/src/sage/algebras/fusion_rings/fusion_double.py b/src/sage/algebras/fusion_rings/fusion_double.py
-index 7ce086f70d0..954513572c3 100644
+index 71277561331..3b681d75d3b 100644
 --- a/src/sage/algebras/fusion_rings/fusion_double.py
 +++ b/src/sage/algebras/fusion_rings/fusion_double.py
 @@ -133,7 +133,7 @@ class FusionDouble(CombinatorialFreeModule):
          sage: G = SmallPermutationGroup(16,9)
-         sage: F = FusionDouble(G, prefix="b",inject_variables=True)
+         sage: F = FusionDouble(G, prefix='b', inject_variables=True)
          sage: b13^2 # long time (4s)
 -        b0 + b2 + b4 + b15 + b16 + b17 + b18 + b24 + b26 + b27
 +        b0 + b3 + b4
- 
      """
      @staticmethod
+     def __classcall_private__(cls, G, prefix='s', inject_variables=False):
 diff --git a/src/sage/categories/simplicial_sets.py b/src/sage/categories/simplicial_sets.py
-index e714a4571c4..a2b87a729d1 100644
+index aabd3cdbb4f..14bebdcd080 100644
 --- a/src/sage/categories/simplicial_sets.py
 +++ b/src/sage/categories/simplicial_sets.py
-@@ -593,9 +593,9 @@ def _canonical_twisting_operator(self):
+@@ -591,9 +591,9 @@ def _canonical_twisting_operator(self):
                      sage: X = simplicial_sets.Torus()
                      sage: d = X._canonical_twisting_operator()
                      sage: d
@@ -27,7 +27,7 @@ index e714a4571c4..a2b87a729d1 100644
                      sage: Y = simplicial_sets.RealProjectiveSpace(2)
                      sage: d2 = Y._canonical_twisting_operator()
                      sage: d2
-@@ -677,10 +677,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
+@@ -674,10 +674,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
                      sage: X = simplicial_sets.Torus()
                      sage: C = X.twisted_chain_complex()
                      sage: C.differential(1)
@@ -41,7 +41,7 @@ index e714a4571c4..a2b87a729d1 100644
                      [      -1       -1]
                      sage: C.differential(3)
                      []
-@@ -848,29 +848,29 @@ def twisted_homology(self, n, reduced=False):
+@@ -844,29 +844,29 @@ def twisted_homology(self, n, reduced=False):
                      sage: # needs sage.graphs
                      sage: Y = simplicial_sets.Torus()
                      sage: Y.twisted_homology(1)
@@ -80,10 +80,10 @@ index e714a4571c4..a2b87a729d1 100644
                      [1 0 0 0 0]
                      [0 1 0 0 0]
 diff --git a/src/sage/combinat/matrices/latin.py b/src/sage/combinat/matrices/latin.py
-index 936edcc6ea4..c06a53d9afd 100644
+index e2d818e9480..84e6c4fcc9b 100644
 --- a/src/sage/combinat/matrices/latin.py
 +++ b/src/sage/combinat/matrices/latin.py
-@@ -2453,7 +2453,7 @@ def p3_group_bitrade_generators(p):
+@@ -2444,7 +2444,7 @@ def p3_group_bitrade_generators(p):
      EXAMPLES::
  
          sage: from sage.combinat.matrices.latin import *
@@ -93,7 +93,7 @@ index 936edcc6ea4..c06a53d9afd 100644
           (1,2,3)(4,7,8)(5,6,9),
           (1,9,2)(3,7,4)(5,8,6),
 diff --git a/src/sage/groups/cubic_braid.py b/src/sage/groups/cubic_braid.py
-index 257b400f1c7..36423c756aa 100644
+index 61db70925e1..521289c7578 100644
 --- a/src/sage/groups/cubic_braid.py
 +++ b/src/sage/groups/cubic_braid.py
 @@ -282,7 +282,7 @@ def _richcmp_(self, other, op):
@@ -106,7 +106,7 @@ index 257b400f1c7..36423c756aa 100644
               c1*c0^-1*c1, c0^-1*c1^-1*c0^-1, c0^-1*c1^-1, c1^-1*c0*c1^-1,
               c0*c1^-1*c0^-1, c0^-1*c1, c0^-1*c1*c0, c0*c1^-1, c1*c0^-1,
 diff --git a/src/sage/groups/finitely_presented.py b/src/sage/groups/finitely_presented.py
-index 4bb52ee4efb..85f572fac6c 100644
+index 4ac2faa783b..7016d08381b 100644
 --- a/src/sage/groups/finitely_presented.py
 +++ b/src/sage/groups/finitely_presented.py
 @@ -1344,8 +1344,8 @@ def abelianization_map(self):
@@ -161,10 +161,10 @@ index 4bb52ee4efb..85f572fac6c 100644
              sage: G.characteristic_varieties(groebner=True)
              {0: [-1 + F1, 1 + F1, 1 - F1 + F1^2, 1 + F1 + F1^2], 1: [1 - F1 + F1^2],  2: []}
 diff --git a/src/sage/groups/perm_gps/permgroup_named.py b/src/sage/groups/perm_gps/permgroup_named.py
-index c1f2683907b..d219e104a2c 100644
+index 5c153b93d4c..bd4afad2942 100644
 --- a/src/sage/groups/perm_gps/permgroup_named.py
 +++ b/src/sage/groups/perm_gps/permgroup_named.py
-@@ -3468,16 +3468,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
+@@ -3465,16 +3465,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
          sage: G = SmallPermutationGroup(12,4); G
          Group of order 12 and GAP Id 4 as a permutation group
          sage: G.gens()
@@ -186,7 +186,7 @@ index c1f2683907b..d219e104a2c 100644
          sage: def numgps(n): return ZZ(libgap.NumberSmallGroups(n))
          sage: all(SmallPermutationGroup(n,k).id() == [n,k]
          ....:     for n in [1..64] for k in [1..numgps(n)])
-@@ -3486,11 +3484,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
+@@ -3483,11 +3481,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
          sage: H.is_abelian()
          False
          sage: [H.centralizer(g) for g in H.conjugacy_classes_representatives()]
diff --git a/srcpkgs/sagemath/patches/38250-numpy_2.0.patch b/srcpkgs/sagemath/patches/38250-numpy_2.0.patch
deleted file mode 100644
index e28fd857afcb75..00000000000000
--- a/srcpkgs/sagemath/patches/38250-numpy_2.0.patch
+++ /dev/null
@@ -1,587 +0,0 @@
-diff --git a/src/sage/arith/misc.py b/src/sage/arith/misc.py
-index 28f81d7b798..d184c52bf19 100644
---- a/src/sage/arith/misc.py
-+++ b/src/sage/arith/misc.py
-@@ -2277,7 +2277,7 @@ def power_mod(a, n, m):
- 
-         sage: from numpy import int32                                                   # needs numpy
-         sage: power_mod(int32(2), int32(390), int32(391))                               # needs numpy
--        285
-+        ...285...
-         sage: from gmpy2 import mpz
-         sage: power_mod(mpz(2), mpz(390), mpz(391))
-         mpz(285)
-diff --git a/src/sage/calculus/interpolators.pyx b/src/sage/calculus/interpolators.pyx
-index 221b52369e2..bb0be7bab0c 100644
---- a/src/sage/calculus/interpolators.pyx
-+++ b/src/sage/calculus/interpolators.pyx
-@@ -27,6 +27,9 @@ Development supported by NSF award No. 0702939.
- import numpy as np
- cimport numpy as np
- 
-+if int(np.version.short_version[0]) > 1:
-+    np.set_printoptions(legacy="1.25")
-+
- from math import pi
- cdef double TWOPI = 2*pi
- 
-diff --git a/src/sage/calculus/riemann.pyx b/src/sage/calculus/riemann.pyx
-index 6ec80d89aa7..c09d93c4260 100644
---- a/src/sage/calculus/riemann.pyx
-+++ b/src/sage/calculus/riemann.pyx
-@@ -44,6 +44,9 @@ from sage.calculus.integration import numerical_integral
- import numpy as np
- cimport numpy as np
- 
-+if int(np.version.short_version[0]) > 1:
-+    np.set_printoptions(legacy="1.25")
-+
- from math import pi
- from math import sin
- from math import cos
-diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index b198fed0c0d..b3ebd206cd2 100644
---- a/src/sage/combinat/fully_packed_loop.py
-+++ b/src/sage/combinat/fully_packed_loop.py
-@@ -66,6 +66,9 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
-     r"""
-     TESTS::
- 
-+        sage: import numpy as np
-+        sage: if int(np.version.short_version[0]) > 1:
-+        ....:     np.set_printoptions(legacy="1.25")
-         sage: from sage.combinat.fully_packed_loop import _make_color_list
-         sage: _make_color_list(5)
-         sage: _make_color_list(5, ['blue', 'red'])
-diff --git a/src/sage/env.py b/src/sage/env.py
-index 722649ab3da..abb9b19f9e3 100644
---- a/src/sage/env.py
-+++ b/src/sage/env.py
-@@ -296,7 +296,7 @@ def sage_include_directories(use_sources=False):
-         sage: import sage.env
-         sage: sage.env.sage_include_directories()
-         ['...',
--         '.../numpy/core/include',
-+         '.../numpy/...core/include',
-          '.../include/python...']
- 
-     To check that C/C++ files are correctly found, we verify that we can
-diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
-index e100ba3ee23..2a03bb68f67 100644
---- a/src/sage/functions/special.py
-+++ b/src/sage/functions/special.py
-@@ -217,6 +217,9 @@ class SphericalHarmonic(BuiltinFunction):
-         sage: spherical_harmonic(1, 1, pi/2, pi).n()  # abs tol 1e-14                   # needs sage.symbolic
-         0.345494149471335
-         sage: from scipy.special import sph_harm  # NB: arguments x and y are swapped   # needs scipy
-+        sage: import numpy as np                                                        # needs scipy
-+        sage: if int(np.version.short_version[0]) > 1:                                  # needs scipy
-+        ....:     np.set_printoptions(legacy="1.25")                                    # needs scipy
-         sage: sph_harm(1, 1, pi.n(), (pi/2).n())  # abs tol 1e-14                       # needs scipy sage.symbolic
-         (0.3454941494713355-4.231083042742082e-17j)
- 
-diff --git a/src/sage/graphs/generators/classical_geometries.py b/src/sage/graphs/generators/classical_geometries.py
-index da04362eef3..957f88d2061 100644
---- a/src/sage/graphs/generators/classical_geometries.py
-+++ b/src/sage/graphs/generators/classical_geometries.py
-@@ -1315,7 +1315,7 @@ def CossidentePenttilaGraph(q):
- 
-     from sage.libs.gap.libgap import libgap
-     adj_list = libgap.function_factory("""function(q)
--        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x;
-+        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x, sqo;
-         LoadPackage("grape");
-         G0:=SO(3,q^2);
-         so:=GeneratorsOfGroup(G0);
-diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
-index 063931ae274..0bafbd00564 100644
---- a/src/sage/graphs/generic_graph.py
-+++ b/src/sage/graphs/generic_graph.py
-@@ -18420,6 +18420,9 @@ def shortest_path_all_pairs(self, by_weight=False, algorithm=None,
-                 M = self.adjacency_matrix(vertices=int_to_vertex)
- 
-             # We call the Floyd-Warshall method from SciPy
-+            import numpy  # to ensure numpy 2.0 compatibility
-+            if int(numpy.version.short_version[0]) > 1:
-+                numpy.set_printoptions(legacy="1.25")
-             from numpy import array as np_array
-             from scipy.sparse.csgraph import floyd_warshall
-             dd, pp = floyd_warshall(np_array(M), directed=self.is_directed(),
-diff --git a/src/sage/graphs/graph_generators_pyx.pyx b/src/sage/graphs/graph_generators_pyx.pyx
-index 033e8b22adc..04b20d3229b 100644
---- a/src/sage/graphs/graph_generators_pyx.pyx
-+++ b/src/sage/graphs/graph_generators_pyx.pyx
-@@ -57,7 +57,7 @@ def RandomGNP(n, p, bint directed=False, bint loops=False, seed=None):
- 
-         sage: from numpy import mean                                                    # needs numpy
-         sage: abs(mean([RandomGNP(200, .2).density() for i in range(30)]) - .2) < .001  # needs numpy
--        True
-+        ...True...
-         sage: RandomGNP(150, .2, loops=True)
-         Traceback (most recent call last):
-         ...
-diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
-index a810418389c..c38df5412f0 100644
---- a/src/sage/matrix/matrix1.pyx
-+++ b/src/sage/matrix/matrix1.pyx
-@@ -705,12 +705,15 @@ cdef class Matrix(Matrix0):
-         Type ``numpy.typecodes`` for a list of the possible
-         typecodes::
- 
--            sage: import numpy                                                          # needs numpy
--            sage: sorted(numpy.typecodes.items())                                       # needs numpy
-+            sage: import numpy                            # needs numpy
-+            sage: numpy.typecodes.items()                 # needs numpy # random
-             [('All', '?bhilqpBHILQPefdgFDGSUVOMm'), ('AllFloat', 'efdgFDG'),
--             ('AllInteger', 'bBhHiIlLqQpP'), ('Character', 'c'), ('Complex', 'FDG'),
--             ('Datetime', 'Mm'), ('Float', 'efdg'), ('Integer', 'bhilqp'),
--             ('UnsignedInteger', 'BHILQP')]
-+            ...
-+
-+        For instance, you can see possibilities for real floating point numbers::
-+
-+            sage: numpy.typecodes['Float']                # needs numpy
-+            'efdg'
- 
-         Alternatively, numpy automatically calls this function (via
-         the magic :meth:`__array__` method) to convert Sage matrices
-diff --git a/src/sage/modules/free_module_element.pyx b/src/sage/modules/free_module_element.pyx
-index d71d22ac1f7..b6f297a3510 100644
---- a/src/sage/modules/free_module_element.pyx
-+++ b/src/sage/modules/free_module_element.pyx
-@@ -555,7 +555,11 @@ def vector(arg0, arg1=None, arg2=None, sparse=None, immutable=False):
-         R = None
- 
-     try:
-+        import numpy
-         from numpy import ndarray
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-+
-     except ImportError:
-         pass
-     else:
-@@ -1188,7 +1192,11 @@ cdef class FreeModuleElement(Vector):   # abstract base class
-             over Rational Field to numpy array of type <... 'float'>:
-             setting an array element with a sequence.
-         """
-+        import numpy
-         from numpy import array
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-+
-         try:
-             return array(self, dtype=dtype)
-         except ValueError as e:
-diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index e3d94d1746e..7ae8ca4966f 100644
---- a/src/sage/numerical/optimize.py
-+++ b/src/sage/numerical/optimize.py
-@@ -155,6 +155,10 @@ def find_root(f, a, b, xtol=10e-13, rtol=2.0**-50, maxiter=100, full_output=Fals
-         b = max(s_1, s_2)
- 
-     import scipy.optimize
-+    import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     g = lambda x: float(f(x))
-     brentqRes = scipy.optimize.brentq(g, a, b,
-                                  full_output=full_output, xtol=xtol, rtol=rtol, maxiter=maxiter)
-@@ -288,6 +292,10 @@ def find_local_minimum(f, a, b, tol=1.48e-08, maxfun=500):
-     a = float(a)
-     b = float(b)
-     import scipy.optimize
-+    import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     xmin, fval, iter, funcalls = scipy.optimize.fminbound(f, a, b, full_output=1, xtol=tol, maxfun=maxfun)
-     return fval, xmin
- 
-@@ -376,6 +384,8 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
-         sage: def rosen(x):  # The Rosenbrock function
-         ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
-         sage: import numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:
-+        ....:     numpy.set_printoptions(legacy="1.25")
-         sage: from numpy import zeros
-         sage: def rosen_der(x):
-         ....:    xm = x[1r:-1r]
-@@ -393,6 +403,9 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
-     from sage.structure.element import Expression
-     from sage.ext.fast_callable import fast_callable
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     from scipy import optimize
-     if isinstance(func, Expression):
-         var_list = func.variables()
-@@ -530,6 +543,8 @@ def minimize_constrained(func,cons,x0,gradient=None,algorithm='default', **args)
-     from sage.structure.element import Expression
-     from sage.ext.fast_callable import fast_callable
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-     from scipy import optimize
-     function_type = type(lambda x,y: x+y)
- 
-@@ -652,6 +667,8 @@ def find_fit(data, model, initial_guess=None, parameters=None, variables=None, s
-     ``lmdif`` and ``lmder`` algorithms.
-     """
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
- 
-     if not isinstance(data, numpy.ndarray):
-         try:
-diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index ac1dc79d802..23e2517ca56 100644
---- a/src/sage/plot/arrow.py
-+++ b/src/sage/plot/arrow.py
-@@ -53,6 +53,9 @@ def get_minmax_data(self):
- 
-         EXAMPLES::
- 
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: from sage.plot.arrow import CurveArrow
-             sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
-             ....:                options={})
-diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx
-index f1f2671a803..4d71414e1c2 100644
---- a/src/sage/plot/complex_plot.pyx
-+++ b/src/sage/plot/complex_plot.pyx
-@@ -1282,15 +1282,13 @@ def rgb_to_hls(rgb):
-         raise ValueError("Last dimension of input array must be 3; "
-                          "shape {} was found.".format(rgb.shape))
-     in_shape = rgb.shape
--    rgb = np.array(
--        rgb, copy=False, dtype=np.dtype(float), ndmin=2
--    )
-+    rgb = np.asarray(rgb, dtype=np.dtype(float))
-     rgb_max = rgb.max(-1)
-     rgb_min = rgb.min(-1)
-     l = (rgb_max + rgb_min)/2.0  # lightness
- 
-     hls = np.zeros_like(rgb)
--    delta = rgb.ptp(-1)
-+    delta = np.ptp(rgb, -1)
-     s = np.zeros_like(delta)
- 
-     ipos = delta > 0
-diff --git a/src/sage/plot/graphics.py b/src/sage/plot/graphics.py
-index a84d162cb56..94f5db09d83 100644
---- a/src/sage/plot/graphics.py
-+++ b/src/sage/plot/graphics.py
-@@ -2754,7 +2754,7 @@ def matplotlib(self, filename=None,
-             sage: xmin, xmax = sub.get_xlim()
-             sage: ymin, ymax = sub.get_ylim()
-             sage: xmin > xmax, ymin > ymax
--            (True, True)
-+            (...True..., ...True...)
-         """
-         if not isinstance(ticks, (list, tuple)):
-             ticks = (ticks, None)
-diff --git a/src/sage/plot/histogram.py b/src/sage/plot/histogram.py
-index fa86a44bd0a..a585cacf9cd 100644
---- a/src/sage/plot/histogram.py
-+++ b/src/sage/plot/histogram.py
-@@ -92,6 +92,8 @@ def get_minmax_data(self):
-             {'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.476190476190..., 'ymin': 0}
-         """
-         import numpy
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
- 
-         # Extract these options (if they are not None) and pass them to
-         # histogram()
-diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
-index b583be32317..6be448f1e04 100644
---- a/src/sage/plot/multigraphics.py
-+++ b/src/sage/plot/multigraphics.py
-@@ -784,6 +784,9 @@ def _add_subplot(self, figure, index, **options):
-             True
-             sage: G.position(1)
-             (0.2, 0.3, 0.4, 0.1)
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: ax1.get_position().bounds  # tol 1.0e-13
-             (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
- 
-@@ -1295,6 +1298,9 @@ def position(self, index):
-             sage: g1 = plot(sin(x), (x, -pi, pi))
-             sage: g2 = circle((0,1), 1.)
-             sage: G = graphics_array([g1, g2])
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: G.position(0)  # tol 5.0e-3
-             (0.025045451349937315,
-              0.03415488992713045,
-diff --git a/src/sage/plot/plot3d/implicit_surface.pyx b/src/sage/plot/plot3d/implicit_surface.pyx
-index ce0da48a4e0..f4d5059b620 100644
---- a/src/sage/plot/plot3d/implicit_surface.pyx
-+++ b/src/sage/plot/plot3d/implicit_surface.pyx
-@@ -468,6 +468,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
-             sage: cube_marcher.y_vertices.tolist()
-             [[[<1.0, 0.5, 0.0>, None]], [[None, None]]]
-             sage: cube_marcher.x_vertices.any() # This shouldn't affect the X vertices.
-+            ...
-         """
-         (self.y_vertices, self.y_vertices_swapped) = \
-             (self.y_vertices_swapped, self.y_vertices)
-@@ -574,6 +575,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
-             sage: cube_marcher.x_vertices.tolist()
-             [[None, None], [None, <1.5, 1.0, 1.0>]]
-             sage: cube_marcher.y_vertices.any() or cube_marcher.z_vertices.any() # This shouldn't affect the Y or Z vertices.
-+            ...
-         """
-         cdef bint has_prev = (_prev is not None)
-         cdef bint has_next = (_next is not None)
-diff --git a/src/sage/plot/scatter_plot.py b/src/sage/plot/scatter_plot.py
-index 4ad418f040b..781854d372c 100644
---- a/src/sage/plot/scatter_plot.py
-+++ b/src/sage/plot/scatter_plot.py
-@@ -63,9 +63,9 @@ def get_minmax_data(self):
-             sage: s = scatter_plot([[0,1],[2,4],[3.2,6]])
-             sage: d = s.get_minmax_data()
-             sage: d['xmin']
--            0.0
-+            ...0.0...
-             sage: d['ymin']
--            1.0
-+            ...1.0...
-         """
-         return {'xmin': self.xdata.min(),
-                 'xmax': self.xdata.max(),
-diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index 663d3aee70b..d2cb11088c7 100644
---- a/src/sage/plot/streamline_plot.py
-+++ b/src/sage/plot/streamline_plot.py
-@@ -71,6 +71,9 @@ def get_minmax_data(self):
-         EXAMPLES::
- 
-             sage: x, y = var('x y')
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: d = streamline_plot((.01*x, x+y), (x,10,20), (y,10,20))[0].get_minmax_data()
-             sage: d['xmin']
-             10.0
-diff --git a/src/sage/probability/probability_distribution.pyx b/src/sage/probability/probability_distribution.pyx
-index e2c71af9c25..59ba4a95ab6 100644
---- a/src/sage/probability/probability_distribution.pyx
-+++ b/src/sage/probability/probability_distribution.pyx
-@@ -140,6 +140,9 @@ cdef class ProbabilityDistribution:
-              1.8,
-              2.0]
-         """
-+        import numpy as np
-+        if int(np.version.short_version[0]) > 1:
-+            np.set_printoptions(legacy="1.25")
-         import pylab
-         ell = [float(self.get_random_element()) for _ in range(num_samples)]
-         S = pylab.hist(ell, bins, density=True)
-diff --git a/src/sage/rings/complex_double.pyx b/src/sage/rings/complex_double.pyx
-index c59a2b46d6f..b4dddebb4dc 100644
---- a/src/sage/rings/complex_double.pyx
-+++ b/src/sage/rings/complex_double.pyx
-@@ -2558,10 +2558,10 @@ cdef class ComplexToCDF(Morphism):
- 
-         sage: # needs numpy
-         sage: import numpy
--        sage: f = CDF.coerce_map_from(numpy.complex_)
--        sage: f(numpy.complex_(I))
-+        sage: f = CDF.coerce_map_from(numpy.complex128)
-+        sage: f(numpy.complex128(I))
-         1.0*I
--        sage: f(numpy.complex_(I)).parent()
-+        sage: f(numpy.complex128(I)).parent()
-         Complex Double Field
-     """
-     def __init__(self, R):
-@@ -2578,7 +2578,7 @@ cdef class ComplexToCDF(Morphism):
-         EXAMPLES::
- 
-             sage: import numpy                                                          # needs numpy
--            sage: CDF(numpy.complex_(I))    # indirect doctest                          # needs numpy
-+            sage: CDF(numpy.complex128(I))    # indirect doctest                          # needs numpy
-             1.0*I
-         """
-         cdef ComplexDoubleElement z = <ComplexDoubleElement>ComplexDoubleElement.__new__(ComplexDoubleElement)
-@@ -2592,7 +2592,7 @@ cdef class ComplexToCDF(Morphism):
-         EXAMPLES::
- 
-             sage: import numpy                                                          # needs numpy
--            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex_)            # needs numpy
-+            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex128)          # needs numpy
-             sage: f._repr_type()                                                        # needs numpy
-             'Native'
-         """
-diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index b4a1fa5039b..38c30f7627b 100644
---- a/src/sage/rings/integer.pyx
-+++ b/src/sage/rings/integer.pyx
-@@ -593,6 +593,8 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
-         Test comparisons with numpy types (see :issue:`13386` and :issue:`18076`)::
- 
-             sage: import numpy                                                          # needs numpy
-+            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
-+            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-             sage: numpy.int8('12') == 12                                                # needs numpy
-             True
-             sage: 12 == numpy.int8('12')                                                # needs numpy
-diff --git a/src/sage/rings/polynomial/polynomial_element.pyx b/src/sage/rings/polynomial/polynomial_element.pyx
-index dcf2af7cdf2..c87eccd44f1 100644
---- a/src/sage/rings/polynomial/polynomial_element.pyx
-+++ b/src/sage/rings/polynomial/polynomial_element.pyx
-@@ -8851,7 +8851,7 @@ cdef class Polynomial(CommutativePolynomial):
-                          'you expect.')
- 
-                 import numpy
--                from numpy.linalg.linalg import LinAlgError
-+                from numpy.linalg import LinAlgError
-                 from sage.rings.complex_double import CDF
- 
-                 numpy_dtype = ('complex' if input_complex else 'double')
-diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
-index 95b472e912c..76fbfedab95 100644
---- a/src/sage/rings/real_mpfi.pyx
-+++ b/src/sage/rings/real_mpfi.pyx
-@@ -231,6 +231,8 @@ specified if given a non-interval and an interval::
- TESTS::
- 
-     sage: import numpy                                                                  # needs numpy
-+    sage: if int(numpy.version.short_version[0]) > 1:                                   # needs numpy
-+    ....:     numpy.set_printoptions(legacy="1.25")                                     # needs numpy
-     sage: RIF(2) == numpy.int8('2')                                                     # needs numpy
-     True
-     sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
-diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-index 8f240627e77..70ce616f92f 100644
---- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-+++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-@@ -77,6 +77,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
-@@ -295,6 +297,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((10, 10))
-             sage: data[1:4,1:4] = True
-@@ -317,6 +321,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1,1] = True
-@@ -370,6 +376,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
- 
-             sage: data = np.zeros((20, 20))
-@@ -520,6 +528,8 @@ cdef class PeriodicRegion:
-         TESTS::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1, 1] = True
-diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index b2e6b301bf7..6937f6cb410 100644
---- a/src/sage/stats/basic_stats.py
-+++ b/src/sage/stats/basic_stats.py
-@@ -227,6 +227,8 @@ def std(v, bias=False):
- 
-         sage: # needs numpy
-         sage: import numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:
-+        ....:     numpy.set_printoptions(legacy="1.25")
-         sage: x = numpy.array([1,2,3,4,5])
-         sage: std(x, bias=False)
-         1.5811388300841898
-@@ -304,6 +306,8 @@ def variance(v, bias=False):
-         sage: variance([RIF(1.0103, 1.0103), RIF(2)])
-         0.4897530450000000?
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-         sage: x = numpy.array([1,2,3,4,5])                                              # needs numpy
-         sage: variance(x, bias=False)                                                   # needs numpy
-         2.5
-diff --git a/src/sage/stats/time_series.pyx b/src/sage/stats/time_series.pyx
-index 2e22ec45c69..23adae84fb4 100644
---- a/src/sage/stats/time_series.pyx
-+++ b/src/sage/stats/time_series.pyx
-@@ -1718,6 +1718,8 @@ cdef class TimeSeries:
-         if len(v0) == 1:
-             return v1[0]/v0[0]
-         import numpy
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-         coeffs = numpy.polyfit(v0,v1,1)
-         return coeffs[0]
- 
-diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
-index dfbd5ff82fa..955a256e9b4 100644
---- a/src/sage/structure/coerce.pyx
-+++ b/src/sage/structure/coerce.pyx
-@@ -520,6 +520,8 @@ cdef class CoercionModel:
-     Check that :issue:`8426` is fixed (see also :issue:`18076`)::
- 
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
- 
-         sage: # needs sage.rings.real_mpfr
-         sage: x = polygen(RR)
-diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
-index 2cb2f09c715..cd89ad2a256 100644
---- a/src/sage/symbolic/function.pyx
-+++ b/src/sage/symbolic/function.pyx
-@@ -964,6 +964,9 @@ cdef class BuiltinFunction(Function):
-             mpc(real='0.83373002513114902', imag='-0.98889770576286506')
- 
-             sage: import numpy                                                          # needs numpy
-+            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
-+            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-+
-             sage: sin(numpy.int32(0))                                                   # needs numpy
-             0.0
-             sage: type(_)                                                               # needs numpy
-diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 501b0920898..5b007d9e5fd 100644
---- a/src/sage/symbolic/ring.pyx
-+++ b/src/sage/symbolic/ring.pyx
-@@ -1162,6 +1162,8 @@ cdef class NumpyToSRMorphism(Morphism):
-     We check that :issue:`8949` and :issue:`9769` are fixed (see also :issue:`18076`)::
- 
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-         sage: f(x) = x^2
-         sage: f(numpy.int8('2'))                                                        # needs numpy
-         4
diff --git a/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch b/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch
deleted file mode 100644
index db0ae9030623b6..00000000000000
--- a/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-diff --git a/src/sage/interfaces/ecm.py b/src/sage/interfaces/ecm.py
-index 99287dec718..98011970404 100644
---- a/src/sage/interfaces/ecm.py
-+++ b/src/sage/interfaces/ecm.py
-@@ -508,7 +508,6 @@ def _find_factor(self, n, factor_digits, B1, **kwds):
-         """
-         n = self._validate(n)
-         kwds.setdefault('c', 1000000000)
--        kwds.setdefault('I', 1)
-         if factor_digits is not None:
-             B1 = self.recommended_B1(factor_digits)
-         kwds['one'] = True
-diff --git a/src/sage/libs/libecm.pyx b/src/sage/libs/libecm.pyx
-index 886a9b816e4..83fb7adaf8d 100644
---- a/src/sage/libs/libecm.pyx
-+++ b/src/sage/libs/libecm.pyx
-@@ -149,11 +149,13 @@ def ecmfactor(number, double B1, verbose=False, sigma=0):
-     Some special cases::
- 
-         sage: ecmfactor(1, 100)
--        (True, 1, ...)
-+        Traceback (most recent call last):
-+        ...
-+        ValueError: Input number (1) must be greater than 1
-         sage: ecmfactor(0, 100)
-         Traceback (most recent call last):
-         ...
--        ValueError: Input number (0) must be positive
-+        ValueError: Input number (0) must be greater than 1
-     """
-     cdef mpz_t n, f
-     cdef int res
-@@ -164,8 +166,8 @@ def ecmfactor(number, double B1, verbose=False, sigma=0):
-     sage_int_number = Integer(number)
-     sage_int_sigma = Integer(sigma)
- 
--    if number <= 0:
--        raise ValueError("Input number (%s) must be positive"%number)
-+    if number <= 1:
-+        raise ValueError("Input number (%s) must be greater than 1"%number)
- 
-     if verbose:
-         print("Performing one curve with B1=%1.0f" % B1)
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 28162dff8a38e1..5cab228f286365 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -19,7 +19,7 @@ get_pr() {
 	echo "curl -sL \"$url\" | filterdiff ... > \"$pr-$desc.patch\""
 	if [ -z "$dry" ]; then
 		curl -sL "$url" |
-			filterdiff -p1 -x src/setup.py -x build/* -x src/doc/* |
+			filterdiff -p1 -x src/setup.py -x environment* -x src/environment* -x build/* -x src/doc/* |
 			cat > "$pr-$desc.patch"
 	fi
 }
@@ -29,8 +29,6 @@ cd $(dirname "$0")
 
 get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
-get_pr 38250 "numpy 2.0"
-get_pr 38344 "ecm 7.0.6"
 
 #get_pr 37645 "fix doctest"
 #get_pr 37885 "cython warnings"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index befe33a0188687..f5e1d8c68cfcbe 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,7 +1,7 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.4
-revision=2
+version=10.5.beta2
+revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
 build_style=python3-pep517
@@ -25,14 +25,14 @@ depends="eclib-devel fflas-ffpack flintlib-devel gcc-fortran meson gd-devel
  python3-sympy python3-traitlets sage-data-combinatorial_designs
  python3-conway-polynomials sage-data-elliptic_curves sage-data-graphs
  sage-data-polytopes_db sympow tachyon threejs-sage"
-checkdepends="$depends pythran python3-Sphinx gdb"
+checkdepends="$depends python3-pytest pythran python3-Sphinx gdb"
 short_desc="Open source mathematics software"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=f6579e85f33bd9bb6e9b991bfc4c49dab1e649858ed9ee41c7cec75cb92d4c62
+checksum=0fe0c82dd6959951fc07d55737d270290f64947e183a403ca25709e21b751dee
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From eb7df4a9f682cf046b5c9666b666cb2d7e8d9a3d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Wed, 14 Aug 2024 00:12:02 -0300
Subject: [PATCH 3/6] sagemath: enable all cython warnings

---
 srcpkgs/sagemath/patches/37885-cython_warnings.patch | 12 ++++++++++++
 srcpkgs/sagemath/patches/get_patches                 |  2 +-
 2 files changed, 13 insertions(+), 1 deletion(-)
 create mode 100644 srcpkgs/sagemath/patches/37885-cython_warnings.patch

diff --git a/srcpkgs/sagemath/patches/37885-cython_warnings.patch b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
new file mode 100644
index 00000000000000..fa4b648cfc1577
--- /dev/null
+++ b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
@@ -0,0 +1,12 @@
+diff --git a/src/sage_setup/command/sage_build_cython.py b/src/sage_setup/command/sage_build_cython.py
+index f4b1357c543..3435c196d49 100644
+--- a/src/sage_setup/command/sage_build_cython.py
++++ b/src/sage_setup/command/sage_build_cython.py
+@@ -226,6 +226,7 @@ def run(self):
+                 compiler_directives=self.cython_directives,
+                 compile_time_env=self.compile_time_env,
+                 create_extension=self.create_extension,
++                show_all_warnings=True,
+                 # Debugging
+                 gdb_debug=self.debug,
+                 output_dir=os.path.join(self.build_lib, "sage"),
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 5cab228f286365..c182576ea553cd 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -31,4 +31,4 @@ get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
 
 #get_pr 37645 "fix doctest"
-#get_pr 37885 "cython warnings"
+get_pr 37885 "cython warnings"

From 6831717a594328f0a6efe163da56f2cf7802e040 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 19 Aug 2024 17:35:53 -0300
Subject: [PATCH 4/6] python3-numpy: update to 2.1.0.

---
 srcpkgs/python3-numpy/template | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/srcpkgs/python3-numpy/template b/srcpkgs/python3-numpy/template
index cab4e3e506df30..7d0e493b32c5bb 100644
--- a/srcpkgs/python3-numpy/template
+++ b/srcpkgs/python3-numpy/template
@@ -1,6 +1,6 @@
 # Template file for 'python3-numpy'
 pkgname=python3-numpy
-version=2.0.1
+version=2.1.0
 revision=1
 build_style=python3-pep517
 build_helper="meson qemu"
@@ -19,7 +19,7 @@ license="BSD-3-Clause"
 homepage="https://www.numpy.org/"
 changelog="https://github.com/numpy/numpy/releases"
 distfiles="${PYPI_SITE}/n/numpy/numpy-${version}.tar.gz"
-checksum=485b87235796410c3519a699cfe1faab097e509e90ebb05dcd098db2ae87e7b3
+checksum=7dc90da0081f7e1da49ec4e398ede6a8e9cc4f5ebe5f9e06b443ed889ee9aaa2
 alternatives="numpy:f2py:/usr/bin/f2py3"
 
 build_options="openblas"

From 33e6757c9f86da2ddf02a07cfd90ec7eb32f86a9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 19 Aug 2024 22:02:54 -0300
Subject: [PATCH 5/6] flintlib: C99 compliance

---
 srcpkgs/flintlib/patches/2027.patch | 322 ++++++++++++++++++++++++++++
 srcpkgs/flintlib/template           |   2 +-
 2 files changed, 323 insertions(+), 1 deletion(-)
 create mode 100644 srcpkgs/flintlib/patches/2027.patch

diff --git a/srcpkgs/flintlib/patches/2027.patch b/srcpkgs/flintlib/patches/2027.patch
new file mode 100644
index 00000000000000..f17ff31f2754d7
--- /dev/null
+++ b/srcpkgs/flintlib/patches/2027.patch
@@ -0,0 +1,322 @@
+See: https://github.com/flintlib/flint/pull/2027
+
+From 1b93e73d00881be12e04b7f13e070214a3c9e1cc Mon Sep 17 00:00:00 2001
+From: Dima Pasechnik <dima@pasechnik.info>
+Date: Wed, 19 Jun 2024 22:16:34 +0100
+Subject: [PATCH] ensure C99 compliance in headers, as 'I' is reserved
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+Note that the following code
+---- cut here: save as t.c
+---- cut here
+
+fails to compile with a suffciently new compiler, e.g. clang 16 or gcc 14.
+
+$ gcc -c t.c
+In file included from t.c:1:
+/usr/include/flint/mpoly.h:1319:43: error: expected ‘)’ before ‘__extension__’
+ 1319 | void mpoly_gcd_info_init(mpoly_gcd_info_t I, slong nvars);
+      |                                           ^
+In file included from /usr/include/flint/fmpz_types.h:15,
+                 from /usr/include/flint/fmpz_mod_types.h:15,
+                 from /usr/include/flint/mpoly_types.h:15,
+                 from /usr/include/flint/mpoly.h:23,
+                 from t.c:2:
+/usr/include/flint/mpoly.h:1319:46: error: expected ‘;’, ‘,’ or ‘)’ before ‘mp_limb_signed_t’
+ 1319 | void mpoly_gcd_info_init(mpoly_gcd_info_t I, slong nvars);
+
+...
+---
+ src/fft_small.h             |  6 +++---
+ src/fmpz_mod_mpoly_factor.h |  8 ++++----
+ src/fmpz_mpoly.h            |  2 +-
+ src/fmpz_mpoly_factor.h     | 18 +++++++++---------
+ src/fq_nmod_mpoly_factor.h  |  6 +++---
+ src/fq_zech_mpoly_factor.h  |  6 +++---
+ src/mpoly.h                 | 18 +++++++++---------
+ src/nmod_mpoly.h            |  4 ++--
+ src/nmod_mpoly_factor.h     |  6 +++---
+ 9 files changed, 37 insertions(+), 37 deletions(-)
+
+diff --git a/src/fft_small.h b/src/fft_small.h
+index 3f62f2e988..b7404f196d 100644
+--- a/src/fft_small.h
++++ b/src/fft_small.h
+@@ -242,10 +242,10 @@ FLINT_INLINE double sd_fft_ctx_get_fft_index(double* d, ulong i)
+ }
+ 
+ /* sd_fft.c */
+-void sd_fft_trunc(const sd_fft_lctx_t Q, ulong I, ulong S, ulong k, ulong j, ulong itrunc, ulong otrunc);
++void sd_fft_trunc(const sd_fft_lctx_t Q, ulong Iv, ulong S, ulong k, ulong j, ulong itrunc, ulong otrunc);
+ 
+ /* sd_ifft.c */
+-void sd_ifft_trunc(const sd_fft_lctx_t Q, ulong I, ulong S, ulong k, ulong j, ulong z, ulong n, int f);
++void sd_ifft_trunc(const sd_fft_lctx_t Q, ulong Iv, ulong S, ulong k, ulong j, ulong z, ulong n, int f);
+ 
+ /* sd_fft_ctx.c */
+ void sd_fft_ctx_clear(sd_fft_ctx_t Q);
+@@ -428,7 +428,7 @@ typedef struct {
+ 
+ typedef mpn_ctx_struct mpn_ctx_t[1];
+ 
+-void _convert_block(ulong* Xs, sd_fft_ctx_struct* Rffts, double* d, ulong dstride, ulong np, ulong I);
++void _convert_block(ulong* Xs, sd_fft_ctx_struct* Rffts, double* d, ulong dstride, ulong np, ulong Iv);
+ ulong flint_mpn_nbits(const ulong* a, ulong an);
+ int flint_mpn_cmp_ui_2exp(const ulong* a, ulong an, ulong b, ulong e);
+ unsigned char flint_mpn_add_inplace_c(ulong* z, ulong zn, ulong* a, ulong an, unsigned char cf);
+diff --git a/src/fmpz_mod_mpoly_factor.h b/src/fmpz_mod_mpoly_factor.h
+index 359fdd1e3d..460695dd23 100644
+--- a/src/fmpz_mod_mpoly_factor.h
++++ b/src/fmpz_mod_mpoly_factor.h
+@@ -1203,15 +1203,15 @@ typedef struct {
+ typedef fmpz_mod_mpoly_pfrac_struct fmpz_mod_mpoly_pfrac_t[1];
+ 
+ 
+-int fmpz_mod_mpoly_pfrac_init(fmpz_mod_mpoly_pfrac_t I,
++int fmpz_mod_mpoly_pfrac_init(fmpz_mod_mpoly_pfrac_t Iv,
+     flint_bitcnt_t bits, slong l, slong r, const fmpz_mod_mpoly_struct * betas,
+                           const fmpz * alpha, const fmpz_mod_mpoly_ctx_t ctx);
+ 
+-void fmpz_mod_mpoly_pfrac_clear(fmpz_mod_mpoly_pfrac_t I,
++void fmpz_mod_mpoly_pfrac_clear(fmpz_mod_mpoly_pfrac_t Iv,
+                                               const fmpz_mod_mpoly_ctx_t ctx);
+ 
+ int fmpz_mod_mpoly_pfrac(slong r, fmpz_mod_mpoly_t t, const slong * deg,
+-                     fmpz_mod_mpoly_pfrac_t I, const fmpz_mod_mpoly_ctx_t ctx);
++                     fmpz_mod_mpoly_pfrac_t Iv, const fmpz_mod_mpoly_ctx_t ctx);
+ 
+ int fmpz_mod_mpoly_hlift(slong m, fmpz_mod_mpoly_struct * f, slong r,
+             const fmpz * alpha, const fmpz_mod_mpoly_t A, const slong * degs,
+@@ -1290,7 +1290,7 @@ int fmpz_mod_mpolyn_gcd_brown_smprime(
+     fmpz_mod_mpolyn_t B,
+     slong var,
+     const fmpz_mod_mpoly_ctx_t ctx,
+-    const mpoly_gcd_info_t I,
++    const mpoly_gcd_info_t Iv,
+     fmpz_mod_poly_polyun_mpolyn_stack_t St);
+ 
+ int fmpz_mod_mpolyl_gcdp_zippel(
+diff --git a/src/fmpz_mpoly.h b/src/fmpz_mpoly.h
+index b7c9677915..4be3d05c56 100644
+--- a/src/fmpz_mpoly.h
++++ b/src/fmpz_mpoly.h
+@@ -1084,7 +1084,7 @@ void fmpz_mpoly_vec_randtest_not_zero(fmpz_mpoly_vec_t vec, flint_rand_t state,
+ 
+ void fmpz_mpoly_spoly(fmpz_mpoly_t res, const fmpz_mpoly_t f, const fmpz_mpoly_t g, const fmpz_mpoly_ctx_t ctx);
+ void fmpz_mpoly_vec_set_primitive_unique(fmpz_mpoly_vec_t G, const fmpz_mpoly_vec_t F, const fmpz_mpoly_ctx_t ctx);
+-void fmpz_mpoly_reduction_primitive_part(fmpz_mpoly_t res, const fmpz_mpoly_t f, const fmpz_mpoly_vec_t I, const fmpz_mpoly_ctx_t ctx);
++void fmpz_mpoly_reduction_primitive_part(fmpz_mpoly_t res, const fmpz_mpoly_t f, const fmpz_mpoly_vec_t Iv, const fmpz_mpoly_ctx_t ctx);
+ int fmpz_mpoly_vec_is_groebner(const fmpz_mpoly_vec_t G, const fmpz_mpoly_vec_t F, const fmpz_mpoly_ctx_t ctx);
+ void fmpz_mpoly_buchberger_naive(fmpz_mpoly_vec_t G, const fmpz_mpoly_vec_t F, const fmpz_mpoly_ctx_t ctx);
+ int fmpz_mpoly_buchberger_naive_with_limits(fmpz_mpoly_vec_t G, const fmpz_mpoly_vec_t F,
+diff --git a/src/fmpz_mpoly_factor.h b/src/fmpz_mpoly_factor.h
+index 0da7c1052b..a04ef8021e 100644
+--- a/src/fmpz_mpoly_factor.h
++++ b/src/fmpz_mpoly_factor.h
+@@ -298,11 +298,11 @@ void fmpz_mpoly_from_mpolyl_perm_inflate(fmpz_mpoly_t A,
+ 
+ int fmpz_mpolyl_gcd_brown(fmpz_mpoly_t G,
+         fmpz_mpoly_t Abar, fmpz_mpoly_t Bbar, fmpz_mpoly_t A, fmpz_mpoly_t B,
+-                         const fmpz_mpoly_ctx_t ctx, const mpoly_gcd_info_t I);
++                         const fmpz_mpoly_ctx_t ctx, const mpoly_gcd_info_t Iv);
+ 
+ int fmpz_mpolyl_gcd_brown_threaded_pool(fmpz_mpoly_t G,
+         fmpz_mpoly_t Abar, fmpz_mpoly_t Bbar, fmpz_mpoly_t A, fmpz_mpoly_t B,
+-                         const fmpz_mpoly_ctx_t ctx, const mpoly_gcd_info_t I,
++                         const fmpz_mpoly_ctx_t ctx, const mpoly_gcd_info_t Iv,
+                         const thread_pool_handle * handles, slong num_handles);
+ 
+ int fmpz_mpolyl_gcd_zippel(fmpz_mpoly_t G, fmpz_mpoly_t Abar,
+@@ -340,15 +340,15 @@ typedef struct {
+ 
+ typedef fmpz_poly_pfrac_struct fmpz_poly_pfrac_t[1];
+ 
+-void fmpz_poly_pfrac_init(fmpz_poly_pfrac_t I);
++void fmpz_poly_pfrac_init(fmpz_poly_pfrac_t Iv);
+ 
+-void fmpz_poly_pfrac_clear(fmpz_poly_pfrac_t I);
++void fmpz_poly_pfrac_clear(fmpz_poly_pfrac_t Iv);
+ 
+-int fmpz_poly_pfrac_precompute(fmpz_poly_pfrac_t I,
++int fmpz_poly_pfrac_precompute(fmpz_poly_pfrac_t Iv,
+                                           const fmpz_poly_struct * b, slong r);
+ 
+ int fmpz_poly_pfrac_precomp(fmpz_poly_struct * c,
+-                                     const fmpz_poly_t A, fmpz_poly_pfrac_t I);
++                                     const fmpz_poly_t A, fmpz_poly_pfrac_t Iv);
+ 
+ typedef struct {
+     flint_bitcnt_t bits;
+@@ -372,15 +372,15 @@ typedef struct {
+ 
+ typedef fmpz_mpoly_pfrac_struct fmpz_mpoly_pfrac_t[1];
+ 
+-int fmpz_mpoly_pfrac_init(fmpz_mpoly_pfrac_t I, flint_bitcnt_t bits,
++int fmpz_mpoly_pfrac_init(fmpz_mpoly_pfrac_t Iv, flint_bitcnt_t bits,
+                             slong r, slong w, const fmpz_mpoly_struct * betas,
+                                const fmpz * alpha, const fmpz_mpoly_ctx_t ctx);
+ 
+-void fmpz_mpoly_pfrac_clear(fmpz_mpoly_pfrac_t I,
++void fmpz_mpoly_pfrac_clear(fmpz_mpoly_pfrac_t Iv,
+                                                    const fmpz_mpoly_ctx_t ctx);
+ 
+ int fmpz_mpoly_pfrac(slong l, fmpz_mpoly_t t, const slong * degs,
+-                             fmpz_mpoly_pfrac_t I, const fmpz_mpoly_ctx_t ctx);
++                             fmpz_mpoly_pfrac_t Iv, const fmpz_mpoly_ctx_t ctx);
+ 
+ int fmpz_mpoly_hlift(slong m, fmpz_mpoly_struct * f, slong r,
+                 const fmpz * alpha, const fmpz_mpoly_t A, const slong * degs,
+diff --git a/src/fq_nmod_mpoly_factor.h b/src/fq_nmod_mpoly_factor.h
+index 6289d3f1c5..29caa99aa4 100644
+--- a/src/fq_nmod_mpoly_factor.h
++++ b/src/fq_nmod_mpoly_factor.h
+@@ -427,7 +427,7 @@ typedef fq_nmod_mpoly_pfrac_struct fq_nmod_mpoly_pfrac_t[1];
+ 
+ 
+ int fq_nmod_mpoly_pfrac_init(
+-    fq_nmod_mpoly_pfrac_t I,
++    fq_nmod_mpoly_pfrac_t Iv,
+     flint_bitcnt_t bits,
+     slong l, slong r,
+     const fq_nmod_mpoly_struct * betas,
+@@ -435,14 +435,14 @@ int fq_nmod_mpoly_pfrac_init(
+     const fq_nmod_mpoly_ctx_t ctx);
+ 
+ void fq_nmod_mpoly_pfrac_clear(
+-    fq_nmod_mpoly_pfrac_t I,
++    fq_nmod_mpoly_pfrac_t Iv,
+     const fq_nmod_mpoly_ctx_t ctx);
+ 
+ int fq_nmod_mpoly_pfrac(
+     slong r,
+     fq_nmod_mpoly_t t,
+     const slong * deg,
+-    fq_nmod_mpoly_pfrac_t I,
++    fq_nmod_mpoly_pfrac_t Iv,
+     const fq_nmod_mpoly_ctx_t ctx);
+ 
+ int fq_nmod_mpoly_hlift(
+diff --git a/src/fq_zech_mpoly_factor.h b/src/fq_zech_mpoly_factor.h
+index 06f31369f9..3d3c51419f 100644
+--- a/src/fq_zech_mpoly_factor.h
++++ b/src/fq_zech_mpoly_factor.h
+@@ -652,7 +652,7 @@ typedef fq_zech_mpoly_pfrac_struct fq_zech_mpoly_pfrac_t[1];
+ 
+ 
+ int fq_zech_mpoly_pfrac_init(
+-    fq_zech_mpoly_pfrac_t I,
++    fq_zech_mpoly_pfrac_t Iv,
+     flint_bitcnt_t bits,
+     slong l, slong r,
+     const fq_zech_mpoly_struct * betas,
+@@ -660,14 +660,14 @@ int fq_zech_mpoly_pfrac_init(
+     const fq_zech_mpoly_ctx_t ctx);
+ 
+ void fq_zech_mpoly_pfrac_clear(
+-    fq_zech_mpoly_pfrac_t I,
++    fq_zech_mpoly_pfrac_t Iv,
+     const fq_zech_mpoly_ctx_t ctx);
+ 
+ int fq_zech_mpoly_pfrac(
+     slong r,
+     fq_zech_mpoly_t t,
+     const slong * deg,
+-    fq_zech_mpoly_pfrac_t I,
++    fq_zech_mpoly_pfrac_t Iv,
+     const fq_zech_mpoly_ctx_t ctx);
+ 
+ int fq_zech_mpoly_hlift(
+diff --git a/src/mpoly.h b/src/mpoly.h
+index b0950e3a48..fe0ccbe7c4 100644
+--- a/src/mpoly.h
++++ b/src/mpoly.h
+@@ -1363,9 +1363,9 @@ typedef struct
+ 
+ typedef mpoly_gcd_info_struct mpoly_gcd_info_t[1];
+ 
+-void mpoly_gcd_info_init(mpoly_gcd_info_t I, slong nvars);
++void mpoly_gcd_info_init(mpoly_gcd_info_t Iv, slong nvars);
+ 
+-void mpoly_gcd_info_clear(mpoly_gcd_info_t I);
++void mpoly_gcd_info_clear(mpoly_gcd_info_t Iv);
+ 
+ void mpoly_gcd_info_limits(ulong * Amax_exp, ulong * Amin_exp,
+                        slong * Amax_exp_count, slong * Amin_exp_count,
+@@ -1378,25 +1378,25 @@ void mpoly_gcd_info_stride(ulong * strides,
+                              const ulong * Bmax_exp, const ulong * Bmin_exp,
+                                                        const mpoly_ctx_t mctx);
+ 
+-void mpoly_gcd_info_set_perm(mpoly_gcd_info_t I,
++void mpoly_gcd_info_set_perm(mpoly_gcd_info_t Iv,
+                          slong Alength, slong Blength, const mpoly_ctx_t mctx);
+ 
+-slong mpoly_gcd_info_get_brown_upper_limit(const mpoly_gcd_info_t I,
++slong mpoly_gcd_info_get_brown_upper_limit(const mpoly_gcd_info_t Iv,
+                                                        slong var, slong bound);
+ 
+-void mpoly_gcd_info_measure_hensel(mpoly_gcd_info_t I,
++void mpoly_gcd_info_measure_hensel(mpoly_gcd_info_t Iv,
+                          slong Alength, slong Blength, const mpoly_ctx_t mctx);
+ 
+-void mpoly_gcd_info_measure_brown(mpoly_gcd_info_t I,
++void mpoly_gcd_info_measure_brown(mpoly_gcd_info_t Iv,
+                          slong Alength, slong Blength, const mpoly_ctx_t mctx);
+ 
+-void mpoly_gcd_info_measure_bma(mpoly_gcd_info_t I,
++void mpoly_gcd_info_measure_bma(mpoly_gcd_info_t Iv,
+                          slong Alength, slong Blength, const mpoly_ctx_t mctx);
+ 
+-void mpoly_gcd_info_measure_zippel(mpoly_gcd_info_t I,
++void mpoly_gcd_info_measure_zippel(mpoly_gcd_info_t Iv,
+                          slong Alength, slong Blength, const mpoly_ctx_t mctx);
+ 
+-void mpoly_gcd_info_measure_zippel2(mpoly_gcd_info_t I,
++void mpoly_gcd_info_measure_zippel2(mpoly_gcd_info_t Iv,
+                          slong Alength, slong Blength, const mpoly_ctx_t mctx);
+ 
+ int mpoly_monomial_cofactors(fmpz * Abarexps, fmpz * Bbarexps,
+diff --git a/src/nmod_mpoly.h b/src/nmod_mpoly.h
+index 2a8136e6eb..716ac9669a 100644
+--- a/src/nmod_mpoly.h
++++ b/src/nmod_mpoly.h
+@@ -1619,13 +1619,13 @@ int nmod_mpolyn_gcd_brown_smprime_bivar(
+ int nmod_mpolyn_gcd_brown_smprime(nmod_mpolyn_t G,
+                                   nmod_mpolyn_t Abar, nmod_mpolyn_t Bbar,
+                                  nmod_mpolyn_t A, nmod_mpolyn_t B, slong var,
+-                         const nmod_mpoly_ctx_t ctx, const mpoly_gcd_info_t I,
++                         const nmod_mpoly_ctx_t ctx, const mpoly_gcd_info_t Iv,
+                                                          nmod_poly_stack_t Sp);
+ 
+ int nmod_mpolyn_gcd_brown_smprime_threaded_pool(nmod_mpolyn_t G,
+                                 nmod_mpolyn_t Abar, nmod_mpolyn_t Bbar,
+                                nmod_mpolyn_t A, nmod_mpolyn_t B, slong var,
+-                         const nmod_mpoly_ctx_t ctx, const mpoly_gcd_info_t I,
++                         const nmod_mpoly_ctx_t ctx, const mpoly_gcd_info_t Iv,
+                         const thread_pool_handle * handles, slong num_workers);
+ 
+ int nmod_mpolyn_gcd_brown_lgprime(nmod_mpolyn_t G,
+diff --git a/src/nmod_mpoly_factor.h b/src/nmod_mpoly_factor.h
+index a46afc860f..b16c802b9b 100644
+--- a/src/nmod_mpoly_factor.h
++++ b/src/nmod_mpoly_factor.h
+@@ -362,15 +362,15 @@ typedef struct {
+ typedef nmod_mpoly_pfrac_struct nmod_mpoly_pfrac_t[1];
+ 
+ 
+-int nmod_mpoly_pfrac_init(nmod_mpoly_pfrac_t I, flint_bitcnt_t bits,
++int nmod_mpoly_pfrac_init(nmod_mpoly_pfrac_t Iv, flint_bitcnt_t bits,
+                          slong l, slong r, const nmod_mpoly_struct * betas,
+                           const mp_limb_t * alpha, const nmod_mpoly_ctx_t ctx);
+ 
+-void nmod_mpoly_pfrac_clear(nmod_mpoly_pfrac_t I,
++void nmod_mpoly_pfrac_clear(nmod_mpoly_pfrac_t Iv,
+                                                    const nmod_mpoly_ctx_t ctx);
+ 
+ int nmod_mpoly_pfrac(slong r, nmod_mpoly_t t, const slong * deg,
+-                             nmod_mpoly_pfrac_t I, const nmod_mpoly_ctx_t ctx);
++                             nmod_mpoly_pfrac_t Iv, const nmod_mpoly_ctx_t ctx);
+ 
+ int nmod_mpoly_hlift(slong m, nmod_mpoly_struct * f, slong r,
+             const mp_limb_t * alpha, const nmod_mpoly_t A, const slong * degs,
diff --git a/srcpkgs/flintlib/template b/srcpkgs/flintlib/template
index 613391a9a0ae1b..465cdf1d0d3f71 100644
--- a/srcpkgs/flintlib/template
+++ b/srcpkgs/flintlib/template
@@ -1,7 +1,7 @@
 # Template file for 'flintlib'
 pkgname=flintlib
 version=3.1.2
-revision=1
+revision=2
 build_style=gnu-configure
 configure_args="--prefix=/usr --disable-arch $(vopt_with ntl)
  $(vopt_if openblas --with-blas-include=${XBPS_CROSS_BASE}/usr/include/openblas)"

From 86dd81ae8b6540ff0ff27c9d3b0686578a802cf3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 20 Aug 2024 17:56:06 -0300
Subject: [PATCH 6/6] sagemath: patch for numpy 2.1

---
 srcpkgs/sagemath/patches/numpy_2.1a.patch |  20 ++
 srcpkgs/sagemath/patches/numpy_2.1b.patch | 223 ++++++++++++++++++++++
 2 files changed, 243 insertions(+)
 create mode 100644 srcpkgs/sagemath/patches/numpy_2.1a.patch
 create mode 100644 srcpkgs/sagemath/patches/numpy_2.1b.patch

diff --git a/srcpkgs/sagemath/patches/numpy_2.1a.patch b/srcpkgs/sagemath/patches/numpy_2.1a.patch
new file mode 100644
index 00000000000000..a2b77d61168bf9
--- /dev/null
+++ b/srcpkgs/sagemath/patches/numpy_2.1a.patch
@@ -0,0 +1,20 @@
+--- a/src/sage/matrix/matrix1.pyx
++++ b/src/sage/matrix/matrix1.pyx
+@@ -670,7 +670,7 @@ cdef class Matrix(Matrix0):
+             entries = [[sib(v, 2) for v in row] for row in self.rows()]
+             return sib.name('matrix')(self.base_ring(), entries)
+ 
+-    def numpy(self, dtype=None):
++    def numpy(self, dtype=None, copy=True):
+         """
+         Return the Numpy matrix associated to this matrix.
+ 
+@@ -731,7 +731,7 @@ cdef class Matrix(Matrix0):
+             (3, 4)
+         """
+         import numpy
+-        A = numpy.matrix(self.list(), dtype=dtype)
++        A = numpy.matrix(self.list(), dtype=dtype, copy=copy)
+         return numpy.resize(A,(self.nrows(), self.ncols()))
+ 
+     # Define the magic "__array__" function so that numpy.array(m) can convert
diff --git a/srcpkgs/sagemath/patches/numpy_2.1b.patch b/srcpkgs/sagemath/patches/numpy_2.1b.patch
new file mode 100644
index 00000000000000..e59b8940e9d9a2
--- /dev/null
+++ b/srcpkgs/sagemath/patches/numpy_2.1b.patch
@@ -0,0 +1,223 @@
+diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
+index b3ebd206cd2..d61242928dc 100644
+--- a/src/sage/combinat/fully_packed_loop.py
++++ b/src/sage/combinat/fully_packed_loop.py
+@@ -68,7 +68,7 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
+ 
+         sage: import numpy as np
+         sage: if int(np.version.short_version[0]) > 1:
+-        ....:     np.set_printoptions(legacy="1.25")
++        ....:     np.set_printoptions(legacy="1.25") and None
+         sage: from sage.combinat.fully_packed_loop import _make_color_list
+         sage: _make_color_list(5)
+         sage: _make_color_list(5, ['blue', 'red'])
+diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
+index 2a03bb68f67..fbde392f954 100644
+--- a/src/sage/functions/special.py
++++ b/src/sage/functions/special.py
+@@ -219,7 +219,7 @@ class SphericalHarmonic(BuiltinFunction):
+         sage: from scipy.special import sph_harm  # NB: arguments x and y are swapped   # needs scipy
+         sage: import numpy as np                                                        # needs scipy
+         sage: if int(np.version.short_version[0]) > 1:                                  # needs scipy
+-        ....:     np.set_printoptions(legacy="1.25")                                    # needs scipy
++        ....:     np.set_printoptions(legacy="1.25") and None                           # needs scipy
+         sage: sph_harm(1, 1, pi.n(), (pi/2).n())  # abs tol 1e-14                       # needs scipy sage.symbolic
+         (0.3454941494713355-4.231083042742082e-17j)
+ 
+diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
+index 7ae8ca4966f..e3633c6c423 100644
+--- a/src/sage/numerical/optimize.py
++++ b/src/sage/numerical/optimize.py
+@@ -385,7 +385,7 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
+         ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
+         sage: import numpy
+         sage: if int(numpy.version.short_version[0]) > 1:
+-        ....:     numpy.set_printoptions(legacy="1.25")
++        ....:     numpy.set_printoptions(legacy="1.25") and None
+         sage: from numpy import zeros
+         sage: def rosen_der(x):
+         ....:    xm = x[1r:-1r]
+diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
+index 23e2517ca56..96f85a4d944 100644
+--- a/src/sage/plot/arrow.py
++++ b/src/sage/plot/arrow.py
+@@ -55,7 +55,7 @@ class CurveArrow(GraphicPrimitive):
+ 
+             sage: import numpy  # to ensure numpy 2.0 compatibility
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     numpy.set_printoptions(legacy="1.25") and None
+             sage: from sage.plot.arrow import CurveArrow
+             sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
+             ....:                options={})
+diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
+index 6be448f1e04..3b44fdd90b1 100644
+--- a/src/sage/plot/multigraphics.py
++++ b/src/sage/plot/multigraphics.py
+@@ -786,7 +786,7 @@ class MultiGraphics(WithEqualityById, SageObject):
+             (0.2, 0.3, 0.4, 0.1)
+             sage: import numpy  # to ensure numpy 2.0 compatibility
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     numpy.set_printoptions(legacy="1.25") and None
+             sage: ax1.get_position().bounds  # tol 1.0e-13
+             (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
+ 
+@@ -1300,7 +1300,7 @@ class GraphicsArray(MultiGraphics):
+             sage: G = graphics_array([g1, g2])
+             sage: import numpy  # to ensure numpy 2.0 compatibility
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     numpy.set_printoptions(legacy="1.25") and None
+             sage: G.position(0)  # tol 5.0e-3
+             (0.025045451349937315,
+              0.03415488992713045,
+diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
+index d2cb11088c7..b05c21692fb 100644
+--- a/src/sage/plot/streamline_plot.py
++++ b/src/sage/plot/streamline_plot.py
+@@ -73,7 +73,7 @@ class StreamlinePlot(GraphicPrimitive):
+             sage: x, y = var('x y')
+             sage: import numpy  # to ensure numpy 2.0 compatibility
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     numpy.set_printoptions(legacy="1.25") and None
+             sage: d = streamline_plot((.01*x, x+y), (x,10,20), (y,10,20))[0].get_minmax_data()
+             sage: d['xmin']
+             10.0
+diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
+index 38c30f7627b..c6d31b51747 100644
+--- a/src/sage/rings/integer.pyx
++++ b/src/sage/rings/integer.pyx
+@@ -594,7 +594,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
+             sage: # needs numpy 
+             sage: import numpy
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     numpy.set_printoptions(legacy="1.25") and None
+             sage: numpy.int8('12') == 12
+             True
+             sage: 12 == numpy.int8('12')
+diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
+index 76fbfedab95..62aa3e60821 100644
+--- a/src/sage/rings/real_mpfi.pyx
++++ b/src/sage/rings/real_mpfi.pyx
+@@ -232,7 +232,7 @@ TESTS::
+ 
+     sage: import numpy                                                                  # needs numpy
+     sage: if int(numpy.version.short_version[0]) > 1:                                   # needs numpy
+-    ....:     numpy.set_printoptions(legacy="1.25")                                     # needs numpy
++    ....:     numpy.set_printoptions(legacy="1.25") and None                            # needs numpy
+     sage: RIF(2) == numpy.int8('2')                                                     # needs numpy
+     True
+     sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
+diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
+index 70ce616f92f..f6db3703307 100644
+--- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
++++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
+@@ -78,7 +78,7 @@ cdef class PeriodicRegion:
+ 
+             sage: import numpy as np
+             sage: if int(np.version.short_version[0]) > 1:
+-            ....:     np.set_printoptions(legacy="1.25")
++            ....:     np.set_printoptions(legacy="1.25") and None
+             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
+             sage: data = np.zeros((4, 4))
+             sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
+@@ -298,7 +298,7 @@ cdef class PeriodicRegion:
+ 
+             sage: import numpy as np
+             sage: if int(np.version.short_version[0]) > 1:
+-            ....:     np.set_printoptions(legacy="1.25")
++            ....:     np.set_printoptions(legacy="1.25") and None
+             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
+             sage: data = np.zeros((10, 10))
+             sage: data[1:4,1:4] = True
+@@ -322,7 +322,7 @@ cdef class PeriodicRegion:
+ 
+             sage: import numpy as np
+             sage: if int(np.version.short_version[0]) > 1:
+-            ....:     np.set_printoptions(legacy="1.25")
++            ....:     np.set_printoptions(legacy="1.25") and None
+             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
+             sage: data = np.zeros((4, 4))
+             sage: data[1,1] = True
+@@ -377,7 +377,7 @@ cdef class PeriodicRegion:
+ 
+             sage: import numpy as np
+             sage: if int(np.version.short_version[0]) > 1:
+-            ....:     np.set_printoptions(legacy="1.25")
++            ....:     np.set_printoptions(legacy="1.25") and None
+             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
+ 
+             sage: data = np.zeros((20, 20))
+@@ -529,7 +529,7 @@ cdef class PeriodicRegion:
+ 
+             sage: import numpy as np
+             sage: if int(np.version.short_version[0]) > 1:
+-            ....:     np.set_printoptions(legacy="1.25")
++            ....:     np.set_printoptions(legacy="1.25") and None
+             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
+             sage: data = np.zeros((4, 4))
+             sage: data[1, 1] = True
+diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
+index 6937f6cb410..154a897b89b 100644
+--- a/src/sage/stats/basic_stats.py
++++ b/src/sage/stats/basic_stats.py
+@@ -228,7 +228,7 @@ def std(v, bias=False):
+         sage: # needs numpy
+         sage: import numpy
+         sage: if int(numpy.version.short_version[0]) > 1:
+-        ....:     numpy.set_printoptions(legacy="1.25")
++        ....:     numpy.set_printoptions(legacy="1.25") and None
+         sage: x = numpy.array([1,2,3,4,5])
+         sage: std(x, bias=False)
+         1.5811388300841898
+@@ -307,7 +307,7 @@ def variance(v, bias=False):
+         0.4897530450000000?
+         sage: import numpy                                                              # needs numpy
+         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
+-        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
++        ....:     numpy.set_printoptions(legacy="1.25") and None                        # needs numpy
+         sage: x = numpy.array([1,2,3,4,5])                                              # needs numpy
+         sage: variance(x, bias=False)                                                   # needs numpy
+         2.5
+diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
+index 955a256e9b4..dfa02de288e 100644
+--- a/src/sage/structure/coerce.pyx
++++ b/src/sage/structure/coerce.pyx
+@@ -521,7 +521,7 @@ cdef class CoercionModel:
+ 
+         sage: import numpy                                                              # needs numpy
+         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
+-        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
++        ....:     numpy.set_printoptions(legacy="1.25") and None                        # needs numpy
+ 
+         sage: # needs sage.rings.real_mpfr
+         sage: x = polygen(RR)
+diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
+index cd89ad2a256..28d9acb8de9 100644
+--- a/src/sage/symbolic/function.pyx
++++ b/src/sage/symbolic/function.pyx
+@@ -965,7 +965,7 @@ cdef class BuiltinFunction(Function):
+ 
+             sage: import numpy                                                          # needs numpy
+             sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
+-            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
++            ....:     numpy.set_printoptions(legacy="1.25") and None                    # needs numpy
+ 
+             sage: sin(numpy.int32(0))                                                   # needs numpy
+             0.0
+diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
+index 5b007d9e5fd..acf7a0c7003 100644
+--- a/src/sage/symbolic/ring.pyx
++++ b/src/sage/symbolic/ring.pyx
+@@ -1163,7 +1163,7 @@ cdef class NumpyToSRMorphism(Morphism):
+ 
+         sage: import numpy                                                              # needs numpy
+         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
+-        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
++        ....:     numpy.set_printoptions(legacy="1.25") and None                        # needs numpy
+         sage: f(x) = x^2
+         sage: f(numpy.int8('2'))                                                        # needs numpy
+         4

^ permalink raw reply	[flat|nested] 13+ messages in thread

* Re: [PR PATCH] [Updated] [BETA] sagemath: update to 10.5.beta2
  2024-08-18 17:54 [PR PATCH] [BETA] sagemath: update to 10.5.beta2 tornaria
  2024-08-20 20:57 ` [PR PATCH] [Updated] " tornaria
@ 2024-08-21  1:11 ` tornaria
  2024-08-22  2:10 ` tornaria
                   ` (9 subsequent siblings)
  11 siblings, 0 replies; 13+ messages in thread
From: tornaria @ 2024-08-21  1:11 UTC (permalink / raw)
  To: ml

[-- Attachment #1: Type: text/plain, Size: 1465 bytes --]

There is an updated pull request by tornaria against master on the void-packages repository

https://github.com/tornaria/void-packages sagemath
https://github.com/void-linux/void-packages/pull/51902

[BETA] sagemath: update to 10.5.beta2
<!-- Uncomment relevant sections and delete options which are not applicable -->

 - python3-Cython: alternative fix for 6122
 - python3-gmpy2: update to 2.2.1.
 - python3-cypari2: update to 2.2.0.
 - python3-sympy: update to 1.13.2.
 - sagemath: enable all cython warnings

#### Testing the changes
- I tested the changes in this PR: **YES**

@dkwo

<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->

<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration
and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
  - aarch64-musl
  - armv7l
  - armv6l-musl
-->


A patch file from https://github.com/void-linux/void-packages/pull/51902.patch is attached

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-sagemath-51902.patch --]
[-- Type: text/x-diff, Size: 75666 bytes --]

From 416e90f2c36dd4a394daaafb63207dba5203c706 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 11 Aug 2024 22:53:42 -0300
Subject: [PATCH 1/6] python3-Cython: alternative fix for 6122

---
 srcpkgs/python3-Cython/patches/fix-regression.patch | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/srcpkgs/python3-Cython/patches/fix-regression.patch b/srcpkgs/python3-Cython/patches/fix-regression.patch
index f2e761608e373b..f5957cfa59c2f5 100644
--- a/srcpkgs/python3-Cython/patches/fix-regression.patch
+++ b/srcpkgs/python3-Cython/patches/fix-regression.patch
@@ -15,3 +15,11 @@ serious regression, e.g. sagemath FTBS with cython 3.0.11
              warning(self.pos,
                      "Implicit noexcept declaration is deprecated."
                      " Function declaration should contain 'noexcept' keyword.",
+@@ -3128,6 +3126,7 @@ class DefNode(FuncDefNode):
+             if scope is None:
+                 scope = cfunc.scope
+             cfunc_type = cfunc.type
++            has_explicit_exc_clause=True
+             if len(self.args) != len(cfunc_type.args) or cfunc_type.has_varargs:
+                 error(self.pos, "wrong number of arguments")
+                 error(cfunc.pos, "previous declaration here")

From 21b3dad478a94fe98ddd4ca793d16eedf424e199 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 5 Aug 2024 00:21:23 -0300
Subject: [PATCH 2/6] sagemath: update to 10.5.beta2.

---
 .../sagemath/patches/36641-sympy_1.13.patch   |  22 +-
 .../sagemath/patches/37884-gap_4.13.1.patch   |  28 +-
 .../sagemath/patches/38250-numpy_2.0.patch    | 587 ------------------
 .../sagemath/patches/38344-ecm_7.0.6.patch    |  43 --
 srcpkgs/sagemath/patches/get_patches          |   4 +-
 srcpkgs/sagemath/template                     |   8 +-
 6 files changed, 22 insertions(+), 670 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/38250-numpy_2.0.patch
 delete mode 100644 srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch

diff --git a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
index 625c582cdd41b7..01e859ad023f4d 100644
--- a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
+++ b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
@@ -1,8 +1,5 @@
-diff --git a/build/pkgs/sympy/requirements.txt b/build/pkgs/sympy/requirements.txt
-new file mode 100644
-index 00000000000..3ef8f90b550
 diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py
-index 7e9eab2ff2e..43365cd645e 100644
+index 823a0d14a41..de1c8531814 100644
 --- a/src/sage/doctest/forker.py
 +++ b/src/sage/doctest/forker.py
 @@ -150,14 +150,15 @@ def init_sage(controller=None):
@@ -28,7 +25,7 @@ index 7e9eab2ff2e..43365cd645e 100644
      The displayhook sorts dictionary keys to simplify doctesting of
      dictionary output::
 diff --git a/src/sage/functions/hypergeometric.py b/src/sage/functions/hypergeometric.py
-index 010c61febe0..bbccbd20032 100644
+index ade7836b310..eb5c6665c0d 100644
 --- a/src/sage/functions/hypergeometric.py
 +++ b/src/sage/functions/hypergeometric.py
 @@ -124,7 +124,7 @@
@@ -40,21 +37,8 @@ index 010c61febe0..bbccbd20032 100644
      sage: hypergeometric((5, 4), (4, 4), 3)._mathematica_init_()                        # needs sage.symbolic
      'HypergeometricPFQ[{5,4},{4,4},3]'
  
-diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx
-index a92fe241355..f62311423be 100644
---- a/src/sage/symbolic/expression.pyx
-+++ b/src/sage/symbolic/expression.pyx
-@@ -1167,7 +1167,7 @@ cdef class Expression(Expression_abc):
-             sage: unicode_art(SR(13 - I))
-             13 - ⅈ
-             sage: unicode_art(SR(1.3 - I))
--            1.3 - ⅈ
-+            1.3 - 1.0⋅ⅈ
-             sage: unicode_art(cos(I))
-             cosh(1)
- 
 diff --git a/src/sage/typeset/ascii_art.py b/src/sage/typeset/ascii_art.py
-index 28024405d27..458fa8724a3 100644
+index 83d92af8959..e470e2bd88d 100644
 --- a/src/sage/typeset/ascii_art.py
 +++ b/src/sage/typeset/ascii_art.py
 @@ -44,11 +44,12 @@
diff --git a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
index 1550d47e2436c6..321e0a94487da3 100644
--- a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
+++ b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
@@ -1,21 +1,21 @@
 diff --git a/src/sage/algebras/fusion_rings/fusion_double.py b/src/sage/algebras/fusion_rings/fusion_double.py
-index 7ce086f70d0..954513572c3 100644
+index 71277561331..3b681d75d3b 100644
 --- a/src/sage/algebras/fusion_rings/fusion_double.py
 +++ b/src/sage/algebras/fusion_rings/fusion_double.py
 @@ -133,7 +133,7 @@ class FusionDouble(CombinatorialFreeModule):
          sage: G = SmallPermutationGroup(16,9)
-         sage: F = FusionDouble(G, prefix="b",inject_variables=True)
+         sage: F = FusionDouble(G, prefix='b', inject_variables=True)
          sage: b13^2 # long time (4s)
 -        b0 + b2 + b4 + b15 + b16 + b17 + b18 + b24 + b26 + b27
 +        b0 + b3 + b4
- 
      """
      @staticmethod
+     def __classcall_private__(cls, G, prefix='s', inject_variables=False):
 diff --git a/src/sage/categories/simplicial_sets.py b/src/sage/categories/simplicial_sets.py
-index e714a4571c4..a2b87a729d1 100644
+index aabd3cdbb4f..14bebdcd080 100644
 --- a/src/sage/categories/simplicial_sets.py
 +++ b/src/sage/categories/simplicial_sets.py
-@@ -593,9 +593,9 @@ def _canonical_twisting_operator(self):
+@@ -591,9 +591,9 @@ def _canonical_twisting_operator(self):
                      sage: X = simplicial_sets.Torus()
                      sage: d = X._canonical_twisting_operator()
                      sage: d
@@ -27,7 +27,7 @@ index e714a4571c4..a2b87a729d1 100644
                      sage: Y = simplicial_sets.RealProjectiveSpace(2)
                      sage: d2 = Y._canonical_twisting_operator()
                      sage: d2
-@@ -677,10 +677,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
+@@ -674,10 +674,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
                      sage: X = simplicial_sets.Torus()
                      sage: C = X.twisted_chain_complex()
                      sage: C.differential(1)
@@ -41,7 +41,7 @@ index e714a4571c4..a2b87a729d1 100644
                      [      -1       -1]
                      sage: C.differential(3)
                      []
-@@ -848,29 +848,29 @@ def twisted_homology(self, n, reduced=False):
+@@ -844,29 +844,29 @@ def twisted_homology(self, n, reduced=False):
                      sage: # needs sage.graphs
                      sage: Y = simplicial_sets.Torus()
                      sage: Y.twisted_homology(1)
@@ -80,10 +80,10 @@ index e714a4571c4..a2b87a729d1 100644
                      [1 0 0 0 0]
                      [0 1 0 0 0]
 diff --git a/src/sage/combinat/matrices/latin.py b/src/sage/combinat/matrices/latin.py
-index 936edcc6ea4..c06a53d9afd 100644
+index e2d818e9480..84e6c4fcc9b 100644
 --- a/src/sage/combinat/matrices/latin.py
 +++ b/src/sage/combinat/matrices/latin.py
-@@ -2453,7 +2453,7 @@ def p3_group_bitrade_generators(p):
+@@ -2444,7 +2444,7 @@ def p3_group_bitrade_generators(p):
      EXAMPLES::
  
          sage: from sage.combinat.matrices.latin import *
@@ -93,7 +93,7 @@ index 936edcc6ea4..c06a53d9afd 100644
           (1,2,3)(4,7,8)(5,6,9),
           (1,9,2)(3,7,4)(5,8,6),
 diff --git a/src/sage/groups/cubic_braid.py b/src/sage/groups/cubic_braid.py
-index 257b400f1c7..36423c756aa 100644
+index 61db70925e1..521289c7578 100644
 --- a/src/sage/groups/cubic_braid.py
 +++ b/src/sage/groups/cubic_braid.py
 @@ -282,7 +282,7 @@ def _richcmp_(self, other, op):
@@ -106,7 +106,7 @@ index 257b400f1c7..36423c756aa 100644
               c1*c0^-1*c1, c0^-1*c1^-1*c0^-1, c0^-1*c1^-1, c1^-1*c0*c1^-1,
               c0*c1^-1*c0^-1, c0^-1*c1, c0^-1*c1*c0, c0*c1^-1, c1*c0^-1,
 diff --git a/src/sage/groups/finitely_presented.py b/src/sage/groups/finitely_presented.py
-index 4bb52ee4efb..85f572fac6c 100644
+index 4ac2faa783b..7016d08381b 100644
 --- a/src/sage/groups/finitely_presented.py
 +++ b/src/sage/groups/finitely_presented.py
 @@ -1344,8 +1344,8 @@ def abelianization_map(self):
@@ -161,10 +161,10 @@ index 4bb52ee4efb..85f572fac6c 100644
              sage: G.characteristic_varieties(groebner=True)
              {0: [-1 + F1, 1 + F1, 1 - F1 + F1^2, 1 + F1 + F1^2], 1: [1 - F1 + F1^2],  2: []}
 diff --git a/src/sage/groups/perm_gps/permgroup_named.py b/src/sage/groups/perm_gps/permgroup_named.py
-index c1f2683907b..d219e104a2c 100644
+index 5c153b93d4c..bd4afad2942 100644
 --- a/src/sage/groups/perm_gps/permgroup_named.py
 +++ b/src/sage/groups/perm_gps/permgroup_named.py
-@@ -3468,16 +3468,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
+@@ -3465,16 +3465,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
          sage: G = SmallPermutationGroup(12,4); G
          Group of order 12 and GAP Id 4 as a permutation group
          sage: G.gens()
@@ -186,7 +186,7 @@ index c1f2683907b..d219e104a2c 100644
          sage: def numgps(n): return ZZ(libgap.NumberSmallGroups(n))
          sage: all(SmallPermutationGroup(n,k).id() == [n,k]
          ....:     for n in [1..64] for k in [1..numgps(n)])
-@@ -3486,11 +3484,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
+@@ -3483,11 +3481,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
          sage: H.is_abelian()
          False
          sage: [H.centralizer(g) for g in H.conjugacy_classes_representatives()]
diff --git a/srcpkgs/sagemath/patches/38250-numpy_2.0.patch b/srcpkgs/sagemath/patches/38250-numpy_2.0.patch
deleted file mode 100644
index e28fd857afcb75..00000000000000
--- a/srcpkgs/sagemath/patches/38250-numpy_2.0.patch
+++ /dev/null
@@ -1,587 +0,0 @@
-diff --git a/src/sage/arith/misc.py b/src/sage/arith/misc.py
-index 28f81d7b798..d184c52bf19 100644
---- a/src/sage/arith/misc.py
-+++ b/src/sage/arith/misc.py
-@@ -2277,7 +2277,7 @@ def power_mod(a, n, m):
- 
-         sage: from numpy import int32                                                   # needs numpy
-         sage: power_mod(int32(2), int32(390), int32(391))                               # needs numpy
--        285
-+        ...285...
-         sage: from gmpy2 import mpz
-         sage: power_mod(mpz(2), mpz(390), mpz(391))
-         mpz(285)
-diff --git a/src/sage/calculus/interpolators.pyx b/src/sage/calculus/interpolators.pyx
-index 221b52369e2..bb0be7bab0c 100644
---- a/src/sage/calculus/interpolators.pyx
-+++ b/src/sage/calculus/interpolators.pyx
-@@ -27,6 +27,9 @@ Development supported by NSF award No. 0702939.
- import numpy as np
- cimport numpy as np
- 
-+if int(np.version.short_version[0]) > 1:
-+    np.set_printoptions(legacy="1.25")
-+
- from math import pi
- cdef double TWOPI = 2*pi
- 
-diff --git a/src/sage/calculus/riemann.pyx b/src/sage/calculus/riemann.pyx
-index 6ec80d89aa7..c09d93c4260 100644
---- a/src/sage/calculus/riemann.pyx
-+++ b/src/sage/calculus/riemann.pyx
-@@ -44,6 +44,9 @@ from sage.calculus.integration import numerical_integral
- import numpy as np
- cimport numpy as np
- 
-+if int(np.version.short_version[0]) > 1:
-+    np.set_printoptions(legacy="1.25")
-+
- from math import pi
- from math import sin
- from math import cos
-diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index b198fed0c0d..b3ebd206cd2 100644
---- a/src/sage/combinat/fully_packed_loop.py
-+++ b/src/sage/combinat/fully_packed_loop.py
-@@ -66,6 +66,9 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
-     r"""
-     TESTS::
- 
-+        sage: import numpy as np
-+        sage: if int(np.version.short_version[0]) > 1:
-+        ....:     np.set_printoptions(legacy="1.25")
-         sage: from sage.combinat.fully_packed_loop import _make_color_list
-         sage: _make_color_list(5)
-         sage: _make_color_list(5, ['blue', 'red'])
-diff --git a/src/sage/env.py b/src/sage/env.py
-index 722649ab3da..abb9b19f9e3 100644
---- a/src/sage/env.py
-+++ b/src/sage/env.py
-@@ -296,7 +296,7 @@ def sage_include_directories(use_sources=False):
-         sage: import sage.env
-         sage: sage.env.sage_include_directories()
-         ['...',
--         '.../numpy/core/include',
-+         '.../numpy/...core/include',
-          '.../include/python...']
- 
-     To check that C/C++ files are correctly found, we verify that we can
-diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
-index e100ba3ee23..2a03bb68f67 100644
---- a/src/sage/functions/special.py
-+++ b/src/sage/functions/special.py
-@@ -217,6 +217,9 @@ class SphericalHarmonic(BuiltinFunction):
-         sage: spherical_harmonic(1, 1, pi/2, pi).n()  # abs tol 1e-14                   # needs sage.symbolic
-         0.345494149471335
-         sage: from scipy.special import sph_harm  # NB: arguments x and y are swapped   # needs scipy
-+        sage: import numpy as np                                                        # needs scipy
-+        sage: if int(np.version.short_version[0]) > 1:                                  # needs scipy
-+        ....:     np.set_printoptions(legacy="1.25")                                    # needs scipy
-         sage: sph_harm(1, 1, pi.n(), (pi/2).n())  # abs tol 1e-14                       # needs scipy sage.symbolic
-         (0.3454941494713355-4.231083042742082e-17j)
- 
-diff --git a/src/sage/graphs/generators/classical_geometries.py b/src/sage/graphs/generators/classical_geometries.py
-index da04362eef3..957f88d2061 100644
---- a/src/sage/graphs/generators/classical_geometries.py
-+++ b/src/sage/graphs/generators/classical_geometries.py
-@@ -1315,7 +1315,7 @@ def CossidentePenttilaGraph(q):
- 
-     from sage.libs.gap.libgap import libgap
-     adj_list = libgap.function_factory("""function(q)
--        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x;
-+        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x, sqo;
-         LoadPackage("grape");
-         G0:=SO(3,q^2);
-         so:=GeneratorsOfGroup(G0);
-diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
-index 063931ae274..0bafbd00564 100644
---- a/src/sage/graphs/generic_graph.py
-+++ b/src/sage/graphs/generic_graph.py
-@@ -18420,6 +18420,9 @@ def shortest_path_all_pairs(self, by_weight=False, algorithm=None,
-                 M = self.adjacency_matrix(vertices=int_to_vertex)
- 
-             # We call the Floyd-Warshall method from SciPy
-+            import numpy  # to ensure numpy 2.0 compatibility
-+            if int(numpy.version.short_version[0]) > 1:
-+                numpy.set_printoptions(legacy="1.25")
-             from numpy import array as np_array
-             from scipy.sparse.csgraph import floyd_warshall
-             dd, pp = floyd_warshall(np_array(M), directed=self.is_directed(),
-diff --git a/src/sage/graphs/graph_generators_pyx.pyx b/src/sage/graphs/graph_generators_pyx.pyx
-index 033e8b22adc..04b20d3229b 100644
---- a/src/sage/graphs/graph_generators_pyx.pyx
-+++ b/src/sage/graphs/graph_generators_pyx.pyx
-@@ -57,7 +57,7 @@ def RandomGNP(n, p, bint directed=False, bint loops=False, seed=None):
- 
-         sage: from numpy import mean                                                    # needs numpy
-         sage: abs(mean([RandomGNP(200, .2).density() for i in range(30)]) - .2) < .001  # needs numpy
--        True
-+        ...True...
-         sage: RandomGNP(150, .2, loops=True)
-         Traceback (most recent call last):
-         ...
-diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
-index a810418389c..c38df5412f0 100644
---- a/src/sage/matrix/matrix1.pyx
-+++ b/src/sage/matrix/matrix1.pyx
-@@ -705,12 +705,15 @@ cdef class Matrix(Matrix0):
-         Type ``numpy.typecodes`` for a list of the possible
-         typecodes::
- 
--            sage: import numpy                                                          # needs numpy
--            sage: sorted(numpy.typecodes.items())                                       # needs numpy
-+            sage: import numpy                            # needs numpy
-+            sage: numpy.typecodes.items()                 # needs numpy # random
-             [('All', '?bhilqpBHILQPefdgFDGSUVOMm'), ('AllFloat', 'efdgFDG'),
--             ('AllInteger', 'bBhHiIlLqQpP'), ('Character', 'c'), ('Complex', 'FDG'),
--             ('Datetime', 'Mm'), ('Float', 'efdg'), ('Integer', 'bhilqp'),
--             ('UnsignedInteger', 'BHILQP')]
-+            ...
-+
-+        For instance, you can see possibilities for real floating point numbers::
-+
-+            sage: numpy.typecodes['Float']                # needs numpy
-+            'efdg'
- 
-         Alternatively, numpy automatically calls this function (via
-         the magic :meth:`__array__` method) to convert Sage matrices
-diff --git a/src/sage/modules/free_module_element.pyx b/src/sage/modules/free_module_element.pyx
-index d71d22ac1f7..b6f297a3510 100644
---- a/src/sage/modules/free_module_element.pyx
-+++ b/src/sage/modules/free_module_element.pyx
-@@ -555,7 +555,11 @@ def vector(arg0, arg1=None, arg2=None, sparse=None, immutable=False):
-         R = None
- 
-     try:
-+        import numpy
-         from numpy import ndarray
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-+
-     except ImportError:
-         pass
-     else:
-@@ -1188,7 +1192,11 @@ cdef class FreeModuleElement(Vector):   # abstract base class
-             over Rational Field to numpy array of type <... 'float'>:
-             setting an array element with a sequence.
-         """
-+        import numpy
-         from numpy import array
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-+
-         try:
-             return array(self, dtype=dtype)
-         except ValueError as e:
-diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index e3d94d1746e..7ae8ca4966f 100644
---- a/src/sage/numerical/optimize.py
-+++ b/src/sage/numerical/optimize.py
-@@ -155,6 +155,10 @@ def find_root(f, a, b, xtol=10e-13, rtol=2.0**-50, maxiter=100, full_output=Fals
-         b = max(s_1, s_2)
- 
-     import scipy.optimize
-+    import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     g = lambda x: float(f(x))
-     brentqRes = scipy.optimize.brentq(g, a, b,
-                                  full_output=full_output, xtol=xtol, rtol=rtol, maxiter=maxiter)
-@@ -288,6 +292,10 @@ def find_local_minimum(f, a, b, tol=1.48e-08, maxfun=500):
-     a = float(a)
-     b = float(b)
-     import scipy.optimize
-+    import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     xmin, fval, iter, funcalls = scipy.optimize.fminbound(f, a, b, full_output=1, xtol=tol, maxfun=maxfun)
-     return fval, xmin
- 
-@@ -376,6 +384,8 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
-         sage: def rosen(x):  # The Rosenbrock function
-         ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
-         sage: import numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:
-+        ....:     numpy.set_printoptions(legacy="1.25")
-         sage: from numpy import zeros
-         sage: def rosen_der(x):
-         ....:    xm = x[1r:-1r]
-@@ -393,6 +403,9 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
-     from sage.structure.element import Expression
-     from sage.ext.fast_callable import fast_callable
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     from scipy import optimize
-     if isinstance(func, Expression):
-         var_list = func.variables()
-@@ -530,6 +543,8 @@ def minimize_constrained(func,cons,x0,gradient=None,algorithm='default', **args)
-     from sage.structure.element import Expression
-     from sage.ext.fast_callable import fast_callable
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-     from scipy import optimize
-     function_type = type(lambda x,y: x+y)
- 
-@@ -652,6 +667,8 @@ def find_fit(data, model, initial_guess=None, parameters=None, variables=None, s
-     ``lmdif`` and ``lmder`` algorithms.
-     """
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
- 
-     if not isinstance(data, numpy.ndarray):
-         try:
-diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index ac1dc79d802..23e2517ca56 100644
---- a/src/sage/plot/arrow.py
-+++ b/src/sage/plot/arrow.py
-@@ -53,6 +53,9 @@ def get_minmax_data(self):
- 
-         EXAMPLES::
- 
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: from sage.plot.arrow import CurveArrow
-             sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
-             ....:                options={})
-diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx
-index f1f2671a803..4d71414e1c2 100644
---- a/src/sage/plot/complex_plot.pyx
-+++ b/src/sage/plot/complex_plot.pyx
-@@ -1282,15 +1282,13 @@ def rgb_to_hls(rgb):
-         raise ValueError("Last dimension of input array must be 3; "
-                          "shape {} was found.".format(rgb.shape))
-     in_shape = rgb.shape
--    rgb = np.array(
--        rgb, copy=False, dtype=np.dtype(float), ndmin=2
--    )
-+    rgb = np.asarray(rgb, dtype=np.dtype(float))
-     rgb_max = rgb.max(-1)
-     rgb_min = rgb.min(-1)
-     l = (rgb_max + rgb_min)/2.0  # lightness
- 
-     hls = np.zeros_like(rgb)
--    delta = rgb.ptp(-1)
-+    delta = np.ptp(rgb, -1)
-     s = np.zeros_like(delta)
- 
-     ipos = delta > 0
-diff --git a/src/sage/plot/graphics.py b/src/sage/plot/graphics.py
-index a84d162cb56..94f5db09d83 100644
---- a/src/sage/plot/graphics.py
-+++ b/src/sage/plot/graphics.py
-@@ -2754,7 +2754,7 @@ def matplotlib(self, filename=None,
-             sage: xmin, xmax = sub.get_xlim()
-             sage: ymin, ymax = sub.get_ylim()
-             sage: xmin > xmax, ymin > ymax
--            (True, True)
-+            (...True..., ...True...)
-         """
-         if not isinstance(ticks, (list, tuple)):
-             ticks = (ticks, None)
-diff --git a/src/sage/plot/histogram.py b/src/sage/plot/histogram.py
-index fa86a44bd0a..a585cacf9cd 100644
---- a/src/sage/plot/histogram.py
-+++ b/src/sage/plot/histogram.py
-@@ -92,6 +92,8 @@ def get_minmax_data(self):
-             {'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.476190476190..., 'ymin': 0}
-         """
-         import numpy
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
- 
-         # Extract these options (if they are not None) and pass them to
-         # histogram()
-diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
-index b583be32317..6be448f1e04 100644
---- a/src/sage/plot/multigraphics.py
-+++ b/src/sage/plot/multigraphics.py
-@@ -784,6 +784,9 @@ def _add_subplot(self, figure, index, **options):
-             True
-             sage: G.position(1)
-             (0.2, 0.3, 0.4, 0.1)
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: ax1.get_position().bounds  # tol 1.0e-13
-             (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
- 
-@@ -1295,6 +1298,9 @@ def position(self, index):
-             sage: g1 = plot(sin(x), (x, -pi, pi))
-             sage: g2 = circle((0,1), 1.)
-             sage: G = graphics_array([g1, g2])
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: G.position(0)  # tol 5.0e-3
-             (0.025045451349937315,
-              0.03415488992713045,
-diff --git a/src/sage/plot/plot3d/implicit_surface.pyx b/src/sage/plot/plot3d/implicit_surface.pyx
-index ce0da48a4e0..f4d5059b620 100644
---- a/src/sage/plot/plot3d/implicit_surface.pyx
-+++ b/src/sage/plot/plot3d/implicit_surface.pyx
-@@ -468,6 +468,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
-             sage: cube_marcher.y_vertices.tolist()
-             [[[<1.0, 0.5, 0.0>, None]], [[None, None]]]
-             sage: cube_marcher.x_vertices.any() # This shouldn't affect the X vertices.
-+            ...
-         """
-         (self.y_vertices, self.y_vertices_swapped) = \
-             (self.y_vertices_swapped, self.y_vertices)
-@@ -574,6 +575,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
-             sage: cube_marcher.x_vertices.tolist()
-             [[None, None], [None, <1.5, 1.0, 1.0>]]
-             sage: cube_marcher.y_vertices.any() or cube_marcher.z_vertices.any() # This shouldn't affect the Y or Z vertices.
-+            ...
-         """
-         cdef bint has_prev = (_prev is not None)
-         cdef bint has_next = (_next is not None)
-diff --git a/src/sage/plot/scatter_plot.py b/src/sage/plot/scatter_plot.py
-index 4ad418f040b..781854d372c 100644
---- a/src/sage/plot/scatter_plot.py
-+++ b/src/sage/plot/scatter_plot.py
-@@ -63,9 +63,9 @@ def get_minmax_data(self):
-             sage: s = scatter_plot([[0,1],[2,4],[3.2,6]])
-             sage: d = s.get_minmax_data()
-             sage: d['xmin']
--            0.0
-+            ...0.0...
-             sage: d['ymin']
--            1.0
-+            ...1.0...
-         """
-         return {'xmin': self.xdata.min(),
-                 'xmax': self.xdata.max(),
-diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index 663d3aee70b..d2cb11088c7 100644
---- a/src/sage/plot/streamline_plot.py
-+++ b/src/sage/plot/streamline_plot.py
-@@ -71,6 +71,9 @@ def get_minmax_data(self):
-         EXAMPLES::
- 
-             sage: x, y = var('x y')
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: d = streamline_plot((.01*x, x+y), (x,10,20), (y,10,20))[0].get_minmax_data()
-             sage: d['xmin']
-             10.0
-diff --git a/src/sage/probability/probability_distribution.pyx b/src/sage/probability/probability_distribution.pyx
-index e2c71af9c25..59ba4a95ab6 100644
---- a/src/sage/probability/probability_distribution.pyx
-+++ b/src/sage/probability/probability_distribution.pyx
-@@ -140,6 +140,9 @@ cdef class ProbabilityDistribution:
-              1.8,
-              2.0]
-         """
-+        import numpy as np
-+        if int(np.version.short_version[0]) > 1:
-+            np.set_printoptions(legacy="1.25")
-         import pylab
-         ell = [float(self.get_random_element()) for _ in range(num_samples)]
-         S = pylab.hist(ell, bins, density=True)
-diff --git a/src/sage/rings/complex_double.pyx b/src/sage/rings/complex_double.pyx
-index c59a2b46d6f..b4dddebb4dc 100644
---- a/src/sage/rings/complex_double.pyx
-+++ b/src/sage/rings/complex_double.pyx
-@@ -2558,10 +2558,10 @@ cdef class ComplexToCDF(Morphism):
- 
-         sage: # needs numpy
-         sage: import numpy
--        sage: f = CDF.coerce_map_from(numpy.complex_)
--        sage: f(numpy.complex_(I))
-+        sage: f = CDF.coerce_map_from(numpy.complex128)
-+        sage: f(numpy.complex128(I))
-         1.0*I
--        sage: f(numpy.complex_(I)).parent()
-+        sage: f(numpy.complex128(I)).parent()
-         Complex Double Field
-     """
-     def __init__(self, R):
-@@ -2578,7 +2578,7 @@ cdef class ComplexToCDF(Morphism):
-         EXAMPLES::
- 
-             sage: import numpy                                                          # needs numpy
--            sage: CDF(numpy.complex_(I))    # indirect doctest                          # needs numpy
-+            sage: CDF(numpy.complex128(I))    # indirect doctest                          # needs numpy
-             1.0*I
-         """
-         cdef ComplexDoubleElement z = <ComplexDoubleElement>ComplexDoubleElement.__new__(ComplexDoubleElement)
-@@ -2592,7 +2592,7 @@ cdef class ComplexToCDF(Morphism):
-         EXAMPLES::
- 
-             sage: import numpy                                                          # needs numpy
--            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex_)            # needs numpy
-+            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex128)          # needs numpy
-             sage: f._repr_type()                                                        # needs numpy
-             'Native'
-         """
-diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index b4a1fa5039b..38c30f7627b 100644
---- a/src/sage/rings/integer.pyx
-+++ b/src/sage/rings/integer.pyx
-@@ -593,6 +593,8 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
-         Test comparisons with numpy types (see :issue:`13386` and :issue:`18076`)::
- 
-             sage: import numpy                                                          # needs numpy
-+            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
-+            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-             sage: numpy.int8('12') == 12                                                # needs numpy
-             True
-             sage: 12 == numpy.int8('12')                                                # needs numpy
-diff --git a/src/sage/rings/polynomial/polynomial_element.pyx b/src/sage/rings/polynomial/polynomial_element.pyx
-index dcf2af7cdf2..c87eccd44f1 100644
---- a/src/sage/rings/polynomial/polynomial_element.pyx
-+++ b/src/sage/rings/polynomial/polynomial_element.pyx
-@@ -8851,7 +8851,7 @@ cdef class Polynomial(CommutativePolynomial):
-                          'you expect.')
- 
-                 import numpy
--                from numpy.linalg.linalg import LinAlgError
-+                from numpy.linalg import LinAlgError
-                 from sage.rings.complex_double import CDF
- 
-                 numpy_dtype = ('complex' if input_complex else 'double')
-diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
-index 95b472e912c..76fbfedab95 100644
---- a/src/sage/rings/real_mpfi.pyx
-+++ b/src/sage/rings/real_mpfi.pyx
-@@ -231,6 +231,8 @@ specified if given a non-interval and an interval::
- TESTS::
- 
-     sage: import numpy                                                                  # needs numpy
-+    sage: if int(numpy.version.short_version[0]) > 1:                                   # needs numpy
-+    ....:     numpy.set_printoptions(legacy="1.25")                                     # needs numpy
-     sage: RIF(2) == numpy.int8('2')                                                     # needs numpy
-     True
-     sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
-diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-index 8f240627e77..70ce616f92f 100644
---- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-+++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-@@ -77,6 +77,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
-@@ -295,6 +297,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((10, 10))
-             sage: data[1:4,1:4] = True
-@@ -317,6 +321,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1,1] = True
-@@ -370,6 +376,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
- 
-             sage: data = np.zeros((20, 20))
-@@ -520,6 +528,8 @@ cdef class PeriodicRegion:
-         TESTS::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1, 1] = True
-diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index b2e6b301bf7..6937f6cb410 100644
---- a/src/sage/stats/basic_stats.py
-+++ b/src/sage/stats/basic_stats.py
-@@ -227,6 +227,8 @@ def std(v, bias=False):
- 
-         sage: # needs numpy
-         sage: import numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:
-+        ....:     numpy.set_printoptions(legacy="1.25")
-         sage: x = numpy.array([1,2,3,4,5])
-         sage: std(x, bias=False)
-         1.5811388300841898
-@@ -304,6 +306,8 @@ def variance(v, bias=False):
-         sage: variance([RIF(1.0103, 1.0103), RIF(2)])
-         0.4897530450000000?
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-         sage: x = numpy.array([1,2,3,4,5])                                              # needs numpy
-         sage: variance(x, bias=False)                                                   # needs numpy
-         2.5
-diff --git a/src/sage/stats/time_series.pyx b/src/sage/stats/time_series.pyx
-index 2e22ec45c69..23adae84fb4 100644
---- a/src/sage/stats/time_series.pyx
-+++ b/src/sage/stats/time_series.pyx
-@@ -1718,6 +1718,8 @@ cdef class TimeSeries:
-         if len(v0) == 1:
-             return v1[0]/v0[0]
-         import numpy
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-         coeffs = numpy.polyfit(v0,v1,1)
-         return coeffs[0]
- 
-diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
-index dfbd5ff82fa..955a256e9b4 100644
---- a/src/sage/structure/coerce.pyx
-+++ b/src/sage/structure/coerce.pyx
-@@ -520,6 +520,8 @@ cdef class CoercionModel:
-     Check that :issue:`8426` is fixed (see also :issue:`18076`)::
- 
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
- 
-         sage: # needs sage.rings.real_mpfr
-         sage: x = polygen(RR)
-diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
-index 2cb2f09c715..cd89ad2a256 100644
---- a/src/sage/symbolic/function.pyx
-+++ b/src/sage/symbolic/function.pyx
-@@ -964,6 +964,9 @@ cdef class BuiltinFunction(Function):
-             mpc(real='0.83373002513114902', imag='-0.98889770576286506')
- 
-             sage: import numpy                                                          # needs numpy
-+            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
-+            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-+
-             sage: sin(numpy.int32(0))                                                   # needs numpy
-             0.0
-             sage: type(_)                                                               # needs numpy
-diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 501b0920898..5b007d9e5fd 100644
---- a/src/sage/symbolic/ring.pyx
-+++ b/src/sage/symbolic/ring.pyx
-@@ -1162,6 +1162,8 @@ cdef class NumpyToSRMorphism(Morphism):
-     We check that :issue:`8949` and :issue:`9769` are fixed (see also :issue:`18076`)::
- 
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-         sage: f(x) = x^2
-         sage: f(numpy.int8('2'))                                                        # needs numpy
-         4
diff --git a/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch b/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch
deleted file mode 100644
index db0ae9030623b6..00000000000000
--- a/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-diff --git a/src/sage/interfaces/ecm.py b/src/sage/interfaces/ecm.py
-index 99287dec718..98011970404 100644
---- a/src/sage/interfaces/ecm.py
-+++ b/src/sage/interfaces/ecm.py
-@@ -508,7 +508,6 @@ def _find_factor(self, n, factor_digits, B1, **kwds):
-         """
-         n = self._validate(n)
-         kwds.setdefault('c', 1000000000)
--        kwds.setdefault('I', 1)
-         if factor_digits is not None:
-             B1 = self.recommended_B1(factor_digits)
-         kwds['one'] = True
-diff --git a/src/sage/libs/libecm.pyx b/src/sage/libs/libecm.pyx
-index 886a9b816e4..83fb7adaf8d 100644
---- a/src/sage/libs/libecm.pyx
-+++ b/src/sage/libs/libecm.pyx
-@@ -149,11 +149,13 @@ def ecmfactor(number, double B1, verbose=False, sigma=0):
-     Some special cases::
- 
-         sage: ecmfactor(1, 100)
--        (True, 1, ...)
-+        Traceback (most recent call last):
-+        ...
-+        ValueError: Input number (1) must be greater than 1
-         sage: ecmfactor(0, 100)
-         Traceback (most recent call last):
-         ...
--        ValueError: Input number (0) must be positive
-+        ValueError: Input number (0) must be greater than 1
-     """
-     cdef mpz_t n, f
-     cdef int res
-@@ -164,8 +166,8 @@ def ecmfactor(number, double B1, verbose=False, sigma=0):
-     sage_int_number = Integer(number)
-     sage_int_sigma = Integer(sigma)
- 
--    if number <= 0:
--        raise ValueError("Input number (%s) must be positive"%number)
-+    if number <= 1:
-+        raise ValueError("Input number (%s) must be greater than 1"%number)
- 
-     if verbose:
-         print("Performing one curve with B1=%1.0f" % B1)
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 28162dff8a38e1..5cab228f286365 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -19,7 +19,7 @@ get_pr() {
 	echo "curl -sL \"$url\" | filterdiff ... > \"$pr-$desc.patch\""
 	if [ -z "$dry" ]; then
 		curl -sL "$url" |
-			filterdiff -p1 -x src/setup.py -x build/* -x src/doc/* |
+			filterdiff -p1 -x src/setup.py -x environment* -x src/environment* -x build/* -x src/doc/* |
 			cat > "$pr-$desc.patch"
 	fi
 }
@@ -29,8 +29,6 @@ cd $(dirname "$0")
 
 get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
-get_pr 38250 "numpy 2.0"
-get_pr 38344 "ecm 7.0.6"
 
 #get_pr 37645 "fix doctest"
 #get_pr 37885 "cython warnings"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index befe33a0188687..f5e1d8c68cfcbe 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,7 +1,7 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.4
-revision=2
+version=10.5.beta2
+revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
 build_style=python3-pep517
@@ -25,14 +25,14 @@ depends="eclib-devel fflas-ffpack flintlib-devel gcc-fortran meson gd-devel
  python3-sympy python3-traitlets sage-data-combinatorial_designs
  python3-conway-polynomials sage-data-elliptic_curves sage-data-graphs
  sage-data-polytopes_db sympow tachyon threejs-sage"
-checkdepends="$depends pythran python3-Sphinx gdb"
+checkdepends="$depends python3-pytest pythran python3-Sphinx gdb"
 short_desc="Open source mathematics software"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=f6579e85f33bd9bb6e9b991bfc4c49dab1e649858ed9ee41c7cec75cb92d4c62
+checksum=0fe0c82dd6959951fc07d55737d270290f64947e183a403ca25709e21b751dee
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From eb7df4a9f682cf046b5c9666b666cb2d7e8d9a3d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Wed, 14 Aug 2024 00:12:02 -0300
Subject: [PATCH 3/6] sagemath: enable all cython warnings

---
 srcpkgs/sagemath/patches/37885-cython_warnings.patch | 12 ++++++++++++
 srcpkgs/sagemath/patches/get_patches                 |  2 +-
 2 files changed, 13 insertions(+), 1 deletion(-)
 create mode 100644 srcpkgs/sagemath/patches/37885-cython_warnings.patch

diff --git a/srcpkgs/sagemath/patches/37885-cython_warnings.patch b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
new file mode 100644
index 00000000000000..fa4b648cfc1577
--- /dev/null
+++ b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
@@ -0,0 +1,12 @@
+diff --git a/src/sage_setup/command/sage_build_cython.py b/src/sage_setup/command/sage_build_cython.py
+index f4b1357c543..3435c196d49 100644
+--- a/src/sage_setup/command/sage_build_cython.py
++++ b/src/sage_setup/command/sage_build_cython.py
+@@ -226,6 +226,7 @@ def run(self):
+                 compiler_directives=self.cython_directives,
+                 compile_time_env=self.compile_time_env,
+                 create_extension=self.create_extension,
++                show_all_warnings=True,
+                 # Debugging
+                 gdb_debug=self.debug,
+                 output_dir=os.path.join(self.build_lib, "sage"),
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 5cab228f286365..c182576ea553cd 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -31,4 +31,4 @@ get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
 
 #get_pr 37645 "fix doctest"
-#get_pr 37885 "cython warnings"
+get_pr 37885 "cython warnings"

From 6831717a594328f0a6efe163da56f2cf7802e040 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 19 Aug 2024 17:35:53 -0300
Subject: [PATCH 4/6] python3-numpy: update to 2.1.0.

---
 srcpkgs/python3-numpy/template | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/srcpkgs/python3-numpy/template b/srcpkgs/python3-numpy/template
index cab4e3e506df30..7d0e493b32c5bb 100644
--- a/srcpkgs/python3-numpy/template
+++ b/srcpkgs/python3-numpy/template
@@ -1,6 +1,6 @@
 # Template file for 'python3-numpy'
 pkgname=python3-numpy
-version=2.0.1
+version=2.1.0
 revision=1
 build_style=python3-pep517
 build_helper="meson qemu"
@@ -19,7 +19,7 @@ license="BSD-3-Clause"
 homepage="https://www.numpy.org/"
 changelog="https://github.com/numpy/numpy/releases"
 distfiles="${PYPI_SITE}/n/numpy/numpy-${version}.tar.gz"
-checksum=485b87235796410c3519a699cfe1faab097e509e90ebb05dcd098db2ae87e7b3
+checksum=7dc90da0081f7e1da49ec4e398ede6a8e9cc4f5ebe5f9e06b443ed889ee9aaa2
 alternatives="numpy:f2py:/usr/bin/f2py3"
 
 build_options="openblas"

From 33e6757c9f86da2ddf02a07cfd90ec7eb32f86a9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 19 Aug 2024 22:02:54 -0300
Subject: [PATCH 5/6] flintlib: C99 compliance

---
 srcpkgs/flintlib/patches/2027.patch | 322 ++++++++++++++++++++++++++++
 srcpkgs/flintlib/template           |   2 +-
 2 files changed, 323 insertions(+), 1 deletion(-)
 create mode 100644 srcpkgs/flintlib/patches/2027.patch

diff --git a/srcpkgs/flintlib/patches/2027.patch b/srcpkgs/flintlib/patches/2027.patch
new file mode 100644
index 00000000000000..f17ff31f2754d7
--- /dev/null
+++ b/srcpkgs/flintlib/patches/2027.patch
@@ -0,0 +1,322 @@
+See: https://github.com/flintlib/flint/pull/2027
+
+From 1b93e73d00881be12e04b7f13e070214a3c9e1cc Mon Sep 17 00:00:00 2001
+From: Dima Pasechnik <dima@pasechnik.info>
+Date: Wed, 19 Jun 2024 22:16:34 +0100
+Subject: [PATCH] ensure C99 compliance in headers, as 'I' is reserved
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+Note that the following code
+---- cut here: save as t.c
+---- cut here
+
+fails to compile with a suffciently new compiler, e.g. clang 16 or gcc 14.
+
+$ gcc -c t.c
+In file included from t.c:1:
+/usr/include/flint/mpoly.h:1319:43: error: expected ‘)’ before ‘__extension__’
+ 1319 | void mpoly_gcd_info_init(mpoly_gcd_info_t I, slong nvars);
+      |                                           ^
+In file included from /usr/include/flint/fmpz_types.h:15,
+                 from /usr/include/flint/fmpz_mod_types.h:15,
+                 from /usr/include/flint/mpoly_types.h:15,
+                 from /usr/include/flint/mpoly.h:23,
+                 from t.c:2:
+/usr/include/flint/mpoly.h:1319:46: error: expected ‘;’, ‘,’ or ‘)’ before ‘mp_limb_signed_t’
+ 1319 | void mpoly_gcd_info_init(mpoly_gcd_info_t I, slong nvars);
+
+...
+---
+ src/fft_small.h             |  6 +++---
+ src/fmpz_mod_mpoly_factor.h |  8 ++++----
+ src/fmpz_mpoly.h            |  2 +-
+ src/fmpz_mpoly_factor.h     | 18 +++++++++---------
+ src/fq_nmod_mpoly_factor.h  |  6 +++---
+ src/fq_zech_mpoly_factor.h  |  6 +++---
+ src/mpoly.h                 | 18 +++++++++---------
+ src/nmod_mpoly.h            |  4 ++--
+ src/nmod_mpoly_factor.h     |  6 +++---
+ 9 files changed, 37 insertions(+), 37 deletions(-)
+
+diff --git a/src/fft_small.h b/src/fft_small.h
+index 3f62f2e988..b7404f196d 100644
+--- a/src/fft_small.h
++++ b/src/fft_small.h
+@@ -242,10 +242,10 @@ FLINT_INLINE double sd_fft_ctx_get_fft_index(double* d, ulong i)
+ }
+ 
+ /* sd_fft.c */
+-void sd_fft_trunc(const sd_fft_lctx_t Q, ulong I, ulong S, ulong k, ulong j, ulong itrunc, ulong otrunc);
++void sd_fft_trunc(const sd_fft_lctx_t Q, ulong Iv, ulong S, ulong k, ulong j, ulong itrunc, ulong otrunc);
+ 
+ /* sd_ifft.c */
+-void sd_ifft_trunc(const sd_fft_lctx_t Q, ulong I, ulong S, ulong k, ulong j, ulong z, ulong n, int f);
++void sd_ifft_trunc(const sd_fft_lctx_t Q, ulong Iv, ulong S, ulong k, ulong j, ulong z, ulong n, int f);
+ 
+ /* sd_fft_ctx.c */
+ void sd_fft_ctx_clear(sd_fft_ctx_t Q);
+@@ -428,7 +428,7 @@ typedef struct {
+ 
+ typedef mpn_ctx_struct mpn_ctx_t[1];
+ 
+-void _convert_block(ulong* Xs, sd_fft_ctx_struct* Rffts, double* d, ulong dstride, ulong np, ulong I);
++void _convert_block(ulong* Xs, sd_fft_ctx_struct* Rffts, double* d, ulong dstride, ulong np, ulong Iv);
+ ulong flint_mpn_nbits(const ulong* a, ulong an);
+ int flint_mpn_cmp_ui_2exp(const ulong* a, ulong an, ulong b, ulong e);
+ unsigned char flint_mpn_add_inplace_c(ulong* z, ulong zn, ulong* a, ulong an, unsigned char cf);
+diff --git a/src/fmpz_mod_mpoly_factor.h b/src/fmpz_mod_mpoly_factor.h
+index 359fdd1e3d..460695dd23 100644
+--- a/src/fmpz_mod_mpoly_factor.h
++++ b/src/fmpz_mod_mpoly_factor.h
+@@ -1203,15 +1203,15 @@ typedef struct {
+ typedef fmpz_mod_mpoly_pfrac_struct fmpz_mod_mpoly_pfrac_t[1];
+ 
+ 
+-int fmpz_mod_mpoly_pfrac_init(fmpz_mod_mpoly_pfrac_t I,
++int fmpz_mod_mpoly_pfrac_init(fmpz_mod_mpoly_pfrac_t Iv,
+     flint_bitcnt_t bits, slong l, slong r, const fmpz_mod_mpoly_struct * betas,
+                           const fmpz * alpha, const fmpz_mod_mpoly_ctx_t ctx);
+ 
+-void fmpz_mod_mpoly_pfrac_clear(fmpz_mod_mpoly_pfrac_t I,
++void fmpz_mod_mpoly_pfrac_clear(fmpz_mod_mpoly_pfrac_t Iv,
+                                               const fmpz_mod_mpoly_ctx_t ctx);
+ 
+ int fmpz_mod_mpoly_pfrac(slong r, fmpz_mod_mpoly_t t, const slong * deg,
+-                     fmpz_mod_mpoly_pfrac_t I, const fmpz_mod_mpoly_ctx_t ctx);
++                     fmpz_mod_mpoly_pfrac_t Iv, const fmpz_mod_mpoly_ctx_t ctx);
+ 
+ int fmpz_mod_mpoly_hlift(slong m, fmpz_mod_mpoly_struct * f, slong r,
+             const fmpz * alpha, const fmpz_mod_mpoly_t A, const slong * degs,
+@@ -1290,7 +1290,7 @@ int fmpz_mod_mpolyn_gcd_brown_smprime(
+     fmpz_mod_mpolyn_t B,
+     slong var,
+     const fmpz_mod_mpoly_ctx_t ctx,
+-    const mpoly_gcd_info_t I,
++    const mpoly_gcd_info_t Iv,
+     fmpz_mod_poly_polyun_mpolyn_stack_t St);
+ 
+ int fmpz_mod_mpolyl_gcdp_zippel(
+diff --git a/src/fmpz_mpoly.h b/src/fmpz_mpoly.h
+index b7c9677915..4be3d05c56 100644
+--- a/src/fmpz_mpoly.h
++++ b/src/fmpz_mpoly.h
+@@ -1084,7 +1084,7 @@ void fmpz_mpoly_vec_randtest_not_zero(fmpz_mpoly_vec_t vec, flint_rand_t state,
+ 
+ void fmpz_mpoly_spoly(fmpz_mpoly_t res, const fmpz_mpoly_t f, const fmpz_mpoly_t g, const fmpz_mpoly_ctx_t ctx);
+ void fmpz_mpoly_vec_set_primitive_unique(fmpz_mpoly_vec_t G, const fmpz_mpoly_vec_t F, const fmpz_mpoly_ctx_t ctx);
+-void fmpz_mpoly_reduction_primitive_part(fmpz_mpoly_t res, const fmpz_mpoly_t f, const fmpz_mpoly_vec_t I, const fmpz_mpoly_ctx_t ctx);
++void fmpz_mpoly_reduction_primitive_part(fmpz_mpoly_t res, const fmpz_mpoly_t f, const fmpz_mpoly_vec_t Iv, const fmpz_mpoly_ctx_t ctx);
+ int fmpz_mpoly_vec_is_groebner(const fmpz_mpoly_vec_t G, const fmpz_mpoly_vec_t F, const fmpz_mpoly_ctx_t ctx);
+ void fmpz_mpoly_buchberger_naive(fmpz_mpoly_vec_t G, const fmpz_mpoly_vec_t F, const fmpz_mpoly_ctx_t ctx);
+ int fmpz_mpoly_buchberger_naive_with_limits(fmpz_mpoly_vec_t G, const fmpz_mpoly_vec_t F,
+diff --git a/src/fmpz_mpoly_factor.h b/src/fmpz_mpoly_factor.h
+index 0da7c1052b..a04ef8021e 100644
+--- a/src/fmpz_mpoly_factor.h
++++ b/src/fmpz_mpoly_factor.h
+@@ -298,11 +298,11 @@ void fmpz_mpoly_from_mpolyl_perm_inflate(fmpz_mpoly_t A,
+ 
+ int fmpz_mpolyl_gcd_brown(fmpz_mpoly_t G,
+         fmpz_mpoly_t Abar, fmpz_mpoly_t Bbar, fmpz_mpoly_t A, fmpz_mpoly_t B,
+-                         const fmpz_mpoly_ctx_t ctx, const mpoly_gcd_info_t I);
++                         const fmpz_mpoly_ctx_t ctx, const mpoly_gcd_info_t Iv);
+ 
+ int fmpz_mpolyl_gcd_brown_threaded_pool(fmpz_mpoly_t G,
+         fmpz_mpoly_t Abar, fmpz_mpoly_t Bbar, fmpz_mpoly_t A, fmpz_mpoly_t B,
+-                         const fmpz_mpoly_ctx_t ctx, const mpoly_gcd_info_t I,
++                         const fmpz_mpoly_ctx_t ctx, const mpoly_gcd_info_t Iv,
+                         const thread_pool_handle * handles, slong num_handles);
+ 
+ int fmpz_mpolyl_gcd_zippel(fmpz_mpoly_t G, fmpz_mpoly_t Abar,
+@@ -340,15 +340,15 @@ typedef struct {
+ 
+ typedef fmpz_poly_pfrac_struct fmpz_poly_pfrac_t[1];
+ 
+-void fmpz_poly_pfrac_init(fmpz_poly_pfrac_t I);
++void fmpz_poly_pfrac_init(fmpz_poly_pfrac_t Iv);
+ 
+-void fmpz_poly_pfrac_clear(fmpz_poly_pfrac_t I);
++void fmpz_poly_pfrac_clear(fmpz_poly_pfrac_t Iv);
+ 
+-int fmpz_poly_pfrac_precompute(fmpz_poly_pfrac_t I,
++int fmpz_poly_pfrac_precompute(fmpz_poly_pfrac_t Iv,
+                                           const fmpz_poly_struct * b, slong r);
+ 
+ int fmpz_poly_pfrac_precomp(fmpz_poly_struct * c,
+-                                     const fmpz_poly_t A, fmpz_poly_pfrac_t I);
++                                     const fmpz_poly_t A, fmpz_poly_pfrac_t Iv);
+ 
+ typedef struct {
+     flint_bitcnt_t bits;
+@@ -372,15 +372,15 @@ typedef struct {
+ 
+ typedef fmpz_mpoly_pfrac_struct fmpz_mpoly_pfrac_t[1];
+ 
+-int fmpz_mpoly_pfrac_init(fmpz_mpoly_pfrac_t I, flint_bitcnt_t bits,
++int fmpz_mpoly_pfrac_init(fmpz_mpoly_pfrac_t Iv, flint_bitcnt_t bits,
+                             slong r, slong w, const fmpz_mpoly_struct * betas,
+                                const fmpz * alpha, const fmpz_mpoly_ctx_t ctx);
+ 
+-void fmpz_mpoly_pfrac_clear(fmpz_mpoly_pfrac_t I,
++void fmpz_mpoly_pfrac_clear(fmpz_mpoly_pfrac_t Iv,
+                                                    const fmpz_mpoly_ctx_t ctx);
+ 
+ int fmpz_mpoly_pfrac(slong l, fmpz_mpoly_t t, const slong * degs,
+-                             fmpz_mpoly_pfrac_t I, const fmpz_mpoly_ctx_t ctx);
++                             fmpz_mpoly_pfrac_t Iv, const fmpz_mpoly_ctx_t ctx);
+ 
+ int fmpz_mpoly_hlift(slong m, fmpz_mpoly_struct * f, slong r,
+                 const fmpz * alpha, const fmpz_mpoly_t A, const slong * degs,
+diff --git a/src/fq_nmod_mpoly_factor.h b/src/fq_nmod_mpoly_factor.h
+index 6289d3f1c5..29caa99aa4 100644
+--- a/src/fq_nmod_mpoly_factor.h
++++ b/src/fq_nmod_mpoly_factor.h
+@@ -427,7 +427,7 @@ typedef fq_nmod_mpoly_pfrac_struct fq_nmod_mpoly_pfrac_t[1];
+ 
+ 
+ int fq_nmod_mpoly_pfrac_init(
+-    fq_nmod_mpoly_pfrac_t I,
++    fq_nmod_mpoly_pfrac_t Iv,
+     flint_bitcnt_t bits,
+     slong l, slong r,
+     const fq_nmod_mpoly_struct * betas,
+@@ -435,14 +435,14 @@ int fq_nmod_mpoly_pfrac_init(
+     const fq_nmod_mpoly_ctx_t ctx);
+ 
+ void fq_nmod_mpoly_pfrac_clear(
+-    fq_nmod_mpoly_pfrac_t I,
++    fq_nmod_mpoly_pfrac_t Iv,
+     const fq_nmod_mpoly_ctx_t ctx);
+ 
+ int fq_nmod_mpoly_pfrac(
+     slong r,
+     fq_nmod_mpoly_t t,
+     const slong * deg,
+-    fq_nmod_mpoly_pfrac_t I,
++    fq_nmod_mpoly_pfrac_t Iv,
+     const fq_nmod_mpoly_ctx_t ctx);
+ 
+ int fq_nmod_mpoly_hlift(
+diff --git a/src/fq_zech_mpoly_factor.h b/src/fq_zech_mpoly_factor.h
+index 06f31369f9..3d3c51419f 100644
+--- a/src/fq_zech_mpoly_factor.h
++++ b/src/fq_zech_mpoly_factor.h
+@@ -652,7 +652,7 @@ typedef fq_zech_mpoly_pfrac_struct fq_zech_mpoly_pfrac_t[1];
+ 
+ 
+ int fq_zech_mpoly_pfrac_init(
+-    fq_zech_mpoly_pfrac_t I,
++    fq_zech_mpoly_pfrac_t Iv,
+     flint_bitcnt_t bits,
+     slong l, slong r,
+     const fq_zech_mpoly_struct * betas,
+@@ -660,14 +660,14 @@ int fq_zech_mpoly_pfrac_init(
+     const fq_zech_mpoly_ctx_t ctx);
+ 
+ void fq_zech_mpoly_pfrac_clear(
+-    fq_zech_mpoly_pfrac_t I,
++    fq_zech_mpoly_pfrac_t Iv,
+     const fq_zech_mpoly_ctx_t ctx);
+ 
+ int fq_zech_mpoly_pfrac(
+     slong r,
+     fq_zech_mpoly_t t,
+     const slong * deg,
+-    fq_zech_mpoly_pfrac_t I,
++    fq_zech_mpoly_pfrac_t Iv,
+     const fq_zech_mpoly_ctx_t ctx);
+ 
+ int fq_zech_mpoly_hlift(
+diff --git a/src/mpoly.h b/src/mpoly.h
+index b0950e3a48..fe0ccbe7c4 100644
+--- a/src/mpoly.h
++++ b/src/mpoly.h
+@@ -1363,9 +1363,9 @@ typedef struct
+ 
+ typedef mpoly_gcd_info_struct mpoly_gcd_info_t[1];
+ 
+-void mpoly_gcd_info_init(mpoly_gcd_info_t I, slong nvars);
++void mpoly_gcd_info_init(mpoly_gcd_info_t Iv, slong nvars);
+ 
+-void mpoly_gcd_info_clear(mpoly_gcd_info_t I);
++void mpoly_gcd_info_clear(mpoly_gcd_info_t Iv);
+ 
+ void mpoly_gcd_info_limits(ulong * Amax_exp, ulong * Amin_exp,
+                        slong * Amax_exp_count, slong * Amin_exp_count,
+@@ -1378,25 +1378,25 @@ void mpoly_gcd_info_stride(ulong * strides,
+                              const ulong * Bmax_exp, const ulong * Bmin_exp,
+                                                        const mpoly_ctx_t mctx);
+ 
+-void mpoly_gcd_info_set_perm(mpoly_gcd_info_t I,
++void mpoly_gcd_info_set_perm(mpoly_gcd_info_t Iv,
+                          slong Alength, slong Blength, const mpoly_ctx_t mctx);
+ 
+-slong mpoly_gcd_info_get_brown_upper_limit(const mpoly_gcd_info_t I,
++slong mpoly_gcd_info_get_brown_upper_limit(const mpoly_gcd_info_t Iv,
+                                                        slong var, slong bound);
+ 
+-void mpoly_gcd_info_measure_hensel(mpoly_gcd_info_t I,
++void mpoly_gcd_info_measure_hensel(mpoly_gcd_info_t Iv,
+                          slong Alength, slong Blength, const mpoly_ctx_t mctx);
+ 
+-void mpoly_gcd_info_measure_brown(mpoly_gcd_info_t I,
++void mpoly_gcd_info_measure_brown(mpoly_gcd_info_t Iv,
+                          slong Alength, slong Blength, const mpoly_ctx_t mctx);
+ 
+-void mpoly_gcd_info_measure_bma(mpoly_gcd_info_t I,
++void mpoly_gcd_info_measure_bma(mpoly_gcd_info_t Iv,
+                          slong Alength, slong Blength, const mpoly_ctx_t mctx);
+ 
+-void mpoly_gcd_info_measure_zippel(mpoly_gcd_info_t I,
++void mpoly_gcd_info_measure_zippel(mpoly_gcd_info_t Iv,
+                          slong Alength, slong Blength, const mpoly_ctx_t mctx);
+ 
+-void mpoly_gcd_info_measure_zippel2(mpoly_gcd_info_t I,
++void mpoly_gcd_info_measure_zippel2(mpoly_gcd_info_t Iv,
+                          slong Alength, slong Blength, const mpoly_ctx_t mctx);
+ 
+ int mpoly_monomial_cofactors(fmpz * Abarexps, fmpz * Bbarexps,
+diff --git a/src/nmod_mpoly.h b/src/nmod_mpoly.h
+index 2a8136e6eb..716ac9669a 100644
+--- a/src/nmod_mpoly.h
++++ b/src/nmod_mpoly.h
+@@ -1619,13 +1619,13 @@ int nmod_mpolyn_gcd_brown_smprime_bivar(
+ int nmod_mpolyn_gcd_brown_smprime(nmod_mpolyn_t G,
+                                   nmod_mpolyn_t Abar, nmod_mpolyn_t Bbar,
+                                  nmod_mpolyn_t A, nmod_mpolyn_t B, slong var,
+-                         const nmod_mpoly_ctx_t ctx, const mpoly_gcd_info_t I,
++                         const nmod_mpoly_ctx_t ctx, const mpoly_gcd_info_t Iv,
+                                                          nmod_poly_stack_t Sp);
+ 
+ int nmod_mpolyn_gcd_brown_smprime_threaded_pool(nmod_mpolyn_t G,
+                                 nmod_mpolyn_t Abar, nmod_mpolyn_t Bbar,
+                                nmod_mpolyn_t A, nmod_mpolyn_t B, slong var,
+-                         const nmod_mpoly_ctx_t ctx, const mpoly_gcd_info_t I,
++                         const nmod_mpoly_ctx_t ctx, const mpoly_gcd_info_t Iv,
+                         const thread_pool_handle * handles, slong num_workers);
+ 
+ int nmod_mpolyn_gcd_brown_lgprime(nmod_mpolyn_t G,
+diff --git a/src/nmod_mpoly_factor.h b/src/nmod_mpoly_factor.h
+index a46afc860f..b16c802b9b 100644
+--- a/src/nmod_mpoly_factor.h
++++ b/src/nmod_mpoly_factor.h
+@@ -362,15 +362,15 @@ typedef struct {
+ typedef nmod_mpoly_pfrac_struct nmod_mpoly_pfrac_t[1];
+ 
+ 
+-int nmod_mpoly_pfrac_init(nmod_mpoly_pfrac_t I, flint_bitcnt_t bits,
++int nmod_mpoly_pfrac_init(nmod_mpoly_pfrac_t Iv, flint_bitcnt_t bits,
+                          slong l, slong r, const nmod_mpoly_struct * betas,
+                           const mp_limb_t * alpha, const nmod_mpoly_ctx_t ctx);
+ 
+-void nmod_mpoly_pfrac_clear(nmod_mpoly_pfrac_t I,
++void nmod_mpoly_pfrac_clear(nmod_mpoly_pfrac_t Iv,
+                                                    const nmod_mpoly_ctx_t ctx);
+ 
+ int nmod_mpoly_pfrac(slong r, nmod_mpoly_t t, const slong * deg,
+-                             nmod_mpoly_pfrac_t I, const nmod_mpoly_ctx_t ctx);
++                             nmod_mpoly_pfrac_t Iv, const nmod_mpoly_ctx_t ctx);
+ 
+ int nmod_mpoly_hlift(slong m, nmod_mpoly_struct * f, slong r,
+             const mp_limb_t * alpha, const nmod_mpoly_t A, const slong * degs,
diff --git a/srcpkgs/flintlib/template b/srcpkgs/flintlib/template
index 613391a9a0ae1b..465cdf1d0d3f71 100644
--- a/srcpkgs/flintlib/template
+++ b/srcpkgs/flintlib/template
@@ -1,7 +1,7 @@
 # Template file for 'flintlib'
 pkgname=flintlib
 version=3.1.2
-revision=1
+revision=2
 build_style=gnu-configure
 configure_args="--prefix=/usr --disable-arch $(vopt_with ntl)
  $(vopt_if openblas --with-blas-include=${XBPS_CROSS_BASE}/usr/include/openblas)"

From e78be426bc1268e87433181f2fee4982b7e8dcf3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 20 Aug 2024 17:56:06 -0300
Subject: [PATCH 6/6] sagemath: patch for numpy 2.1

---
 srcpkgs/sagemath/patches/numpy_2.1a.patch |  28 +++
 srcpkgs/sagemath/patches/numpy_2.1b.patch | 229 ++++++++++++++++++++++
 2 files changed, 257 insertions(+)
 create mode 100644 srcpkgs/sagemath/patches/numpy_2.1a.patch
 create mode 100644 srcpkgs/sagemath/patches/numpy_2.1b.patch

diff --git a/srcpkgs/sagemath/patches/numpy_2.1a.patch b/srcpkgs/sagemath/patches/numpy_2.1a.patch
new file mode 100644
index 00000000000000..493c75e2f8f8e0
--- /dev/null
+++ b/srcpkgs/sagemath/patches/numpy_2.1a.patch
@@ -0,0 +1,28 @@
+commit d755b32cbed462abf01a1cd782ba57cb92fbf713
+Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
+Date:   Mon Aug 19 23:25:32 2024 -0300
+
+    add copy parameter to numpy (needed for v2.1)
+
+diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
+index 3edb9ead54d..2c76fd1e557 100644
+--- a/src/sage/matrix/matrix1.pyx
++++ b/src/sage/matrix/matrix1.pyx
+@@ -670,7 +670,7 @@ cdef class Matrix(Matrix0):
+             entries = [[sib(v, 2) for v in row] for row in self.rows()]
+             return sib.name('matrix')(self.base_ring(), entries)
+ 
+-    def numpy(self, dtype=None):
++    def numpy(self, dtype=None, copy=True):
+         """
+         Return the Numpy matrix associated to this matrix.
+ 
+@@ -731,7 +731,7 @@ cdef class Matrix(Matrix0):
+             (3, 4)
+         """
+         import numpy
+-        A = numpy.matrix(self.list(), dtype=dtype)
++        A = numpy.matrix(self.list(), dtype=dtype, copy=copy)
+         return numpy.resize(A,(self.nrows(), self.ncols()))
+ 
+     # Define the magic "__array__" function so that numpy.array(m) can convert
diff --git a/srcpkgs/sagemath/patches/numpy_2.1b.patch b/srcpkgs/sagemath/patches/numpy_2.1b.patch
new file mode 100644
index 00000000000000..8dc0eec2b5a9d8
--- /dev/null
+++ b/srcpkgs/sagemath/patches/numpy_2.1b.patch
@@ -0,0 +1,229 @@
+commit 8260d18c3cf8e356db3d95fc46f6e68f75b453fd
+Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
+Date:   Tue Aug 20 00:05:33 2024 -0300
+
+    silence np.set_printoptions (for numpy 2.1)
+
+diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
+index 74a14fa1ecd..82e6c7eb3c8 100644
+--- a/src/sage/combinat/fully_packed_loop.py
++++ b/src/sage/combinat/fully_packed_loop.py
+@@ -68,7 +68,7 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
+ 
+         sage: import numpy as np
+         sage: if int(np.version.short_version[0]) > 1:
+-        ....:     np.set_printoptions(legacy="1.25")
++        ....:     _token = np.set_printoptions(legacy="1.25")
+         sage: from sage.combinat.fully_packed_loop import _make_color_list
+         sage: _make_color_list(5)
+         sage: _make_color_list(5, ['blue', 'red'])
+diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
+index 308171af3cd..6f66624ef87 100644
+--- a/src/sage/functions/special.py
++++ b/src/sage/functions/special.py
+@@ -219,7 +219,7 @@ class SphericalHarmonic(BuiltinFunction):
+         sage: from scipy.special import sph_harm  # NB: arguments x and y are swapped   # needs scipy
+         sage: import numpy as np                                                        # needs scipy
+         sage: if int(np.version.short_version[0]) > 1:                                  # needs scipy
+-        ....:     np.set_printoptions(legacy="1.25")                                    # needs scipy
++        ....:     _token = np.set_printoptions(legacy="1.25")                           # needs scipy
+         sage: sph_harm(1, 1, pi.n(), (pi/2).n())  # abs tol 1e-14                       # needs scipy sage.symbolic
+         (0.3454941494713355-4.231083042742082e-17j)
+ 
+diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
+index b3e42a6a6a2..13ffa4d1789 100644
+--- a/src/sage/numerical/optimize.py
++++ b/src/sage/numerical/optimize.py
+@@ -381,7 +381,7 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm='default',
+         ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
+         sage: import numpy
+         sage: if int(numpy.version.short_version[0]) > 1:
+-        ....:     numpy.set_printoptions(legacy="1.25")
++        ....:     _token = numpy.set_printoptions(legacy="1.25")
+         sage: from numpy import zeros
+         sage: def rosen_der(x):
+         ....:    xm = x[1r:-1r]
+diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
+index 02442f90ba4..1fe3f0b051a 100644
+--- a/src/sage/plot/arrow.py
++++ b/src/sage/plot/arrow.py
+@@ -55,7 +55,7 @@ class CurveArrow(GraphicPrimitive):
+ 
+             sage: import numpy  # to ensure numpy 2.0 compatibility
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     _token = numpy.set_printoptions(legacy="1.25")
+             sage: from sage.plot.arrow import CurveArrow
+             sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
+             ....:                options={})
+diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
+index d2f70b44526..2eaacc6879e 100644
+--- a/src/sage/plot/multigraphics.py
++++ b/src/sage/plot/multigraphics.py
+@@ -766,7 +766,7 @@ class MultiGraphics(WithEqualityById, SageObject):
+             (0.2, 0.3, 0.4, 0.1)
+             sage: import numpy  # to ensure numpy 2.0 compatibility
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     _token = numpy.set_printoptions(legacy="1.25")
+             sage: ax1.get_position().bounds  # tol 1.0e-13
+             (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
+         """
+@@ -1269,7 +1269,7 @@ class GraphicsArray(MultiGraphics):
+             sage: G = graphics_array([g1, g2])
+             sage: import numpy  # to ensure numpy 2.0 compatibility
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     _token = numpy.set_printoptions(legacy="1.25")
+             sage: G.position(0)  # tol 5.0e-3
+             (0.025045451349937315,
+              0.03415488992713045,
+diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
+index b69a05b37bf..25e404bfc7d 100644
+--- a/src/sage/plot/streamline_plot.py
++++ b/src/sage/plot/streamline_plot.py
+@@ -72,7 +72,7 @@ class StreamlinePlot(GraphicPrimitive):
+             sage: x, y = var('x y')
+             sage: import numpy  # to ensure numpy 2.0 compatibility
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     _token = numpy.set_printoptions(legacy="1.25")
+             sage: d = streamline_plot((.01*x, x+y), (x,10,20), (y,10,20))[0].get_minmax_data()
+             sage: d['xmin']
+             10.0
+diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
+index 11811b9587f..8ce0f7f2683 100644
+--- a/src/sage/rings/integer.pyx
++++ b/src/sage/rings/integer.pyx
+@@ -595,7 +595,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
+             sage: # needs numpy
+             sage: import numpy
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     _token = numpy.set_printoptions(legacy="1.25")
+             sage: numpy.int8('12') == 12
+             True
+             sage: 12 == numpy.int8('12')
+diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
+index 11953a50ab5..6aafcceed89 100644
+--- a/src/sage/rings/real_mpfi.pyx
++++ b/src/sage/rings/real_mpfi.pyx
+@@ -232,7 +232,7 @@ TESTS::
+ 
+     sage: import numpy                                                                  # needs numpy
+     sage: if int(numpy.version.short_version[0]) > 1:                                   # needs numpy
+-    ....:     numpy.set_printoptions(legacy="1.25")                                     # needs numpy
++    ....:     _token = numpy.set_printoptions(legacy="1.25")                            # needs numpy
+     sage: RIF(2) == numpy.int8('2')                                                     # needs numpy
+     True
+     sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
+diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
+index 40b92ab23eb..3838bcccb8a 100755
+--- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
++++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
+@@ -78,7 +78,7 @@ cdef class PeriodicRegion:
+ 
+             sage: import numpy as np
+             sage: if int(np.version.short_version[0]) > 1:
+-            ....:     np.set_printoptions(legacy="1.25")
++            ....:     _token = np.set_printoptions(legacy="1.25")
+             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
+             sage: data = np.zeros((4, 4))
+             sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
+@@ -296,7 +296,7 @@ cdef class PeriodicRegion:
+ 
+             sage: import numpy as np
+             sage: if int(np.version.short_version[0]) > 1:
+-            ....:     np.set_printoptions(legacy="1.25")
++            ....:     _token = np.set_printoptions(legacy="1.25")
+             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
+             sage: data = np.zeros((10, 10))
+             sage: data[1:4,1:4] = True
+@@ -320,7 +320,7 @@ cdef class PeriodicRegion:
+ 
+             sage: import numpy as np
+             sage: if int(np.version.short_version[0]) > 1:
+-            ....:     np.set_printoptions(legacy="1.25")
++            ....:     _token = np.set_printoptions(legacy="1.25")
+             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
+             sage: data = np.zeros((4, 4))
+             sage: data[1,1] = True
+@@ -375,7 +375,7 @@ cdef class PeriodicRegion:
+ 
+             sage: import numpy as np
+             sage: if int(np.version.short_version[0]) > 1:
+-            ....:     np.set_printoptions(legacy="1.25")
++            ....:     _token = np.set_printoptions(legacy="1.25")
+             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
+ 
+             sage: data = np.zeros((20, 20))
+@@ -528,7 +528,7 @@ cdef class PeriodicRegion:
+ 
+             sage: import numpy as np
+             sage: if int(np.version.short_version[0]) > 1:
+-            ....:     np.set_printoptions(legacy="1.25")
++            ....:     _token = np.set_printoptions(legacy="1.25")
+             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
+             sage: data = np.zeros((4, 4))
+             sage: data[1, 1] = True
+diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
+index 47d890cf0ab..ba7f0cdb0f9 100644
+--- a/src/sage/stats/basic_stats.py
++++ b/src/sage/stats/basic_stats.py
+@@ -222,7 +222,7 @@ def std(v, bias=False):
+         sage: # needs numpy
+         sage: import numpy
+         sage: if int(numpy.version.short_version[0]) > 1:
+-        ....:     numpy.set_printoptions(legacy="1.25")
++        ....:     _token = numpy.set_printoptions(legacy="1.25")
+         sage: x = numpy.array([1,2,3,4,5])
+         sage: std(x, bias=False)
+         1.5811388300841898
+@@ -299,7 +299,7 @@ def variance(v, bias=False):
+         0.4897530450000000?
+         sage: import numpy                                                              # needs numpy
+         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
+-        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
++        ....:     _token = numpy.set_printoptions(legacy="1.25")                        # needs numpy
+         sage: x = numpy.array([1,2,3,4,5])                                              # needs numpy
+         sage: variance(x, bias=False)                                                   # needs numpy
+         2.5
+diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
+index cc15eff82e9..e32e7fd28b3 100644
+--- a/src/sage/structure/coerce.pyx
++++ b/src/sage/structure/coerce.pyx
+@@ -521,7 +521,7 @@ cdef class CoercionModel:
+ 
+         sage: import numpy                                                              # needs numpy
+         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
+-        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
++        ....:     _token = numpy.set_printoptions(legacy="1.25")                        # needs numpy
+ 
+         sage: # needs sage.rings.real_mpfr
+         sage: x = polygen(RR)
+diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
+index 362d01ea297..92bce28b032 100644
+--- a/src/sage/symbolic/function.pyx
++++ b/src/sage/symbolic/function.pyx
+@@ -962,7 +962,7 @@ cdef class BuiltinFunction(Function):
+ 
+             sage: import numpy                                                          # needs numpy
+             sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
+-            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
++            ....:     _token = numpy.set_printoptions(legacy="1.25")                    # needs numpy
+ 
+             sage: sin(numpy.int32(0))                                                   # needs numpy
+             0.0
+diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
+index 32afe8d3a62..63734e68f63 100644
+--- a/src/sage/symbolic/ring.pyx
++++ b/src/sage/symbolic/ring.pyx
+@@ -1154,7 +1154,7 @@ cdef class NumpyToSRMorphism(Morphism):
+ 
+         sage: import numpy                                                              # needs numpy
+         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
+-        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
++        ....:     _token = numpy.set_printoptions(legacy="1.25")                        # needs numpy
+         sage: f(x) = x^2
+         sage: f(numpy.int8('2'))                                                        # needs numpy
+         4

^ permalink raw reply	[flat|nested] 13+ messages in thread

* Re: [PR PATCH] [Updated] [BETA] sagemath: update to 10.5.beta2
  2024-08-18 17:54 [PR PATCH] [BETA] sagemath: update to 10.5.beta2 tornaria
  2024-08-20 20:57 ` [PR PATCH] [Updated] " tornaria
  2024-08-21  1:11 ` tornaria
@ 2024-08-22  2:10 ` tornaria
  2024-08-24  4:03 ` tornaria
                   ` (8 subsequent siblings)
  11 siblings, 0 replies; 13+ messages in thread
From: tornaria @ 2024-08-22  2:10 UTC (permalink / raw)
  To: ml

[-- Attachment #1: Type: text/plain, Size: 1465 bytes --]

There is an updated pull request by tornaria against master on the void-packages repository

https://github.com/tornaria/void-packages sagemath
https://github.com/void-linux/void-packages/pull/51902

[BETA] sagemath: update to 10.5.beta2
<!-- Uncomment relevant sections and delete options which are not applicable -->

 - python3-Cython: alternative fix for 6122
 - python3-gmpy2: update to 2.2.1.
 - python3-cypari2: update to 2.2.0.
 - python3-sympy: update to 1.13.2.
 - sagemath: enable all cython warnings

#### Testing the changes
- I tested the changes in this PR: **YES**

@dkwo

<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->

<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration
and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
  - aarch64-musl
  - armv7l
  - armv6l-musl
-->


A patch file from https://github.com/void-linux/void-packages/pull/51902.patch is attached

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-sagemath-51902.patch --]
[-- Type: text/x-diff, Size: 77011 bytes --]

From 1825ad833745404dc45dd4a3b82386c30db78513 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 11 Aug 2024 22:53:42 -0300
Subject: [PATCH 1/7] python3-Cython: alternative fix for 6122

---
 srcpkgs/python3-Cython/patches/fix-regression.patch | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/srcpkgs/python3-Cython/patches/fix-regression.patch b/srcpkgs/python3-Cython/patches/fix-regression.patch
index f2e761608e373b..f5957cfa59c2f5 100644
--- a/srcpkgs/python3-Cython/patches/fix-regression.patch
+++ b/srcpkgs/python3-Cython/patches/fix-regression.patch
@@ -15,3 +15,11 @@ serious regression, e.g. sagemath FTBS with cython 3.0.11
              warning(self.pos,
                      "Implicit noexcept declaration is deprecated."
                      " Function declaration should contain 'noexcept' keyword.",
+@@ -3128,6 +3126,7 @@ class DefNode(FuncDefNode):
+             if scope is None:
+                 scope = cfunc.scope
+             cfunc_type = cfunc.type
++            has_explicit_exc_clause=True
+             if len(self.args) != len(cfunc_type.args) or cfunc_type.has_varargs:
+                 error(self.pos, "wrong number of arguments")
+                 error(cfunc.pos, "previous declaration here")

From 1f322f47ed3beb3b916289142d680bbe1cb4ea4f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 19 Aug 2024 22:02:54 -0300
Subject: [PATCH 2/7] flintlib: C99 compliance

---
 srcpkgs/flintlib/patches/2027.patch | 322 ++++++++++++++++++++++++++++
 srcpkgs/flintlib/template           |   2 +-
 2 files changed, 323 insertions(+), 1 deletion(-)
 create mode 100644 srcpkgs/flintlib/patches/2027.patch

diff --git a/srcpkgs/flintlib/patches/2027.patch b/srcpkgs/flintlib/patches/2027.patch
new file mode 100644
index 00000000000000..f17ff31f2754d7
--- /dev/null
+++ b/srcpkgs/flintlib/patches/2027.patch
@@ -0,0 +1,322 @@
+See: https://github.com/flintlib/flint/pull/2027
+
+From 1b93e73d00881be12e04b7f13e070214a3c9e1cc Mon Sep 17 00:00:00 2001
+From: Dima Pasechnik <dima@pasechnik.info>
+Date: Wed, 19 Jun 2024 22:16:34 +0100
+Subject: [PATCH] ensure C99 compliance in headers, as 'I' is reserved
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+Note that the following code
+---- cut here: save as t.c
+---- cut here
+
+fails to compile with a suffciently new compiler, e.g. clang 16 or gcc 14.
+
+$ gcc -c t.c
+In file included from t.c:1:
+/usr/include/flint/mpoly.h:1319:43: error: expected ‘)’ before ‘__extension__’
+ 1319 | void mpoly_gcd_info_init(mpoly_gcd_info_t I, slong nvars);
+      |                                           ^
+In file included from /usr/include/flint/fmpz_types.h:15,
+                 from /usr/include/flint/fmpz_mod_types.h:15,
+                 from /usr/include/flint/mpoly_types.h:15,
+                 from /usr/include/flint/mpoly.h:23,
+                 from t.c:2:
+/usr/include/flint/mpoly.h:1319:46: error: expected ‘;’, ‘,’ or ‘)’ before ‘mp_limb_signed_t’
+ 1319 | void mpoly_gcd_info_init(mpoly_gcd_info_t I, slong nvars);
+
+...
+---
+ src/fft_small.h             |  6 +++---
+ src/fmpz_mod_mpoly_factor.h |  8 ++++----
+ src/fmpz_mpoly.h            |  2 +-
+ src/fmpz_mpoly_factor.h     | 18 +++++++++---------
+ src/fq_nmod_mpoly_factor.h  |  6 +++---
+ src/fq_zech_mpoly_factor.h  |  6 +++---
+ src/mpoly.h                 | 18 +++++++++---------
+ src/nmod_mpoly.h            |  4 ++--
+ src/nmod_mpoly_factor.h     |  6 +++---
+ 9 files changed, 37 insertions(+), 37 deletions(-)
+
+diff --git a/src/fft_small.h b/src/fft_small.h
+index 3f62f2e988..b7404f196d 100644
+--- a/src/fft_small.h
++++ b/src/fft_small.h
+@@ -242,10 +242,10 @@ FLINT_INLINE double sd_fft_ctx_get_fft_index(double* d, ulong i)
+ }
+ 
+ /* sd_fft.c */
+-void sd_fft_trunc(const sd_fft_lctx_t Q, ulong I, ulong S, ulong k, ulong j, ulong itrunc, ulong otrunc);
++void sd_fft_trunc(const sd_fft_lctx_t Q, ulong Iv, ulong S, ulong k, ulong j, ulong itrunc, ulong otrunc);
+ 
+ /* sd_ifft.c */
+-void sd_ifft_trunc(const sd_fft_lctx_t Q, ulong I, ulong S, ulong k, ulong j, ulong z, ulong n, int f);
++void sd_ifft_trunc(const sd_fft_lctx_t Q, ulong Iv, ulong S, ulong k, ulong j, ulong z, ulong n, int f);
+ 
+ /* sd_fft_ctx.c */
+ void sd_fft_ctx_clear(sd_fft_ctx_t Q);
+@@ -428,7 +428,7 @@ typedef struct {
+ 
+ typedef mpn_ctx_struct mpn_ctx_t[1];
+ 
+-void _convert_block(ulong* Xs, sd_fft_ctx_struct* Rffts, double* d, ulong dstride, ulong np, ulong I);
++void _convert_block(ulong* Xs, sd_fft_ctx_struct* Rffts, double* d, ulong dstride, ulong np, ulong Iv);
+ ulong flint_mpn_nbits(const ulong* a, ulong an);
+ int flint_mpn_cmp_ui_2exp(const ulong* a, ulong an, ulong b, ulong e);
+ unsigned char flint_mpn_add_inplace_c(ulong* z, ulong zn, ulong* a, ulong an, unsigned char cf);
+diff --git a/src/fmpz_mod_mpoly_factor.h b/src/fmpz_mod_mpoly_factor.h
+index 359fdd1e3d..460695dd23 100644
+--- a/src/fmpz_mod_mpoly_factor.h
++++ b/src/fmpz_mod_mpoly_factor.h
+@@ -1203,15 +1203,15 @@ typedef struct {
+ typedef fmpz_mod_mpoly_pfrac_struct fmpz_mod_mpoly_pfrac_t[1];
+ 
+ 
+-int fmpz_mod_mpoly_pfrac_init(fmpz_mod_mpoly_pfrac_t I,
++int fmpz_mod_mpoly_pfrac_init(fmpz_mod_mpoly_pfrac_t Iv,
+     flint_bitcnt_t bits, slong l, slong r, const fmpz_mod_mpoly_struct * betas,
+                           const fmpz * alpha, const fmpz_mod_mpoly_ctx_t ctx);
+ 
+-void fmpz_mod_mpoly_pfrac_clear(fmpz_mod_mpoly_pfrac_t I,
++void fmpz_mod_mpoly_pfrac_clear(fmpz_mod_mpoly_pfrac_t Iv,
+                                               const fmpz_mod_mpoly_ctx_t ctx);
+ 
+ int fmpz_mod_mpoly_pfrac(slong r, fmpz_mod_mpoly_t t, const slong * deg,
+-                     fmpz_mod_mpoly_pfrac_t I, const fmpz_mod_mpoly_ctx_t ctx);
++                     fmpz_mod_mpoly_pfrac_t Iv, const fmpz_mod_mpoly_ctx_t ctx);
+ 
+ int fmpz_mod_mpoly_hlift(slong m, fmpz_mod_mpoly_struct * f, slong r,
+             const fmpz * alpha, const fmpz_mod_mpoly_t A, const slong * degs,
+@@ -1290,7 +1290,7 @@ int fmpz_mod_mpolyn_gcd_brown_smprime(
+     fmpz_mod_mpolyn_t B,
+     slong var,
+     const fmpz_mod_mpoly_ctx_t ctx,
+-    const mpoly_gcd_info_t I,
++    const mpoly_gcd_info_t Iv,
+     fmpz_mod_poly_polyun_mpolyn_stack_t St);
+ 
+ int fmpz_mod_mpolyl_gcdp_zippel(
+diff --git a/src/fmpz_mpoly.h b/src/fmpz_mpoly.h
+index b7c9677915..4be3d05c56 100644
+--- a/src/fmpz_mpoly.h
++++ b/src/fmpz_mpoly.h
+@@ -1084,7 +1084,7 @@ void fmpz_mpoly_vec_randtest_not_zero(fmpz_mpoly_vec_t vec, flint_rand_t state,
+ 
+ void fmpz_mpoly_spoly(fmpz_mpoly_t res, const fmpz_mpoly_t f, const fmpz_mpoly_t g, const fmpz_mpoly_ctx_t ctx);
+ void fmpz_mpoly_vec_set_primitive_unique(fmpz_mpoly_vec_t G, const fmpz_mpoly_vec_t F, const fmpz_mpoly_ctx_t ctx);
+-void fmpz_mpoly_reduction_primitive_part(fmpz_mpoly_t res, const fmpz_mpoly_t f, const fmpz_mpoly_vec_t I, const fmpz_mpoly_ctx_t ctx);
++void fmpz_mpoly_reduction_primitive_part(fmpz_mpoly_t res, const fmpz_mpoly_t f, const fmpz_mpoly_vec_t Iv, const fmpz_mpoly_ctx_t ctx);
+ int fmpz_mpoly_vec_is_groebner(const fmpz_mpoly_vec_t G, const fmpz_mpoly_vec_t F, const fmpz_mpoly_ctx_t ctx);
+ void fmpz_mpoly_buchberger_naive(fmpz_mpoly_vec_t G, const fmpz_mpoly_vec_t F, const fmpz_mpoly_ctx_t ctx);
+ int fmpz_mpoly_buchberger_naive_with_limits(fmpz_mpoly_vec_t G, const fmpz_mpoly_vec_t F,
+diff --git a/src/fmpz_mpoly_factor.h b/src/fmpz_mpoly_factor.h
+index 0da7c1052b..a04ef8021e 100644
+--- a/src/fmpz_mpoly_factor.h
++++ b/src/fmpz_mpoly_factor.h
+@@ -298,11 +298,11 @@ void fmpz_mpoly_from_mpolyl_perm_inflate(fmpz_mpoly_t A,
+ 
+ int fmpz_mpolyl_gcd_brown(fmpz_mpoly_t G,
+         fmpz_mpoly_t Abar, fmpz_mpoly_t Bbar, fmpz_mpoly_t A, fmpz_mpoly_t B,
+-                         const fmpz_mpoly_ctx_t ctx, const mpoly_gcd_info_t I);
++                         const fmpz_mpoly_ctx_t ctx, const mpoly_gcd_info_t Iv);
+ 
+ int fmpz_mpolyl_gcd_brown_threaded_pool(fmpz_mpoly_t G,
+         fmpz_mpoly_t Abar, fmpz_mpoly_t Bbar, fmpz_mpoly_t A, fmpz_mpoly_t B,
+-                         const fmpz_mpoly_ctx_t ctx, const mpoly_gcd_info_t I,
++                         const fmpz_mpoly_ctx_t ctx, const mpoly_gcd_info_t Iv,
+                         const thread_pool_handle * handles, slong num_handles);
+ 
+ int fmpz_mpolyl_gcd_zippel(fmpz_mpoly_t G, fmpz_mpoly_t Abar,
+@@ -340,15 +340,15 @@ typedef struct {
+ 
+ typedef fmpz_poly_pfrac_struct fmpz_poly_pfrac_t[1];
+ 
+-void fmpz_poly_pfrac_init(fmpz_poly_pfrac_t I);
++void fmpz_poly_pfrac_init(fmpz_poly_pfrac_t Iv);
+ 
+-void fmpz_poly_pfrac_clear(fmpz_poly_pfrac_t I);
++void fmpz_poly_pfrac_clear(fmpz_poly_pfrac_t Iv);
+ 
+-int fmpz_poly_pfrac_precompute(fmpz_poly_pfrac_t I,
++int fmpz_poly_pfrac_precompute(fmpz_poly_pfrac_t Iv,
+                                           const fmpz_poly_struct * b, slong r);
+ 
+ int fmpz_poly_pfrac_precomp(fmpz_poly_struct * c,
+-                                     const fmpz_poly_t A, fmpz_poly_pfrac_t I);
++                                     const fmpz_poly_t A, fmpz_poly_pfrac_t Iv);
+ 
+ typedef struct {
+     flint_bitcnt_t bits;
+@@ -372,15 +372,15 @@ typedef struct {
+ 
+ typedef fmpz_mpoly_pfrac_struct fmpz_mpoly_pfrac_t[1];
+ 
+-int fmpz_mpoly_pfrac_init(fmpz_mpoly_pfrac_t I, flint_bitcnt_t bits,
++int fmpz_mpoly_pfrac_init(fmpz_mpoly_pfrac_t Iv, flint_bitcnt_t bits,
+                             slong r, slong w, const fmpz_mpoly_struct * betas,
+                                const fmpz * alpha, const fmpz_mpoly_ctx_t ctx);
+ 
+-void fmpz_mpoly_pfrac_clear(fmpz_mpoly_pfrac_t I,
++void fmpz_mpoly_pfrac_clear(fmpz_mpoly_pfrac_t Iv,
+                                                    const fmpz_mpoly_ctx_t ctx);
+ 
+ int fmpz_mpoly_pfrac(slong l, fmpz_mpoly_t t, const slong * degs,
+-                             fmpz_mpoly_pfrac_t I, const fmpz_mpoly_ctx_t ctx);
++                             fmpz_mpoly_pfrac_t Iv, const fmpz_mpoly_ctx_t ctx);
+ 
+ int fmpz_mpoly_hlift(slong m, fmpz_mpoly_struct * f, slong r,
+                 const fmpz * alpha, const fmpz_mpoly_t A, const slong * degs,
+diff --git a/src/fq_nmod_mpoly_factor.h b/src/fq_nmod_mpoly_factor.h
+index 6289d3f1c5..29caa99aa4 100644
+--- a/src/fq_nmod_mpoly_factor.h
++++ b/src/fq_nmod_mpoly_factor.h
+@@ -427,7 +427,7 @@ typedef fq_nmod_mpoly_pfrac_struct fq_nmod_mpoly_pfrac_t[1];
+ 
+ 
+ int fq_nmod_mpoly_pfrac_init(
+-    fq_nmod_mpoly_pfrac_t I,
++    fq_nmod_mpoly_pfrac_t Iv,
+     flint_bitcnt_t bits,
+     slong l, slong r,
+     const fq_nmod_mpoly_struct * betas,
+@@ -435,14 +435,14 @@ int fq_nmod_mpoly_pfrac_init(
+     const fq_nmod_mpoly_ctx_t ctx);
+ 
+ void fq_nmod_mpoly_pfrac_clear(
+-    fq_nmod_mpoly_pfrac_t I,
++    fq_nmod_mpoly_pfrac_t Iv,
+     const fq_nmod_mpoly_ctx_t ctx);
+ 
+ int fq_nmod_mpoly_pfrac(
+     slong r,
+     fq_nmod_mpoly_t t,
+     const slong * deg,
+-    fq_nmod_mpoly_pfrac_t I,
++    fq_nmod_mpoly_pfrac_t Iv,
+     const fq_nmod_mpoly_ctx_t ctx);
+ 
+ int fq_nmod_mpoly_hlift(
+diff --git a/src/fq_zech_mpoly_factor.h b/src/fq_zech_mpoly_factor.h
+index 06f31369f9..3d3c51419f 100644
+--- a/src/fq_zech_mpoly_factor.h
++++ b/src/fq_zech_mpoly_factor.h
+@@ -652,7 +652,7 @@ typedef fq_zech_mpoly_pfrac_struct fq_zech_mpoly_pfrac_t[1];
+ 
+ 
+ int fq_zech_mpoly_pfrac_init(
+-    fq_zech_mpoly_pfrac_t I,
++    fq_zech_mpoly_pfrac_t Iv,
+     flint_bitcnt_t bits,
+     slong l, slong r,
+     const fq_zech_mpoly_struct * betas,
+@@ -660,14 +660,14 @@ int fq_zech_mpoly_pfrac_init(
+     const fq_zech_mpoly_ctx_t ctx);
+ 
+ void fq_zech_mpoly_pfrac_clear(
+-    fq_zech_mpoly_pfrac_t I,
++    fq_zech_mpoly_pfrac_t Iv,
+     const fq_zech_mpoly_ctx_t ctx);
+ 
+ int fq_zech_mpoly_pfrac(
+     slong r,
+     fq_zech_mpoly_t t,
+     const slong * deg,
+-    fq_zech_mpoly_pfrac_t I,
++    fq_zech_mpoly_pfrac_t Iv,
+     const fq_zech_mpoly_ctx_t ctx);
+ 
+ int fq_zech_mpoly_hlift(
+diff --git a/src/mpoly.h b/src/mpoly.h
+index b0950e3a48..fe0ccbe7c4 100644
+--- a/src/mpoly.h
++++ b/src/mpoly.h
+@@ -1363,9 +1363,9 @@ typedef struct
+ 
+ typedef mpoly_gcd_info_struct mpoly_gcd_info_t[1];
+ 
+-void mpoly_gcd_info_init(mpoly_gcd_info_t I, slong nvars);
++void mpoly_gcd_info_init(mpoly_gcd_info_t Iv, slong nvars);
+ 
+-void mpoly_gcd_info_clear(mpoly_gcd_info_t I);
++void mpoly_gcd_info_clear(mpoly_gcd_info_t Iv);
+ 
+ void mpoly_gcd_info_limits(ulong * Amax_exp, ulong * Amin_exp,
+                        slong * Amax_exp_count, slong * Amin_exp_count,
+@@ -1378,25 +1378,25 @@ void mpoly_gcd_info_stride(ulong * strides,
+                              const ulong * Bmax_exp, const ulong * Bmin_exp,
+                                                        const mpoly_ctx_t mctx);
+ 
+-void mpoly_gcd_info_set_perm(mpoly_gcd_info_t I,
++void mpoly_gcd_info_set_perm(mpoly_gcd_info_t Iv,
+                          slong Alength, slong Blength, const mpoly_ctx_t mctx);
+ 
+-slong mpoly_gcd_info_get_brown_upper_limit(const mpoly_gcd_info_t I,
++slong mpoly_gcd_info_get_brown_upper_limit(const mpoly_gcd_info_t Iv,
+                                                        slong var, slong bound);
+ 
+-void mpoly_gcd_info_measure_hensel(mpoly_gcd_info_t I,
++void mpoly_gcd_info_measure_hensel(mpoly_gcd_info_t Iv,
+                          slong Alength, slong Blength, const mpoly_ctx_t mctx);
+ 
+-void mpoly_gcd_info_measure_brown(mpoly_gcd_info_t I,
++void mpoly_gcd_info_measure_brown(mpoly_gcd_info_t Iv,
+                          slong Alength, slong Blength, const mpoly_ctx_t mctx);
+ 
+-void mpoly_gcd_info_measure_bma(mpoly_gcd_info_t I,
++void mpoly_gcd_info_measure_bma(mpoly_gcd_info_t Iv,
+                          slong Alength, slong Blength, const mpoly_ctx_t mctx);
+ 
+-void mpoly_gcd_info_measure_zippel(mpoly_gcd_info_t I,
++void mpoly_gcd_info_measure_zippel(mpoly_gcd_info_t Iv,
+                          slong Alength, slong Blength, const mpoly_ctx_t mctx);
+ 
+-void mpoly_gcd_info_measure_zippel2(mpoly_gcd_info_t I,
++void mpoly_gcd_info_measure_zippel2(mpoly_gcd_info_t Iv,
+                          slong Alength, slong Blength, const mpoly_ctx_t mctx);
+ 
+ int mpoly_monomial_cofactors(fmpz * Abarexps, fmpz * Bbarexps,
+diff --git a/src/nmod_mpoly.h b/src/nmod_mpoly.h
+index 2a8136e6eb..716ac9669a 100644
+--- a/src/nmod_mpoly.h
++++ b/src/nmod_mpoly.h
+@@ -1619,13 +1619,13 @@ int nmod_mpolyn_gcd_brown_smprime_bivar(
+ int nmod_mpolyn_gcd_brown_smprime(nmod_mpolyn_t G,
+                                   nmod_mpolyn_t Abar, nmod_mpolyn_t Bbar,
+                                  nmod_mpolyn_t A, nmod_mpolyn_t B, slong var,
+-                         const nmod_mpoly_ctx_t ctx, const mpoly_gcd_info_t I,
++                         const nmod_mpoly_ctx_t ctx, const mpoly_gcd_info_t Iv,
+                                                          nmod_poly_stack_t Sp);
+ 
+ int nmod_mpolyn_gcd_brown_smprime_threaded_pool(nmod_mpolyn_t G,
+                                 nmod_mpolyn_t Abar, nmod_mpolyn_t Bbar,
+                                nmod_mpolyn_t A, nmod_mpolyn_t B, slong var,
+-                         const nmod_mpoly_ctx_t ctx, const mpoly_gcd_info_t I,
++                         const nmod_mpoly_ctx_t ctx, const mpoly_gcd_info_t Iv,
+                         const thread_pool_handle * handles, slong num_workers);
+ 
+ int nmod_mpolyn_gcd_brown_lgprime(nmod_mpolyn_t G,
+diff --git a/src/nmod_mpoly_factor.h b/src/nmod_mpoly_factor.h
+index a46afc860f..b16c802b9b 100644
+--- a/src/nmod_mpoly_factor.h
++++ b/src/nmod_mpoly_factor.h
+@@ -362,15 +362,15 @@ typedef struct {
+ typedef nmod_mpoly_pfrac_struct nmod_mpoly_pfrac_t[1];
+ 
+ 
+-int nmod_mpoly_pfrac_init(nmod_mpoly_pfrac_t I, flint_bitcnt_t bits,
++int nmod_mpoly_pfrac_init(nmod_mpoly_pfrac_t Iv, flint_bitcnt_t bits,
+                          slong l, slong r, const nmod_mpoly_struct * betas,
+                           const mp_limb_t * alpha, const nmod_mpoly_ctx_t ctx);
+ 
+-void nmod_mpoly_pfrac_clear(nmod_mpoly_pfrac_t I,
++void nmod_mpoly_pfrac_clear(nmod_mpoly_pfrac_t Iv,
+                                                    const nmod_mpoly_ctx_t ctx);
+ 
+ int nmod_mpoly_pfrac(slong r, nmod_mpoly_t t, const slong * deg,
+-                             nmod_mpoly_pfrac_t I, const nmod_mpoly_ctx_t ctx);
++                             nmod_mpoly_pfrac_t Iv, const nmod_mpoly_ctx_t ctx);
+ 
+ int nmod_mpoly_hlift(slong m, nmod_mpoly_struct * f, slong r,
+             const mp_limb_t * alpha, const nmod_mpoly_t A, const slong * degs,
diff --git a/srcpkgs/flintlib/template b/srcpkgs/flintlib/template
index 613391a9a0ae1b..465cdf1d0d3f71 100644
--- a/srcpkgs/flintlib/template
+++ b/srcpkgs/flintlib/template
@@ -1,7 +1,7 @@
 # Template file for 'flintlib'
 pkgname=flintlib
 version=3.1.2
-revision=1
+revision=2
 build_style=gnu-configure
 configure_args="--prefix=/usr --disable-arch $(vopt_with ntl)
  $(vopt_if openblas --with-blas-include=${XBPS_CROSS_BASE}/usr/include/openblas)"

From bcd8e6b405a9eb73e52a4273f74b1e445e2dffc6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 19 Aug 2024 17:35:53 -0300
Subject: [PATCH 3/7] python3-numpy: update to 2.1.0.

---
 srcpkgs/python3-numpy/template | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/srcpkgs/python3-numpy/template b/srcpkgs/python3-numpy/template
index cab4e3e506df30..7d0e493b32c5bb 100644
--- a/srcpkgs/python3-numpy/template
+++ b/srcpkgs/python3-numpy/template
@@ -1,6 +1,6 @@
 # Template file for 'python3-numpy'
 pkgname=python3-numpy
-version=2.0.1
+version=2.1.0
 revision=1
 build_style=python3-pep517
 build_helper="meson qemu"
@@ -19,7 +19,7 @@ license="BSD-3-Clause"
 homepage="https://www.numpy.org/"
 changelog="https://github.com/numpy/numpy/releases"
 distfiles="${PYPI_SITE}/n/numpy/numpy-${version}.tar.gz"
-checksum=485b87235796410c3519a699cfe1faab097e509e90ebb05dcd098db2ae87e7b3
+checksum=7dc90da0081f7e1da49ec4e398ede6a8e9cc4f5ebe5f9e06b443ed889ee9aaa2
 alternatives="numpy:f2py:/usr/bin/f2py3"
 
 build_options="openblas"

From b4542c50776ceb0a1274d38b7e04697470f81a29 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Wed, 21 Aug 2024 00:00:46 -0300
Subject: [PATCH 4/7] python3-scipy: update to 1.14.1.

---
 srcpkgs/python3-scipy/template | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/srcpkgs/python3-scipy/template b/srcpkgs/python3-scipy/template
index e35cd25b4595c6..00aa693110b985 100644
--- a/srcpkgs/python3-scipy/template
+++ b/srcpkgs/python3-scipy/template
@@ -1,7 +1,7 @@
 # Template file for 'python3-scipy'
 pkgname=python3-scipy
-version=1.14.0
-revision=2
+version=1.14.1
+revision=1
 build_style=python3-pep517
 build_helper="meson numpy"
 # SciPy imposes strict and unnecessary restrictions on build dependencies
@@ -19,8 +19,9 @@ short_desc="Scientific library for Python3"
 maintainer="Andrew J. Hesford <ajh@sideband.org>"
 license="BSD-3-Clause"
 homepage="https://scipy.org/"
+changelog="https://github.com/scipy/scipy/releases"
 distfiles="${PYPI_SITE}/s/scipy/scipy-${version}.tar.gz"
-checksum=b5923f48cb840380f9854339176ef21763118a7300a88203ccd0bdd26e58527b
+checksum=5a275584e726026a5699459aa72f828a610821006228e841b94275c4a7c08417
 # must be tested from site dir of installed version (see dev.py:739)
 make_check_pre='eval env -C "${testdir}/${py3_sitelib}"'
 

From 4b37959f5e5083977b44f6e598d17cf4b4438784 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 5 Aug 2024 00:21:23 -0300
Subject: [PATCH 5/7] sagemath: update to 10.5.beta2.

---
 .../sagemath/patches/36641-sympy_1.13.patch   |  22 +-
 .../sagemath/patches/37884-gap_4.13.1.patch   |  28 +-
 .../sagemath/patches/38250-numpy_2.0.patch    | 587 ------------------
 .../sagemath/patches/38344-ecm_7.0.6.patch    |  43 --
 srcpkgs/sagemath/patches/get_patches          |   4 +-
 srcpkgs/sagemath/template                     |   8 +-
 6 files changed, 22 insertions(+), 670 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/38250-numpy_2.0.patch
 delete mode 100644 srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch

diff --git a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
index 625c582cdd41b7..01e859ad023f4d 100644
--- a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
+++ b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
@@ -1,8 +1,5 @@
-diff --git a/build/pkgs/sympy/requirements.txt b/build/pkgs/sympy/requirements.txt
-new file mode 100644
-index 00000000000..3ef8f90b550
 diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py
-index 7e9eab2ff2e..43365cd645e 100644
+index 823a0d14a41..de1c8531814 100644
 --- a/src/sage/doctest/forker.py
 +++ b/src/sage/doctest/forker.py
 @@ -150,14 +150,15 @@ def init_sage(controller=None):
@@ -28,7 +25,7 @@ index 7e9eab2ff2e..43365cd645e 100644
      The displayhook sorts dictionary keys to simplify doctesting of
      dictionary output::
 diff --git a/src/sage/functions/hypergeometric.py b/src/sage/functions/hypergeometric.py
-index 010c61febe0..bbccbd20032 100644
+index ade7836b310..eb5c6665c0d 100644
 --- a/src/sage/functions/hypergeometric.py
 +++ b/src/sage/functions/hypergeometric.py
 @@ -124,7 +124,7 @@
@@ -40,21 +37,8 @@ index 010c61febe0..bbccbd20032 100644
      sage: hypergeometric((5, 4), (4, 4), 3)._mathematica_init_()                        # needs sage.symbolic
      'HypergeometricPFQ[{5,4},{4,4},3]'
  
-diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx
-index a92fe241355..f62311423be 100644
---- a/src/sage/symbolic/expression.pyx
-+++ b/src/sage/symbolic/expression.pyx
-@@ -1167,7 +1167,7 @@ cdef class Expression(Expression_abc):
-             sage: unicode_art(SR(13 - I))
-             13 - ⅈ
-             sage: unicode_art(SR(1.3 - I))
--            1.3 - ⅈ
-+            1.3 - 1.0⋅ⅈ
-             sage: unicode_art(cos(I))
-             cosh(1)
- 
 diff --git a/src/sage/typeset/ascii_art.py b/src/sage/typeset/ascii_art.py
-index 28024405d27..458fa8724a3 100644
+index 83d92af8959..e470e2bd88d 100644
 --- a/src/sage/typeset/ascii_art.py
 +++ b/src/sage/typeset/ascii_art.py
 @@ -44,11 +44,12 @@
diff --git a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
index 1550d47e2436c6..321e0a94487da3 100644
--- a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
+++ b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
@@ -1,21 +1,21 @@
 diff --git a/src/sage/algebras/fusion_rings/fusion_double.py b/src/sage/algebras/fusion_rings/fusion_double.py
-index 7ce086f70d0..954513572c3 100644
+index 71277561331..3b681d75d3b 100644
 --- a/src/sage/algebras/fusion_rings/fusion_double.py
 +++ b/src/sage/algebras/fusion_rings/fusion_double.py
 @@ -133,7 +133,7 @@ class FusionDouble(CombinatorialFreeModule):
          sage: G = SmallPermutationGroup(16,9)
-         sage: F = FusionDouble(G, prefix="b",inject_variables=True)
+         sage: F = FusionDouble(G, prefix='b', inject_variables=True)
          sage: b13^2 # long time (4s)
 -        b0 + b2 + b4 + b15 + b16 + b17 + b18 + b24 + b26 + b27
 +        b0 + b3 + b4
- 
      """
      @staticmethod
+     def __classcall_private__(cls, G, prefix='s', inject_variables=False):
 diff --git a/src/sage/categories/simplicial_sets.py b/src/sage/categories/simplicial_sets.py
-index e714a4571c4..a2b87a729d1 100644
+index aabd3cdbb4f..14bebdcd080 100644
 --- a/src/sage/categories/simplicial_sets.py
 +++ b/src/sage/categories/simplicial_sets.py
-@@ -593,9 +593,9 @@ def _canonical_twisting_operator(self):
+@@ -591,9 +591,9 @@ def _canonical_twisting_operator(self):
                      sage: X = simplicial_sets.Torus()
                      sage: d = X._canonical_twisting_operator()
                      sage: d
@@ -27,7 +27,7 @@ index e714a4571c4..a2b87a729d1 100644
                      sage: Y = simplicial_sets.RealProjectiveSpace(2)
                      sage: d2 = Y._canonical_twisting_operator()
                      sage: d2
-@@ -677,10 +677,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
+@@ -674,10 +674,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
                      sage: X = simplicial_sets.Torus()
                      sage: C = X.twisted_chain_complex()
                      sage: C.differential(1)
@@ -41,7 +41,7 @@ index e714a4571c4..a2b87a729d1 100644
                      [      -1       -1]
                      sage: C.differential(3)
                      []
-@@ -848,29 +848,29 @@ def twisted_homology(self, n, reduced=False):
+@@ -844,29 +844,29 @@ def twisted_homology(self, n, reduced=False):
                      sage: # needs sage.graphs
                      sage: Y = simplicial_sets.Torus()
                      sage: Y.twisted_homology(1)
@@ -80,10 +80,10 @@ index e714a4571c4..a2b87a729d1 100644
                      [1 0 0 0 0]
                      [0 1 0 0 0]
 diff --git a/src/sage/combinat/matrices/latin.py b/src/sage/combinat/matrices/latin.py
-index 936edcc6ea4..c06a53d9afd 100644
+index e2d818e9480..84e6c4fcc9b 100644
 --- a/src/sage/combinat/matrices/latin.py
 +++ b/src/sage/combinat/matrices/latin.py
-@@ -2453,7 +2453,7 @@ def p3_group_bitrade_generators(p):
+@@ -2444,7 +2444,7 @@ def p3_group_bitrade_generators(p):
      EXAMPLES::
  
          sage: from sage.combinat.matrices.latin import *
@@ -93,7 +93,7 @@ index 936edcc6ea4..c06a53d9afd 100644
           (1,2,3)(4,7,8)(5,6,9),
           (1,9,2)(3,7,4)(5,8,6),
 diff --git a/src/sage/groups/cubic_braid.py b/src/sage/groups/cubic_braid.py
-index 257b400f1c7..36423c756aa 100644
+index 61db70925e1..521289c7578 100644
 --- a/src/sage/groups/cubic_braid.py
 +++ b/src/sage/groups/cubic_braid.py
 @@ -282,7 +282,7 @@ def _richcmp_(self, other, op):
@@ -106,7 +106,7 @@ index 257b400f1c7..36423c756aa 100644
               c1*c0^-1*c1, c0^-1*c1^-1*c0^-1, c0^-1*c1^-1, c1^-1*c0*c1^-1,
               c0*c1^-1*c0^-1, c0^-1*c1, c0^-1*c1*c0, c0*c1^-1, c1*c0^-1,
 diff --git a/src/sage/groups/finitely_presented.py b/src/sage/groups/finitely_presented.py
-index 4bb52ee4efb..85f572fac6c 100644
+index 4ac2faa783b..7016d08381b 100644
 --- a/src/sage/groups/finitely_presented.py
 +++ b/src/sage/groups/finitely_presented.py
 @@ -1344,8 +1344,8 @@ def abelianization_map(self):
@@ -161,10 +161,10 @@ index 4bb52ee4efb..85f572fac6c 100644
              sage: G.characteristic_varieties(groebner=True)
              {0: [-1 + F1, 1 + F1, 1 - F1 + F1^2, 1 + F1 + F1^2], 1: [1 - F1 + F1^2],  2: []}
 diff --git a/src/sage/groups/perm_gps/permgroup_named.py b/src/sage/groups/perm_gps/permgroup_named.py
-index c1f2683907b..d219e104a2c 100644
+index 5c153b93d4c..bd4afad2942 100644
 --- a/src/sage/groups/perm_gps/permgroup_named.py
 +++ b/src/sage/groups/perm_gps/permgroup_named.py
-@@ -3468,16 +3468,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
+@@ -3465,16 +3465,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
          sage: G = SmallPermutationGroup(12,4); G
          Group of order 12 and GAP Id 4 as a permutation group
          sage: G.gens()
@@ -186,7 +186,7 @@ index c1f2683907b..d219e104a2c 100644
          sage: def numgps(n): return ZZ(libgap.NumberSmallGroups(n))
          sage: all(SmallPermutationGroup(n,k).id() == [n,k]
          ....:     for n in [1..64] for k in [1..numgps(n)])
-@@ -3486,11 +3484,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
+@@ -3483,11 +3481,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
          sage: H.is_abelian()
          False
          sage: [H.centralizer(g) for g in H.conjugacy_classes_representatives()]
diff --git a/srcpkgs/sagemath/patches/38250-numpy_2.0.patch b/srcpkgs/sagemath/patches/38250-numpy_2.0.patch
deleted file mode 100644
index e28fd857afcb75..00000000000000
--- a/srcpkgs/sagemath/patches/38250-numpy_2.0.patch
+++ /dev/null
@@ -1,587 +0,0 @@
-diff --git a/src/sage/arith/misc.py b/src/sage/arith/misc.py
-index 28f81d7b798..d184c52bf19 100644
---- a/src/sage/arith/misc.py
-+++ b/src/sage/arith/misc.py
-@@ -2277,7 +2277,7 @@ def power_mod(a, n, m):
- 
-         sage: from numpy import int32                                                   # needs numpy
-         sage: power_mod(int32(2), int32(390), int32(391))                               # needs numpy
--        285
-+        ...285...
-         sage: from gmpy2 import mpz
-         sage: power_mod(mpz(2), mpz(390), mpz(391))
-         mpz(285)
-diff --git a/src/sage/calculus/interpolators.pyx b/src/sage/calculus/interpolators.pyx
-index 221b52369e2..bb0be7bab0c 100644
---- a/src/sage/calculus/interpolators.pyx
-+++ b/src/sage/calculus/interpolators.pyx
-@@ -27,6 +27,9 @@ Development supported by NSF award No. 0702939.
- import numpy as np
- cimport numpy as np
- 
-+if int(np.version.short_version[0]) > 1:
-+    np.set_printoptions(legacy="1.25")
-+
- from math import pi
- cdef double TWOPI = 2*pi
- 
-diff --git a/src/sage/calculus/riemann.pyx b/src/sage/calculus/riemann.pyx
-index 6ec80d89aa7..c09d93c4260 100644
---- a/src/sage/calculus/riemann.pyx
-+++ b/src/sage/calculus/riemann.pyx
-@@ -44,6 +44,9 @@ from sage.calculus.integration import numerical_integral
- import numpy as np
- cimport numpy as np
- 
-+if int(np.version.short_version[0]) > 1:
-+    np.set_printoptions(legacy="1.25")
-+
- from math import pi
- from math import sin
- from math import cos
-diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index b198fed0c0d..b3ebd206cd2 100644
---- a/src/sage/combinat/fully_packed_loop.py
-+++ b/src/sage/combinat/fully_packed_loop.py
-@@ -66,6 +66,9 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
-     r"""
-     TESTS::
- 
-+        sage: import numpy as np
-+        sage: if int(np.version.short_version[0]) > 1:
-+        ....:     np.set_printoptions(legacy="1.25")
-         sage: from sage.combinat.fully_packed_loop import _make_color_list
-         sage: _make_color_list(5)
-         sage: _make_color_list(5, ['blue', 'red'])
-diff --git a/src/sage/env.py b/src/sage/env.py
-index 722649ab3da..abb9b19f9e3 100644
---- a/src/sage/env.py
-+++ b/src/sage/env.py
-@@ -296,7 +296,7 @@ def sage_include_directories(use_sources=False):
-         sage: import sage.env
-         sage: sage.env.sage_include_directories()
-         ['...',
--         '.../numpy/core/include',
-+         '.../numpy/...core/include',
-          '.../include/python...']
- 
-     To check that C/C++ files are correctly found, we verify that we can
-diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
-index e100ba3ee23..2a03bb68f67 100644
---- a/src/sage/functions/special.py
-+++ b/src/sage/functions/special.py
-@@ -217,6 +217,9 @@ class SphericalHarmonic(BuiltinFunction):
-         sage: spherical_harmonic(1, 1, pi/2, pi).n()  # abs tol 1e-14                   # needs sage.symbolic
-         0.345494149471335
-         sage: from scipy.special import sph_harm  # NB: arguments x and y are swapped   # needs scipy
-+        sage: import numpy as np                                                        # needs scipy
-+        sage: if int(np.version.short_version[0]) > 1:                                  # needs scipy
-+        ....:     np.set_printoptions(legacy="1.25")                                    # needs scipy
-         sage: sph_harm(1, 1, pi.n(), (pi/2).n())  # abs tol 1e-14                       # needs scipy sage.symbolic
-         (0.3454941494713355-4.231083042742082e-17j)
- 
-diff --git a/src/sage/graphs/generators/classical_geometries.py b/src/sage/graphs/generators/classical_geometries.py
-index da04362eef3..957f88d2061 100644
---- a/src/sage/graphs/generators/classical_geometries.py
-+++ b/src/sage/graphs/generators/classical_geometries.py
-@@ -1315,7 +1315,7 @@ def CossidentePenttilaGraph(q):
- 
-     from sage.libs.gap.libgap import libgap
-     adj_list = libgap.function_factory("""function(q)
--        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x;
-+        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x, sqo;
-         LoadPackage("grape");
-         G0:=SO(3,q^2);
-         so:=GeneratorsOfGroup(G0);
-diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
-index 063931ae274..0bafbd00564 100644
---- a/src/sage/graphs/generic_graph.py
-+++ b/src/sage/graphs/generic_graph.py
-@@ -18420,6 +18420,9 @@ def shortest_path_all_pairs(self, by_weight=False, algorithm=None,
-                 M = self.adjacency_matrix(vertices=int_to_vertex)
- 
-             # We call the Floyd-Warshall method from SciPy
-+            import numpy  # to ensure numpy 2.0 compatibility
-+            if int(numpy.version.short_version[0]) > 1:
-+                numpy.set_printoptions(legacy="1.25")
-             from numpy import array as np_array
-             from scipy.sparse.csgraph import floyd_warshall
-             dd, pp = floyd_warshall(np_array(M), directed=self.is_directed(),
-diff --git a/src/sage/graphs/graph_generators_pyx.pyx b/src/sage/graphs/graph_generators_pyx.pyx
-index 033e8b22adc..04b20d3229b 100644
---- a/src/sage/graphs/graph_generators_pyx.pyx
-+++ b/src/sage/graphs/graph_generators_pyx.pyx
-@@ -57,7 +57,7 @@ def RandomGNP(n, p, bint directed=False, bint loops=False, seed=None):
- 
-         sage: from numpy import mean                                                    # needs numpy
-         sage: abs(mean([RandomGNP(200, .2).density() for i in range(30)]) - .2) < .001  # needs numpy
--        True
-+        ...True...
-         sage: RandomGNP(150, .2, loops=True)
-         Traceback (most recent call last):
-         ...
-diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
-index a810418389c..c38df5412f0 100644
---- a/src/sage/matrix/matrix1.pyx
-+++ b/src/sage/matrix/matrix1.pyx
-@@ -705,12 +705,15 @@ cdef class Matrix(Matrix0):
-         Type ``numpy.typecodes`` for a list of the possible
-         typecodes::
- 
--            sage: import numpy                                                          # needs numpy
--            sage: sorted(numpy.typecodes.items())                                       # needs numpy
-+            sage: import numpy                            # needs numpy
-+            sage: numpy.typecodes.items()                 # needs numpy # random
-             [('All', '?bhilqpBHILQPefdgFDGSUVOMm'), ('AllFloat', 'efdgFDG'),
--             ('AllInteger', 'bBhHiIlLqQpP'), ('Character', 'c'), ('Complex', 'FDG'),
--             ('Datetime', 'Mm'), ('Float', 'efdg'), ('Integer', 'bhilqp'),
--             ('UnsignedInteger', 'BHILQP')]
-+            ...
-+
-+        For instance, you can see possibilities for real floating point numbers::
-+
-+            sage: numpy.typecodes['Float']                # needs numpy
-+            'efdg'
- 
-         Alternatively, numpy automatically calls this function (via
-         the magic :meth:`__array__` method) to convert Sage matrices
-diff --git a/src/sage/modules/free_module_element.pyx b/src/sage/modules/free_module_element.pyx
-index d71d22ac1f7..b6f297a3510 100644
---- a/src/sage/modules/free_module_element.pyx
-+++ b/src/sage/modules/free_module_element.pyx
-@@ -555,7 +555,11 @@ def vector(arg0, arg1=None, arg2=None, sparse=None, immutable=False):
-         R = None
- 
-     try:
-+        import numpy
-         from numpy import ndarray
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-+
-     except ImportError:
-         pass
-     else:
-@@ -1188,7 +1192,11 @@ cdef class FreeModuleElement(Vector):   # abstract base class
-             over Rational Field to numpy array of type <... 'float'>:
-             setting an array element with a sequence.
-         """
-+        import numpy
-         from numpy import array
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-+
-         try:
-             return array(self, dtype=dtype)
-         except ValueError as e:
-diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index e3d94d1746e..7ae8ca4966f 100644
---- a/src/sage/numerical/optimize.py
-+++ b/src/sage/numerical/optimize.py
-@@ -155,6 +155,10 @@ def find_root(f, a, b, xtol=10e-13, rtol=2.0**-50, maxiter=100, full_output=Fals
-         b = max(s_1, s_2)
- 
-     import scipy.optimize
-+    import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     g = lambda x: float(f(x))
-     brentqRes = scipy.optimize.brentq(g, a, b,
-                                  full_output=full_output, xtol=xtol, rtol=rtol, maxiter=maxiter)
-@@ -288,6 +292,10 @@ def find_local_minimum(f, a, b, tol=1.48e-08, maxfun=500):
-     a = float(a)
-     b = float(b)
-     import scipy.optimize
-+    import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     xmin, fval, iter, funcalls = scipy.optimize.fminbound(f, a, b, full_output=1, xtol=tol, maxfun=maxfun)
-     return fval, xmin
- 
-@@ -376,6 +384,8 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
-         sage: def rosen(x):  # The Rosenbrock function
-         ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
-         sage: import numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:
-+        ....:     numpy.set_printoptions(legacy="1.25")
-         sage: from numpy import zeros
-         sage: def rosen_der(x):
-         ....:    xm = x[1r:-1r]
-@@ -393,6 +403,9 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
-     from sage.structure.element import Expression
-     from sage.ext.fast_callable import fast_callable
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     from scipy import optimize
-     if isinstance(func, Expression):
-         var_list = func.variables()
-@@ -530,6 +543,8 @@ def minimize_constrained(func,cons,x0,gradient=None,algorithm='default', **args)
-     from sage.structure.element import Expression
-     from sage.ext.fast_callable import fast_callable
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-     from scipy import optimize
-     function_type = type(lambda x,y: x+y)
- 
-@@ -652,6 +667,8 @@ def find_fit(data, model, initial_guess=None, parameters=None, variables=None, s
-     ``lmdif`` and ``lmder`` algorithms.
-     """
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
- 
-     if not isinstance(data, numpy.ndarray):
-         try:
-diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index ac1dc79d802..23e2517ca56 100644
---- a/src/sage/plot/arrow.py
-+++ b/src/sage/plot/arrow.py
-@@ -53,6 +53,9 @@ def get_minmax_data(self):
- 
-         EXAMPLES::
- 
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: from sage.plot.arrow import CurveArrow
-             sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
-             ....:                options={})
-diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx
-index f1f2671a803..4d71414e1c2 100644
---- a/src/sage/plot/complex_plot.pyx
-+++ b/src/sage/plot/complex_plot.pyx
-@@ -1282,15 +1282,13 @@ def rgb_to_hls(rgb):
-         raise ValueError("Last dimension of input array must be 3; "
-                          "shape {} was found.".format(rgb.shape))
-     in_shape = rgb.shape
--    rgb = np.array(
--        rgb, copy=False, dtype=np.dtype(float), ndmin=2
--    )
-+    rgb = np.asarray(rgb, dtype=np.dtype(float))
-     rgb_max = rgb.max(-1)
-     rgb_min = rgb.min(-1)
-     l = (rgb_max + rgb_min)/2.0  # lightness
- 
-     hls = np.zeros_like(rgb)
--    delta = rgb.ptp(-1)
-+    delta = np.ptp(rgb, -1)
-     s = np.zeros_like(delta)
- 
-     ipos = delta > 0
-diff --git a/src/sage/plot/graphics.py b/src/sage/plot/graphics.py
-index a84d162cb56..94f5db09d83 100644
---- a/src/sage/plot/graphics.py
-+++ b/src/sage/plot/graphics.py
-@@ -2754,7 +2754,7 @@ def matplotlib(self, filename=None,
-             sage: xmin, xmax = sub.get_xlim()
-             sage: ymin, ymax = sub.get_ylim()
-             sage: xmin > xmax, ymin > ymax
--            (True, True)
-+            (...True..., ...True...)
-         """
-         if not isinstance(ticks, (list, tuple)):
-             ticks = (ticks, None)
-diff --git a/src/sage/plot/histogram.py b/src/sage/plot/histogram.py
-index fa86a44bd0a..a585cacf9cd 100644
---- a/src/sage/plot/histogram.py
-+++ b/src/sage/plot/histogram.py
-@@ -92,6 +92,8 @@ def get_minmax_data(self):
-             {'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.476190476190..., 'ymin': 0}
-         """
-         import numpy
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
- 
-         # Extract these options (if they are not None) and pass them to
-         # histogram()
-diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
-index b583be32317..6be448f1e04 100644
---- a/src/sage/plot/multigraphics.py
-+++ b/src/sage/plot/multigraphics.py
-@@ -784,6 +784,9 @@ def _add_subplot(self, figure, index, **options):
-             True
-             sage: G.position(1)
-             (0.2, 0.3, 0.4, 0.1)
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: ax1.get_position().bounds  # tol 1.0e-13
-             (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
- 
-@@ -1295,6 +1298,9 @@ def position(self, index):
-             sage: g1 = plot(sin(x), (x, -pi, pi))
-             sage: g2 = circle((0,1), 1.)
-             sage: G = graphics_array([g1, g2])
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: G.position(0)  # tol 5.0e-3
-             (0.025045451349937315,
-              0.03415488992713045,
-diff --git a/src/sage/plot/plot3d/implicit_surface.pyx b/src/sage/plot/plot3d/implicit_surface.pyx
-index ce0da48a4e0..f4d5059b620 100644
---- a/src/sage/plot/plot3d/implicit_surface.pyx
-+++ b/src/sage/plot/plot3d/implicit_surface.pyx
-@@ -468,6 +468,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
-             sage: cube_marcher.y_vertices.tolist()
-             [[[<1.0, 0.5, 0.0>, None]], [[None, None]]]
-             sage: cube_marcher.x_vertices.any() # This shouldn't affect the X vertices.
-+            ...
-         """
-         (self.y_vertices, self.y_vertices_swapped) = \
-             (self.y_vertices_swapped, self.y_vertices)
-@@ -574,6 +575,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
-             sage: cube_marcher.x_vertices.tolist()
-             [[None, None], [None, <1.5, 1.0, 1.0>]]
-             sage: cube_marcher.y_vertices.any() or cube_marcher.z_vertices.any() # This shouldn't affect the Y or Z vertices.
-+            ...
-         """
-         cdef bint has_prev = (_prev is not None)
-         cdef bint has_next = (_next is not None)
-diff --git a/src/sage/plot/scatter_plot.py b/src/sage/plot/scatter_plot.py
-index 4ad418f040b..781854d372c 100644
---- a/src/sage/plot/scatter_plot.py
-+++ b/src/sage/plot/scatter_plot.py
-@@ -63,9 +63,9 @@ def get_minmax_data(self):
-             sage: s = scatter_plot([[0,1],[2,4],[3.2,6]])
-             sage: d = s.get_minmax_data()
-             sage: d['xmin']
--            0.0
-+            ...0.0...
-             sage: d['ymin']
--            1.0
-+            ...1.0...
-         """
-         return {'xmin': self.xdata.min(),
-                 'xmax': self.xdata.max(),
-diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index 663d3aee70b..d2cb11088c7 100644
---- a/src/sage/plot/streamline_plot.py
-+++ b/src/sage/plot/streamline_plot.py
-@@ -71,6 +71,9 @@ def get_minmax_data(self):
-         EXAMPLES::
- 
-             sage: x, y = var('x y')
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: d = streamline_plot((.01*x, x+y), (x,10,20), (y,10,20))[0].get_minmax_data()
-             sage: d['xmin']
-             10.0
-diff --git a/src/sage/probability/probability_distribution.pyx b/src/sage/probability/probability_distribution.pyx
-index e2c71af9c25..59ba4a95ab6 100644
---- a/src/sage/probability/probability_distribution.pyx
-+++ b/src/sage/probability/probability_distribution.pyx
-@@ -140,6 +140,9 @@ cdef class ProbabilityDistribution:
-              1.8,
-              2.0]
-         """
-+        import numpy as np
-+        if int(np.version.short_version[0]) > 1:
-+            np.set_printoptions(legacy="1.25")
-         import pylab
-         ell = [float(self.get_random_element()) for _ in range(num_samples)]
-         S = pylab.hist(ell, bins, density=True)
-diff --git a/src/sage/rings/complex_double.pyx b/src/sage/rings/complex_double.pyx
-index c59a2b46d6f..b4dddebb4dc 100644
---- a/src/sage/rings/complex_double.pyx
-+++ b/src/sage/rings/complex_double.pyx
-@@ -2558,10 +2558,10 @@ cdef class ComplexToCDF(Morphism):
- 
-         sage: # needs numpy
-         sage: import numpy
--        sage: f = CDF.coerce_map_from(numpy.complex_)
--        sage: f(numpy.complex_(I))
-+        sage: f = CDF.coerce_map_from(numpy.complex128)
-+        sage: f(numpy.complex128(I))
-         1.0*I
--        sage: f(numpy.complex_(I)).parent()
-+        sage: f(numpy.complex128(I)).parent()
-         Complex Double Field
-     """
-     def __init__(self, R):
-@@ -2578,7 +2578,7 @@ cdef class ComplexToCDF(Morphism):
-         EXAMPLES::
- 
-             sage: import numpy                                                          # needs numpy
--            sage: CDF(numpy.complex_(I))    # indirect doctest                          # needs numpy
-+            sage: CDF(numpy.complex128(I))    # indirect doctest                          # needs numpy
-             1.0*I
-         """
-         cdef ComplexDoubleElement z = <ComplexDoubleElement>ComplexDoubleElement.__new__(ComplexDoubleElement)
-@@ -2592,7 +2592,7 @@ cdef class ComplexToCDF(Morphism):
-         EXAMPLES::
- 
-             sage: import numpy                                                          # needs numpy
--            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex_)            # needs numpy
-+            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex128)          # needs numpy
-             sage: f._repr_type()                                                        # needs numpy
-             'Native'
-         """
-diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index b4a1fa5039b..38c30f7627b 100644
---- a/src/sage/rings/integer.pyx
-+++ b/src/sage/rings/integer.pyx
-@@ -593,6 +593,8 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
-         Test comparisons with numpy types (see :issue:`13386` and :issue:`18076`)::
- 
-             sage: import numpy                                                          # needs numpy
-+            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
-+            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-             sage: numpy.int8('12') == 12                                                # needs numpy
-             True
-             sage: 12 == numpy.int8('12')                                                # needs numpy
-diff --git a/src/sage/rings/polynomial/polynomial_element.pyx b/src/sage/rings/polynomial/polynomial_element.pyx
-index dcf2af7cdf2..c87eccd44f1 100644
---- a/src/sage/rings/polynomial/polynomial_element.pyx
-+++ b/src/sage/rings/polynomial/polynomial_element.pyx
-@@ -8851,7 +8851,7 @@ cdef class Polynomial(CommutativePolynomial):
-                          'you expect.')
- 
-                 import numpy
--                from numpy.linalg.linalg import LinAlgError
-+                from numpy.linalg import LinAlgError
-                 from sage.rings.complex_double import CDF
- 
-                 numpy_dtype = ('complex' if input_complex else 'double')
-diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
-index 95b472e912c..76fbfedab95 100644
---- a/src/sage/rings/real_mpfi.pyx
-+++ b/src/sage/rings/real_mpfi.pyx
-@@ -231,6 +231,8 @@ specified if given a non-interval and an interval::
- TESTS::
- 
-     sage: import numpy                                                                  # needs numpy
-+    sage: if int(numpy.version.short_version[0]) > 1:                                   # needs numpy
-+    ....:     numpy.set_printoptions(legacy="1.25")                                     # needs numpy
-     sage: RIF(2) == numpy.int8('2')                                                     # needs numpy
-     True
-     sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
-diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-index 8f240627e77..70ce616f92f 100644
---- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-+++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-@@ -77,6 +77,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
-@@ -295,6 +297,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((10, 10))
-             sage: data[1:4,1:4] = True
-@@ -317,6 +321,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1,1] = True
-@@ -370,6 +376,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
- 
-             sage: data = np.zeros((20, 20))
-@@ -520,6 +528,8 @@ cdef class PeriodicRegion:
-         TESTS::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1, 1] = True
-diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index b2e6b301bf7..6937f6cb410 100644
---- a/src/sage/stats/basic_stats.py
-+++ b/src/sage/stats/basic_stats.py
-@@ -227,6 +227,8 @@ def std(v, bias=False):
- 
-         sage: # needs numpy
-         sage: import numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:
-+        ....:     numpy.set_printoptions(legacy="1.25")
-         sage: x = numpy.array([1,2,3,4,5])
-         sage: std(x, bias=False)
-         1.5811388300841898
-@@ -304,6 +306,8 @@ def variance(v, bias=False):
-         sage: variance([RIF(1.0103, 1.0103), RIF(2)])
-         0.4897530450000000?
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-         sage: x = numpy.array([1,2,3,4,5])                                              # needs numpy
-         sage: variance(x, bias=False)                                                   # needs numpy
-         2.5
-diff --git a/src/sage/stats/time_series.pyx b/src/sage/stats/time_series.pyx
-index 2e22ec45c69..23adae84fb4 100644
---- a/src/sage/stats/time_series.pyx
-+++ b/src/sage/stats/time_series.pyx
-@@ -1718,6 +1718,8 @@ cdef class TimeSeries:
-         if len(v0) == 1:
-             return v1[0]/v0[0]
-         import numpy
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-         coeffs = numpy.polyfit(v0,v1,1)
-         return coeffs[0]
- 
-diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
-index dfbd5ff82fa..955a256e9b4 100644
---- a/src/sage/structure/coerce.pyx
-+++ b/src/sage/structure/coerce.pyx
-@@ -520,6 +520,8 @@ cdef class CoercionModel:
-     Check that :issue:`8426` is fixed (see also :issue:`18076`)::
- 
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
- 
-         sage: # needs sage.rings.real_mpfr
-         sage: x = polygen(RR)
-diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
-index 2cb2f09c715..cd89ad2a256 100644
---- a/src/sage/symbolic/function.pyx
-+++ b/src/sage/symbolic/function.pyx
-@@ -964,6 +964,9 @@ cdef class BuiltinFunction(Function):
-             mpc(real='0.83373002513114902', imag='-0.98889770576286506')
- 
-             sage: import numpy                                                          # needs numpy
-+            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
-+            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-+
-             sage: sin(numpy.int32(0))                                                   # needs numpy
-             0.0
-             sage: type(_)                                                               # needs numpy
-diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 501b0920898..5b007d9e5fd 100644
---- a/src/sage/symbolic/ring.pyx
-+++ b/src/sage/symbolic/ring.pyx
-@@ -1162,6 +1162,8 @@ cdef class NumpyToSRMorphism(Morphism):
-     We check that :issue:`8949` and :issue:`9769` are fixed (see also :issue:`18076`)::
- 
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-         sage: f(x) = x^2
-         sage: f(numpy.int8('2'))                                                        # needs numpy
-         4
diff --git a/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch b/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch
deleted file mode 100644
index db0ae9030623b6..00000000000000
--- a/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-diff --git a/src/sage/interfaces/ecm.py b/src/sage/interfaces/ecm.py
-index 99287dec718..98011970404 100644
---- a/src/sage/interfaces/ecm.py
-+++ b/src/sage/interfaces/ecm.py
-@@ -508,7 +508,6 @@ def _find_factor(self, n, factor_digits, B1, **kwds):
-         """
-         n = self._validate(n)
-         kwds.setdefault('c', 1000000000)
--        kwds.setdefault('I', 1)
-         if factor_digits is not None:
-             B1 = self.recommended_B1(factor_digits)
-         kwds['one'] = True
-diff --git a/src/sage/libs/libecm.pyx b/src/sage/libs/libecm.pyx
-index 886a9b816e4..83fb7adaf8d 100644
---- a/src/sage/libs/libecm.pyx
-+++ b/src/sage/libs/libecm.pyx
-@@ -149,11 +149,13 @@ def ecmfactor(number, double B1, verbose=False, sigma=0):
-     Some special cases::
- 
-         sage: ecmfactor(1, 100)
--        (True, 1, ...)
-+        Traceback (most recent call last):
-+        ...
-+        ValueError: Input number (1) must be greater than 1
-         sage: ecmfactor(0, 100)
-         Traceback (most recent call last):
-         ...
--        ValueError: Input number (0) must be positive
-+        ValueError: Input number (0) must be greater than 1
-     """
-     cdef mpz_t n, f
-     cdef int res
-@@ -164,8 +166,8 @@ def ecmfactor(number, double B1, verbose=False, sigma=0):
-     sage_int_number = Integer(number)
-     sage_int_sigma = Integer(sigma)
- 
--    if number <= 0:
--        raise ValueError("Input number (%s) must be positive"%number)
-+    if number <= 1:
-+        raise ValueError("Input number (%s) must be greater than 1"%number)
- 
-     if verbose:
-         print("Performing one curve with B1=%1.0f" % B1)
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 28162dff8a38e1..5cab228f286365 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -19,7 +19,7 @@ get_pr() {
 	echo "curl -sL \"$url\" | filterdiff ... > \"$pr-$desc.patch\""
 	if [ -z "$dry" ]; then
 		curl -sL "$url" |
-			filterdiff -p1 -x src/setup.py -x build/* -x src/doc/* |
+			filterdiff -p1 -x src/setup.py -x environment* -x src/environment* -x build/* -x src/doc/* |
 			cat > "$pr-$desc.patch"
 	fi
 }
@@ -29,8 +29,6 @@ cd $(dirname "$0")
 
 get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
-get_pr 38250 "numpy 2.0"
-get_pr 38344 "ecm 7.0.6"
 
 #get_pr 37645 "fix doctest"
 #get_pr 37885 "cython warnings"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index befe33a0188687..f5e1d8c68cfcbe 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,7 +1,7 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.4
-revision=2
+version=10.5.beta2
+revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
 build_style=python3-pep517
@@ -25,14 +25,14 @@ depends="eclib-devel fflas-ffpack flintlib-devel gcc-fortran meson gd-devel
  python3-sympy python3-traitlets sage-data-combinatorial_designs
  python3-conway-polynomials sage-data-elliptic_curves sage-data-graphs
  sage-data-polytopes_db sympow tachyon threejs-sage"
-checkdepends="$depends pythran python3-Sphinx gdb"
+checkdepends="$depends python3-pytest pythran python3-Sphinx gdb"
 short_desc="Open source mathematics software"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=f6579e85f33bd9bb6e9b991bfc4c49dab1e649858ed9ee41c7cec75cb92d4c62
+checksum=0fe0c82dd6959951fc07d55737d270290f64947e183a403ca25709e21b751dee
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From 69c04f99d3fa1bae9c234e3a161e4dba41ec275e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Wed, 14 Aug 2024 00:12:02 -0300
Subject: [PATCH 6/7] sagemath: enable all cython warnings

---
 srcpkgs/sagemath/patches/37885-cython_warnings.patch | 12 ++++++++++++
 srcpkgs/sagemath/patches/get_patches                 |  2 +-
 2 files changed, 13 insertions(+), 1 deletion(-)
 create mode 100644 srcpkgs/sagemath/patches/37885-cython_warnings.patch

diff --git a/srcpkgs/sagemath/patches/37885-cython_warnings.patch b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
new file mode 100644
index 00000000000000..fa4b648cfc1577
--- /dev/null
+++ b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
@@ -0,0 +1,12 @@
+diff --git a/src/sage_setup/command/sage_build_cython.py b/src/sage_setup/command/sage_build_cython.py
+index f4b1357c543..3435c196d49 100644
+--- a/src/sage_setup/command/sage_build_cython.py
++++ b/src/sage_setup/command/sage_build_cython.py
+@@ -226,6 +226,7 @@ def run(self):
+                 compiler_directives=self.cython_directives,
+                 compile_time_env=self.compile_time_env,
+                 create_extension=self.create_extension,
++                show_all_warnings=True,
+                 # Debugging
+                 gdb_debug=self.debug,
+                 output_dir=os.path.join(self.build_lib, "sage"),
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 5cab228f286365..c182576ea553cd 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -31,4 +31,4 @@ get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
 
 #get_pr 37645 "fix doctest"
-#get_pr 37885 "cython warnings"
+get_pr 37885 "cython warnings"

From 7b24a6d2d50891008f6ffa4e4ca5b1de276e1a7f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 20 Aug 2024 17:56:06 -0300
Subject: [PATCH 7/7] sagemath: patch for numpy 2.1

---
 srcpkgs/sagemath/patches/numpy_2.1a.patch |  28 +++
 srcpkgs/sagemath/patches/numpy_2.1b.patch | 229 ++++++++++++++++++++++
 2 files changed, 257 insertions(+)
 create mode 100644 srcpkgs/sagemath/patches/numpy_2.1a.patch
 create mode 100644 srcpkgs/sagemath/patches/numpy_2.1b.patch

diff --git a/srcpkgs/sagemath/patches/numpy_2.1a.patch b/srcpkgs/sagemath/patches/numpy_2.1a.patch
new file mode 100644
index 00000000000000..493c75e2f8f8e0
--- /dev/null
+++ b/srcpkgs/sagemath/patches/numpy_2.1a.patch
@@ -0,0 +1,28 @@
+commit d755b32cbed462abf01a1cd782ba57cb92fbf713
+Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
+Date:   Mon Aug 19 23:25:32 2024 -0300
+
+    add copy parameter to numpy (needed for v2.1)
+
+diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
+index 3edb9ead54d..2c76fd1e557 100644
+--- a/src/sage/matrix/matrix1.pyx
++++ b/src/sage/matrix/matrix1.pyx
+@@ -670,7 +670,7 @@ cdef class Matrix(Matrix0):
+             entries = [[sib(v, 2) for v in row] for row in self.rows()]
+             return sib.name('matrix')(self.base_ring(), entries)
+ 
+-    def numpy(self, dtype=None):
++    def numpy(self, dtype=None, copy=True):
+         """
+         Return the Numpy matrix associated to this matrix.
+ 
+@@ -731,7 +731,7 @@ cdef class Matrix(Matrix0):
+             (3, 4)
+         """
+         import numpy
+-        A = numpy.matrix(self.list(), dtype=dtype)
++        A = numpy.matrix(self.list(), dtype=dtype, copy=copy)
+         return numpy.resize(A,(self.nrows(), self.ncols()))
+ 
+     # Define the magic "__array__" function so that numpy.array(m) can convert
diff --git a/srcpkgs/sagemath/patches/numpy_2.1b.patch b/srcpkgs/sagemath/patches/numpy_2.1b.patch
new file mode 100644
index 00000000000000..8dc0eec2b5a9d8
--- /dev/null
+++ b/srcpkgs/sagemath/patches/numpy_2.1b.patch
@@ -0,0 +1,229 @@
+commit 8260d18c3cf8e356db3d95fc46f6e68f75b453fd
+Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
+Date:   Tue Aug 20 00:05:33 2024 -0300
+
+    silence np.set_printoptions (for numpy 2.1)
+
+diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
+index 74a14fa1ecd..82e6c7eb3c8 100644
+--- a/src/sage/combinat/fully_packed_loop.py
++++ b/src/sage/combinat/fully_packed_loop.py
+@@ -68,7 +68,7 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
+ 
+         sage: import numpy as np
+         sage: if int(np.version.short_version[0]) > 1:
+-        ....:     np.set_printoptions(legacy="1.25")
++        ....:     _token = np.set_printoptions(legacy="1.25")
+         sage: from sage.combinat.fully_packed_loop import _make_color_list
+         sage: _make_color_list(5)
+         sage: _make_color_list(5, ['blue', 'red'])
+diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
+index 308171af3cd..6f66624ef87 100644
+--- a/src/sage/functions/special.py
++++ b/src/sage/functions/special.py
+@@ -219,7 +219,7 @@ class SphericalHarmonic(BuiltinFunction):
+         sage: from scipy.special import sph_harm  # NB: arguments x and y are swapped   # needs scipy
+         sage: import numpy as np                                                        # needs scipy
+         sage: if int(np.version.short_version[0]) > 1:                                  # needs scipy
+-        ....:     np.set_printoptions(legacy="1.25")                                    # needs scipy
++        ....:     _token = np.set_printoptions(legacy="1.25")                           # needs scipy
+         sage: sph_harm(1, 1, pi.n(), (pi/2).n())  # abs tol 1e-14                       # needs scipy sage.symbolic
+         (0.3454941494713355-4.231083042742082e-17j)
+ 
+diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
+index b3e42a6a6a2..13ffa4d1789 100644
+--- a/src/sage/numerical/optimize.py
++++ b/src/sage/numerical/optimize.py
+@@ -381,7 +381,7 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm='default',
+         ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
+         sage: import numpy
+         sage: if int(numpy.version.short_version[0]) > 1:
+-        ....:     numpy.set_printoptions(legacy="1.25")
++        ....:     _token = numpy.set_printoptions(legacy="1.25")
+         sage: from numpy import zeros
+         sage: def rosen_der(x):
+         ....:    xm = x[1r:-1r]
+diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
+index 02442f90ba4..1fe3f0b051a 100644
+--- a/src/sage/plot/arrow.py
++++ b/src/sage/plot/arrow.py
+@@ -55,7 +55,7 @@ class CurveArrow(GraphicPrimitive):
+ 
+             sage: import numpy  # to ensure numpy 2.0 compatibility
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     _token = numpy.set_printoptions(legacy="1.25")
+             sage: from sage.plot.arrow import CurveArrow
+             sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
+             ....:                options={})
+diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
+index d2f70b44526..2eaacc6879e 100644
+--- a/src/sage/plot/multigraphics.py
++++ b/src/sage/plot/multigraphics.py
+@@ -766,7 +766,7 @@ class MultiGraphics(WithEqualityById, SageObject):
+             (0.2, 0.3, 0.4, 0.1)
+             sage: import numpy  # to ensure numpy 2.0 compatibility
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     _token = numpy.set_printoptions(legacy="1.25")
+             sage: ax1.get_position().bounds  # tol 1.0e-13
+             (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
+         """
+@@ -1269,7 +1269,7 @@ class GraphicsArray(MultiGraphics):
+             sage: G = graphics_array([g1, g2])
+             sage: import numpy  # to ensure numpy 2.0 compatibility
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     _token = numpy.set_printoptions(legacy="1.25")
+             sage: G.position(0)  # tol 5.0e-3
+             (0.025045451349937315,
+              0.03415488992713045,
+diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
+index b69a05b37bf..25e404bfc7d 100644
+--- a/src/sage/plot/streamline_plot.py
++++ b/src/sage/plot/streamline_plot.py
+@@ -72,7 +72,7 @@ class StreamlinePlot(GraphicPrimitive):
+             sage: x, y = var('x y')
+             sage: import numpy  # to ensure numpy 2.0 compatibility
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     _token = numpy.set_printoptions(legacy="1.25")
+             sage: d = streamline_plot((.01*x, x+y), (x,10,20), (y,10,20))[0].get_minmax_data()
+             sage: d['xmin']
+             10.0
+diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
+index 11811b9587f..8ce0f7f2683 100644
+--- a/src/sage/rings/integer.pyx
++++ b/src/sage/rings/integer.pyx
+@@ -595,7 +595,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
+             sage: # needs numpy
+             sage: import numpy
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     _token = numpy.set_printoptions(legacy="1.25")
+             sage: numpy.int8('12') == 12
+             True
+             sage: 12 == numpy.int8('12')
+diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
+index 11953a50ab5..6aafcceed89 100644
+--- a/src/sage/rings/real_mpfi.pyx
++++ b/src/sage/rings/real_mpfi.pyx
+@@ -232,7 +232,7 @@ TESTS::
+ 
+     sage: import numpy                                                                  # needs numpy
+     sage: if int(numpy.version.short_version[0]) > 1:                                   # needs numpy
+-    ....:     numpy.set_printoptions(legacy="1.25")                                     # needs numpy
++    ....:     _token = numpy.set_printoptions(legacy="1.25")                            # needs numpy
+     sage: RIF(2) == numpy.int8('2')                                                     # needs numpy
+     True
+     sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
+diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
+index 40b92ab23eb..3838bcccb8a 100755
+--- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
++++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
+@@ -78,7 +78,7 @@ cdef class PeriodicRegion:
+ 
+             sage: import numpy as np
+             sage: if int(np.version.short_version[0]) > 1:
+-            ....:     np.set_printoptions(legacy="1.25")
++            ....:     _token = np.set_printoptions(legacy="1.25")
+             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
+             sage: data = np.zeros((4, 4))
+             sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
+@@ -296,7 +296,7 @@ cdef class PeriodicRegion:
+ 
+             sage: import numpy as np
+             sage: if int(np.version.short_version[0]) > 1:
+-            ....:     np.set_printoptions(legacy="1.25")
++            ....:     _token = np.set_printoptions(legacy="1.25")
+             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
+             sage: data = np.zeros((10, 10))
+             sage: data[1:4,1:4] = True
+@@ -320,7 +320,7 @@ cdef class PeriodicRegion:
+ 
+             sage: import numpy as np
+             sage: if int(np.version.short_version[0]) > 1:
+-            ....:     np.set_printoptions(legacy="1.25")
++            ....:     _token = np.set_printoptions(legacy="1.25")
+             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
+             sage: data = np.zeros((4, 4))
+             sage: data[1,1] = True
+@@ -375,7 +375,7 @@ cdef class PeriodicRegion:
+ 
+             sage: import numpy as np
+             sage: if int(np.version.short_version[0]) > 1:
+-            ....:     np.set_printoptions(legacy="1.25")
++            ....:     _token = np.set_printoptions(legacy="1.25")
+             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
+ 
+             sage: data = np.zeros((20, 20))
+@@ -528,7 +528,7 @@ cdef class PeriodicRegion:
+ 
+             sage: import numpy as np
+             sage: if int(np.version.short_version[0]) > 1:
+-            ....:     np.set_printoptions(legacy="1.25")
++            ....:     _token = np.set_printoptions(legacy="1.25")
+             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
+             sage: data = np.zeros((4, 4))
+             sage: data[1, 1] = True
+diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
+index 47d890cf0ab..ba7f0cdb0f9 100644
+--- a/src/sage/stats/basic_stats.py
++++ b/src/sage/stats/basic_stats.py
+@@ -222,7 +222,7 @@ def std(v, bias=False):
+         sage: # needs numpy
+         sage: import numpy
+         sage: if int(numpy.version.short_version[0]) > 1:
+-        ....:     numpy.set_printoptions(legacy="1.25")
++        ....:     _token = numpy.set_printoptions(legacy="1.25")
+         sage: x = numpy.array([1,2,3,4,5])
+         sage: std(x, bias=False)
+         1.5811388300841898
+@@ -299,7 +299,7 @@ def variance(v, bias=False):
+         0.4897530450000000?
+         sage: import numpy                                                              # needs numpy
+         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
+-        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
++        ....:     _token = numpy.set_printoptions(legacy="1.25")                        # needs numpy
+         sage: x = numpy.array([1,2,3,4,5])                                              # needs numpy
+         sage: variance(x, bias=False)                                                   # needs numpy
+         2.5
+diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
+index cc15eff82e9..e32e7fd28b3 100644
+--- a/src/sage/structure/coerce.pyx
++++ b/src/sage/structure/coerce.pyx
+@@ -521,7 +521,7 @@ cdef class CoercionModel:
+ 
+         sage: import numpy                                                              # needs numpy
+         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
+-        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
++        ....:     _token = numpy.set_printoptions(legacy="1.25")                        # needs numpy
+ 
+         sage: # needs sage.rings.real_mpfr
+         sage: x = polygen(RR)
+diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
+index 362d01ea297..92bce28b032 100644
+--- a/src/sage/symbolic/function.pyx
++++ b/src/sage/symbolic/function.pyx
+@@ -962,7 +962,7 @@ cdef class BuiltinFunction(Function):
+ 
+             sage: import numpy                                                          # needs numpy
+             sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
+-            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
++            ....:     _token = numpy.set_printoptions(legacy="1.25")                    # needs numpy
+ 
+             sage: sin(numpy.int32(0))                                                   # needs numpy
+             0.0
+diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
+index 32afe8d3a62..63734e68f63 100644
+--- a/src/sage/symbolic/ring.pyx
++++ b/src/sage/symbolic/ring.pyx
+@@ -1154,7 +1154,7 @@ cdef class NumpyToSRMorphism(Morphism):
+ 
+         sage: import numpy                                                              # needs numpy
+         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
+-        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
++        ....:     _token = numpy.set_printoptions(legacy="1.25")                        # needs numpy
+         sage: f(x) = x^2
+         sage: f(numpy.int8('2'))                                                        # needs numpy
+         4

^ permalink raw reply	[flat|nested] 13+ messages in thread

* Re: [PR PATCH] [Updated] [BETA] sagemath: update to 10.5.beta2
  2024-08-18 17:54 [PR PATCH] [BETA] sagemath: update to 10.5.beta2 tornaria
                   ` (2 preceding siblings ...)
  2024-08-22  2:10 ` tornaria
@ 2024-08-24  4:03 ` tornaria
  2024-09-08 16:10 ` tornaria
                   ` (7 subsequent siblings)
  11 siblings, 0 replies; 13+ messages in thread
From: tornaria @ 2024-08-24  4:03 UTC (permalink / raw)
  To: ml

[-- Attachment #1: Type: text/plain, Size: 1465 bytes --]

There is an updated pull request by tornaria against master on the void-packages repository

https://github.com/tornaria/void-packages sagemath
https://github.com/void-linux/void-packages/pull/51902

[BETA] sagemath: update to 10.5.beta2
<!-- Uncomment relevant sections and delete options which are not applicable -->

 - python3-Cython: alternative fix for 6122
 - python3-gmpy2: update to 2.2.1.
 - python3-cypari2: update to 2.2.0.
 - python3-sympy: update to 1.13.2.
 - sagemath: enable all cython warnings

#### Testing the changes
- I tested the changes in this PR: **YES**

@dkwo

<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->

<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration
and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
  - aarch64-musl
  - armv7l
  - armv6l-musl
-->


A patch file from https://github.com/void-linux/void-packages/pull/51902.patch is attached

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-sagemath-51902.patch --]
[-- Type: text/x-diff, Size: 56398 bytes --]

From 5552d7472e2439f30f5150fd6f43a7e7702cfc80 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 11 Aug 2024 22:53:42 -0300
Subject: [PATCH 1/4] python3-Cython: alternative fix for 6122

---
 srcpkgs/python3-Cython/patches/fix-regression.patch | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/srcpkgs/python3-Cython/patches/fix-regression.patch b/srcpkgs/python3-Cython/patches/fix-regression.patch
index f2e761608e373b..f5957cfa59c2f5 100644
--- a/srcpkgs/python3-Cython/patches/fix-regression.patch
+++ b/srcpkgs/python3-Cython/patches/fix-regression.patch
@@ -15,3 +15,11 @@ serious regression, e.g. sagemath FTBS with cython 3.0.11
              warning(self.pos,
                      "Implicit noexcept declaration is deprecated."
                      " Function declaration should contain 'noexcept' keyword.",
+@@ -3128,6 +3126,7 @@ class DefNode(FuncDefNode):
+             if scope is None:
+                 scope = cfunc.scope
+             cfunc_type = cfunc.type
++            has_explicit_exc_clause=True
+             if len(self.args) != len(cfunc_type.args) or cfunc_type.has_varargs:
+                 error(self.pos, "wrong number of arguments")
+                 error(cfunc.pos, "previous declaration here")

From 84dfd2776f3b306beaabf613896707ba1886679d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 5 Aug 2024 00:21:23 -0300
Subject: [PATCH 2/4] sagemath: update to 10.5.beta2.

---
 .../sagemath/patches/36641-sympy_1.13.patch   |  22 +-
 .../sagemath/patches/37884-gap_4.13.1.patch   |  28 +-
 .../sagemath/patches/38250-numpy_2.0.patch    | 587 ------------------
 .../sagemath/patches/38344-ecm_7.0.6.patch    |  43 --
 srcpkgs/sagemath/patches/get_patches          |   4 +-
 srcpkgs/sagemath/template                     |   6 +-
 6 files changed, 21 insertions(+), 669 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/38250-numpy_2.0.patch
 delete mode 100644 srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch

diff --git a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
index 625c582cdd41b7..01e859ad023f4d 100644
--- a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
+++ b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
@@ -1,8 +1,5 @@
-diff --git a/build/pkgs/sympy/requirements.txt b/build/pkgs/sympy/requirements.txt
-new file mode 100644
-index 00000000000..3ef8f90b550
 diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py
-index 7e9eab2ff2e..43365cd645e 100644
+index 823a0d14a41..de1c8531814 100644
 --- a/src/sage/doctest/forker.py
 +++ b/src/sage/doctest/forker.py
 @@ -150,14 +150,15 @@ def init_sage(controller=None):
@@ -28,7 +25,7 @@ index 7e9eab2ff2e..43365cd645e 100644
      The displayhook sorts dictionary keys to simplify doctesting of
      dictionary output::
 diff --git a/src/sage/functions/hypergeometric.py b/src/sage/functions/hypergeometric.py
-index 010c61febe0..bbccbd20032 100644
+index ade7836b310..eb5c6665c0d 100644
 --- a/src/sage/functions/hypergeometric.py
 +++ b/src/sage/functions/hypergeometric.py
 @@ -124,7 +124,7 @@
@@ -40,21 +37,8 @@ index 010c61febe0..bbccbd20032 100644
      sage: hypergeometric((5, 4), (4, 4), 3)._mathematica_init_()                        # needs sage.symbolic
      'HypergeometricPFQ[{5,4},{4,4},3]'
  
-diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx
-index a92fe241355..f62311423be 100644
---- a/src/sage/symbolic/expression.pyx
-+++ b/src/sage/symbolic/expression.pyx
-@@ -1167,7 +1167,7 @@ cdef class Expression(Expression_abc):
-             sage: unicode_art(SR(13 - I))
-             13 - ⅈ
-             sage: unicode_art(SR(1.3 - I))
--            1.3 - ⅈ
-+            1.3 - 1.0⋅ⅈ
-             sage: unicode_art(cos(I))
-             cosh(1)
- 
 diff --git a/src/sage/typeset/ascii_art.py b/src/sage/typeset/ascii_art.py
-index 28024405d27..458fa8724a3 100644
+index 83d92af8959..e470e2bd88d 100644
 --- a/src/sage/typeset/ascii_art.py
 +++ b/src/sage/typeset/ascii_art.py
 @@ -44,11 +44,12 @@
diff --git a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
index 1550d47e2436c6..321e0a94487da3 100644
--- a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
+++ b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
@@ -1,21 +1,21 @@
 diff --git a/src/sage/algebras/fusion_rings/fusion_double.py b/src/sage/algebras/fusion_rings/fusion_double.py
-index 7ce086f70d0..954513572c3 100644
+index 71277561331..3b681d75d3b 100644
 --- a/src/sage/algebras/fusion_rings/fusion_double.py
 +++ b/src/sage/algebras/fusion_rings/fusion_double.py
 @@ -133,7 +133,7 @@ class FusionDouble(CombinatorialFreeModule):
          sage: G = SmallPermutationGroup(16,9)
-         sage: F = FusionDouble(G, prefix="b",inject_variables=True)
+         sage: F = FusionDouble(G, prefix='b', inject_variables=True)
          sage: b13^2 # long time (4s)
 -        b0 + b2 + b4 + b15 + b16 + b17 + b18 + b24 + b26 + b27
 +        b0 + b3 + b4
- 
      """
      @staticmethod
+     def __classcall_private__(cls, G, prefix='s', inject_variables=False):
 diff --git a/src/sage/categories/simplicial_sets.py b/src/sage/categories/simplicial_sets.py
-index e714a4571c4..a2b87a729d1 100644
+index aabd3cdbb4f..14bebdcd080 100644
 --- a/src/sage/categories/simplicial_sets.py
 +++ b/src/sage/categories/simplicial_sets.py
-@@ -593,9 +593,9 @@ def _canonical_twisting_operator(self):
+@@ -591,9 +591,9 @@ def _canonical_twisting_operator(self):
                      sage: X = simplicial_sets.Torus()
                      sage: d = X._canonical_twisting_operator()
                      sage: d
@@ -27,7 +27,7 @@ index e714a4571c4..a2b87a729d1 100644
                      sage: Y = simplicial_sets.RealProjectiveSpace(2)
                      sage: d2 = Y._canonical_twisting_operator()
                      sage: d2
-@@ -677,10 +677,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
+@@ -674,10 +674,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
                      sage: X = simplicial_sets.Torus()
                      sage: C = X.twisted_chain_complex()
                      sage: C.differential(1)
@@ -41,7 +41,7 @@ index e714a4571c4..a2b87a729d1 100644
                      [      -1       -1]
                      sage: C.differential(3)
                      []
-@@ -848,29 +848,29 @@ def twisted_homology(self, n, reduced=False):
+@@ -844,29 +844,29 @@ def twisted_homology(self, n, reduced=False):
                      sage: # needs sage.graphs
                      sage: Y = simplicial_sets.Torus()
                      sage: Y.twisted_homology(1)
@@ -80,10 +80,10 @@ index e714a4571c4..a2b87a729d1 100644
                      [1 0 0 0 0]
                      [0 1 0 0 0]
 diff --git a/src/sage/combinat/matrices/latin.py b/src/sage/combinat/matrices/latin.py
-index 936edcc6ea4..c06a53d9afd 100644
+index e2d818e9480..84e6c4fcc9b 100644
 --- a/src/sage/combinat/matrices/latin.py
 +++ b/src/sage/combinat/matrices/latin.py
-@@ -2453,7 +2453,7 @@ def p3_group_bitrade_generators(p):
+@@ -2444,7 +2444,7 @@ def p3_group_bitrade_generators(p):
      EXAMPLES::
  
          sage: from sage.combinat.matrices.latin import *
@@ -93,7 +93,7 @@ index 936edcc6ea4..c06a53d9afd 100644
           (1,2,3)(4,7,8)(5,6,9),
           (1,9,2)(3,7,4)(5,8,6),
 diff --git a/src/sage/groups/cubic_braid.py b/src/sage/groups/cubic_braid.py
-index 257b400f1c7..36423c756aa 100644
+index 61db70925e1..521289c7578 100644
 --- a/src/sage/groups/cubic_braid.py
 +++ b/src/sage/groups/cubic_braid.py
 @@ -282,7 +282,7 @@ def _richcmp_(self, other, op):
@@ -106,7 +106,7 @@ index 257b400f1c7..36423c756aa 100644
               c1*c0^-1*c1, c0^-1*c1^-1*c0^-1, c0^-1*c1^-1, c1^-1*c0*c1^-1,
               c0*c1^-1*c0^-1, c0^-1*c1, c0^-1*c1*c0, c0*c1^-1, c1*c0^-1,
 diff --git a/src/sage/groups/finitely_presented.py b/src/sage/groups/finitely_presented.py
-index 4bb52ee4efb..85f572fac6c 100644
+index 4ac2faa783b..7016d08381b 100644
 --- a/src/sage/groups/finitely_presented.py
 +++ b/src/sage/groups/finitely_presented.py
 @@ -1344,8 +1344,8 @@ def abelianization_map(self):
@@ -161,10 +161,10 @@ index 4bb52ee4efb..85f572fac6c 100644
              sage: G.characteristic_varieties(groebner=True)
              {0: [-1 + F1, 1 + F1, 1 - F1 + F1^2, 1 + F1 + F1^2], 1: [1 - F1 + F1^2],  2: []}
 diff --git a/src/sage/groups/perm_gps/permgroup_named.py b/src/sage/groups/perm_gps/permgroup_named.py
-index c1f2683907b..d219e104a2c 100644
+index 5c153b93d4c..bd4afad2942 100644
 --- a/src/sage/groups/perm_gps/permgroup_named.py
 +++ b/src/sage/groups/perm_gps/permgroup_named.py
-@@ -3468,16 +3468,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
+@@ -3465,16 +3465,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
          sage: G = SmallPermutationGroup(12,4); G
          Group of order 12 and GAP Id 4 as a permutation group
          sage: G.gens()
@@ -186,7 +186,7 @@ index c1f2683907b..d219e104a2c 100644
          sage: def numgps(n): return ZZ(libgap.NumberSmallGroups(n))
          sage: all(SmallPermutationGroup(n,k).id() == [n,k]
          ....:     for n in [1..64] for k in [1..numgps(n)])
-@@ -3486,11 +3484,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
+@@ -3483,11 +3481,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
          sage: H.is_abelian()
          False
          sage: [H.centralizer(g) for g in H.conjugacy_classes_representatives()]
diff --git a/srcpkgs/sagemath/patches/38250-numpy_2.0.patch b/srcpkgs/sagemath/patches/38250-numpy_2.0.patch
deleted file mode 100644
index e28fd857afcb75..00000000000000
--- a/srcpkgs/sagemath/patches/38250-numpy_2.0.patch
+++ /dev/null
@@ -1,587 +0,0 @@
-diff --git a/src/sage/arith/misc.py b/src/sage/arith/misc.py
-index 28f81d7b798..d184c52bf19 100644
---- a/src/sage/arith/misc.py
-+++ b/src/sage/arith/misc.py
-@@ -2277,7 +2277,7 @@ def power_mod(a, n, m):
- 
-         sage: from numpy import int32                                                   # needs numpy
-         sage: power_mod(int32(2), int32(390), int32(391))                               # needs numpy
--        285
-+        ...285...
-         sage: from gmpy2 import mpz
-         sage: power_mod(mpz(2), mpz(390), mpz(391))
-         mpz(285)
-diff --git a/src/sage/calculus/interpolators.pyx b/src/sage/calculus/interpolators.pyx
-index 221b52369e2..bb0be7bab0c 100644
---- a/src/sage/calculus/interpolators.pyx
-+++ b/src/sage/calculus/interpolators.pyx
-@@ -27,6 +27,9 @@ Development supported by NSF award No. 0702939.
- import numpy as np
- cimport numpy as np
- 
-+if int(np.version.short_version[0]) > 1:
-+    np.set_printoptions(legacy="1.25")
-+
- from math import pi
- cdef double TWOPI = 2*pi
- 
-diff --git a/src/sage/calculus/riemann.pyx b/src/sage/calculus/riemann.pyx
-index 6ec80d89aa7..c09d93c4260 100644
---- a/src/sage/calculus/riemann.pyx
-+++ b/src/sage/calculus/riemann.pyx
-@@ -44,6 +44,9 @@ from sage.calculus.integration import numerical_integral
- import numpy as np
- cimport numpy as np
- 
-+if int(np.version.short_version[0]) > 1:
-+    np.set_printoptions(legacy="1.25")
-+
- from math import pi
- from math import sin
- from math import cos
-diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index b198fed0c0d..b3ebd206cd2 100644
---- a/src/sage/combinat/fully_packed_loop.py
-+++ b/src/sage/combinat/fully_packed_loop.py
-@@ -66,6 +66,9 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
-     r"""
-     TESTS::
- 
-+        sage: import numpy as np
-+        sage: if int(np.version.short_version[0]) > 1:
-+        ....:     np.set_printoptions(legacy="1.25")
-         sage: from sage.combinat.fully_packed_loop import _make_color_list
-         sage: _make_color_list(5)
-         sage: _make_color_list(5, ['blue', 'red'])
-diff --git a/src/sage/env.py b/src/sage/env.py
-index 722649ab3da..abb9b19f9e3 100644
---- a/src/sage/env.py
-+++ b/src/sage/env.py
-@@ -296,7 +296,7 @@ def sage_include_directories(use_sources=False):
-         sage: import sage.env
-         sage: sage.env.sage_include_directories()
-         ['...',
--         '.../numpy/core/include',
-+         '.../numpy/...core/include',
-          '.../include/python...']
- 
-     To check that C/C++ files are correctly found, we verify that we can
-diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
-index e100ba3ee23..2a03bb68f67 100644
---- a/src/sage/functions/special.py
-+++ b/src/sage/functions/special.py
-@@ -217,6 +217,9 @@ class SphericalHarmonic(BuiltinFunction):
-         sage: spherical_harmonic(1, 1, pi/2, pi).n()  # abs tol 1e-14                   # needs sage.symbolic
-         0.345494149471335
-         sage: from scipy.special import sph_harm  # NB: arguments x and y are swapped   # needs scipy
-+        sage: import numpy as np                                                        # needs scipy
-+        sage: if int(np.version.short_version[0]) > 1:                                  # needs scipy
-+        ....:     np.set_printoptions(legacy="1.25")                                    # needs scipy
-         sage: sph_harm(1, 1, pi.n(), (pi/2).n())  # abs tol 1e-14                       # needs scipy sage.symbolic
-         (0.3454941494713355-4.231083042742082e-17j)
- 
-diff --git a/src/sage/graphs/generators/classical_geometries.py b/src/sage/graphs/generators/classical_geometries.py
-index da04362eef3..957f88d2061 100644
---- a/src/sage/graphs/generators/classical_geometries.py
-+++ b/src/sage/graphs/generators/classical_geometries.py
-@@ -1315,7 +1315,7 @@ def CossidentePenttilaGraph(q):
- 
-     from sage.libs.gap.libgap import libgap
-     adj_list = libgap.function_factory("""function(q)
--        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x;
-+        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x, sqo;
-         LoadPackage("grape");
-         G0:=SO(3,q^2);
-         so:=GeneratorsOfGroup(G0);
-diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
-index 063931ae274..0bafbd00564 100644
---- a/src/sage/graphs/generic_graph.py
-+++ b/src/sage/graphs/generic_graph.py
-@@ -18420,6 +18420,9 @@ def shortest_path_all_pairs(self, by_weight=False, algorithm=None,
-                 M = self.adjacency_matrix(vertices=int_to_vertex)
- 
-             # We call the Floyd-Warshall method from SciPy
-+            import numpy  # to ensure numpy 2.0 compatibility
-+            if int(numpy.version.short_version[0]) > 1:
-+                numpy.set_printoptions(legacy="1.25")
-             from numpy import array as np_array
-             from scipy.sparse.csgraph import floyd_warshall
-             dd, pp = floyd_warshall(np_array(M), directed=self.is_directed(),
-diff --git a/src/sage/graphs/graph_generators_pyx.pyx b/src/sage/graphs/graph_generators_pyx.pyx
-index 033e8b22adc..04b20d3229b 100644
---- a/src/sage/graphs/graph_generators_pyx.pyx
-+++ b/src/sage/graphs/graph_generators_pyx.pyx
-@@ -57,7 +57,7 @@ def RandomGNP(n, p, bint directed=False, bint loops=False, seed=None):
- 
-         sage: from numpy import mean                                                    # needs numpy
-         sage: abs(mean([RandomGNP(200, .2).density() for i in range(30)]) - .2) < .001  # needs numpy
--        True
-+        ...True...
-         sage: RandomGNP(150, .2, loops=True)
-         Traceback (most recent call last):
-         ...
-diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
-index a810418389c..c38df5412f0 100644
---- a/src/sage/matrix/matrix1.pyx
-+++ b/src/sage/matrix/matrix1.pyx
-@@ -705,12 +705,15 @@ cdef class Matrix(Matrix0):
-         Type ``numpy.typecodes`` for a list of the possible
-         typecodes::
- 
--            sage: import numpy                                                          # needs numpy
--            sage: sorted(numpy.typecodes.items())                                       # needs numpy
-+            sage: import numpy                            # needs numpy
-+            sage: numpy.typecodes.items()                 # needs numpy # random
-             [('All', '?bhilqpBHILQPefdgFDGSUVOMm'), ('AllFloat', 'efdgFDG'),
--             ('AllInteger', 'bBhHiIlLqQpP'), ('Character', 'c'), ('Complex', 'FDG'),
--             ('Datetime', 'Mm'), ('Float', 'efdg'), ('Integer', 'bhilqp'),
--             ('UnsignedInteger', 'BHILQP')]
-+            ...
-+
-+        For instance, you can see possibilities for real floating point numbers::
-+
-+            sage: numpy.typecodes['Float']                # needs numpy
-+            'efdg'
- 
-         Alternatively, numpy automatically calls this function (via
-         the magic :meth:`__array__` method) to convert Sage matrices
-diff --git a/src/sage/modules/free_module_element.pyx b/src/sage/modules/free_module_element.pyx
-index d71d22ac1f7..b6f297a3510 100644
---- a/src/sage/modules/free_module_element.pyx
-+++ b/src/sage/modules/free_module_element.pyx
-@@ -555,7 +555,11 @@ def vector(arg0, arg1=None, arg2=None, sparse=None, immutable=False):
-         R = None
- 
-     try:
-+        import numpy
-         from numpy import ndarray
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-+
-     except ImportError:
-         pass
-     else:
-@@ -1188,7 +1192,11 @@ cdef class FreeModuleElement(Vector):   # abstract base class
-             over Rational Field to numpy array of type <... 'float'>:
-             setting an array element with a sequence.
-         """
-+        import numpy
-         from numpy import array
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-+
-         try:
-             return array(self, dtype=dtype)
-         except ValueError as e:
-diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index e3d94d1746e..7ae8ca4966f 100644
---- a/src/sage/numerical/optimize.py
-+++ b/src/sage/numerical/optimize.py
-@@ -155,6 +155,10 @@ def find_root(f, a, b, xtol=10e-13, rtol=2.0**-50, maxiter=100, full_output=Fals
-         b = max(s_1, s_2)
- 
-     import scipy.optimize
-+    import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     g = lambda x: float(f(x))
-     brentqRes = scipy.optimize.brentq(g, a, b,
-                                  full_output=full_output, xtol=xtol, rtol=rtol, maxiter=maxiter)
-@@ -288,6 +292,10 @@ def find_local_minimum(f, a, b, tol=1.48e-08, maxfun=500):
-     a = float(a)
-     b = float(b)
-     import scipy.optimize
-+    import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     xmin, fval, iter, funcalls = scipy.optimize.fminbound(f, a, b, full_output=1, xtol=tol, maxfun=maxfun)
-     return fval, xmin
- 
-@@ -376,6 +384,8 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
-         sage: def rosen(x):  # The Rosenbrock function
-         ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
-         sage: import numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:
-+        ....:     numpy.set_printoptions(legacy="1.25")
-         sage: from numpy import zeros
-         sage: def rosen_der(x):
-         ....:    xm = x[1r:-1r]
-@@ -393,6 +403,9 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
-     from sage.structure.element import Expression
-     from sage.ext.fast_callable import fast_callable
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     from scipy import optimize
-     if isinstance(func, Expression):
-         var_list = func.variables()
-@@ -530,6 +543,8 @@ def minimize_constrained(func,cons,x0,gradient=None,algorithm='default', **args)
-     from sage.structure.element import Expression
-     from sage.ext.fast_callable import fast_callable
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-     from scipy import optimize
-     function_type = type(lambda x,y: x+y)
- 
-@@ -652,6 +667,8 @@ def find_fit(data, model, initial_guess=None, parameters=None, variables=None, s
-     ``lmdif`` and ``lmder`` algorithms.
-     """
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
- 
-     if not isinstance(data, numpy.ndarray):
-         try:
-diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index ac1dc79d802..23e2517ca56 100644
---- a/src/sage/plot/arrow.py
-+++ b/src/sage/plot/arrow.py
-@@ -53,6 +53,9 @@ def get_minmax_data(self):
- 
-         EXAMPLES::
- 
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: from sage.plot.arrow import CurveArrow
-             sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
-             ....:                options={})
-diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx
-index f1f2671a803..4d71414e1c2 100644
---- a/src/sage/plot/complex_plot.pyx
-+++ b/src/sage/plot/complex_plot.pyx
-@@ -1282,15 +1282,13 @@ def rgb_to_hls(rgb):
-         raise ValueError("Last dimension of input array must be 3; "
-                          "shape {} was found.".format(rgb.shape))
-     in_shape = rgb.shape
--    rgb = np.array(
--        rgb, copy=False, dtype=np.dtype(float), ndmin=2
--    )
-+    rgb = np.asarray(rgb, dtype=np.dtype(float))
-     rgb_max = rgb.max(-1)
-     rgb_min = rgb.min(-1)
-     l = (rgb_max + rgb_min)/2.0  # lightness
- 
-     hls = np.zeros_like(rgb)
--    delta = rgb.ptp(-1)
-+    delta = np.ptp(rgb, -1)
-     s = np.zeros_like(delta)
- 
-     ipos = delta > 0
-diff --git a/src/sage/plot/graphics.py b/src/sage/plot/graphics.py
-index a84d162cb56..94f5db09d83 100644
---- a/src/sage/plot/graphics.py
-+++ b/src/sage/plot/graphics.py
-@@ -2754,7 +2754,7 @@ def matplotlib(self, filename=None,
-             sage: xmin, xmax = sub.get_xlim()
-             sage: ymin, ymax = sub.get_ylim()
-             sage: xmin > xmax, ymin > ymax
--            (True, True)
-+            (...True..., ...True...)
-         """
-         if not isinstance(ticks, (list, tuple)):
-             ticks = (ticks, None)
-diff --git a/src/sage/plot/histogram.py b/src/sage/plot/histogram.py
-index fa86a44bd0a..a585cacf9cd 100644
---- a/src/sage/plot/histogram.py
-+++ b/src/sage/plot/histogram.py
-@@ -92,6 +92,8 @@ def get_minmax_data(self):
-             {'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.476190476190..., 'ymin': 0}
-         """
-         import numpy
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
- 
-         # Extract these options (if they are not None) and pass them to
-         # histogram()
-diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
-index b583be32317..6be448f1e04 100644
---- a/src/sage/plot/multigraphics.py
-+++ b/src/sage/plot/multigraphics.py
-@@ -784,6 +784,9 @@ def _add_subplot(self, figure, index, **options):
-             True
-             sage: G.position(1)
-             (0.2, 0.3, 0.4, 0.1)
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: ax1.get_position().bounds  # tol 1.0e-13
-             (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
- 
-@@ -1295,6 +1298,9 @@ def position(self, index):
-             sage: g1 = plot(sin(x), (x, -pi, pi))
-             sage: g2 = circle((0,1), 1.)
-             sage: G = graphics_array([g1, g2])
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: G.position(0)  # tol 5.0e-3
-             (0.025045451349937315,
-              0.03415488992713045,
-diff --git a/src/sage/plot/plot3d/implicit_surface.pyx b/src/sage/plot/plot3d/implicit_surface.pyx
-index ce0da48a4e0..f4d5059b620 100644
---- a/src/sage/plot/plot3d/implicit_surface.pyx
-+++ b/src/sage/plot/plot3d/implicit_surface.pyx
-@@ -468,6 +468,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
-             sage: cube_marcher.y_vertices.tolist()
-             [[[<1.0, 0.5, 0.0>, None]], [[None, None]]]
-             sage: cube_marcher.x_vertices.any() # This shouldn't affect the X vertices.
-+            ...
-         """
-         (self.y_vertices, self.y_vertices_swapped) = \
-             (self.y_vertices_swapped, self.y_vertices)
-@@ -574,6 +575,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
-             sage: cube_marcher.x_vertices.tolist()
-             [[None, None], [None, <1.5, 1.0, 1.0>]]
-             sage: cube_marcher.y_vertices.any() or cube_marcher.z_vertices.any() # This shouldn't affect the Y or Z vertices.
-+            ...
-         """
-         cdef bint has_prev = (_prev is not None)
-         cdef bint has_next = (_next is not None)
-diff --git a/src/sage/plot/scatter_plot.py b/src/sage/plot/scatter_plot.py
-index 4ad418f040b..781854d372c 100644
---- a/src/sage/plot/scatter_plot.py
-+++ b/src/sage/plot/scatter_plot.py
-@@ -63,9 +63,9 @@ def get_minmax_data(self):
-             sage: s = scatter_plot([[0,1],[2,4],[3.2,6]])
-             sage: d = s.get_minmax_data()
-             sage: d['xmin']
--            0.0
-+            ...0.0...
-             sage: d['ymin']
--            1.0
-+            ...1.0...
-         """
-         return {'xmin': self.xdata.min(),
-                 'xmax': self.xdata.max(),
-diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index 663d3aee70b..d2cb11088c7 100644
---- a/src/sage/plot/streamline_plot.py
-+++ b/src/sage/plot/streamline_plot.py
-@@ -71,6 +71,9 @@ def get_minmax_data(self):
-         EXAMPLES::
- 
-             sage: x, y = var('x y')
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: d = streamline_plot((.01*x, x+y), (x,10,20), (y,10,20))[0].get_minmax_data()
-             sage: d['xmin']
-             10.0
-diff --git a/src/sage/probability/probability_distribution.pyx b/src/sage/probability/probability_distribution.pyx
-index e2c71af9c25..59ba4a95ab6 100644
---- a/src/sage/probability/probability_distribution.pyx
-+++ b/src/sage/probability/probability_distribution.pyx
-@@ -140,6 +140,9 @@ cdef class ProbabilityDistribution:
-              1.8,
-              2.0]
-         """
-+        import numpy as np
-+        if int(np.version.short_version[0]) > 1:
-+            np.set_printoptions(legacy="1.25")
-         import pylab
-         ell = [float(self.get_random_element()) for _ in range(num_samples)]
-         S = pylab.hist(ell, bins, density=True)
-diff --git a/src/sage/rings/complex_double.pyx b/src/sage/rings/complex_double.pyx
-index c59a2b46d6f..b4dddebb4dc 100644
---- a/src/sage/rings/complex_double.pyx
-+++ b/src/sage/rings/complex_double.pyx
-@@ -2558,10 +2558,10 @@ cdef class ComplexToCDF(Morphism):
- 
-         sage: # needs numpy
-         sage: import numpy
--        sage: f = CDF.coerce_map_from(numpy.complex_)
--        sage: f(numpy.complex_(I))
-+        sage: f = CDF.coerce_map_from(numpy.complex128)
-+        sage: f(numpy.complex128(I))
-         1.0*I
--        sage: f(numpy.complex_(I)).parent()
-+        sage: f(numpy.complex128(I)).parent()
-         Complex Double Field
-     """
-     def __init__(self, R):
-@@ -2578,7 +2578,7 @@ cdef class ComplexToCDF(Morphism):
-         EXAMPLES::
- 
-             sage: import numpy                                                          # needs numpy
--            sage: CDF(numpy.complex_(I))    # indirect doctest                          # needs numpy
-+            sage: CDF(numpy.complex128(I))    # indirect doctest                          # needs numpy
-             1.0*I
-         """
-         cdef ComplexDoubleElement z = <ComplexDoubleElement>ComplexDoubleElement.__new__(ComplexDoubleElement)
-@@ -2592,7 +2592,7 @@ cdef class ComplexToCDF(Morphism):
-         EXAMPLES::
- 
-             sage: import numpy                                                          # needs numpy
--            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex_)            # needs numpy
-+            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex128)          # needs numpy
-             sage: f._repr_type()                                                        # needs numpy
-             'Native'
-         """
-diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index b4a1fa5039b..38c30f7627b 100644
---- a/src/sage/rings/integer.pyx
-+++ b/src/sage/rings/integer.pyx
-@@ -593,6 +593,8 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
-         Test comparisons with numpy types (see :issue:`13386` and :issue:`18076`)::
- 
-             sage: import numpy                                                          # needs numpy
-+            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
-+            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-             sage: numpy.int8('12') == 12                                                # needs numpy
-             True
-             sage: 12 == numpy.int8('12')                                                # needs numpy
-diff --git a/src/sage/rings/polynomial/polynomial_element.pyx b/src/sage/rings/polynomial/polynomial_element.pyx
-index dcf2af7cdf2..c87eccd44f1 100644
---- a/src/sage/rings/polynomial/polynomial_element.pyx
-+++ b/src/sage/rings/polynomial/polynomial_element.pyx
-@@ -8851,7 +8851,7 @@ cdef class Polynomial(CommutativePolynomial):
-                          'you expect.')
- 
-                 import numpy
--                from numpy.linalg.linalg import LinAlgError
-+                from numpy.linalg import LinAlgError
-                 from sage.rings.complex_double import CDF
- 
-                 numpy_dtype = ('complex' if input_complex else 'double')
-diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
-index 95b472e912c..76fbfedab95 100644
---- a/src/sage/rings/real_mpfi.pyx
-+++ b/src/sage/rings/real_mpfi.pyx
-@@ -231,6 +231,8 @@ specified if given a non-interval and an interval::
- TESTS::
- 
-     sage: import numpy                                                                  # needs numpy
-+    sage: if int(numpy.version.short_version[0]) > 1:                                   # needs numpy
-+    ....:     numpy.set_printoptions(legacy="1.25")                                     # needs numpy
-     sage: RIF(2) == numpy.int8('2')                                                     # needs numpy
-     True
-     sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
-diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-index 8f240627e77..70ce616f92f 100644
---- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-+++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-@@ -77,6 +77,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
-@@ -295,6 +297,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((10, 10))
-             sage: data[1:4,1:4] = True
-@@ -317,6 +321,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1,1] = True
-@@ -370,6 +376,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
- 
-             sage: data = np.zeros((20, 20))
-@@ -520,6 +528,8 @@ cdef class PeriodicRegion:
-         TESTS::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1, 1] = True
-diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index b2e6b301bf7..6937f6cb410 100644
---- a/src/sage/stats/basic_stats.py
-+++ b/src/sage/stats/basic_stats.py
-@@ -227,6 +227,8 @@ def std(v, bias=False):
- 
-         sage: # needs numpy
-         sage: import numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:
-+        ....:     numpy.set_printoptions(legacy="1.25")
-         sage: x = numpy.array([1,2,3,4,5])
-         sage: std(x, bias=False)
-         1.5811388300841898
-@@ -304,6 +306,8 @@ def variance(v, bias=False):
-         sage: variance([RIF(1.0103, 1.0103), RIF(2)])
-         0.4897530450000000?
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-         sage: x = numpy.array([1,2,3,4,5])                                              # needs numpy
-         sage: variance(x, bias=False)                                                   # needs numpy
-         2.5
-diff --git a/src/sage/stats/time_series.pyx b/src/sage/stats/time_series.pyx
-index 2e22ec45c69..23adae84fb4 100644
---- a/src/sage/stats/time_series.pyx
-+++ b/src/sage/stats/time_series.pyx
-@@ -1718,6 +1718,8 @@ cdef class TimeSeries:
-         if len(v0) == 1:
-             return v1[0]/v0[0]
-         import numpy
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-         coeffs = numpy.polyfit(v0,v1,1)
-         return coeffs[0]
- 
-diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
-index dfbd5ff82fa..955a256e9b4 100644
---- a/src/sage/structure/coerce.pyx
-+++ b/src/sage/structure/coerce.pyx
-@@ -520,6 +520,8 @@ cdef class CoercionModel:
-     Check that :issue:`8426` is fixed (see also :issue:`18076`)::
- 
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
- 
-         sage: # needs sage.rings.real_mpfr
-         sage: x = polygen(RR)
-diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
-index 2cb2f09c715..cd89ad2a256 100644
---- a/src/sage/symbolic/function.pyx
-+++ b/src/sage/symbolic/function.pyx
-@@ -964,6 +964,9 @@ cdef class BuiltinFunction(Function):
-             mpc(real='0.83373002513114902', imag='-0.98889770576286506')
- 
-             sage: import numpy                                                          # needs numpy
-+            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
-+            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-+
-             sage: sin(numpy.int32(0))                                                   # needs numpy
-             0.0
-             sage: type(_)                                                               # needs numpy
-diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 501b0920898..5b007d9e5fd 100644
---- a/src/sage/symbolic/ring.pyx
-+++ b/src/sage/symbolic/ring.pyx
-@@ -1162,6 +1162,8 @@ cdef class NumpyToSRMorphism(Morphism):
-     We check that :issue:`8949` and :issue:`9769` are fixed (see also :issue:`18076`)::
- 
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-         sage: f(x) = x^2
-         sage: f(numpy.int8('2'))                                                        # needs numpy
-         4
diff --git a/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch b/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch
deleted file mode 100644
index db0ae9030623b6..00000000000000
--- a/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-diff --git a/src/sage/interfaces/ecm.py b/src/sage/interfaces/ecm.py
-index 99287dec718..98011970404 100644
---- a/src/sage/interfaces/ecm.py
-+++ b/src/sage/interfaces/ecm.py
-@@ -508,7 +508,6 @@ def _find_factor(self, n, factor_digits, B1, **kwds):
-         """
-         n = self._validate(n)
-         kwds.setdefault('c', 1000000000)
--        kwds.setdefault('I', 1)
-         if factor_digits is not None:
-             B1 = self.recommended_B1(factor_digits)
-         kwds['one'] = True
-diff --git a/src/sage/libs/libecm.pyx b/src/sage/libs/libecm.pyx
-index 886a9b816e4..83fb7adaf8d 100644
---- a/src/sage/libs/libecm.pyx
-+++ b/src/sage/libs/libecm.pyx
-@@ -149,11 +149,13 @@ def ecmfactor(number, double B1, verbose=False, sigma=0):
-     Some special cases::
- 
-         sage: ecmfactor(1, 100)
--        (True, 1, ...)
-+        Traceback (most recent call last):
-+        ...
-+        ValueError: Input number (1) must be greater than 1
-         sage: ecmfactor(0, 100)
-         Traceback (most recent call last):
-         ...
--        ValueError: Input number (0) must be positive
-+        ValueError: Input number (0) must be greater than 1
-     """
-     cdef mpz_t n, f
-     cdef int res
-@@ -164,8 +166,8 @@ def ecmfactor(number, double B1, verbose=False, sigma=0):
-     sage_int_number = Integer(number)
-     sage_int_sigma = Integer(sigma)
- 
--    if number <= 0:
--        raise ValueError("Input number (%s) must be positive"%number)
-+    if number <= 1:
-+        raise ValueError("Input number (%s) must be greater than 1"%number)
- 
-     if verbose:
-         print("Performing one curve with B1=%1.0f" % B1)
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 28162dff8a38e1..5cab228f286365 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -19,7 +19,7 @@ get_pr() {
 	echo "curl -sL \"$url\" | filterdiff ... > \"$pr-$desc.patch\""
 	if [ -z "$dry" ]; then
 		curl -sL "$url" |
-			filterdiff -p1 -x src/setup.py -x build/* -x src/doc/* |
+			filterdiff -p1 -x src/setup.py -x environment* -x src/environment* -x build/* -x src/doc/* |
 			cat > "$pr-$desc.patch"
 	fi
 }
@@ -29,8 +29,6 @@ cd $(dirname "$0")
 
 get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
-get_pr 38250 "numpy 2.0"
-get_pr 38344 "ecm 7.0.6"
 
 #get_pr 37645 "fix doctest"
 #get_pr 37885 "cython warnings"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index b116e62bc67a5a..f5e1d8c68cfcbe 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,7 +1,7 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.4
-revision=3
+version=10.5.beta2
+revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
 build_style=python3-pep517
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=f6579e85f33bd9bb6e9b991bfc4c49dab1e649858ed9ee41c7cec75cb92d4c62
+checksum=0fe0c82dd6959951fc07d55737d270290f64947e183a403ca25709e21b751dee
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From de0157b766efbd205f9f0a53294951959bd11015 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Wed, 14 Aug 2024 00:12:02 -0300
Subject: [PATCH 3/4] sagemath: enable all cython warnings

---
 srcpkgs/sagemath/patches/37885-cython_warnings.patch | 12 ++++++++++++
 srcpkgs/sagemath/patches/get_patches                 |  2 +-
 2 files changed, 13 insertions(+), 1 deletion(-)
 create mode 100644 srcpkgs/sagemath/patches/37885-cython_warnings.patch

diff --git a/srcpkgs/sagemath/patches/37885-cython_warnings.patch b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
new file mode 100644
index 00000000000000..fa4b648cfc1577
--- /dev/null
+++ b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
@@ -0,0 +1,12 @@
+diff --git a/src/sage_setup/command/sage_build_cython.py b/src/sage_setup/command/sage_build_cython.py
+index f4b1357c543..3435c196d49 100644
+--- a/src/sage_setup/command/sage_build_cython.py
++++ b/src/sage_setup/command/sage_build_cython.py
+@@ -226,6 +226,7 @@ def run(self):
+                 compiler_directives=self.cython_directives,
+                 compile_time_env=self.compile_time_env,
+                 create_extension=self.create_extension,
++                show_all_warnings=True,
+                 # Debugging
+                 gdb_debug=self.debug,
+                 output_dir=os.path.join(self.build_lib, "sage"),
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 5cab228f286365..c182576ea553cd 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -31,4 +31,4 @@ get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
 
 #get_pr 37645 "fix doctest"
-#get_pr 37885 "cython warnings"
+get_pr 37885 "cython warnings"

From 377d7d959c52b13b6873c45b7350aecd172fffa1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 20 Aug 2024 17:56:06 -0300
Subject: [PATCH 4/4] sagemath: patch for numpy 2.1

---
 srcpkgs/sagemath/patches/numpy_2.1a.patch |  8 +--
 srcpkgs/sagemath/patches/numpy_2.1b.patch | 70 +++++++++++------------
 2 files changed, 39 insertions(+), 39 deletions(-)

diff --git a/srcpkgs/sagemath/patches/numpy_2.1a.patch b/srcpkgs/sagemath/patches/numpy_2.1a.patch
index 30e2de99d84536..493c75e2f8f8e0 100644
--- a/srcpkgs/sagemath/patches/numpy_2.1a.patch
+++ b/srcpkgs/sagemath/patches/numpy_2.1a.patch
@@ -1,14 +1,14 @@
-commit 241dc39bd0ba1c056f88bee46a0345d59093eaff
+commit d755b32cbed462abf01a1cd782ba57cb92fbf713
 Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
 Date:   Mon Aug 19 23:25:32 2024 -0300
 
     add copy parameter to numpy (needed for v2.1)
 
 diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
-index c38df5412f0..f587cef651a 100644
+index 3edb9ead54d..2c76fd1e557 100644
 --- a/src/sage/matrix/matrix1.pyx
 +++ b/src/sage/matrix/matrix1.pyx
-@@ -671,7 +671,7 @@ cdef class Matrix(Matrix0):
+@@ -670,7 +670,7 @@ cdef class Matrix(Matrix0):
              entries = [[sib(v, 2) for v in row] for row in self.rows()]
              return sib.name('matrix')(self.base_ring(), entries)
  
@@ -17,7 +17,7 @@ index c38df5412f0..f587cef651a 100644
          """
          Return the Numpy matrix associated to this matrix.
  
-@@ -732,7 +732,7 @@ cdef class Matrix(Matrix0):
+@@ -731,7 +731,7 @@ cdef class Matrix(Matrix0):
              (3, 4)
          """
          import numpy
diff --git a/srcpkgs/sagemath/patches/numpy_2.1b.patch b/srcpkgs/sagemath/patches/numpy_2.1b.patch
index b77e28361d2e74..8dc0eec2b5a9d8 100644
--- a/srcpkgs/sagemath/patches/numpy_2.1b.patch
+++ b/srcpkgs/sagemath/patches/numpy_2.1b.patch
@@ -1,11 +1,11 @@
-commit 8b32fdb87725c1d67ffb51dadec1c331c7c35f3c
+commit 8260d18c3cf8e356db3d95fc46f6e68f75b453fd
 Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
 Date:   Tue Aug 20 00:05:33 2024 -0300
 
     silence np.set_printoptions (for numpy 2.1)
 
 diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index b3ebd206cd2..48866824224 100644
+index 74a14fa1ecd..82e6c7eb3c8 100644
 --- a/src/sage/combinat/fully_packed_loop.py
 +++ b/src/sage/combinat/fully_packed_loop.py
 @@ -68,7 +68,7 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
@@ -18,7 +18,7 @@ index b3ebd206cd2..48866824224 100644
          sage: _make_color_list(5)
          sage: _make_color_list(5, ['blue', 'red'])
 diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
-index 2a03bb68f67..30b56722e66 100644
+index 308171af3cd..6f66624ef87 100644
 --- a/src/sage/functions/special.py
 +++ b/src/sage/functions/special.py
 @@ -219,7 +219,7 @@ class SphericalHarmonic(BuiltinFunction):
@@ -31,10 +31,10 @@ index 2a03bb68f67..30b56722e66 100644
          (0.3454941494713355-4.231083042742082e-17j)
  
 diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index 7ae8ca4966f..4cba22efdba 100644
+index b3e42a6a6a2..13ffa4d1789 100644
 --- a/src/sage/numerical/optimize.py
 +++ b/src/sage/numerical/optimize.py
-@@ -385,7 +385,7 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
+@@ -381,7 +381,7 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm='default',
          ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
          sage: import numpy
          sage: if int(numpy.version.short_version[0]) > 1:
@@ -44,7 +44,7 @@ index 7ae8ca4966f..4cba22efdba 100644
          sage: def rosen_der(x):
          ....:    xm = x[1r:-1r]
 diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index 23e2517ca56..7375dcd5d1c 100644
+index 02442f90ba4..1fe3f0b051a 100644
 --- a/src/sage/plot/arrow.py
 +++ b/src/sage/plot/arrow.py
 @@ -55,7 +55,7 @@ class CurveArrow(GraphicPrimitive):
@@ -57,10 +57,10 @@ index 23e2517ca56..7375dcd5d1c 100644
              sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
              ....:                options={})
 diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
-index 6be448f1e04..004594b77c4 100644
+index d2f70b44526..2eaacc6879e 100644
 --- a/src/sage/plot/multigraphics.py
 +++ b/src/sage/plot/multigraphics.py
-@@ -786,7 +786,7 @@ class MultiGraphics(WithEqualityById, SageObject):
+@@ -766,7 +766,7 @@ class MultiGraphics(WithEqualityById, SageObject):
              (0.2, 0.3, 0.4, 0.1)
              sage: import numpy  # to ensure numpy 2.0 compatibility
              sage: if int(numpy.version.short_version[0]) > 1:
@@ -68,8 +68,8 @@ index 6be448f1e04..004594b77c4 100644
 +            ....:     _token = numpy.set_printoptions(legacy="1.25")
              sage: ax1.get_position().bounds  # tol 1.0e-13
              (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
- 
-@@ -1300,7 +1300,7 @@ class GraphicsArray(MultiGraphics):
+         """
+@@ -1269,7 +1269,7 @@ class GraphicsArray(MultiGraphics):
              sage: G = graphics_array([g1, g2])
              sage: import numpy  # to ensure numpy 2.0 compatibility
              sage: if int(numpy.version.short_version[0]) > 1:
@@ -79,10 +79,10 @@ index 6be448f1e04..004594b77c4 100644
              (0.025045451349937315,
               0.03415488992713045,
 diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index d2cb11088c7..6d88517cc15 100644
+index b69a05b37bf..25e404bfc7d 100644
 --- a/src/sage/plot/streamline_plot.py
 +++ b/src/sage/plot/streamline_plot.py
-@@ -73,7 +73,7 @@ class StreamlinePlot(GraphicPrimitive):
+@@ -72,7 +72,7 @@ class StreamlinePlot(GraphicPrimitive):
              sage: x, y = var('x y')
              sage: import numpy  # to ensure numpy 2.0 compatibility
              sage: if int(numpy.version.short_version[0]) > 1:
@@ -92,20 +92,20 @@ index d2cb11088c7..6d88517cc15 100644
              sage: d['xmin']
              10.0
 diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index 38c30f7627b..cfb8a5ff5f7 100644
+index 11811b9587f..8ce0f7f2683 100644
 --- a/src/sage/rings/integer.pyx
 +++ b/src/sage/rings/integer.pyx
-@@ -594,7 +594,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
- 
-             sage: import numpy                                                          # needs numpy
-             sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
--            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")                    # needs numpy
-             sage: numpy.int8('12') == 12                                                # needs numpy
+@@ -595,7 +595,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
+             sage: # needs numpy
+             sage: import numpy
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     _token = numpy.set_printoptions(legacy="1.25")
+             sage: numpy.int8('12') == 12
              True
-             sage: 12 == numpy.int8('12')                                                # needs numpy
+             sage: 12 == numpy.int8('12')
 diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
-index 76fbfedab95..57de30c9d18 100644
+index 11953a50ab5..6aafcceed89 100644
 --- a/src/sage/rings/real_mpfi.pyx
 +++ b/src/sage/rings/real_mpfi.pyx
 @@ -232,7 +232,7 @@ TESTS::
@@ -118,7 +118,7 @@ index 76fbfedab95..57de30c9d18 100644
      True
      sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
 diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-index 70ce616f92f..f604c6d3785 100644
+index 40b92ab23eb..3838bcccb8a 100755
 --- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
 +++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
 @@ -78,7 +78,7 @@ cdef class PeriodicRegion:
@@ -130,7 +130,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
              sage: data = np.zeros((4, 4))
              sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
-@@ -298,7 +298,7 @@ cdef class PeriodicRegion:
+@@ -296,7 +296,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -139,7 +139,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
              sage: data = np.zeros((10, 10))
              sage: data[1:4,1:4] = True
-@@ -322,7 +322,7 @@ cdef class PeriodicRegion:
+@@ -320,7 +320,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -148,7 +148,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
              sage: data = np.zeros((4, 4))
              sage: data[1,1] = True
-@@ -377,7 +377,7 @@ cdef class PeriodicRegion:
+@@ -375,7 +375,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -157,7 +157,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
  
              sage: data = np.zeros((20, 20))
-@@ -529,7 +529,7 @@ cdef class PeriodicRegion:
+@@ -528,7 +528,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -167,10 +167,10 @@ index 70ce616f92f..f604c6d3785 100644
              sage: data = np.zeros((4, 4))
              sage: data[1, 1] = True
 diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index 6937f6cb410..fb296e00fb6 100644
+index 47d890cf0ab..ba7f0cdb0f9 100644
 --- a/src/sage/stats/basic_stats.py
 +++ b/src/sage/stats/basic_stats.py
-@@ -228,7 +228,7 @@ def std(v, bias=False):
+@@ -222,7 +222,7 @@ def std(v, bias=False):
          sage: # needs numpy
          sage: import numpy
          sage: if int(numpy.version.short_version[0]) > 1:
@@ -179,7 +179,7 @@ index 6937f6cb410..fb296e00fb6 100644
          sage: x = numpy.array([1,2,3,4,5])
          sage: std(x, bias=False)
          1.5811388300841898
-@@ -307,7 +307,7 @@ def variance(v, bias=False):
+@@ -299,7 +299,7 @@ def variance(v, bias=False):
          0.4897530450000000?
          sage: import numpy                                                              # needs numpy
          sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
@@ -189,7 +189,7 @@ index 6937f6cb410..fb296e00fb6 100644
          sage: variance(x, bias=False)                                                   # needs numpy
          2.5
 diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
-index 955a256e9b4..e5ed6160b79 100644
+index cc15eff82e9..e32e7fd28b3 100644
 --- a/src/sage/structure/coerce.pyx
 +++ b/src/sage/structure/coerce.pyx
 @@ -521,7 +521,7 @@ cdef class CoercionModel:
@@ -202,10 +202,10 @@ index 955a256e9b4..e5ed6160b79 100644
          sage: # needs sage.rings.real_mpfr
          sage: x = polygen(RR)
 diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
-index cd89ad2a256..6fdf6d8ef23 100644
+index 362d01ea297..92bce28b032 100644
 --- a/src/sage/symbolic/function.pyx
 +++ b/src/sage/symbolic/function.pyx
-@@ -965,7 +965,7 @@ cdef class BuiltinFunction(Function):
+@@ -962,7 +962,7 @@ cdef class BuiltinFunction(Function):
  
              sage: import numpy                                                          # needs numpy
              sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
@@ -215,10 +215,10 @@ index cd89ad2a256..6fdf6d8ef23 100644
              sage: sin(numpy.int32(0))                                                   # needs numpy
              0.0
 diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 5b007d9e5fd..4a096d317e7 100644
+index 32afe8d3a62..63734e68f63 100644
 --- a/src/sage/symbolic/ring.pyx
 +++ b/src/sage/symbolic/ring.pyx
-@@ -1163,7 +1163,7 @@ cdef class NumpyToSRMorphism(Morphism):
+@@ -1154,7 +1154,7 @@ cdef class NumpyToSRMorphism(Morphism):
  
          sage: import numpy                                                              # needs numpy
          sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy

^ permalink raw reply	[flat|nested] 13+ messages in thread

* Re: [PR PATCH] [Updated] [BETA] sagemath: update to 10.5.beta2
  2024-08-18 17:54 [PR PATCH] [BETA] sagemath: update to 10.5.beta2 tornaria
                   ` (3 preceding siblings ...)
  2024-08-24  4:03 ` tornaria
@ 2024-09-08 16:10 ` tornaria
  2024-09-09  1:13 ` [BETA] sagemath: update to 10.5.beta3 dkwo
                   ` (6 subsequent siblings)
  11 siblings, 0 replies; 13+ messages in thread
From: tornaria @ 2024-09-08 16:10 UTC (permalink / raw)
  To: ml

[-- Attachment #1: Type: text/plain, Size: 1465 bytes --]

There is an updated pull request by tornaria against master on the void-packages repository

https://github.com/tornaria/void-packages sagemath
https://github.com/void-linux/void-packages/pull/51902

[BETA] sagemath: update to 10.5.beta2
<!-- Uncomment relevant sections and delete options which are not applicable -->

 - python3-Cython: alternative fix for 6122
 - python3-gmpy2: update to 2.2.1.
 - python3-cypari2: update to 2.2.0.
 - python3-sympy: update to 1.13.2.
 - sagemath: enable all cython warnings

#### Testing the changes
- I tested the changes in this PR: **YES**

@dkwo

<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->

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- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
  - aarch64-musl
  - armv7l
  - armv6l-musl
-->


A patch file from https://github.com/void-linux/void-packages/pull/51902.patch is attached

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-sagemath-51902.patch --]
[-- Type: text/x-diff, Size: 65319 bytes --]

From 026f7e0ddb57ddb60467a26e256ab961f5e49c96 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 11 Aug 2024 22:53:42 -0300
Subject: [PATCH 1/6] python3-Cython: alternative fix for 6122

---
 srcpkgs/python3-Cython/patches/fix-regression.patch | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/srcpkgs/python3-Cython/patches/fix-regression.patch b/srcpkgs/python3-Cython/patches/fix-regression.patch
index f2e761608e373b..f5957cfa59c2f5 100644
--- a/srcpkgs/python3-Cython/patches/fix-regression.patch
+++ b/srcpkgs/python3-Cython/patches/fix-regression.patch
@@ -15,3 +15,11 @@ serious regression, e.g. sagemath FTBS with cython 3.0.11
              warning(self.pos,
                      "Implicit noexcept declaration is deprecated."
                      " Function declaration should contain 'noexcept' keyword.",
+@@ -3128,6 +3126,7 @@ class DefNode(FuncDefNode):
+             if scope is None:
+                 scope = cfunc.scope
+             cfunc_type = cfunc.type
++            has_explicit_exc_clause=True
+             if len(self.args) != len(cfunc_type.args) or cfunc_type.has_varargs:
+                 error(self.pos, "wrong number of arguments")
+                 error(cfunc.pos, "previous declaration here")

From 05ecf46ead5f27871a9b1ac7afbd972c93589e93 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 5 Aug 2024 00:21:23 -0300
Subject: [PATCH 2/6] sagemath: update to 10.5.beta2.

---
 .../sagemath/patches/36641-sympy_1.13.patch   |  22 +-
 .../sagemath/patches/37884-gap_4.13.1.patch   |  28 +-
 .../sagemath/patches/38250-numpy_2.0.patch    | 587 ------------------
 .../sagemath/patches/38344-ecm_7.0.6.patch    |  43 --
 srcpkgs/sagemath/patches/get_patches          |   4 +-
 srcpkgs/sagemath/template                     |   6 +-
 6 files changed, 21 insertions(+), 669 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/38250-numpy_2.0.patch
 delete mode 100644 srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch

diff --git a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
index 625c582cdd41b7..01e859ad023f4d 100644
--- a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
+++ b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
@@ -1,8 +1,5 @@
-diff --git a/build/pkgs/sympy/requirements.txt b/build/pkgs/sympy/requirements.txt
-new file mode 100644
-index 00000000000..3ef8f90b550
 diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py
-index 7e9eab2ff2e..43365cd645e 100644
+index 823a0d14a41..de1c8531814 100644
 --- a/src/sage/doctest/forker.py
 +++ b/src/sage/doctest/forker.py
 @@ -150,14 +150,15 @@ def init_sage(controller=None):
@@ -28,7 +25,7 @@ index 7e9eab2ff2e..43365cd645e 100644
      The displayhook sorts dictionary keys to simplify doctesting of
      dictionary output::
 diff --git a/src/sage/functions/hypergeometric.py b/src/sage/functions/hypergeometric.py
-index 010c61febe0..bbccbd20032 100644
+index ade7836b310..eb5c6665c0d 100644
 --- a/src/sage/functions/hypergeometric.py
 +++ b/src/sage/functions/hypergeometric.py
 @@ -124,7 +124,7 @@
@@ -40,21 +37,8 @@ index 010c61febe0..bbccbd20032 100644
      sage: hypergeometric((5, 4), (4, 4), 3)._mathematica_init_()                        # needs sage.symbolic
      'HypergeometricPFQ[{5,4},{4,4},3]'
  
-diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx
-index a92fe241355..f62311423be 100644
---- a/src/sage/symbolic/expression.pyx
-+++ b/src/sage/symbolic/expression.pyx
-@@ -1167,7 +1167,7 @@ cdef class Expression(Expression_abc):
-             sage: unicode_art(SR(13 - I))
-             13 - ⅈ
-             sage: unicode_art(SR(1.3 - I))
--            1.3 - ⅈ
-+            1.3 - 1.0⋅ⅈ
-             sage: unicode_art(cos(I))
-             cosh(1)
- 
 diff --git a/src/sage/typeset/ascii_art.py b/src/sage/typeset/ascii_art.py
-index 28024405d27..458fa8724a3 100644
+index 83d92af8959..e470e2bd88d 100644
 --- a/src/sage/typeset/ascii_art.py
 +++ b/src/sage/typeset/ascii_art.py
 @@ -44,11 +44,12 @@
diff --git a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
index 1550d47e2436c6..321e0a94487da3 100644
--- a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
+++ b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
@@ -1,21 +1,21 @@
 diff --git a/src/sage/algebras/fusion_rings/fusion_double.py b/src/sage/algebras/fusion_rings/fusion_double.py
-index 7ce086f70d0..954513572c3 100644
+index 71277561331..3b681d75d3b 100644
 --- a/src/sage/algebras/fusion_rings/fusion_double.py
 +++ b/src/sage/algebras/fusion_rings/fusion_double.py
 @@ -133,7 +133,7 @@ class FusionDouble(CombinatorialFreeModule):
          sage: G = SmallPermutationGroup(16,9)
-         sage: F = FusionDouble(G, prefix="b",inject_variables=True)
+         sage: F = FusionDouble(G, prefix='b', inject_variables=True)
          sage: b13^2 # long time (4s)
 -        b0 + b2 + b4 + b15 + b16 + b17 + b18 + b24 + b26 + b27
 +        b0 + b3 + b4
- 
      """
      @staticmethod
+     def __classcall_private__(cls, G, prefix='s', inject_variables=False):
 diff --git a/src/sage/categories/simplicial_sets.py b/src/sage/categories/simplicial_sets.py
-index e714a4571c4..a2b87a729d1 100644
+index aabd3cdbb4f..14bebdcd080 100644
 --- a/src/sage/categories/simplicial_sets.py
 +++ b/src/sage/categories/simplicial_sets.py
-@@ -593,9 +593,9 @@ def _canonical_twisting_operator(self):
+@@ -591,9 +591,9 @@ def _canonical_twisting_operator(self):
                      sage: X = simplicial_sets.Torus()
                      sage: d = X._canonical_twisting_operator()
                      sage: d
@@ -27,7 +27,7 @@ index e714a4571c4..a2b87a729d1 100644
                      sage: Y = simplicial_sets.RealProjectiveSpace(2)
                      sage: d2 = Y._canonical_twisting_operator()
                      sage: d2
-@@ -677,10 +677,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
+@@ -674,10 +674,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
                      sage: X = simplicial_sets.Torus()
                      sage: C = X.twisted_chain_complex()
                      sage: C.differential(1)
@@ -41,7 +41,7 @@ index e714a4571c4..a2b87a729d1 100644
                      [      -1       -1]
                      sage: C.differential(3)
                      []
-@@ -848,29 +848,29 @@ def twisted_homology(self, n, reduced=False):
+@@ -844,29 +844,29 @@ def twisted_homology(self, n, reduced=False):
                      sage: # needs sage.graphs
                      sage: Y = simplicial_sets.Torus()
                      sage: Y.twisted_homology(1)
@@ -80,10 +80,10 @@ index e714a4571c4..a2b87a729d1 100644
                      [1 0 0 0 0]
                      [0 1 0 0 0]
 diff --git a/src/sage/combinat/matrices/latin.py b/src/sage/combinat/matrices/latin.py
-index 936edcc6ea4..c06a53d9afd 100644
+index e2d818e9480..84e6c4fcc9b 100644
 --- a/src/sage/combinat/matrices/latin.py
 +++ b/src/sage/combinat/matrices/latin.py
-@@ -2453,7 +2453,7 @@ def p3_group_bitrade_generators(p):
+@@ -2444,7 +2444,7 @@ def p3_group_bitrade_generators(p):
      EXAMPLES::
  
          sage: from sage.combinat.matrices.latin import *
@@ -93,7 +93,7 @@ index 936edcc6ea4..c06a53d9afd 100644
           (1,2,3)(4,7,8)(5,6,9),
           (1,9,2)(3,7,4)(5,8,6),
 diff --git a/src/sage/groups/cubic_braid.py b/src/sage/groups/cubic_braid.py
-index 257b400f1c7..36423c756aa 100644
+index 61db70925e1..521289c7578 100644
 --- a/src/sage/groups/cubic_braid.py
 +++ b/src/sage/groups/cubic_braid.py
 @@ -282,7 +282,7 @@ def _richcmp_(self, other, op):
@@ -106,7 +106,7 @@ index 257b400f1c7..36423c756aa 100644
               c1*c0^-1*c1, c0^-1*c1^-1*c0^-1, c0^-1*c1^-1, c1^-1*c0*c1^-1,
               c0*c1^-1*c0^-1, c0^-1*c1, c0^-1*c1*c0, c0*c1^-1, c1*c0^-1,
 diff --git a/src/sage/groups/finitely_presented.py b/src/sage/groups/finitely_presented.py
-index 4bb52ee4efb..85f572fac6c 100644
+index 4ac2faa783b..7016d08381b 100644
 --- a/src/sage/groups/finitely_presented.py
 +++ b/src/sage/groups/finitely_presented.py
 @@ -1344,8 +1344,8 @@ def abelianization_map(self):
@@ -161,10 +161,10 @@ index 4bb52ee4efb..85f572fac6c 100644
              sage: G.characteristic_varieties(groebner=True)
              {0: [-1 + F1, 1 + F1, 1 - F1 + F1^2, 1 + F1 + F1^2], 1: [1 - F1 + F1^2],  2: []}
 diff --git a/src/sage/groups/perm_gps/permgroup_named.py b/src/sage/groups/perm_gps/permgroup_named.py
-index c1f2683907b..d219e104a2c 100644
+index 5c153b93d4c..bd4afad2942 100644
 --- a/src/sage/groups/perm_gps/permgroup_named.py
 +++ b/src/sage/groups/perm_gps/permgroup_named.py
-@@ -3468,16 +3468,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
+@@ -3465,16 +3465,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
          sage: G = SmallPermutationGroup(12,4); G
          Group of order 12 and GAP Id 4 as a permutation group
          sage: G.gens()
@@ -186,7 +186,7 @@ index c1f2683907b..d219e104a2c 100644
          sage: def numgps(n): return ZZ(libgap.NumberSmallGroups(n))
          sage: all(SmallPermutationGroup(n,k).id() == [n,k]
          ....:     for n in [1..64] for k in [1..numgps(n)])
-@@ -3486,11 +3484,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
+@@ -3483,11 +3481,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
          sage: H.is_abelian()
          False
          sage: [H.centralizer(g) for g in H.conjugacy_classes_representatives()]
diff --git a/srcpkgs/sagemath/patches/38250-numpy_2.0.patch b/srcpkgs/sagemath/patches/38250-numpy_2.0.patch
deleted file mode 100644
index e28fd857afcb75..00000000000000
--- a/srcpkgs/sagemath/patches/38250-numpy_2.0.patch
+++ /dev/null
@@ -1,587 +0,0 @@
-diff --git a/src/sage/arith/misc.py b/src/sage/arith/misc.py
-index 28f81d7b798..d184c52bf19 100644
---- a/src/sage/arith/misc.py
-+++ b/src/sage/arith/misc.py
-@@ -2277,7 +2277,7 @@ def power_mod(a, n, m):
- 
-         sage: from numpy import int32                                                   # needs numpy
-         sage: power_mod(int32(2), int32(390), int32(391))                               # needs numpy
--        285
-+        ...285...
-         sage: from gmpy2 import mpz
-         sage: power_mod(mpz(2), mpz(390), mpz(391))
-         mpz(285)
-diff --git a/src/sage/calculus/interpolators.pyx b/src/sage/calculus/interpolators.pyx
-index 221b52369e2..bb0be7bab0c 100644
---- a/src/sage/calculus/interpolators.pyx
-+++ b/src/sage/calculus/interpolators.pyx
-@@ -27,6 +27,9 @@ Development supported by NSF award No. 0702939.
- import numpy as np
- cimport numpy as np
- 
-+if int(np.version.short_version[0]) > 1:
-+    np.set_printoptions(legacy="1.25")
-+
- from math import pi
- cdef double TWOPI = 2*pi
- 
-diff --git a/src/sage/calculus/riemann.pyx b/src/sage/calculus/riemann.pyx
-index 6ec80d89aa7..c09d93c4260 100644
---- a/src/sage/calculus/riemann.pyx
-+++ b/src/sage/calculus/riemann.pyx
-@@ -44,6 +44,9 @@ from sage.calculus.integration import numerical_integral
- import numpy as np
- cimport numpy as np
- 
-+if int(np.version.short_version[0]) > 1:
-+    np.set_printoptions(legacy="1.25")
-+
- from math import pi
- from math import sin
- from math import cos
-diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index b198fed0c0d..b3ebd206cd2 100644
---- a/src/sage/combinat/fully_packed_loop.py
-+++ b/src/sage/combinat/fully_packed_loop.py
-@@ -66,6 +66,9 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
-     r"""
-     TESTS::
- 
-+        sage: import numpy as np
-+        sage: if int(np.version.short_version[0]) > 1:
-+        ....:     np.set_printoptions(legacy="1.25")
-         sage: from sage.combinat.fully_packed_loop import _make_color_list
-         sage: _make_color_list(5)
-         sage: _make_color_list(5, ['blue', 'red'])
-diff --git a/src/sage/env.py b/src/sage/env.py
-index 722649ab3da..abb9b19f9e3 100644
---- a/src/sage/env.py
-+++ b/src/sage/env.py
-@@ -296,7 +296,7 @@ def sage_include_directories(use_sources=False):
-         sage: import sage.env
-         sage: sage.env.sage_include_directories()
-         ['...',
--         '.../numpy/core/include',
-+         '.../numpy/...core/include',
-          '.../include/python...']
- 
-     To check that C/C++ files are correctly found, we verify that we can
-diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
-index e100ba3ee23..2a03bb68f67 100644
---- a/src/sage/functions/special.py
-+++ b/src/sage/functions/special.py
-@@ -217,6 +217,9 @@ class SphericalHarmonic(BuiltinFunction):
-         sage: spherical_harmonic(1, 1, pi/2, pi).n()  # abs tol 1e-14                   # needs sage.symbolic
-         0.345494149471335
-         sage: from scipy.special import sph_harm  # NB: arguments x and y are swapped   # needs scipy
-+        sage: import numpy as np                                                        # needs scipy
-+        sage: if int(np.version.short_version[0]) > 1:                                  # needs scipy
-+        ....:     np.set_printoptions(legacy="1.25")                                    # needs scipy
-         sage: sph_harm(1, 1, pi.n(), (pi/2).n())  # abs tol 1e-14                       # needs scipy sage.symbolic
-         (0.3454941494713355-4.231083042742082e-17j)
- 
-diff --git a/src/sage/graphs/generators/classical_geometries.py b/src/sage/graphs/generators/classical_geometries.py
-index da04362eef3..957f88d2061 100644
---- a/src/sage/graphs/generators/classical_geometries.py
-+++ b/src/sage/graphs/generators/classical_geometries.py
-@@ -1315,7 +1315,7 @@ def CossidentePenttilaGraph(q):
- 
-     from sage.libs.gap.libgap import libgap
-     adj_list = libgap.function_factory("""function(q)
--        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x;
-+        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x, sqo;
-         LoadPackage("grape");
-         G0:=SO(3,q^2);
-         so:=GeneratorsOfGroup(G0);
-diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
-index 063931ae274..0bafbd00564 100644
---- a/src/sage/graphs/generic_graph.py
-+++ b/src/sage/graphs/generic_graph.py
-@@ -18420,6 +18420,9 @@ def shortest_path_all_pairs(self, by_weight=False, algorithm=None,
-                 M = self.adjacency_matrix(vertices=int_to_vertex)
- 
-             # We call the Floyd-Warshall method from SciPy
-+            import numpy  # to ensure numpy 2.0 compatibility
-+            if int(numpy.version.short_version[0]) > 1:
-+                numpy.set_printoptions(legacy="1.25")
-             from numpy import array as np_array
-             from scipy.sparse.csgraph import floyd_warshall
-             dd, pp = floyd_warshall(np_array(M), directed=self.is_directed(),
-diff --git a/src/sage/graphs/graph_generators_pyx.pyx b/src/sage/graphs/graph_generators_pyx.pyx
-index 033e8b22adc..04b20d3229b 100644
---- a/src/sage/graphs/graph_generators_pyx.pyx
-+++ b/src/sage/graphs/graph_generators_pyx.pyx
-@@ -57,7 +57,7 @@ def RandomGNP(n, p, bint directed=False, bint loops=False, seed=None):
- 
-         sage: from numpy import mean                                                    # needs numpy
-         sage: abs(mean([RandomGNP(200, .2).density() for i in range(30)]) - .2) < .001  # needs numpy
--        True
-+        ...True...
-         sage: RandomGNP(150, .2, loops=True)
-         Traceback (most recent call last):
-         ...
-diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
-index a810418389c..c38df5412f0 100644
---- a/src/sage/matrix/matrix1.pyx
-+++ b/src/sage/matrix/matrix1.pyx
-@@ -705,12 +705,15 @@ cdef class Matrix(Matrix0):
-         Type ``numpy.typecodes`` for a list of the possible
-         typecodes::
- 
--            sage: import numpy                                                          # needs numpy
--            sage: sorted(numpy.typecodes.items())                                       # needs numpy
-+            sage: import numpy                            # needs numpy
-+            sage: numpy.typecodes.items()                 # needs numpy # random
-             [('All', '?bhilqpBHILQPefdgFDGSUVOMm'), ('AllFloat', 'efdgFDG'),
--             ('AllInteger', 'bBhHiIlLqQpP'), ('Character', 'c'), ('Complex', 'FDG'),
--             ('Datetime', 'Mm'), ('Float', 'efdg'), ('Integer', 'bhilqp'),
--             ('UnsignedInteger', 'BHILQP')]
-+            ...
-+
-+        For instance, you can see possibilities for real floating point numbers::
-+
-+            sage: numpy.typecodes['Float']                # needs numpy
-+            'efdg'
- 
-         Alternatively, numpy automatically calls this function (via
-         the magic :meth:`__array__` method) to convert Sage matrices
-diff --git a/src/sage/modules/free_module_element.pyx b/src/sage/modules/free_module_element.pyx
-index d71d22ac1f7..b6f297a3510 100644
---- a/src/sage/modules/free_module_element.pyx
-+++ b/src/sage/modules/free_module_element.pyx
-@@ -555,7 +555,11 @@ def vector(arg0, arg1=None, arg2=None, sparse=None, immutable=False):
-         R = None
- 
-     try:
-+        import numpy
-         from numpy import ndarray
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-+
-     except ImportError:
-         pass
-     else:
-@@ -1188,7 +1192,11 @@ cdef class FreeModuleElement(Vector):   # abstract base class
-             over Rational Field to numpy array of type <... 'float'>:
-             setting an array element with a sequence.
-         """
-+        import numpy
-         from numpy import array
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-+
-         try:
-             return array(self, dtype=dtype)
-         except ValueError as e:
-diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index e3d94d1746e..7ae8ca4966f 100644
---- a/src/sage/numerical/optimize.py
-+++ b/src/sage/numerical/optimize.py
-@@ -155,6 +155,10 @@ def find_root(f, a, b, xtol=10e-13, rtol=2.0**-50, maxiter=100, full_output=Fals
-         b = max(s_1, s_2)
- 
-     import scipy.optimize
-+    import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     g = lambda x: float(f(x))
-     brentqRes = scipy.optimize.brentq(g, a, b,
-                                  full_output=full_output, xtol=xtol, rtol=rtol, maxiter=maxiter)
-@@ -288,6 +292,10 @@ def find_local_minimum(f, a, b, tol=1.48e-08, maxfun=500):
-     a = float(a)
-     b = float(b)
-     import scipy.optimize
-+    import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     xmin, fval, iter, funcalls = scipy.optimize.fminbound(f, a, b, full_output=1, xtol=tol, maxfun=maxfun)
-     return fval, xmin
- 
-@@ -376,6 +384,8 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
-         sage: def rosen(x):  # The Rosenbrock function
-         ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
-         sage: import numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:
-+        ....:     numpy.set_printoptions(legacy="1.25")
-         sage: from numpy import zeros
-         sage: def rosen_der(x):
-         ....:    xm = x[1r:-1r]
-@@ -393,6 +403,9 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
-     from sage.structure.element import Expression
-     from sage.ext.fast_callable import fast_callable
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     from scipy import optimize
-     if isinstance(func, Expression):
-         var_list = func.variables()
-@@ -530,6 +543,8 @@ def minimize_constrained(func,cons,x0,gradient=None,algorithm='default', **args)
-     from sage.structure.element import Expression
-     from sage.ext.fast_callable import fast_callable
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-     from scipy import optimize
-     function_type = type(lambda x,y: x+y)
- 
-@@ -652,6 +667,8 @@ def find_fit(data, model, initial_guess=None, parameters=None, variables=None, s
-     ``lmdif`` and ``lmder`` algorithms.
-     """
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
- 
-     if not isinstance(data, numpy.ndarray):
-         try:
-diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index ac1dc79d802..23e2517ca56 100644
---- a/src/sage/plot/arrow.py
-+++ b/src/sage/plot/arrow.py
-@@ -53,6 +53,9 @@ def get_minmax_data(self):
- 
-         EXAMPLES::
- 
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: from sage.plot.arrow import CurveArrow
-             sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
-             ....:                options={})
-diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx
-index f1f2671a803..4d71414e1c2 100644
---- a/src/sage/plot/complex_plot.pyx
-+++ b/src/sage/plot/complex_plot.pyx
-@@ -1282,15 +1282,13 @@ def rgb_to_hls(rgb):
-         raise ValueError("Last dimension of input array must be 3; "
-                          "shape {} was found.".format(rgb.shape))
-     in_shape = rgb.shape
--    rgb = np.array(
--        rgb, copy=False, dtype=np.dtype(float), ndmin=2
--    )
-+    rgb = np.asarray(rgb, dtype=np.dtype(float))
-     rgb_max = rgb.max(-1)
-     rgb_min = rgb.min(-1)
-     l = (rgb_max + rgb_min)/2.0  # lightness
- 
-     hls = np.zeros_like(rgb)
--    delta = rgb.ptp(-1)
-+    delta = np.ptp(rgb, -1)
-     s = np.zeros_like(delta)
- 
-     ipos = delta > 0
-diff --git a/src/sage/plot/graphics.py b/src/sage/plot/graphics.py
-index a84d162cb56..94f5db09d83 100644
---- a/src/sage/plot/graphics.py
-+++ b/src/sage/plot/graphics.py
-@@ -2754,7 +2754,7 @@ def matplotlib(self, filename=None,
-             sage: xmin, xmax = sub.get_xlim()
-             sage: ymin, ymax = sub.get_ylim()
-             sage: xmin > xmax, ymin > ymax
--            (True, True)
-+            (...True..., ...True...)
-         """
-         if not isinstance(ticks, (list, tuple)):
-             ticks = (ticks, None)
-diff --git a/src/sage/plot/histogram.py b/src/sage/plot/histogram.py
-index fa86a44bd0a..a585cacf9cd 100644
---- a/src/sage/plot/histogram.py
-+++ b/src/sage/plot/histogram.py
-@@ -92,6 +92,8 @@ def get_minmax_data(self):
-             {'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.476190476190..., 'ymin': 0}
-         """
-         import numpy
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
- 
-         # Extract these options (if they are not None) and pass them to
-         # histogram()
-diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
-index b583be32317..6be448f1e04 100644
---- a/src/sage/plot/multigraphics.py
-+++ b/src/sage/plot/multigraphics.py
-@@ -784,6 +784,9 @@ def _add_subplot(self, figure, index, **options):
-             True
-             sage: G.position(1)
-             (0.2, 0.3, 0.4, 0.1)
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: ax1.get_position().bounds  # tol 1.0e-13
-             (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
- 
-@@ -1295,6 +1298,9 @@ def position(self, index):
-             sage: g1 = plot(sin(x), (x, -pi, pi))
-             sage: g2 = circle((0,1), 1.)
-             sage: G = graphics_array([g1, g2])
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: G.position(0)  # tol 5.0e-3
-             (0.025045451349937315,
-              0.03415488992713045,
-diff --git a/src/sage/plot/plot3d/implicit_surface.pyx b/src/sage/plot/plot3d/implicit_surface.pyx
-index ce0da48a4e0..f4d5059b620 100644
---- a/src/sage/plot/plot3d/implicit_surface.pyx
-+++ b/src/sage/plot/plot3d/implicit_surface.pyx
-@@ -468,6 +468,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
-             sage: cube_marcher.y_vertices.tolist()
-             [[[<1.0, 0.5, 0.0>, None]], [[None, None]]]
-             sage: cube_marcher.x_vertices.any() # This shouldn't affect the X vertices.
-+            ...
-         """
-         (self.y_vertices, self.y_vertices_swapped) = \
-             (self.y_vertices_swapped, self.y_vertices)
-@@ -574,6 +575,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
-             sage: cube_marcher.x_vertices.tolist()
-             [[None, None], [None, <1.5, 1.0, 1.0>]]
-             sage: cube_marcher.y_vertices.any() or cube_marcher.z_vertices.any() # This shouldn't affect the Y or Z vertices.
-+            ...
-         """
-         cdef bint has_prev = (_prev is not None)
-         cdef bint has_next = (_next is not None)
-diff --git a/src/sage/plot/scatter_plot.py b/src/sage/plot/scatter_plot.py
-index 4ad418f040b..781854d372c 100644
---- a/src/sage/plot/scatter_plot.py
-+++ b/src/sage/plot/scatter_plot.py
-@@ -63,9 +63,9 @@ def get_minmax_data(self):
-             sage: s = scatter_plot([[0,1],[2,4],[3.2,6]])
-             sage: d = s.get_minmax_data()
-             sage: d['xmin']
--            0.0
-+            ...0.0...
-             sage: d['ymin']
--            1.0
-+            ...1.0...
-         """
-         return {'xmin': self.xdata.min(),
-                 'xmax': self.xdata.max(),
-diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index 663d3aee70b..d2cb11088c7 100644
---- a/src/sage/plot/streamline_plot.py
-+++ b/src/sage/plot/streamline_plot.py
-@@ -71,6 +71,9 @@ def get_minmax_data(self):
-         EXAMPLES::
- 
-             sage: x, y = var('x y')
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: d = streamline_plot((.01*x, x+y), (x,10,20), (y,10,20))[0].get_minmax_data()
-             sage: d['xmin']
-             10.0
-diff --git a/src/sage/probability/probability_distribution.pyx b/src/sage/probability/probability_distribution.pyx
-index e2c71af9c25..59ba4a95ab6 100644
---- a/src/sage/probability/probability_distribution.pyx
-+++ b/src/sage/probability/probability_distribution.pyx
-@@ -140,6 +140,9 @@ cdef class ProbabilityDistribution:
-              1.8,
-              2.0]
-         """
-+        import numpy as np
-+        if int(np.version.short_version[0]) > 1:
-+            np.set_printoptions(legacy="1.25")
-         import pylab
-         ell = [float(self.get_random_element()) for _ in range(num_samples)]
-         S = pylab.hist(ell, bins, density=True)
-diff --git a/src/sage/rings/complex_double.pyx b/src/sage/rings/complex_double.pyx
-index c59a2b46d6f..b4dddebb4dc 100644
---- a/src/sage/rings/complex_double.pyx
-+++ b/src/sage/rings/complex_double.pyx
-@@ -2558,10 +2558,10 @@ cdef class ComplexToCDF(Morphism):
- 
-         sage: # needs numpy
-         sage: import numpy
--        sage: f = CDF.coerce_map_from(numpy.complex_)
--        sage: f(numpy.complex_(I))
-+        sage: f = CDF.coerce_map_from(numpy.complex128)
-+        sage: f(numpy.complex128(I))
-         1.0*I
--        sage: f(numpy.complex_(I)).parent()
-+        sage: f(numpy.complex128(I)).parent()
-         Complex Double Field
-     """
-     def __init__(self, R):
-@@ -2578,7 +2578,7 @@ cdef class ComplexToCDF(Morphism):
-         EXAMPLES::
- 
-             sage: import numpy                                                          # needs numpy
--            sage: CDF(numpy.complex_(I))    # indirect doctest                          # needs numpy
-+            sage: CDF(numpy.complex128(I))    # indirect doctest                          # needs numpy
-             1.0*I
-         """
-         cdef ComplexDoubleElement z = <ComplexDoubleElement>ComplexDoubleElement.__new__(ComplexDoubleElement)
-@@ -2592,7 +2592,7 @@ cdef class ComplexToCDF(Morphism):
-         EXAMPLES::
- 
-             sage: import numpy                                                          # needs numpy
--            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex_)            # needs numpy
-+            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex128)          # needs numpy
-             sage: f._repr_type()                                                        # needs numpy
-             'Native'
-         """
-diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index b4a1fa5039b..38c30f7627b 100644
---- a/src/sage/rings/integer.pyx
-+++ b/src/sage/rings/integer.pyx
-@@ -593,6 +593,8 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
-         Test comparisons with numpy types (see :issue:`13386` and :issue:`18076`)::
- 
-             sage: import numpy                                                          # needs numpy
-+            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
-+            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-             sage: numpy.int8('12') == 12                                                # needs numpy
-             True
-             sage: 12 == numpy.int8('12')                                                # needs numpy
-diff --git a/src/sage/rings/polynomial/polynomial_element.pyx b/src/sage/rings/polynomial/polynomial_element.pyx
-index dcf2af7cdf2..c87eccd44f1 100644
---- a/src/sage/rings/polynomial/polynomial_element.pyx
-+++ b/src/sage/rings/polynomial/polynomial_element.pyx
-@@ -8851,7 +8851,7 @@ cdef class Polynomial(CommutativePolynomial):
-                          'you expect.')
- 
-                 import numpy
--                from numpy.linalg.linalg import LinAlgError
-+                from numpy.linalg import LinAlgError
-                 from sage.rings.complex_double import CDF
- 
-                 numpy_dtype = ('complex' if input_complex else 'double')
-diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
-index 95b472e912c..76fbfedab95 100644
---- a/src/sage/rings/real_mpfi.pyx
-+++ b/src/sage/rings/real_mpfi.pyx
-@@ -231,6 +231,8 @@ specified if given a non-interval and an interval::
- TESTS::
- 
-     sage: import numpy                                                                  # needs numpy
-+    sage: if int(numpy.version.short_version[0]) > 1:                                   # needs numpy
-+    ....:     numpy.set_printoptions(legacy="1.25")                                     # needs numpy
-     sage: RIF(2) == numpy.int8('2')                                                     # needs numpy
-     True
-     sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
-diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-index 8f240627e77..70ce616f92f 100644
---- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-+++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-@@ -77,6 +77,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
-@@ -295,6 +297,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((10, 10))
-             sage: data[1:4,1:4] = True
-@@ -317,6 +321,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1,1] = True
-@@ -370,6 +376,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
- 
-             sage: data = np.zeros((20, 20))
-@@ -520,6 +528,8 @@ cdef class PeriodicRegion:
-         TESTS::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1, 1] = True
-diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index b2e6b301bf7..6937f6cb410 100644
---- a/src/sage/stats/basic_stats.py
-+++ b/src/sage/stats/basic_stats.py
-@@ -227,6 +227,8 @@ def std(v, bias=False):
- 
-         sage: # needs numpy
-         sage: import numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:
-+        ....:     numpy.set_printoptions(legacy="1.25")
-         sage: x = numpy.array([1,2,3,4,5])
-         sage: std(x, bias=False)
-         1.5811388300841898
-@@ -304,6 +306,8 @@ def variance(v, bias=False):
-         sage: variance([RIF(1.0103, 1.0103), RIF(2)])
-         0.4897530450000000?
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-         sage: x = numpy.array([1,2,3,4,5])                                              # needs numpy
-         sage: variance(x, bias=False)                                                   # needs numpy
-         2.5
-diff --git a/src/sage/stats/time_series.pyx b/src/sage/stats/time_series.pyx
-index 2e22ec45c69..23adae84fb4 100644
---- a/src/sage/stats/time_series.pyx
-+++ b/src/sage/stats/time_series.pyx
-@@ -1718,6 +1718,8 @@ cdef class TimeSeries:
-         if len(v0) == 1:
-             return v1[0]/v0[0]
-         import numpy
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-         coeffs = numpy.polyfit(v0,v1,1)
-         return coeffs[0]
- 
-diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
-index dfbd5ff82fa..955a256e9b4 100644
---- a/src/sage/structure/coerce.pyx
-+++ b/src/sage/structure/coerce.pyx
-@@ -520,6 +520,8 @@ cdef class CoercionModel:
-     Check that :issue:`8426` is fixed (see also :issue:`18076`)::
- 
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
- 
-         sage: # needs sage.rings.real_mpfr
-         sage: x = polygen(RR)
-diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
-index 2cb2f09c715..cd89ad2a256 100644
---- a/src/sage/symbolic/function.pyx
-+++ b/src/sage/symbolic/function.pyx
-@@ -964,6 +964,9 @@ cdef class BuiltinFunction(Function):
-             mpc(real='0.83373002513114902', imag='-0.98889770576286506')
- 
-             sage: import numpy                                                          # needs numpy
-+            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
-+            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-+
-             sage: sin(numpy.int32(0))                                                   # needs numpy
-             0.0
-             sage: type(_)                                                               # needs numpy
-diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 501b0920898..5b007d9e5fd 100644
---- a/src/sage/symbolic/ring.pyx
-+++ b/src/sage/symbolic/ring.pyx
-@@ -1162,6 +1162,8 @@ cdef class NumpyToSRMorphism(Morphism):
-     We check that :issue:`8949` and :issue:`9769` are fixed (see also :issue:`18076`)::
- 
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-         sage: f(x) = x^2
-         sage: f(numpy.int8('2'))                                                        # needs numpy
-         4
diff --git a/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch b/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch
deleted file mode 100644
index db0ae9030623b6..00000000000000
--- a/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-diff --git a/src/sage/interfaces/ecm.py b/src/sage/interfaces/ecm.py
-index 99287dec718..98011970404 100644
---- a/src/sage/interfaces/ecm.py
-+++ b/src/sage/interfaces/ecm.py
-@@ -508,7 +508,6 @@ def _find_factor(self, n, factor_digits, B1, **kwds):
-         """
-         n = self._validate(n)
-         kwds.setdefault('c', 1000000000)
--        kwds.setdefault('I', 1)
-         if factor_digits is not None:
-             B1 = self.recommended_B1(factor_digits)
-         kwds['one'] = True
-diff --git a/src/sage/libs/libecm.pyx b/src/sage/libs/libecm.pyx
-index 886a9b816e4..83fb7adaf8d 100644
---- a/src/sage/libs/libecm.pyx
-+++ b/src/sage/libs/libecm.pyx
-@@ -149,11 +149,13 @@ def ecmfactor(number, double B1, verbose=False, sigma=0):
-     Some special cases::
- 
-         sage: ecmfactor(1, 100)
--        (True, 1, ...)
-+        Traceback (most recent call last):
-+        ...
-+        ValueError: Input number (1) must be greater than 1
-         sage: ecmfactor(0, 100)
-         Traceback (most recent call last):
-         ...
--        ValueError: Input number (0) must be positive
-+        ValueError: Input number (0) must be greater than 1
-     """
-     cdef mpz_t n, f
-     cdef int res
-@@ -164,8 +166,8 @@ def ecmfactor(number, double B1, verbose=False, sigma=0):
-     sage_int_number = Integer(number)
-     sage_int_sigma = Integer(sigma)
- 
--    if number <= 0:
--        raise ValueError("Input number (%s) must be positive"%number)
-+    if number <= 1:
-+        raise ValueError("Input number (%s) must be greater than 1"%number)
- 
-     if verbose:
-         print("Performing one curve with B1=%1.0f" % B1)
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 28162dff8a38e1..5cab228f286365 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -19,7 +19,7 @@ get_pr() {
 	echo "curl -sL \"$url\" | filterdiff ... > \"$pr-$desc.patch\""
 	if [ -z "$dry" ]; then
 		curl -sL "$url" |
-			filterdiff -p1 -x src/setup.py -x build/* -x src/doc/* |
+			filterdiff -p1 -x src/setup.py -x environment* -x src/environment* -x build/* -x src/doc/* |
 			cat > "$pr-$desc.patch"
 	fi
 }
@@ -29,8 +29,6 @@ cd $(dirname "$0")
 
 get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
-get_pr 38250 "numpy 2.0"
-get_pr 38344 "ecm 7.0.6"
 
 #get_pr 37645 "fix doctest"
 #get_pr 37885 "cython warnings"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index b116e62bc67a5a..f5e1d8c68cfcbe 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,7 +1,7 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.4
-revision=3
+version=10.5.beta2
+revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
 build_style=python3-pep517
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=f6579e85f33bd9bb6e9b991bfc4c49dab1e649858ed9ee41c7cec75cb92d4c62
+checksum=0fe0c82dd6959951fc07d55737d270290f64947e183a403ca25709e21b751dee
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From 9652567cec7902789934a0749377271355c1027c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Wed, 14 Aug 2024 00:12:02 -0300
Subject: [PATCH 3/6] sagemath: enable all cython warnings

---
 srcpkgs/sagemath/patches/37885-cython_warnings.patch | 12 ++++++++++++
 srcpkgs/sagemath/patches/get_patches                 |  2 +-
 2 files changed, 13 insertions(+), 1 deletion(-)
 create mode 100644 srcpkgs/sagemath/patches/37885-cython_warnings.patch

diff --git a/srcpkgs/sagemath/patches/37885-cython_warnings.patch b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
new file mode 100644
index 00000000000000..fa4b648cfc1577
--- /dev/null
+++ b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
@@ -0,0 +1,12 @@
+diff --git a/src/sage_setup/command/sage_build_cython.py b/src/sage_setup/command/sage_build_cython.py
+index f4b1357c543..3435c196d49 100644
+--- a/src/sage_setup/command/sage_build_cython.py
++++ b/src/sage_setup/command/sage_build_cython.py
+@@ -226,6 +226,7 @@ def run(self):
+                 compiler_directives=self.cython_directives,
+                 compile_time_env=self.compile_time_env,
+                 create_extension=self.create_extension,
++                show_all_warnings=True,
+                 # Debugging
+                 gdb_debug=self.debug,
+                 output_dir=os.path.join(self.build_lib, "sage"),
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 5cab228f286365..c182576ea553cd 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -31,4 +31,4 @@ get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
 
 #get_pr 37645 "fix doctest"
-#get_pr 37885 "cython warnings"
+get_pr 37885 "cython warnings"

From 61f8cb5b9f6605b6c48ec6ddfca82eab809f3ced Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 20 Aug 2024 17:56:06 -0300
Subject: [PATCH 4/6] sagemath: patch for numpy 2.1

---
 srcpkgs/sagemath/patches/numpy_2.1a.patch |  8 +--
 srcpkgs/sagemath/patches/numpy_2.1b.patch | 70 +++++++++++------------
 2 files changed, 39 insertions(+), 39 deletions(-)

diff --git a/srcpkgs/sagemath/patches/numpy_2.1a.patch b/srcpkgs/sagemath/patches/numpy_2.1a.patch
index 30e2de99d84536..493c75e2f8f8e0 100644
--- a/srcpkgs/sagemath/patches/numpy_2.1a.patch
+++ b/srcpkgs/sagemath/patches/numpy_2.1a.patch
@@ -1,14 +1,14 @@
-commit 241dc39bd0ba1c056f88bee46a0345d59093eaff
+commit d755b32cbed462abf01a1cd782ba57cb92fbf713
 Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
 Date:   Mon Aug 19 23:25:32 2024 -0300
 
     add copy parameter to numpy (needed for v2.1)
 
 diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
-index c38df5412f0..f587cef651a 100644
+index 3edb9ead54d..2c76fd1e557 100644
 --- a/src/sage/matrix/matrix1.pyx
 +++ b/src/sage/matrix/matrix1.pyx
-@@ -671,7 +671,7 @@ cdef class Matrix(Matrix0):
+@@ -670,7 +670,7 @@ cdef class Matrix(Matrix0):
              entries = [[sib(v, 2) for v in row] for row in self.rows()]
              return sib.name('matrix')(self.base_ring(), entries)
  
@@ -17,7 +17,7 @@ index c38df5412f0..f587cef651a 100644
          """
          Return the Numpy matrix associated to this matrix.
  
-@@ -732,7 +732,7 @@ cdef class Matrix(Matrix0):
+@@ -731,7 +731,7 @@ cdef class Matrix(Matrix0):
              (3, 4)
          """
          import numpy
diff --git a/srcpkgs/sagemath/patches/numpy_2.1b.patch b/srcpkgs/sagemath/patches/numpy_2.1b.patch
index b77e28361d2e74..8dc0eec2b5a9d8 100644
--- a/srcpkgs/sagemath/patches/numpy_2.1b.patch
+++ b/srcpkgs/sagemath/patches/numpy_2.1b.patch
@@ -1,11 +1,11 @@
-commit 8b32fdb87725c1d67ffb51dadec1c331c7c35f3c
+commit 8260d18c3cf8e356db3d95fc46f6e68f75b453fd
 Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
 Date:   Tue Aug 20 00:05:33 2024 -0300
 
     silence np.set_printoptions (for numpy 2.1)
 
 diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index b3ebd206cd2..48866824224 100644
+index 74a14fa1ecd..82e6c7eb3c8 100644
 --- a/src/sage/combinat/fully_packed_loop.py
 +++ b/src/sage/combinat/fully_packed_loop.py
 @@ -68,7 +68,7 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
@@ -18,7 +18,7 @@ index b3ebd206cd2..48866824224 100644
          sage: _make_color_list(5)
          sage: _make_color_list(5, ['blue', 'red'])
 diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
-index 2a03bb68f67..30b56722e66 100644
+index 308171af3cd..6f66624ef87 100644
 --- a/src/sage/functions/special.py
 +++ b/src/sage/functions/special.py
 @@ -219,7 +219,7 @@ class SphericalHarmonic(BuiltinFunction):
@@ -31,10 +31,10 @@ index 2a03bb68f67..30b56722e66 100644
          (0.3454941494713355-4.231083042742082e-17j)
  
 diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index 7ae8ca4966f..4cba22efdba 100644
+index b3e42a6a6a2..13ffa4d1789 100644
 --- a/src/sage/numerical/optimize.py
 +++ b/src/sage/numerical/optimize.py
-@@ -385,7 +385,7 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
+@@ -381,7 +381,7 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm='default',
          ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
          sage: import numpy
          sage: if int(numpy.version.short_version[0]) > 1:
@@ -44,7 +44,7 @@ index 7ae8ca4966f..4cba22efdba 100644
          sage: def rosen_der(x):
          ....:    xm = x[1r:-1r]
 diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index 23e2517ca56..7375dcd5d1c 100644
+index 02442f90ba4..1fe3f0b051a 100644
 --- a/src/sage/plot/arrow.py
 +++ b/src/sage/plot/arrow.py
 @@ -55,7 +55,7 @@ class CurveArrow(GraphicPrimitive):
@@ -57,10 +57,10 @@ index 23e2517ca56..7375dcd5d1c 100644
              sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
              ....:                options={})
 diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
-index 6be448f1e04..004594b77c4 100644
+index d2f70b44526..2eaacc6879e 100644
 --- a/src/sage/plot/multigraphics.py
 +++ b/src/sage/plot/multigraphics.py
-@@ -786,7 +786,7 @@ class MultiGraphics(WithEqualityById, SageObject):
+@@ -766,7 +766,7 @@ class MultiGraphics(WithEqualityById, SageObject):
              (0.2, 0.3, 0.4, 0.1)
              sage: import numpy  # to ensure numpy 2.0 compatibility
              sage: if int(numpy.version.short_version[0]) > 1:
@@ -68,8 +68,8 @@ index 6be448f1e04..004594b77c4 100644
 +            ....:     _token = numpy.set_printoptions(legacy="1.25")
              sage: ax1.get_position().bounds  # tol 1.0e-13
              (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
- 
-@@ -1300,7 +1300,7 @@ class GraphicsArray(MultiGraphics):
+         """
+@@ -1269,7 +1269,7 @@ class GraphicsArray(MultiGraphics):
              sage: G = graphics_array([g1, g2])
              sage: import numpy  # to ensure numpy 2.0 compatibility
              sage: if int(numpy.version.short_version[0]) > 1:
@@ -79,10 +79,10 @@ index 6be448f1e04..004594b77c4 100644
              (0.025045451349937315,
               0.03415488992713045,
 diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index d2cb11088c7..6d88517cc15 100644
+index b69a05b37bf..25e404bfc7d 100644
 --- a/src/sage/plot/streamline_plot.py
 +++ b/src/sage/plot/streamline_plot.py
-@@ -73,7 +73,7 @@ class StreamlinePlot(GraphicPrimitive):
+@@ -72,7 +72,7 @@ class StreamlinePlot(GraphicPrimitive):
              sage: x, y = var('x y')
              sage: import numpy  # to ensure numpy 2.0 compatibility
              sage: if int(numpy.version.short_version[0]) > 1:
@@ -92,20 +92,20 @@ index d2cb11088c7..6d88517cc15 100644
              sage: d['xmin']
              10.0
 diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index 38c30f7627b..cfb8a5ff5f7 100644
+index 11811b9587f..8ce0f7f2683 100644
 --- a/src/sage/rings/integer.pyx
 +++ b/src/sage/rings/integer.pyx
-@@ -594,7 +594,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
- 
-             sage: import numpy                                                          # needs numpy
-             sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
--            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")                    # needs numpy
-             sage: numpy.int8('12') == 12                                                # needs numpy
+@@ -595,7 +595,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
+             sage: # needs numpy
+             sage: import numpy
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     _token = numpy.set_printoptions(legacy="1.25")
+             sage: numpy.int8('12') == 12
              True
-             sage: 12 == numpy.int8('12')                                                # needs numpy
+             sage: 12 == numpy.int8('12')
 diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
-index 76fbfedab95..57de30c9d18 100644
+index 11953a50ab5..6aafcceed89 100644
 --- a/src/sage/rings/real_mpfi.pyx
 +++ b/src/sage/rings/real_mpfi.pyx
 @@ -232,7 +232,7 @@ TESTS::
@@ -118,7 +118,7 @@ index 76fbfedab95..57de30c9d18 100644
      True
      sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
 diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-index 70ce616f92f..f604c6d3785 100644
+index 40b92ab23eb..3838bcccb8a 100755
 --- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
 +++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
 @@ -78,7 +78,7 @@ cdef class PeriodicRegion:
@@ -130,7 +130,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
              sage: data = np.zeros((4, 4))
              sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
-@@ -298,7 +298,7 @@ cdef class PeriodicRegion:
+@@ -296,7 +296,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -139,7 +139,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
              sage: data = np.zeros((10, 10))
              sage: data[1:4,1:4] = True
-@@ -322,7 +322,7 @@ cdef class PeriodicRegion:
+@@ -320,7 +320,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -148,7 +148,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
              sage: data = np.zeros((4, 4))
              sage: data[1,1] = True
-@@ -377,7 +377,7 @@ cdef class PeriodicRegion:
+@@ -375,7 +375,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -157,7 +157,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
  
              sage: data = np.zeros((20, 20))
-@@ -529,7 +529,7 @@ cdef class PeriodicRegion:
+@@ -528,7 +528,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -167,10 +167,10 @@ index 70ce616f92f..f604c6d3785 100644
              sage: data = np.zeros((4, 4))
              sage: data[1, 1] = True
 diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index 6937f6cb410..fb296e00fb6 100644
+index 47d890cf0ab..ba7f0cdb0f9 100644
 --- a/src/sage/stats/basic_stats.py
 +++ b/src/sage/stats/basic_stats.py
-@@ -228,7 +228,7 @@ def std(v, bias=False):
+@@ -222,7 +222,7 @@ def std(v, bias=False):
          sage: # needs numpy
          sage: import numpy
          sage: if int(numpy.version.short_version[0]) > 1:
@@ -179,7 +179,7 @@ index 6937f6cb410..fb296e00fb6 100644
          sage: x = numpy.array([1,2,3,4,5])
          sage: std(x, bias=False)
          1.5811388300841898
-@@ -307,7 +307,7 @@ def variance(v, bias=False):
+@@ -299,7 +299,7 @@ def variance(v, bias=False):
          0.4897530450000000?
          sage: import numpy                                                              # needs numpy
          sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
@@ -189,7 +189,7 @@ index 6937f6cb410..fb296e00fb6 100644
          sage: variance(x, bias=False)                                                   # needs numpy
          2.5
 diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
-index 955a256e9b4..e5ed6160b79 100644
+index cc15eff82e9..e32e7fd28b3 100644
 --- a/src/sage/structure/coerce.pyx
 +++ b/src/sage/structure/coerce.pyx
 @@ -521,7 +521,7 @@ cdef class CoercionModel:
@@ -202,10 +202,10 @@ index 955a256e9b4..e5ed6160b79 100644
          sage: # needs sage.rings.real_mpfr
          sage: x = polygen(RR)
 diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
-index cd89ad2a256..6fdf6d8ef23 100644
+index 362d01ea297..92bce28b032 100644
 --- a/src/sage/symbolic/function.pyx
 +++ b/src/sage/symbolic/function.pyx
-@@ -965,7 +965,7 @@ cdef class BuiltinFunction(Function):
+@@ -962,7 +962,7 @@ cdef class BuiltinFunction(Function):
  
              sage: import numpy                                                          # needs numpy
              sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
@@ -215,10 +215,10 @@ index cd89ad2a256..6fdf6d8ef23 100644
              sage: sin(numpy.int32(0))                                                   # needs numpy
              0.0
 diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 5b007d9e5fd..4a096d317e7 100644
+index 32afe8d3a62..63734e68f63 100644
 --- a/src/sage/symbolic/ring.pyx
 +++ b/src/sage/symbolic/ring.pyx
-@@ -1163,7 +1163,7 @@ cdef class NumpyToSRMorphism(Morphism):
+@@ -1154,7 +1154,7 @@ cdef class NumpyToSRMorphism(Morphism):
  
          sage: import numpy                                                              # needs numpy
          sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy

From 684281e3c47dd422cd38271872a639ace5f4cc7c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 8 Sep 2024 09:35:16 -0300
Subject: [PATCH 5/6] nauty: update to 2.8.9.

---
 srcpkgs/nauty/patches/fix-runalltests.patch | 11 +++++++++++
 srcpkgs/nauty/template                      |  7 ++++---
 2 files changed, 15 insertions(+), 3 deletions(-)
 create mode 100644 srcpkgs/nauty/patches/fix-runalltests.patch

diff --git a/srcpkgs/nauty/patches/fix-runalltests.patch b/srcpkgs/nauty/patches/fix-runalltests.patch
new file mode 100644
index 00000000000000..34e1692cf6e6e3
--- /dev/null
+++ b/srcpkgs/nauty/patches/fix-runalltests.patch
@@ -0,0 +1,11 @@
+--- a/runalltests.in	2024-08-26 00:55:55.000000000 -0300
++++ b/runalltests.in	2024-09-08 09:30:04.032719770 -0300
+@@ -121,7 +121,7 @@
+ runonetest "./geng -q -TD6 10 | ./ransubg -qS765 -P9/10 | ./countg --NN,A,G,GG" "" nautestv.ans
+ runonetest "./genrang -q -P3 -S1234 70 1000 | ./countg --G,GG" "" nautestw.ans
+ runonetest "./genrang -q -P4 -z -S1234 70 500 | ./countg --G,GG" "" nautestx.ans
+-runonetest "./geng -q -bT 12 | ./ranlabg -qS7654 -m5 | uniqg -u" "" nautesty.ans
++runonetest "./geng -q -bT 12 | ./ranlabg -qS7654 -m5 | ./uniqg -u" "" nautesty.ans
+ 
+ echo " "
+ 
diff --git a/srcpkgs/nauty/template b/srcpkgs/nauty/template
index 6f85b1d064d4e5..aea4e4a6eb0294 100644
--- a/srcpkgs/nauty/template
+++ b/srcpkgs/nauty/template
@@ -1,18 +1,18 @@
 # Template file for 'nauty'
 pkgname=nauty
-version=2.8.8
+version=2.8.9
 revision=1
 build_style=gnu-configure
 make_install_args="includedir=/usr/include/nauty
  pkgconfigexecdir=/usr/lib/pkgconfig"
-hostmakedepends="automake"
+hostmakedepends="automake libtool"
 short_desc="Compute the automorphism groups of graphs and digraphs"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="Apache-2.0"
 homepage="https://pallini.di.uniroma1.it/"
 changelog="https://pallini.di.uniroma1.it/changes24-28.txt"
 distfiles="https://pallini.di.uniroma1.it/nauty${version//./_}.tar.gz"
-checksum=159d2156810a6bb240410cd61eb641add85088d9f15c888cdaa37b8681f929ce
+checksum=c97ab42bf48796a86a598bce3e9269047ca2b32c14fc23e07208a244fe52c4ee
 
 build_options="native_build"
 
@@ -21,6 +21,7 @@ if [ -z "$build_option_native_build" ]; then
 fi
 
 pre_configure() {
+	aclocal
 	autoreconf -fi
 }
 

From 2a81fcf283a9514c99342ed1ca93e8bbdc2a8b3d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sat, 7 Sep 2024 14:32:41 -0300
Subject: [PATCH 6/6] sagemath: update to 10.5.beta3.

---
 .../sagemath/patches/36641-sympy_1.13.patch   | 60 -------------------
 .../sagemath/patches/38572-nauty_2.8.9.patch  | 13 ++++
 srcpkgs/sagemath/patches/get_patches          |  4 +-
 srcpkgs/sagemath/template                     |  4 +-
 4 files changed, 17 insertions(+), 64 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/36641-sympy_1.13.patch
 create mode 100644 srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch

diff --git a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
deleted file mode 100644
index 01e859ad023f4d..00000000000000
--- a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
+++ /dev/null
@@ -1,60 +0,0 @@
-diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py
-index 823a0d14a41..de1c8531814 100644
---- a/src/sage/doctest/forker.py
-+++ b/src/sage/doctest/forker.py
-@@ -150,14 +150,15 @@ def init_sage(controller=None):
-         sage: from sympy.printing.pretty.pretty import PrettyPrinter
-         sage: s = sympify('+x^'.join(str(i) for i in range(30)))
-         sage: print(PrettyPrinter(settings={'wrap_line': True}).doprint(s))
--         29    28    27    26    25    24    23    22    21    20    19    18    17
--        x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   +
-+         29    28    27    26    25    24    23    22    21    20    19    18    17    ↪
-+        x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   +  ↪
-         <BLANKLINE>
--         16    15    14    13    12    11    10    9    8    7    6    5    4    3
--        x   + x   + x   + x   + x   + x   + x   + x  + x  + x  + x  + x  + x  + x  + x
-+        ↪  16    15    14    13    12    11    10    9    8    7    6    5    4    3   ↪
-+        ↪ x   + x   + x   + x   + x   + x   + x   + x  + x  + x  + x  + x  + x  + x  + ↪
-         <BLANKLINE>
--        2
--          + x
-+        ↪   2
-+        ↪  x  + x
-+
- 
-     The displayhook sorts dictionary keys to simplify doctesting of
-     dictionary output::
-diff --git a/src/sage/functions/hypergeometric.py b/src/sage/functions/hypergeometric.py
-index ade7836b310..eb5c6665c0d 100644
---- a/src/sage/functions/hypergeometric.py
-+++ b/src/sage/functions/hypergeometric.py
-@@ -124,7 +124,7 @@
-     sage: maxima(hypergeometric([1, 1, 1], [3, 3, 3], x))                               # needs sage.symbolic
-     hypergeometric([1,1,1],[3,3,3],_SAGE_VAR_x)
-     sage: hypergeometric((5, 4), (4, 4), 3)._sympy_()                                   # needs sympy sage.symbolic
--    hyper((5, 4), (4, 4), 3)
-+    hyper((5,), (4,), 3)
-     sage: hypergeometric((5, 4), (4, 4), 3)._mathematica_init_()                        # needs sage.symbolic
-     'HypergeometricPFQ[{5,4},{4,4},3]'
- 
-diff --git a/src/sage/typeset/ascii_art.py b/src/sage/typeset/ascii_art.py
-index 83d92af8959..e470e2bd88d 100644
---- a/src/sage/typeset/ascii_art.py
-+++ b/src/sage/typeset/ascii_art.py
-@@ -44,11 +44,12 @@
-     sage: shell.run_cell('%display ascii_art')
-     sage: shell.run_cell("i = var('i')")                                                # needs sage.symbolic
-     sage: shell.run_cell('sum(factorial(i)*x^i, i, 0, 10)')                             # needs sage.symbolic
--             10           9          8         7        6        5       4      3
--    3628800*x   + 362880*x  + 40320*x  + 5040*x  + 720*x  + 120*x  + 24*x  + 6*x
-+             10           9          8         7        6        5       4      3  >
-+    3628800*x   + 362880*x  + 40320*x  + 5040*x  + 720*x  + 120*x  + 24*x  + 6*x   >
-     <BLANKLINE>
--         2
--    + 2*x  + x + 1
-+    >      2
-+    > + 2*x  + x + 1
-+
-     sage: shell.run_cell('3/(7*x)')                                                     # needs sage.symbolic
-      3
-     ---
diff --git a/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch b/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
new file mode 100644
index 00000000000000..5f75a8bef5556a
--- /dev/null
+++ b/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
@@ -0,0 +1,13 @@
+diff --git a/src/sage/graphs/generators/families.py b/src/sage/graphs/generators/families.py
+index e6e5312b8a8..aa10d15d4d8 100644
+--- a/src/sage/graphs/generators/families.py
++++ b/src/sage/graphs/generators/families.py
+@@ -3710,7 +3710,7 @@ def nauty_gentreeg(options='', debug=False):
+         ...
+         ValueError: wrong format of parameter options
+         sage: list(graphs.nauty_gentreeg("3 -x", debug=True))
+-        ['>E Usage: ...gentreeg [-D#] [-Z#:#] [-ulps] [-q] n [res/mod] ...
++        ['>E Usage: ...gentreeg [-D#] [-Z#:#] [-ulps] [-q] n... [res/mod] ...
+         sage: list(graphs.nauty_gentreeg("3", debug=True))
+         ['>A ...gentreeg ...\n', Graph on 3 vertices]
+     """
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index c182576ea553cd..8f540dad14bfd1 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -1,6 +1,6 @@
 #! /bin/sh
 
-version=10.4
+version=10.5
 
 URL_BASE_PR="https://github.com/sagemath/sage/pull/"
 URL_BASE_COMPARE="https://github.com/sagemath/sage/compare/${version}..."
@@ -27,8 +27,8 @@ get_pr() {
 # run from patches dir
 cd $(dirname "$0")
 
-get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
+get_pr 38572 "nauty 2.8.9"
 
 #get_pr 37645 "fix doctest"
 get_pr 37885 "cython warnings"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index f5e1d8c68cfcbe..709a3ea4262101 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,6 +1,6 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.5.beta2
+version=10.5.beta3
 revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=0fe0c82dd6959951fc07d55737d270290f64947e183a403ca25709e21b751dee
+checksum=cbf3614c1b9be5f0a0756b0a5480c2ebfa663bd87bd66eefd162a755979bcb3d
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

^ permalink raw reply	[flat|nested] 13+ messages in thread

* Re: [BETA] sagemath: update to 10.5.beta3
  2024-08-18 17:54 [PR PATCH] [BETA] sagemath: update to 10.5.beta2 tornaria
                   ` (4 preceding siblings ...)
  2024-09-08 16:10 ` tornaria
@ 2024-09-09  1:13 ` dkwo
  2024-09-10  0:07 ` tornaria
                   ` (5 subsequent siblings)
  11 siblings, 0 replies; 13+ messages in thread
From: dkwo @ 2024-09-09  1:13 UTC (permalink / raw)
  To: ml

[-- Attachment #1: Type: text/plain, Size: 363 bytes --]

New comment by dkwo on void-packages repository

https://github.com/void-linux/void-packages/pull/51902#issuecomment-2336920228

Comment:
I tried to crosscompile sagemath from aarch64 to x86_64: it looks like we should add to hostmakedepends "python3-gmpy2 python3-memory_allocator python3-numpy ecl python3-cypari2 python3-cysignals python3-devel". Makes sense?

^ permalink raw reply	[flat|nested] 13+ messages in thread

* Re: [BETA] sagemath: update to 10.5.beta3
  2024-08-18 17:54 [PR PATCH] [BETA] sagemath: update to 10.5.beta2 tornaria
                   ` (5 preceding siblings ...)
  2024-09-09  1:13 ` [BETA] sagemath: update to 10.5.beta3 dkwo
@ 2024-09-10  0:07 ` tornaria
  2024-09-10 20:23 ` dkwo
                   ` (4 subsequent siblings)
  11 siblings, 0 replies; 13+ messages in thread
From: tornaria @ 2024-09-10  0:07 UTC (permalink / raw)
  To: ml

[-- Attachment #1: Type: text/plain, Size: 468 bytes --]

New comment by tornaria on void-packages repository

https://github.com/void-linux/void-packages/pull/51902#issuecomment-2339362703

Comment:
> I tried to crosscompile sagemath from aarch64 to x86_64: it looks like we should add to hostmakedepends "python3-gmpy2 python3-memory_allocator python3-numpy ecl python3-cypari2 python3-cysignals python3-devel". Makes sense?

Sure, but we still don't have cross for ntl and others, does it make sense to bother with this?

^ permalink raw reply	[flat|nested] 13+ messages in thread

* Re: [BETA] sagemath: update to 10.5.beta3
  2024-08-18 17:54 [PR PATCH] [BETA] sagemath: update to 10.5.beta2 tornaria
                   ` (6 preceding siblings ...)
  2024-09-10  0:07 ` tornaria
@ 2024-09-10 20:23 ` dkwo
  2024-09-22 12:01 ` [PR PATCH] [Updated] " tornaria
                   ` (3 subsequent siblings)
  11 siblings, 0 replies; 13+ messages in thread
From: dkwo @ 2024-09-10 20:23 UTC (permalink / raw)
  To: ml

[-- Attachment #1: Type: text/plain, Size: 260 bytes --]

New comment by dkwo on void-packages repository

https://github.com/void-linux/void-packages/pull/51902#issuecomment-2341944247

Comment:
True. It's still useful to know in general, and it could be useful later, if we decide e.g. to use qemu to build ntl etc.

^ permalink raw reply	[flat|nested] 13+ messages in thread

* Re: [PR PATCH] [Updated] [BETA] sagemath: update to 10.5.beta3
  2024-08-18 17:54 [PR PATCH] [BETA] sagemath: update to 10.5.beta2 tornaria
                   ` (7 preceding siblings ...)
  2024-09-10 20:23 ` dkwo
@ 2024-09-22 12:01 ` tornaria
  2024-10-15 19:18 ` [PR PATCH] [Updated] [BETA] sagemath: update to 10.5.beta5 tornaria
                   ` (2 subsequent siblings)
  11 siblings, 0 replies; 13+ messages in thread
From: tornaria @ 2024-09-22 12:01 UTC (permalink / raw)
  To: ml

[-- Attachment #1: Type: text/plain, Size: 1465 bytes --]

There is an updated pull request by tornaria against master on the void-packages repository

https://github.com/tornaria/void-packages sagemath
https://github.com/void-linux/void-packages/pull/51902

[BETA] sagemath: update to 10.5.beta3
<!-- Uncomment relevant sections and delete options which are not applicable -->

 - python3-Cython: alternative fix for 6122
 - python3-gmpy2: update to 2.2.1.
 - python3-cypari2: update to 2.2.0.
 - python3-sympy: update to 1.13.2.
 - sagemath: enable all cython warnings

#### Testing the changes
- I tested the changes in this PR: **YES**

@dkwo

<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->

<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration
and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
  - aarch64-musl
  - armv7l
  - armv6l-musl
-->


A patch file from https://github.com/void-linux/void-packages/pull/51902.patch is attached

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-sagemath-51902.patch --]
[-- Type: text/x-diff, Size: 82306 bytes --]

From ecfba27920ba6beeb1e7b95162087cfdf899bc2f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 11 Aug 2024 22:53:42 -0300
Subject: [PATCH 1/7] python3-Cython: alternative fix for 6122

---
 srcpkgs/python3-Cython/patches/fix-regression.patch | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/srcpkgs/python3-Cython/patches/fix-regression.patch b/srcpkgs/python3-Cython/patches/fix-regression.patch
index f2e761608e373b..f5957cfa59c2f5 100644
--- a/srcpkgs/python3-Cython/patches/fix-regression.patch
+++ b/srcpkgs/python3-Cython/patches/fix-regression.patch
@@ -15,3 +15,11 @@ serious regression, e.g. sagemath FTBS with cython 3.0.11
              warning(self.pos,
                      "Implicit noexcept declaration is deprecated."
                      " Function declaration should contain 'noexcept' keyword.",
+@@ -3128,6 +3126,7 @@ class DefNode(FuncDefNode):
+             if scope is None:
+                 scope = cfunc.scope
+             cfunc_type = cfunc.type
++            has_explicit_exc_clause=True
+             if len(self.args) != len(cfunc_type.args) or cfunc_type.has_varargs:
+                 error(self.pos, "wrong number of arguments")
+                 error(cfunc.pos, "previous declaration here")

From 0f1b17f2a82bd8d725d3958c0d6f5428a5715e65 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 5 Aug 2024 00:21:23 -0300
Subject: [PATCH 2/7] sagemath: update to 10.5.beta2.

---
 .../sagemath/patches/36641-sympy_1.13.patch   |  22 +-
 .../sagemath/patches/37884-gap_4.13.1.patch   |  28 +-
 .../sagemath/patches/38250-numpy_2.0.patch    | 587 ------------------
 .../sagemath/patches/38344-ecm_7.0.6.patch    |  43 --
 srcpkgs/sagemath/patches/get_patches          |   4 +-
 srcpkgs/sagemath/template                     |   6 +-
 6 files changed, 21 insertions(+), 669 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/38250-numpy_2.0.patch
 delete mode 100644 srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch

diff --git a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
index 625c582cdd41b7..01e859ad023f4d 100644
--- a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
+++ b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
@@ -1,8 +1,5 @@
-diff --git a/build/pkgs/sympy/requirements.txt b/build/pkgs/sympy/requirements.txt
-new file mode 100644
-index 00000000000..3ef8f90b550
 diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py
-index 7e9eab2ff2e..43365cd645e 100644
+index 823a0d14a41..de1c8531814 100644
 --- a/src/sage/doctest/forker.py
 +++ b/src/sage/doctest/forker.py
 @@ -150,14 +150,15 @@ def init_sage(controller=None):
@@ -28,7 +25,7 @@ index 7e9eab2ff2e..43365cd645e 100644
      The displayhook sorts dictionary keys to simplify doctesting of
      dictionary output::
 diff --git a/src/sage/functions/hypergeometric.py b/src/sage/functions/hypergeometric.py
-index 010c61febe0..bbccbd20032 100644
+index ade7836b310..eb5c6665c0d 100644
 --- a/src/sage/functions/hypergeometric.py
 +++ b/src/sage/functions/hypergeometric.py
 @@ -124,7 +124,7 @@
@@ -40,21 +37,8 @@ index 010c61febe0..bbccbd20032 100644
      sage: hypergeometric((5, 4), (4, 4), 3)._mathematica_init_()                        # needs sage.symbolic
      'HypergeometricPFQ[{5,4},{4,4},3]'
  
-diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx
-index a92fe241355..f62311423be 100644
---- a/src/sage/symbolic/expression.pyx
-+++ b/src/sage/symbolic/expression.pyx
-@@ -1167,7 +1167,7 @@ cdef class Expression(Expression_abc):
-             sage: unicode_art(SR(13 - I))
-             13 - ⅈ
-             sage: unicode_art(SR(1.3 - I))
--            1.3 - ⅈ
-+            1.3 - 1.0⋅ⅈ
-             sage: unicode_art(cos(I))
-             cosh(1)
- 
 diff --git a/src/sage/typeset/ascii_art.py b/src/sage/typeset/ascii_art.py
-index 28024405d27..458fa8724a3 100644
+index 83d92af8959..e470e2bd88d 100644
 --- a/src/sage/typeset/ascii_art.py
 +++ b/src/sage/typeset/ascii_art.py
 @@ -44,11 +44,12 @@
diff --git a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
index 1550d47e2436c6..321e0a94487da3 100644
--- a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
+++ b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
@@ -1,21 +1,21 @@
 diff --git a/src/sage/algebras/fusion_rings/fusion_double.py b/src/sage/algebras/fusion_rings/fusion_double.py
-index 7ce086f70d0..954513572c3 100644
+index 71277561331..3b681d75d3b 100644
 --- a/src/sage/algebras/fusion_rings/fusion_double.py
 +++ b/src/sage/algebras/fusion_rings/fusion_double.py
 @@ -133,7 +133,7 @@ class FusionDouble(CombinatorialFreeModule):
          sage: G = SmallPermutationGroup(16,9)
-         sage: F = FusionDouble(G, prefix="b",inject_variables=True)
+         sage: F = FusionDouble(G, prefix='b', inject_variables=True)
          sage: b13^2 # long time (4s)
 -        b0 + b2 + b4 + b15 + b16 + b17 + b18 + b24 + b26 + b27
 +        b0 + b3 + b4
- 
      """
      @staticmethod
+     def __classcall_private__(cls, G, prefix='s', inject_variables=False):
 diff --git a/src/sage/categories/simplicial_sets.py b/src/sage/categories/simplicial_sets.py
-index e714a4571c4..a2b87a729d1 100644
+index aabd3cdbb4f..14bebdcd080 100644
 --- a/src/sage/categories/simplicial_sets.py
 +++ b/src/sage/categories/simplicial_sets.py
-@@ -593,9 +593,9 @@ def _canonical_twisting_operator(self):
+@@ -591,9 +591,9 @@ def _canonical_twisting_operator(self):
                      sage: X = simplicial_sets.Torus()
                      sage: d = X._canonical_twisting_operator()
                      sage: d
@@ -27,7 +27,7 @@ index e714a4571c4..a2b87a729d1 100644
                      sage: Y = simplicial_sets.RealProjectiveSpace(2)
                      sage: d2 = Y._canonical_twisting_operator()
                      sage: d2
-@@ -677,10 +677,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
+@@ -674,10 +674,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
                      sage: X = simplicial_sets.Torus()
                      sage: C = X.twisted_chain_complex()
                      sage: C.differential(1)
@@ -41,7 +41,7 @@ index e714a4571c4..a2b87a729d1 100644
                      [      -1       -1]
                      sage: C.differential(3)
                      []
-@@ -848,29 +848,29 @@ def twisted_homology(self, n, reduced=False):
+@@ -844,29 +844,29 @@ def twisted_homology(self, n, reduced=False):
                      sage: # needs sage.graphs
                      sage: Y = simplicial_sets.Torus()
                      sage: Y.twisted_homology(1)
@@ -80,10 +80,10 @@ index e714a4571c4..a2b87a729d1 100644
                      [1 0 0 0 0]
                      [0 1 0 0 0]
 diff --git a/src/sage/combinat/matrices/latin.py b/src/sage/combinat/matrices/latin.py
-index 936edcc6ea4..c06a53d9afd 100644
+index e2d818e9480..84e6c4fcc9b 100644
 --- a/src/sage/combinat/matrices/latin.py
 +++ b/src/sage/combinat/matrices/latin.py
-@@ -2453,7 +2453,7 @@ def p3_group_bitrade_generators(p):
+@@ -2444,7 +2444,7 @@ def p3_group_bitrade_generators(p):
      EXAMPLES::
  
          sage: from sage.combinat.matrices.latin import *
@@ -93,7 +93,7 @@ index 936edcc6ea4..c06a53d9afd 100644
           (1,2,3)(4,7,8)(5,6,9),
           (1,9,2)(3,7,4)(5,8,6),
 diff --git a/src/sage/groups/cubic_braid.py b/src/sage/groups/cubic_braid.py
-index 257b400f1c7..36423c756aa 100644
+index 61db70925e1..521289c7578 100644
 --- a/src/sage/groups/cubic_braid.py
 +++ b/src/sage/groups/cubic_braid.py
 @@ -282,7 +282,7 @@ def _richcmp_(self, other, op):
@@ -106,7 +106,7 @@ index 257b400f1c7..36423c756aa 100644
               c1*c0^-1*c1, c0^-1*c1^-1*c0^-1, c0^-1*c1^-1, c1^-1*c0*c1^-1,
               c0*c1^-1*c0^-1, c0^-1*c1, c0^-1*c1*c0, c0*c1^-1, c1*c0^-1,
 diff --git a/src/sage/groups/finitely_presented.py b/src/sage/groups/finitely_presented.py
-index 4bb52ee4efb..85f572fac6c 100644
+index 4ac2faa783b..7016d08381b 100644
 --- a/src/sage/groups/finitely_presented.py
 +++ b/src/sage/groups/finitely_presented.py
 @@ -1344,8 +1344,8 @@ def abelianization_map(self):
@@ -161,10 +161,10 @@ index 4bb52ee4efb..85f572fac6c 100644
              sage: G.characteristic_varieties(groebner=True)
              {0: [-1 + F1, 1 + F1, 1 - F1 + F1^2, 1 + F1 + F1^2], 1: [1 - F1 + F1^2],  2: []}
 diff --git a/src/sage/groups/perm_gps/permgroup_named.py b/src/sage/groups/perm_gps/permgroup_named.py
-index c1f2683907b..d219e104a2c 100644
+index 5c153b93d4c..bd4afad2942 100644
 --- a/src/sage/groups/perm_gps/permgroup_named.py
 +++ b/src/sage/groups/perm_gps/permgroup_named.py
-@@ -3468,16 +3468,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
+@@ -3465,16 +3465,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
          sage: G = SmallPermutationGroup(12,4); G
          Group of order 12 and GAP Id 4 as a permutation group
          sage: G.gens()
@@ -186,7 +186,7 @@ index c1f2683907b..d219e104a2c 100644
          sage: def numgps(n): return ZZ(libgap.NumberSmallGroups(n))
          sage: all(SmallPermutationGroup(n,k).id() == [n,k]
          ....:     for n in [1..64] for k in [1..numgps(n)])
-@@ -3486,11 +3484,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
+@@ -3483,11 +3481,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
          sage: H.is_abelian()
          False
          sage: [H.centralizer(g) for g in H.conjugacy_classes_representatives()]
diff --git a/srcpkgs/sagemath/patches/38250-numpy_2.0.patch b/srcpkgs/sagemath/patches/38250-numpy_2.0.patch
deleted file mode 100644
index e28fd857afcb75..00000000000000
--- a/srcpkgs/sagemath/patches/38250-numpy_2.0.patch
+++ /dev/null
@@ -1,587 +0,0 @@
-diff --git a/src/sage/arith/misc.py b/src/sage/arith/misc.py
-index 28f81d7b798..d184c52bf19 100644
---- a/src/sage/arith/misc.py
-+++ b/src/sage/arith/misc.py
-@@ -2277,7 +2277,7 @@ def power_mod(a, n, m):
- 
-         sage: from numpy import int32                                                   # needs numpy
-         sage: power_mod(int32(2), int32(390), int32(391))                               # needs numpy
--        285
-+        ...285...
-         sage: from gmpy2 import mpz
-         sage: power_mod(mpz(2), mpz(390), mpz(391))
-         mpz(285)
-diff --git a/src/sage/calculus/interpolators.pyx b/src/sage/calculus/interpolators.pyx
-index 221b52369e2..bb0be7bab0c 100644
---- a/src/sage/calculus/interpolators.pyx
-+++ b/src/sage/calculus/interpolators.pyx
-@@ -27,6 +27,9 @@ Development supported by NSF award No. 0702939.
- import numpy as np
- cimport numpy as np
- 
-+if int(np.version.short_version[0]) > 1:
-+    np.set_printoptions(legacy="1.25")
-+
- from math import pi
- cdef double TWOPI = 2*pi
- 
-diff --git a/src/sage/calculus/riemann.pyx b/src/sage/calculus/riemann.pyx
-index 6ec80d89aa7..c09d93c4260 100644
---- a/src/sage/calculus/riemann.pyx
-+++ b/src/sage/calculus/riemann.pyx
-@@ -44,6 +44,9 @@ from sage.calculus.integration import numerical_integral
- import numpy as np
- cimport numpy as np
- 
-+if int(np.version.short_version[0]) > 1:
-+    np.set_printoptions(legacy="1.25")
-+
- from math import pi
- from math import sin
- from math import cos
-diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index b198fed0c0d..b3ebd206cd2 100644
---- a/src/sage/combinat/fully_packed_loop.py
-+++ b/src/sage/combinat/fully_packed_loop.py
-@@ -66,6 +66,9 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
-     r"""
-     TESTS::
- 
-+        sage: import numpy as np
-+        sage: if int(np.version.short_version[0]) > 1:
-+        ....:     np.set_printoptions(legacy="1.25")
-         sage: from sage.combinat.fully_packed_loop import _make_color_list
-         sage: _make_color_list(5)
-         sage: _make_color_list(5, ['blue', 'red'])
-diff --git a/src/sage/env.py b/src/sage/env.py
-index 722649ab3da..abb9b19f9e3 100644
---- a/src/sage/env.py
-+++ b/src/sage/env.py
-@@ -296,7 +296,7 @@ def sage_include_directories(use_sources=False):
-         sage: import sage.env
-         sage: sage.env.sage_include_directories()
-         ['...',
--         '.../numpy/core/include',
-+         '.../numpy/...core/include',
-          '.../include/python...']
- 
-     To check that C/C++ files are correctly found, we verify that we can
-diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
-index e100ba3ee23..2a03bb68f67 100644
---- a/src/sage/functions/special.py
-+++ b/src/sage/functions/special.py
-@@ -217,6 +217,9 @@ class SphericalHarmonic(BuiltinFunction):
-         sage: spherical_harmonic(1, 1, pi/2, pi).n()  # abs tol 1e-14                   # needs sage.symbolic
-         0.345494149471335
-         sage: from scipy.special import sph_harm  # NB: arguments x and y are swapped   # needs scipy
-+        sage: import numpy as np                                                        # needs scipy
-+        sage: if int(np.version.short_version[0]) > 1:                                  # needs scipy
-+        ....:     np.set_printoptions(legacy="1.25")                                    # needs scipy
-         sage: sph_harm(1, 1, pi.n(), (pi/2).n())  # abs tol 1e-14                       # needs scipy sage.symbolic
-         (0.3454941494713355-4.231083042742082e-17j)
- 
-diff --git a/src/sage/graphs/generators/classical_geometries.py b/src/sage/graphs/generators/classical_geometries.py
-index da04362eef3..957f88d2061 100644
---- a/src/sage/graphs/generators/classical_geometries.py
-+++ b/src/sage/graphs/generators/classical_geometries.py
-@@ -1315,7 +1315,7 @@ def CossidentePenttilaGraph(q):
- 
-     from sage.libs.gap.libgap import libgap
-     adj_list = libgap.function_factory("""function(q)
--        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x;
-+        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x, sqo;
-         LoadPackage("grape");
-         G0:=SO(3,q^2);
-         so:=GeneratorsOfGroup(G0);
-diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
-index 063931ae274..0bafbd00564 100644
---- a/src/sage/graphs/generic_graph.py
-+++ b/src/sage/graphs/generic_graph.py
-@@ -18420,6 +18420,9 @@ def shortest_path_all_pairs(self, by_weight=False, algorithm=None,
-                 M = self.adjacency_matrix(vertices=int_to_vertex)
- 
-             # We call the Floyd-Warshall method from SciPy
-+            import numpy  # to ensure numpy 2.0 compatibility
-+            if int(numpy.version.short_version[0]) > 1:
-+                numpy.set_printoptions(legacy="1.25")
-             from numpy import array as np_array
-             from scipy.sparse.csgraph import floyd_warshall
-             dd, pp = floyd_warshall(np_array(M), directed=self.is_directed(),
-diff --git a/src/sage/graphs/graph_generators_pyx.pyx b/src/sage/graphs/graph_generators_pyx.pyx
-index 033e8b22adc..04b20d3229b 100644
---- a/src/sage/graphs/graph_generators_pyx.pyx
-+++ b/src/sage/graphs/graph_generators_pyx.pyx
-@@ -57,7 +57,7 @@ def RandomGNP(n, p, bint directed=False, bint loops=False, seed=None):
- 
-         sage: from numpy import mean                                                    # needs numpy
-         sage: abs(mean([RandomGNP(200, .2).density() for i in range(30)]) - .2) < .001  # needs numpy
--        True
-+        ...True...
-         sage: RandomGNP(150, .2, loops=True)
-         Traceback (most recent call last):
-         ...
-diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
-index a810418389c..c38df5412f0 100644
---- a/src/sage/matrix/matrix1.pyx
-+++ b/src/sage/matrix/matrix1.pyx
-@@ -705,12 +705,15 @@ cdef class Matrix(Matrix0):
-         Type ``numpy.typecodes`` for a list of the possible
-         typecodes::
- 
--            sage: import numpy                                                          # needs numpy
--            sage: sorted(numpy.typecodes.items())                                       # needs numpy
-+            sage: import numpy                            # needs numpy
-+            sage: numpy.typecodes.items()                 # needs numpy # random
-             [('All', '?bhilqpBHILQPefdgFDGSUVOMm'), ('AllFloat', 'efdgFDG'),
--             ('AllInteger', 'bBhHiIlLqQpP'), ('Character', 'c'), ('Complex', 'FDG'),
--             ('Datetime', 'Mm'), ('Float', 'efdg'), ('Integer', 'bhilqp'),
--             ('UnsignedInteger', 'BHILQP')]
-+            ...
-+
-+        For instance, you can see possibilities for real floating point numbers::
-+
-+            sage: numpy.typecodes['Float']                # needs numpy
-+            'efdg'
- 
-         Alternatively, numpy automatically calls this function (via
-         the magic :meth:`__array__` method) to convert Sage matrices
-diff --git a/src/sage/modules/free_module_element.pyx b/src/sage/modules/free_module_element.pyx
-index d71d22ac1f7..b6f297a3510 100644
---- a/src/sage/modules/free_module_element.pyx
-+++ b/src/sage/modules/free_module_element.pyx
-@@ -555,7 +555,11 @@ def vector(arg0, arg1=None, arg2=None, sparse=None, immutable=False):
-         R = None
- 
-     try:
-+        import numpy
-         from numpy import ndarray
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-+
-     except ImportError:
-         pass
-     else:
-@@ -1188,7 +1192,11 @@ cdef class FreeModuleElement(Vector):   # abstract base class
-             over Rational Field to numpy array of type <... 'float'>:
-             setting an array element with a sequence.
-         """
-+        import numpy
-         from numpy import array
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-+
-         try:
-             return array(self, dtype=dtype)
-         except ValueError as e:
-diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index e3d94d1746e..7ae8ca4966f 100644
---- a/src/sage/numerical/optimize.py
-+++ b/src/sage/numerical/optimize.py
-@@ -155,6 +155,10 @@ def find_root(f, a, b, xtol=10e-13, rtol=2.0**-50, maxiter=100, full_output=Fals
-         b = max(s_1, s_2)
- 
-     import scipy.optimize
-+    import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     g = lambda x: float(f(x))
-     brentqRes = scipy.optimize.brentq(g, a, b,
-                                  full_output=full_output, xtol=xtol, rtol=rtol, maxiter=maxiter)
-@@ -288,6 +292,10 @@ def find_local_minimum(f, a, b, tol=1.48e-08, maxfun=500):
-     a = float(a)
-     b = float(b)
-     import scipy.optimize
-+    import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     xmin, fval, iter, funcalls = scipy.optimize.fminbound(f, a, b, full_output=1, xtol=tol, maxfun=maxfun)
-     return fval, xmin
- 
-@@ -376,6 +384,8 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
-         sage: def rosen(x):  # The Rosenbrock function
-         ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
-         sage: import numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:
-+        ....:     numpy.set_printoptions(legacy="1.25")
-         sage: from numpy import zeros
-         sage: def rosen_der(x):
-         ....:    xm = x[1r:-1r]
-@@ -393,6 +403,9 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
-     from sage.structure.element import Expression
-     from sage.ext.fast_callable import fast_callable
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     from scipy import optimize
-     if isinstance(func, Expression):
-         var_list = func.variables()
-@@ -530,6 +543,8 @@ def minimize_constrained(func,cons,x0,gradient=None,algorithm='default', **args)
-     from sage.structure.element import Expression
-     from sage.ext.fast_callable import fast_callable
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-     from scipy import optimize
-     function_type = type(lambda x,y: x+y)
- 
-@@ -652,6 +667,8 @@ def find_fit(data, model, initial_guess=None, parameters=None, variables=None, s
-     ``lmdif`` and ``lmder`` algorithms.
-     """
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
- 
-     if not isinstance(data, numpy.ndarray):
-         try:
-diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index ac1dc79d802..23e2517ca56 100644
---- a/src/sage/plot/arrow.py
-+++ b/src/sage/plot/arrow.py
-@@ -53,6 +53,9 @@ def get_minmax_data(self):
- 
-         EXAMPLES::
- 
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: from sage.plot.arrow import CurveArrow
-             sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
-             ....:                options={})
-diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx
-index f1f2671a803..4d71414e1c2 100644
---- a/src/sage/plot/complex_plot.pyx
-+++ b/src/sage/plot/complex_plot.pyx
-@@ -1282,15 +1282,13 @@ def rgb_to_hls(rgb):
-         raise ValueError("Last dimension of input array must be 3; "
-                          "shape {} was found.".format(rgb.shape))
-     in_shape = rgb.shape
--    rgb = np.array(
--        rgb, copy=False, dtype=np.dtype(float), ndmin=2
--    )
-+    rgb = np.asarray(rgb, dtype=np.dtype(float))
-     rgb_max = rgb.max(-1)
-     rgb_min = rgb.min(-1)
-     l = (rgb_max + rgb_min)/2.0  # lightness
- 
-     hls = np.zeros_like(rgb)
--    delta = rgb.ptp(-1)
-+    delta = np.ptp(rgb, -1)
-     s = np.zeros_like(delta)
- 
-     ipos = delta > 0
-diff --git a/src/sage/plot/graphics.py b/src/sage/plot/graphics.py
-index a84d162cb56..94f5db09d83 100644
---- a/src/sage/plot/graphics.py
-+++ b/src/sage/plot/graphics.py
-@@ -2754,7 +2754,7 @@ def matplotlib(self, filename=None,
-             sage: xmin, xmax = sub.get_xlim()
-             sage: ymin, ymax = sub.get_ylim()
-             sage: xmin > xmax, ymin > ymax
--            (True, True)
-+            (...True..., ...True...)
-         """
-         if not isinstance(ticks, (list, tuple)):
-             ticks = (ticks, None)
-diff --git a/src/sage/plot/histogram.py b/src/sage/plot/histogram.py
-index fa86a44bd0a..a585cacf9cd 100644
---- a/src/sage/plot/histogram.py
-+++ b/src/sage/plot/histogram.py
-@@ -92,6 +92,8 @@ def get_minmax_data(self):
-             {'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.476190476190..., 'ymin': 0}
-         """
-         import numpy
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
- 
-         # Extract these options (if they are not None) and pass them to
-         # histogram()
-diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
-index b583be32317..6be448f1e04 100644
---- a/src/sage/plot/multigraphics.py
-+++ b/src/sage/plot/multigraphics.py
-@@ -784,6 +784,9 @@ def _add_subplot(self, figure, index, **options):
-             True
-             sage: G.position(1)
-             (0.2, 0.3, 0.4, 0.1)
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: ax1.get_position().bounds  # tol 1.0e-13
-             (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
- 
-@@ -1295,6 +1298,9 @@ def position(self, index):
-             sage: g1 = plot(sin(x), (x, -pi, pi))
-             sage: g2 = circle((0,1), 1.)
-             sage: G = graphics_array([g1, g2])
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: G.position(0)  # tol 5.0e-3
-             (0.025045451349937315,
-              0.03415488992713045,
-diff --git a/src/sage/plot/plot3d/implicit_surface.pyx b/src/sage/plot/plot3d/implicit_surface.pyx
-index ce0da48a4e0..f4d5059b620 100644
---- a/src/sage/plot/plot3d/implicit_surface.pyx
-+++ b/src/sage/plot/plot3d/implicit_surface.pyx
-@@ -468,6 +468,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
-             sage: cube_marcher.y_vertices.tolist()
-             [[[<1.0, 0.5, 0.0>, None]], [[None, None]]]
-             sage: cube_marcher.x_vertices.any() # This shouldn't affect the X vertices.
-+            ...
-         """
-         (self.y_vertices, self.y_vertices_swapped) = \
-             (self.y_vertices_swapped, self.y_vertices)
-@@ -574,6 +575,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
-             sage: cube_marcher.x_vertices.tolist()
-             [[None, None], [None, <1.5, 1.0, 1.0>]]
-             sage: cube_marcher.y_vertices.any() or cube_marcher.z_vertices.any() # This shouldn't affect the Y or Z vertices.
-+            ...
-         """
-         cdef bint has_prev = (_prev is not None)
-         cdef bint has_next = (_next is not None)
-diff --git a/src/sage/plot/scatter_plot.py b/src/sage/plot/scatter_plot.py
-index 4ad418f040b..781854d372c 100644
---- a/src/sage/plot/scatter_plot.py
-+++ b/src/sage/plot/scatter_plot.py
-@@ -63,9 +63,9 @@ def get_minmax_data(self):
-             sage: s = scatter_plot([[0,1],[2,4],[3.2,6]])
-             sage: d = s.get_minmax_data()
-             sage: d['xmin']
--            0.0
-+            ...0.0...
-             sage: d['ymin']
--            1.0
-+            ...1.0...
-         """
-         return {'xmin': self.xdata.min(),
-                 'xmax': self.xdata.max(),
-diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index 663d3aee70b..d2cb11088c7 100644
---- a/src/sage/plot/streamline_plot.py
-+++ b/src/sage/plot/streamline_plot.py
-@@ -71,6 +71,9 @@ def get_minmax_data(self):
-         EXAMPLES::
- 
-             sage: x, y = var('x y')
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: d = streamline_plot((.01*x, x+y), (x,10,20), (y,10,20))[0].get_minmax_data()
-             sage: d['xmin']
-             10.0
-diff --git a/src/sage/probability/probability_distribution.pyx b/src/sage/probability/probability_distribution.pyx
-index e2c71af9c25..59ba4a95ab6 100644
---- a/src/sage/probability/probability_distribution.pyx
-+++ b/src/sage/probability/probability_distribution.pyx
-@@ -140,6 +140,9 @@ cdef class ProbabilityDistribution:
-              1.8,
-              2.0]
-         """
-+        import numpy as np
-+        if int(np.version.short_version[0]) > 1:
-+            np.set_printoptions(legacy="1.25")
-         import pylab
-         ell = [float(self.get_random_element()) for _ in range(num_samples)]
-         S = pylab.hist(ell, bins, density=True)
-diff --git a/src/sage/rings/complex_double.pyx b/src/sage/rings/complex_double.pyx
-index c59a2b46d6f..b4dddebb4dc 100644
---- a/src/sage/rings/complex_double.pyx
-+++ b/src/sage/rings/complex_double.pyx
-@@ -2558,10 +2558,10 @@ cdef class ComplexToCDF(Morphism):
- 
-         sage: # needs numpy
-         sage: import numpy
--        sage: f = CDF.coerce_map_from(numpy.complex_)
--        sage: f(numpy.complex_(I))
-+        sage: f = CDF.coerce_map_from(numpy.complex128)
-+        sage: f(numpy.complex128(I))
-         1.0*I
--        sage: f(numpy.complex_(I)).parent()
-+        sage: f(numpy.complex128(I)).parent()
-         Complex Double Field
-     """
-     def __init__(self, R):
-@@ -2578,7 +2578,7 @@ cdef class ComplexToCDF(Morphism):
-         EXAMPLES::
- 
-             sage: import numpy                                                          # needs numpy
--            sage: CDF(numpy.complex_(I))    # indirect doctest                          # needs numpy
-+            sage: CDF(numpy.complex128(I))    # indirect doctest                          # needs numpy
-             1.0*I
-         """
-         cdef ComplexDoubleElement z = <ComplexDoubleElement>ComplexDoubleElement.__new__(ComplexDoubleElement)
-@@ -2592,7 +2592,7 @@ cdef class ComplexToCDF(Morphism):
-         EXAMPLES::
- 
-             sage: import numpy                                                          # needs numpy
--            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex_)            # needs numpy
-+            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex128)          # needs numpy
-             sage: f._repr_type()                                                        # needs numpy
-             'Native'
-         """
-diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index b4a1fa5039b..38c30f7627b 100644
---- a/src/sage/rings/integer.pyx
-+++ b/src/sage/rings/integer.pyx
-@@ -593,6 +593,8 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
-         Test comparisons with numpy types (see :issue:`13386` and :issue:`18076`)::
- 
-             sage: import numpy                                                          # needs numpy
-+            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
-+            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-             sage: numpy.int8('12') == 12                                                # needs numpy
-             True
-             sage: 12 == numpy.int8('12')                                                # needs numpy
-diff --git a/src/sage/rings/polynomial/polynomial_element.pyx b/src/sage/rings/polynomial/polynomial_element.pyx
-index dcf2af7cdf2..c87eccd44f1 100644
---- a/src/sage/rings/polynomial/polynomial_element.pyx
-+++ b/src/sage/rings/polynomial/polynomial_element.pyx
-@@ -8851,7 +8851,7 @@ cdef class Polynomial(CommutativePolynomial):
-                          'you expect.')
- 
-                 import numpy
--                from numpy.linalg.linalg import LinAlgError
-+                from numpy.linalg import LinAlgError
-                 from sage.rings.complex_double import CDF
- 
-                 numpy_dtype = ('complex' if input_complex else 'double')
-diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
-index 95b472e912c..76fbfedab95 100644
---- a/src/sage/rings/real_mpfi.pyx
-+++ b/src/sage/rings/real_mpfi.pyx
-@@ -231,6 +231,8 @@ specified if given a non-interval and an interval::
- TESTS::
- 
-     sage: import numpy                                                                  # needs numpy
-+    sage: if int(numpy.version.short_version[0]) > 1:                                   # needs numpy
-+    ....:     numpy.set_printoptions(legacy="1.25")                                     # needs numpy
-     sage: RIF(2) == numpy.int8('2')                                                     # needs numpy
-     True
-     sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
-diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-index 8f240627e77..70ce616f92f 100644
---- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-+++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-@@ -77,6 +77,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
-@@ -295,6 +297,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((10, 10))
-             sage: data[1:4,1:4] = True
-@@ -317,6 +321,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1,1] = True
-@@ -370,6 +376,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
- 
-             sage: data = np.zeros((20, 20))
-@@ -520,6 +528,8 @@ cdef class PeriodicRegion:
-         TESTS::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1, 1] = True
-diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index b2e6b301bf7..6937f6cb410 100644
---- a/src/sage/stats/basic_stats.py
-+++ b/src/sage/stats/basic_stats.py
-@@ -227,6 +227,8 @@ def std(v, bias=False):
- 
-         sage: # needs numpy
-         sage: import numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:
-+        ....:     numpy.set_printoptions(legacy="1.25")
-         sage: x = numpy.array([1,2,3,4,5])
-         sage: std(x, bias=False)
-         1.5811388300841898
-@@ -304,6 +306,8 @@ def variance(v, bias=False):
-         sage: variance([RIF(1.0103, 1.0103), RIF(2)])
-         0.4897530450000000?
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-         sage: x = numpy.array([1,2,3,4,5])                                              # needs numpy
-         sage: variance(x, bias=False)                                                   # needs numpy
-         2.5
-diff --git a/src/sage/stats/time_series.pyx b/src/sage/stats/time_series.pyx
-index 2e22ec45c69..23adae84fb4 100644
---- a/src/sage/stats/time_series.pyx
-+++ b/src/sage/stats/time_series.pyx
-@@ -1718,6 +1718,8 @@ cdef class TimeSeries:
-         if len(v0) == 1:
-             return v1[0]/v0[0]
-         import numpy
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-         coeffs = numpy.polyfit(v0,v1,1)
-         return coeffs[0]
- 
-diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
-index dfbd5ff82fa..955a256e9b4 100644
---- a/src/sage/structure/coerce.pyx
-+++ b/src/sage/structure/coerce.pyx
-@@ -520,6 +520,8 @@ cdef class CoercionModel:
-     Check that :issue:`8426` is fixed (see also :issue:`18076`)::
- 
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
- 
-         sage: # needs sage.rings.real_mpfr
-         sage: x = polygen(RR)
-diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
-index 2cb2f09c715..cd89ad2a256 100644
---- a/src/sage/symbolic/function.pyx
-+++ b/src/sage/symbolic/function.pyx
-@@ -964,6 +964,9 @@ cdef class BuiltinFunction(Function):
-             mpc(real='0.83373002513114902', imag='-0.98889770576286506')
- 
-             sage: import numpy                                                          # needs numpy
-+            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
-+            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-+
-             sage: sin(numpy.int32(0))                                                   # needs numpy
-             0.0
-             sage: type(_)                                                               # needs numpy
-diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 501b0920898..5b007d9e5fd 100644
---- a/src/sage/symbolic/ring.pyx
-+++ b/src/sage/symbolic/ring.pyx
-@@ -1162,6 +1162,8 @@ cdef class NumpyToSRMorphism(Morphism):
-     We check that :issue:`8949` and :issue:`9769` are fixed (see also :issue:`18076`)::
- 
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-         sage: f(x) = x^2
-         sage: f(numpy.int8('2'))                                                        # needs numpy
-         4
diff --git a/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch b/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch
deleted file mode 100644
index db0ae9030623b6..00000000000000
--- a/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-diff --git a/src/sage/interfaces/ecm.py b/src/sage/interfaces/ecm.py
-index 99287dec718..98011970404 100644
---- a/src/sage/interfaces/ecm.py
-+++ b/src/sage/interfaces/ecm.py
-@@ -508,7 +508,6 @@ def _find_factor(self, n, factor_digits, B1, **kwds):
-         """
-         n = self._validate(n)
-         kwds.setdefault('c', 1000000000)
--        kwds.setdefault('I', 1)
-         if factor_digits is not None:
-             B1 = self.recommended_B1(factor_digits)
-         kwds['one'] = True
-diff --git a/src/sage/libs/libecm.pyx b/src/sage/libs/libecm.pyx
-index 886a9b816e4..83fb7adaf8d 100644
---- a/src/sage/libs/libecm.pyx
-+++ b/src/sage/libs/libecm.pyx
-@@ -149,11 +149,13 @@ def ecmfactor(number, double B1, verbose=False, sigma=0):
-     Some special cases::
- 
-         sage: ecmfactor(1, 100)
--        (True, 1, ...)
-+        Traceback (most recent call last):
-+        ...
-+        ValueError: Input number (1) must be greater than 1
-         sage: ecmfactor(0, 100)
-         Traceback (most recent call last):
-         ...
--        ValueError: Input number (0) must be positive
-+        ValueError: Input number (0) must be greater than 1
-     """
-     cdef mpz_t n, f
-     cdef int res
-@@ -164,8 +166,8 @@ def ecmfactor(number, double B1, verbose=False, sigma=0):
-     sage_int_number = Integer(number)
-     sage_int_sigma = Integer(sigma)
- 
--    if number <= 0:
--        raise ValueError("Input number (%s) must be positive"%number)
-+    if number <= 1:
-+        raise ValueError("Input number (%s) must be greater than 1"%number)
- 
-     if verbose:
-         print("Performing one curve with B1=%1.0f" % B1)
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 28162dff8a38e1..5cab228f286365 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -19,7 +19,7 @@ get_pr() {
 	echo "curl -sL \"$url\" | filterdiff ... > \"$pr-$desc.patch\""
 	if [ -z "$dry" ]; then
 		curl -sL "$url" |
-			filterdiff -p1 -x src/setup.py -x build/* -x src/doc/* |
+			filterdiff -p1 -x src/setup.py -x environment* -x src/environment* -x build/* -x src/doc/* |
 			cat > "$pr-$desc.patch"
 	fi
 }
@@ -29,8 +29,6 @@ cd $(dirname "$0")
 
 get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
-get_pr 38250 "numpy 2.0"
-get_pr 38344 "ecm 7.0.6"
 
 #get_pr 37645 "fix doctest"
 #get_pr 37885 "cython warnings"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index b116e62bc67a5a..f5e1d8c68cfcbe 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,7 +1,7 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.4
-revision=3
+version=10.5.beta2
+revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
 build_style=python3-pep517
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=f6579e85f33bd9bb6e9b991bfc4c49dab1e649858ed9ee41c7cec75cb92d4c62
+checksum=0fe0c82dd6959951fc07d55737d270290f64947e183a403ca25709e21b751dee
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From 994c1355b7fac7403f8eb2e2d26609e8df3f879f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Wed, 14 Aug 2024 00:12:02 -0300
Subject: [PATCH 3/7] sagemath: enable all cython warnings

---
 srcpkgs/sagemath/patches/37885-cython_warnings.patch | 12 ++++++++++++
 srcpkgs/sagemath/patches/get_patches                 |  2 +-
 2 files changed, 13 insertions(+), 1 deletion(-)
 create mode 100644 srcpkgs/sagemath/patches/37885-cython_warnings.patch

diff --git a/srcpkgs/sagemath/patches/37885-cython_warnings.patch b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
new file mode 100644
index 00000000000000..fa4b648cfc1577
--- /dev/null
+++ b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
@@ -0,0 +1,12 @@
+diff --git a/src/sage_setup/command/sage_build_cython.py b/src/sage_setup/command/sage_build_cython.py
+index f4b1357c543..3435c196d49 100644
+--- a/src/sage_setup/command/sage_build_cython.py
++++ b/src/sage_setup/command/sage_build_cython.py
+@@ -226,6 +226,7 @@ def run(self):
+                 compiler_directives=self.cython_directives,
+                 compile_time_env=self.compile_time_env,
+                 create_extension=self.create_extension,
++                show_all_warnings=True,
+                 # Debugging
+                 gdb_debug=self.debug,
+                 output_dir=os.path.join(self.build_lib, "sage"),
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 5cab228f286365..c182576ea553cd 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -31,4 +31,4 @@ get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
 
 #get_pr 37645 "fix doctest"
-#get_pr 37885 "cython warnings"
+get_pr 37885 "cython warnings"

From e085459b89cb1758450884986d08d01ab83d2b11 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 20 Aug 2024 17:56:06 -0300
Subject: [PATCH 4/7] sagemath: patch for numpy 2.1

---
 srcpkgs/sagemath/patches/numpy_2.1a.patch |  8 +--
 srcpkgs/sagemath/patches/numpy_2.1b.patch | 70 +++++++++++------------
 2 files changed, 39 insertions(+), 39 deletions(-)

diff --git a/srcpkgs/sagemath/patches/numpy_2.1a.patch b/srcpkgs/sagemath/patches/numpy_2.1a.patch
index 30e2de99d84536..493c75e2f8f8e0 100644
--- a/srcpkgs/sagemath/patches/numpy_2.1a.patch
+++ b/srcpkgs/sagemath/patches/numpy_2.1a.patch
@@ -1,14 +1,14 @@
-commit 241dc39bd0ba1c056f88bee46a0345d59093eaff
+commit d755b32cbed462abf01a1cd782ba57cb92fbf713
 Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
 Date:   Mon Aug 19 23:25:32 2024 -0300
 
     add copy parameter to numpy (needed for v2.1)
 
 diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
-index c38df5412f0..f587cef651a 100644
+index 3edb9ead54d..2c76fd1e557 100644
 --- a/src/sage/matrix/matrix1.pyx
 +++ b/src/sage/matrix/matrix1.pyx
-@@ -671,7 +671,7 @@ cdef class Matrix(Matrix0):
+@@ -670,7 +670,7 @@ cdef class Matrix(Matrix0):
              entries = [[sib(v, 2) for v in row] for row in self.rows()]
              return sib.name('matrix')(self.base_ring(), entries)
  
@@ -17,7 +17,7 @@ index c38df5412f0..f587cef651a 100644
          """
          Return the Numpy matrix associated to this matrix.
  
-@@ -732,7 +732,7 @@ cdef class Matrix(Matrix0):
+@@ -731,7 +731,7 @@ cdef class Matrix(Matrix0):
              (3, 4)
          """
          import numpy
diff --git a/srcpkgs/sagemath/patches/numpy_2.1b.patch b/srcpkgs/sagemath/patches/numpy_2.1b.patch
index b77e28361d2e74..8dc0eec2b5a9d8 100644
--- a/srcpkgs/sagemath/patches/numpy_2.1b.patch
+++ b/srcpkgs/sagemath/patches/numpy_2.1b.patch
@@ -1,11 +1,11 @@
-commit 8b32fdb87725c1d67ffb51dadec1c331c7c35f3c
+commit 8260d18c3cf8e356db3d95fc46f6e68f75b453fd
 Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
 Date:   Tue Aug 20 00:05:33 2024 -0300
 
     silence np.set_printoptions (for numpy 2.1)
 
 diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index b3ebd206cd2..48866824224 100644
+index 74a14fa1ecd..82e6c7eb3c8 100644
 --- a/src/sage/combinat/fully_packed_loop.py
 +++ b/src/sage/combinat/fully_packed_loop.py
 @@ -68,7 +68,7 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
@@ -18,7 +18,7 @@ index b3ebd206cd2..48866824224 100644
          sage: _make_color_list(5)
          sage: _make_color_list(5, ['blue', 'red'])
 diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
-index 2a03bb68f67..30b56722e66 100644
+index 308171af3cd..6f66624ef87 100644
 --- a/src/sage/functions/special.py
 +++ b/src/sage/functions/special.py
 @@ -219,7 +219,7 @@ class SphericalHarmonic(BuiltinFunction):
@@ -31,10 +31,10 @@ index 2a03bb68f67..30b56722e66 100644
          (0.3454941494713355-4.231083042742082e-17j)
  
 diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index 7ae8ca4966f..4cba22efdba 100644
+index b3e42a6a6a2..13ffa4d1789 100644
 --- a/src/sage/numerical/optimize.py
 +++ b/src/sage/numerical/optimize.py
-@@ -385,7 +385,7 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
+@@ -381,7 +381,7 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm='default',
          ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
          sage: import numpy
          sage: if int(numpy.version.short_version[0]) > 1:
@@ -44,7 +44,7 @@ index 7ae8ca4966f..4cba22efdba 100644
          sage: def rosen_der(x):
          ....:    xm = x[1r:-1r]
 diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index 23e2517ca56..7375dcd5d1c 100644
+index 02442f90ba4..1fe3f0b051a 100644
 --- a/src/sage/plot/arrow.py
 +++ b/src/sage/plot/arrow.py
 @@ -55,7 +55,7 @@ class CurveArrow(GraphicPrimitive):
@@ -57,10 +57,10 @@ index 23e2517ca56..7375dcd5d1c 100644
              sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
              ....:                options={})
 diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
-index 6be448f1e04..004594b77c4 100644
+index d2f70b44526..2eaacc6879e 100644
 --- a/src/sage/plot/multigraphics.py
 +++ b/src/sage/plot/multigraphics.py
-@@ -786,7 +786,7 @@ class MultiGraphics(WithEqualityById, SageObject):
+@@ -766,7 +766,7 @@ class MultiGraphics(WithEqualityById, SageObject):
              (0.2, 0.3, 0.4, 0.1)
              sage: import numpy  # to ensure numpy 2.0 compatibility
              sage: if int(numpy.version.short_version[0]) > 1:
@@ -68,8 +68,8 @@ index 6be448f1e04..004594b77c4 100644
 +            ....:     _token = numpy.set_printoptions(legacy="1.25")
              sage: ax1.get_position().bounds  # tol 1.0e-13
              (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
- 
-@@ -1300,7 +1300,7 @@ class GraphicsArray(MultiGraphics):
+         """
+@@ -1269,7 +1269,7 @@ class GraphicsArray(MultiGraphics):
              sage: G = graphics_array([g1, g2])
              sage: import numpy  # to ensure numpy 2.0 compatibility
              sage: if int(numpy.version.short_version[0]) > 1:
@@ -79,10 +79,10 @@ index 6be448f1e04..004594b77c4 100644
              (0.025045451349937315,
               0.03415488992713045,
 diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index d2cb11088c7..6d88517cc15 100644
+index b69a05b37bf..25e404bfc7d 100644
 --- a/src/sage/plot/streamline_plot.py
 +++ b/src/sage/plot/streamline_plot.py
-@@ -73,7 +73,7 @@ class StreamlinePlot(GraphicPrimitive):
+@@ -72,7 +72,7 @@ class StreamlinePlot(GraphicPrimitive):
              sage: x, y = var('x y')
              sage: import numpy  # to ensure numpy 2.0 compatibility
              sage: if int(numpy.version.short_version[0]) > 1:
@@ -92,20 +92,20 @@ index d2cb11088c7..6d88517cc15 100644
              sage: d['xmin']
              10.0
 diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index 38c30f7627b..cfb8a5ff5f7 100644
+index 11811b9587f..8ce0f7f2683 100644
 --- a/src/sage/rings/integer.pyx
 +++ b/src/sage/rings/integer.pyx
-@@ -594,7 +594,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
- 
-             sage: import numpy                                                          # needs numpy
-             sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
--            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")                    # needs numpy
-             sage: numpy.int8('12') == 12                                                # needs numpy
+@@ -595,7 +595,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
+             sage: # needs numpy
+             sage: import numpy
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     _token = numpy.set_printoptions(legacy="1.25")
+             sage: numpy.int8('12') == 12
              True
-             sage: 12 == numpy.int8('12')                                                # needs numpy
+             sage: 12 == numpy.int8('12')
 diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
-index 76fbfedab95..57de30c9d18 100644
+index 11953a50ab5..6aafcceed89 100644
 --- a/src/sage/rings/real_mpfi.pyx
 +++ b/src/sage/rings/real_mpfi.pyx
 @@ -232,7 +232,7 @@ TESTS::
@@ -118,7 +118,7 @@ index 76fbfedab95..57de30c9d18 100644
      True
      sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
 diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-index 70ce616f92f..f604c6d3785 100644
+index 40b92ab23eb..3838bcccb8a 100755
 --- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
 +++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
 @@ -78,7 +78,7 @@ cdef class PeriodicRegion:
@@ -130,7 +130,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
              sage: data = np.zeros((4, 4))
              sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
-@@ -298,7 +298,7 @@ cdef class PeriodicRegion:
+@@ -296,7 +296,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -139,7 +139,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
              sage: data = np.zeros((10, 10))
              sage: data[1:4,1:4] = True
-@@ -322,7 +322,7 @@ cdef class PeriodicRegion:
+@@ -320,7 +320,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -148,7 +148,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
              sage: data = np.zeros((4, 4))
              sage: data[1,1] = True
-@@ -377,7 +377,7 @@ cdef class PeriodicRegion:
+@@ -375,7 +375,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -157,7 +157,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
  
              sage: data = np.zeros((20, 20))
-@@ -529,7 +529,7 @@ cdef class PeriodicRegion:
+@@ -528,7 +528,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -167,10 +167,10 @@ index 70ce616f92f..f604c6d3785 100644
              sage: data = np.zeros((4, 4))
              sage: data[1, 1] = True
 diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index 6937f6cb410..fb296e00fb6 100644
+index 47d890cf0ab..ba7f0cdb0f9 100644
 --- a/src/sage/stats/basic_stats.py
 +++ b/src/sage/stats/basic_stats.py
-@@ -228,7 +228,7 @@ def std(v, bias=False):
+@@ -222,7 +222,7 @@ def std(v, bias=False):
          sage: # needs numpy
          sage: import numpy
          sage: if int(numpy.version.short_version[0]) > 1:
@@ -179,7 +179,7 @@ index 6937f6cb410..fb296e00fb6 100644
          sage: x = numpy.array([1,2,3,4,5])
          sage: std(x, bias=False)
          1.5811388300841898
-@@ -307,7 +307,7 @@ def variance(v, bias=False):
+@@ -299,7 +299,7 @@ def variance(v, bias=False):
          0.4897530450000000?
          sage: import numpy                                                              # needs numpy
          sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
@@ -189,7 +189,7 @@ index 6937f6cb410..fb296e00fb6 100644
          sage: variance(x, bias=False)                                                   # needs numpy
          2.5
 diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
-index 955a256e9b4..e5ed6160b79 100644
+index cc15eff82e9..e32e7fd28b3 100644
 --- a/src/sage/structure/coerce.pyx
 +++ b/src/sage/structure/coerce.pyx
 @@ -521,7 +521,7 @@ cdef class CoercionModel:
@@ -202,10 +202,10 @@ index 955a256e9b4..e5ed6160b79 100644
          sage: # needs sage.rings.real_mpfr
          sage: x = polygen(RR)
 diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
-index cd89ad2a256..6fdf6d8ef23 100644
+index 362d01ea297..92bce28b032 100644
 --- a/src/sage/symbolic/function.pyx
 +++ b/src/sage/symbolic/function.pyx
-@@ -965,7 +965,7 @@ cdef class BuiltinFunction(Function):
+@@ -962,7 +962,7 @@ cdef class BuiltinFunction(Function):
  
              sage: import numpy                                                          # needs numpy
              sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
@@ -215,10 +215,10 @@ index cd89ad2a256..6fdf6d8ef23 100644
              sage: sin(numpy.int32(0))                                                   # needs numpy
              0.0
 diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 5b007d9e5fd..4a096d317e7 100644
+index 32afe8d3a62..63734e68f63 100644
 --- a/src/sage/symbolic/ring.pyx
 +++ b/src/sage/symbolic/ring.pyx
-@@ -1163,7 +1163,7 @@ cdef class NumpyToSRMorphism(Morphism):
+@@ -1154,7 +1154,7 @@ cdef class NumpyToSRMorphism(Morphism):
  
          sage: import numpy                                                              # needs numpy
          sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy

From 2bbc53d3fe97b01a51e86df082736217ad2fd22e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 8 Sep 2024 09:35:16 -0300
Subject: [PATCH 5/7] nauty: update to 2.8.9.

---
 srcpkgs/nauty/patches/fix-runalltests.patch | 11 +++++++++++
 srcpkgs/nauty/template                      |  7 ++++---
 2 files changed, 15 insertions(+), 3 deletions(-)
 create mode 100644 srcpkgs/nauty/patches/fix-runalltests.patch

diff --git a/srcpkgs/nauty/patches/fix-runalltests.patch b/srcpkgs/nauty/patches/fix-runalltests.patch
new file mode 100644
index 00000000000000..34e1692cf6e6e3
--- /dev/null
+++ b/srcpkgs/nauty/patches/fix-runalltests.patch
@@ -0,0 +1,11 @@
+--- a/runalltests.in	2024-08-26 00:55:55.000000000 -0300
++++ b/runalltests.in	2024-09-08 09:30:04.032719770 -0300
+@@ -121,7 +121,7 @@
+ runonetest "./geng -q -TD6 10 | ./ransubg -qS765 -P9/10 | ./countg --NN,A,G,GG" "" nautestv.ans
+ runonetest "./genrang -q -P3 -S1234 70 1000 | ./countg --G,GG" "" nautestw.ans
+ runonetest "./genrang -q -P4 -z -S1234 70 500 | ./countg --G,GG" "" nautestx.ans
+-runonetest "./geng -q -bT 12 | ./ranlabg -qS7654 -m5 | uniqg -u" "" nautesty.ans
++runonetest "./geng -q -bT 12 | ./ranlabg -qS7654 -m5 | ./uniqg -u" "" nautesty.ans
+ 
+ echo " "
+ 
diff --git a/srcpkgs/nauty/template b/srcpkgs/nauty/template
index 6f85b1d064d4e5..aea4e4a6eb0294 100644
--- a/srcpkgs/nauty/template
+++ b/srcpkgs/nauty/template
@@ -1,18 +1,18 @@
 # Template file for 'nauty'
 pkgname=nauty
-version=2.8.8
+version=2.8.9
 revision=1
 build_style=gnu-configure
 make_install_args="includedir=/usr/include/nauty
  pkgconfigexecdir=/usr/lib/pkgconfig"
-hostmakedepends="automake"
+hostmakedepends="automake libtool"
 short_desc="Compute the automorphism groups of graphs and digraphs"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="Apache-2.0"
 homepage="https://pallini.di.uniroma1.it/"
 changelog="https://pallini.di.uniroma1.it/changes24-28.txt"
 distfiles="https://pallini.di.uniroma1.it/nauty${version//./_}.tar.gz"
-checksum=159d2156810a6bb240410cd61eb641add85088d9f15c888cdaa37b8681f929ce
+checksum=c97ab42bf48796a86a598bce3e9269047ca2b32c14fc23e07208a244fe52c4ee
 
 build_options="native_build"
 
@@ -21,6 +21,7 @@ if [ -z "$build_option_native_build" ]; then
 fi
 
 pre_configure() {
+	aclocal
 	autoreconf -fi
 }
 

From c20a4820602587b652b607e3f938062b9e3f551d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sat, 7 Sep 2024 14:32:41 -0300
Subject: [PATCH 6/7] sagemath: update to 10.5.beta3.

---
 .../sagemath/patches/36641-sympy_1.13.patch   | 60 -------------------
 .../sagemath/patches/38572-nauty_2.8.9.patch  | 13 ++++
 srcpkgs/sagemath/patches/get_patches          |  4 +-
 srcpkgs/sagemath/template                     |  4 +-
 4 files changed, 17 insertions(+), 64 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/36641-sympy_1.13.patch
 create mode 100644 srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch

diff --git a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
deleted file mode 100644
index 01e859ad023f4d..00000000000000
--- a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
+++ /dev/null
@@ -1,60 +0,0 @@
-diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py
-index 823a0d14a41..de1c8531814 100644
---- a/src/sage/doctest/forker.py
-+++ b/src/sage/doctest/forker.py
-@@ -150,14 +150,15 @@ def init_sage(controller=None):
-         sage: from sympy.printing.pretty.pretty import PrettyPrinter
-         sage: s = sympify('+x^'.join(str(i) for i in range(30)))
-         sage: print(PrettyPrinter(settings={'wrap_line': True}).doprint(s))
--         29    28    27    26    25    24    23    22    21    20    19    18    17
--        x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   +
-+         29    28    27    26    25    24    23    22    21    20    19    18    17    ↪
-+        x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   +  ↪
-         <BLANKLINE>
--         16    15    14    13    12    11    10    9    8    7    6    5    4    3
--        x   + x   + x   + x   + x   + x   + x   + x  + x  + x  + x  + x  + x  + x  + x
-+        ↪  16    15    14    13    12    11    10    9    8    7    6    5    4    3   ↪
-+        ↪ x   + x   + x   + x   + x   + x   + x   + x  + x  + x  + x  + x  + x  + x  + ↪
-         <BLANKLINE>
--        2
--          + x
-+        ↪   2
-+        ↪  x  + x
-+
- 
-     The displayhook sorts dictionary keys to simplify doctesting of
-     dictionary output::
-diff --git a/src/sage/functions/hypergeometric.py b/src/sage/functions/hypergeometric.py
-index ade7836b310..eb5c6665c0d 100644
---- a/src/sage/functions/hypergeometric.py
-+++ b/src/sage/functions/hypergeometric.py
-@@ -124,7 +124,7 @@
-     sage: maxima(hypergeometric([1, 1, 1], [3, 3, 3], x))                               # needs sage.symbolic
-     hypergeometric([1,1,1],[3,3,3],_SAGE_VAR_x)
-     sage: hypergeometric((5, 4), (4, 4), 3)._sympy_()                                   # needs sympy sage.symbolic
--    hyper((5, 4), (4, 4), 3)
-+    hyper((5,), (4,), 3)
-     sage: hypergeometric((5, 4), (4, 4), 3)._mathematica_init_()                        # needs sage.symbolic
-     'HypergeometricPFQ[{5,4},{4,4},3]'
- 
-diff --git a/src/sage/typeset/ascii_art.py b/src/sage/typeset/ascii_art.py
-index 83d92af8959..e470e2bd88d 100644
---- a/src/sage/typeset/ascii_art.py
-+++ b/src/sage/typeset/ascii_art.py
-@@ -44,11 +44,12 @@
-     sage: shell.run_cell('%display ascii_art')
-     sage: shell.run_cell("i = var('i')")                                                # needs sage.symbolic
-     sage: shell.run_cell('sum(factorial(i)*x^i, i, 0, 10)')                             # needs sage.symbolic
--             10           9          8         7        6        5       4      3
--    3628800*x   + 362880*x  + 40320*x  + 5040*x  + 720*x  + 120*x  + 24*x  + 6*x
-+             10           9          8         7        6        5       4      3  >
-+    3628800*x   + 362880*x  + 40320*x  + 5040*x  + 720*x  + 120*x  + 24*x  + 6*x   >
-     <BLANKLINE>
--         2
--    + 2*x  + x + 1
-+    >      2
-+    > + 2*x  + x + 1
-+
-     sage: shell.run_cell('3/(7*x)')                                                     # needs sage.symbolic
-      3
-     ---
diff --git a/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch b/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
new file mode 100644
index 00000000000000..5f75a8bef5556a
--- /dev/null
+++ b/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
@@ -0,0 +1,13 @@
+diff --git a/src/sage/graphs/generators/families.py b/src/sage/graphs/generators/families.py
+index e6e5312b8a8..aa10d15d4d8 100644
+--- a/src/sage/graphs/generators/families.py
++++ b/src/sage/graphs/generators/families.py
+@@ -3710,7 +3710,7 @@ def nauty_gentreeg(options='', debug=False):
+         ...
+         ValueError: wrong format of parameter options
+         sage: list(graphs.nauty_gentreeg("3 -x", debug=True))
+-        ['>E Usage: ...gentreeg [-D#] [-Z#:#] [-ulps] [-q] n [res/mod] ...
++        ['>E Usage: ...gentreeg [-D#] [-Z#:#] [-ulps] [-q] n... [res/mod] ...
+         sage: list(graphs.nauty_gentreeg("3", debug=True))
+         ['>A ...gentreeg ...\n', Graph on 3 vertices]
+     """
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index c182576ea553cd..8f540dad14bfd1 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -1,6 +1,6 @@
 #! /bin/sh
 
-version=10.4
+version=10.5
 
 URL_BASE_PR="https://github.com/sagemath/sage/pull/"
 URL_BASE_COMPARE="https://github.com/sagemath/sage/compare/${version}..."
@@ -27,8 +27,8 @@ get_pr() {
 # run from patches dir
 cd $(dirname "$0")
 
-get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
+get_pr 38572 "nauty 2.8.9"
 
 #get_pr 37645 "fix doctest"
 get_pr 37885 "cython warnings"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index f5e1d8c68cfcbe..709a3ea4262101 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,6 +1,6 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.5.beta2
+version=10.5.beta3
 revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=0fe0c82dd6959951fc07d55737d270290f64947e183a403ca25709e21b751dee
+checksum=cbf3614c1b9be5f0a0756b0a5480c2ebfa663bd87bd66eefd162a755979bcb3d
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From a1b9d7ea1e4fce08e00593060b08e6eec4c0c641 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 22 Sep 2024 08:19:39 -0300
Subject: [PATCH 7/7] sagemath: update to 10.5.beta5.

---
 .../sagemath/patches/38572-nauty_2.8.9.patch  |  13 -
 srcpkgs/sagemath/patches/numpy_2.1a.patch     |  28 ---
 srcpkgs/sagemath/patches/numpy_2.1b.patch     | 229 ------------------
 srcpkgs/sagemath/template                     |   4 +-
 4 files changed, 2 insertions(+), 272 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
 delete mode 100644 srcpkgs/sagemath/patches/numpy_2.1a.patch
 delete mode 100644 srcpkgs/sagemath/patches/numpy_2.1b.patch

diff --git a/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch b/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
deleted file mode 100644
index 5f75a8bef5556a..00000000000000
--- a/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/src/sage/graphs/generators/families.py b/src/sage/graphs/generators/families.py
-index e6e5312b8a8..aa10d15d4d8 100644
---- a/src/sage/graphs/generators/families.py
-+++ b/src/sage/graphs/generators/families.py
-@@ -3710,7 +3710,7 @@ def nauty_gentreeg(options='', debug=False):
-         ...
-         ValueError: wrong format of parameter options
-         sage: list(graphs.nauty_gentreeg("3 -x", debug=True))
--        ['>E Usage: ...gentreeg [-D#] [-Z#:#] [-ulps] [-q] n [res/mod] ...
-+        ['>E Usage: ...gentreeg [-D#] [-Z#:#] [-ulps] [-q] n... [res/mod] ...
-         sage: list(graphs.nauty_gentreeg("3", debug=True))
-         ['>A ...gentreeg ...\n', Graph on 3 vertices]
-     """
diff --git a/srcpkgs/sagemath/patches/numpy_2.1a.patch b/srcpkgs/sagemath/patches/numpy_2.1a.patch
deleted file mode 100644
index 493c75e2f8f8e0..00000000000000
--- a/srcpkgs/sagemath/patches/numpy_2.1a.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-commit d755b32cbed462abf01a1cd782ba57cb92fbf713
-Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
-Date:   Mon Aug 19 23:25:32 2024 -0300
-
-    add copy parameter to numpy (needed for v2.1)
-
-diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
-index 3edb9ead54d..2c76fd1e557 100644
---- a/src/sage/matrix/matrix1.pyx
-+++ b/src/sage/matrix/matrix1.pyx
-@@ -670,7 +670,7 @@ cdef class Matrix(Matrix0):
-             entries = [[sib(v, 2) for v in row] for row in self.rows()]
-             return sib.name('matrix')(self.base_ring(), entries)
- 
--    def numpy(self, dtype=None):
-+    def numpy(self, dtype=None, copy=True):
-         """
-         Return the Numpy matrix associated to this matrix.
- 
-@@ -731,7 +731,7 @@ cdef class Matrix(Matrix0):
-             (3, 4)
-         """
-         import numpy
--        A = numpy.matrix(self.list(), dtype=dtype)
-+        A = numpy.matrix(self.list(), dtype=dtype, copy=copy)
-         return numpy.resize(A,(self.nrows(), self.ncols()))
- 
-     # Define the magic "__array__" function so that numpy.array(m) can convert
diff --git a/srcpkgs/sagemath/patches/numpy_2.1b.patch b/srcpkgs/sagemath/patches/numpy_2.1b.patch
deleted file mode 100644
index 8dc0eec2b5a9d8..00000000000000
--- a/srcpkgs/sagemath/patches/numpy_2.1b.patch
+++ /dev/null
@@ -1,229 +0,0 @@
-commit 8260d18c3cf8e356db3d95fc46f6e68f75b453fd
-Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
-Date:   Tue Aug 20 00:05:33 2024 -0300
-
-    silence np.set_printoptions (for numpy 2.1)
-
-diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index 74a14fa1ecd..82e6c7eb3c8 100644
---- a/src/sage/combinat/fully_packed_loop.py
-+++ b/src/sage/combinat/fully_packed_loop.py
-@@ -68,7 +68,7 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
- 
-         sage: import numpy as np
-         sage: if int(np.version.short_version[0]) > 1:
--        ....:     np.set_printoptions(legacy="1.25")
-+        ....:     _token = np.set_printoptions(legacy="1.25")
-         sage: from sage.combinat.fully_packed_loop import _make_color_list
-         sage: _make_color_list(5)
-         sage: _make_color_list(5, ['blue', 'red'])
-diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
-index 308171af3cd..6f66624ef87 100644
---- a/src/sage/functions/special.py
-+++ b/src/sage/functions/special.py
-@@ -219,7 +219,7 @@ class SphericalHarmonic(BuiltinFunction):
-         sage: from scipy.special import sph_harm  # NB: arguments x and y are swapped   # needs scipy
-         sage: import numpy as np                                                        # needs scipy
-         sage: if int(np.version.short_version[0]) > 1:                                  # needs scipy
--        ....:     np.set_printoptions(legacy="1.25")                                    # needs scipy
-+        ....:     _token = np.set_printoptions(legacy="1.25")                           # needs scipy
-         sage: sph_harm(1, 1, pi.n(), (pi/2).n())  # abs tol 1e-14                       # needs scipy sage.symbolic
-         (0.3454941494713355-4.231083042742082e-17j)
- 
-diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index b3e42a6a6a2..13ffa4d1789 100644
---- a/src/sage/numerical/optimize.py
-+++ b/src/sage/numerical/optimize.py
-@@ -381,7 +381,7 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm='default',
-         ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
-         sage: import numpy
-         sage: if int(numpy.version.short_version[0]) > 1:
--        ....:     numpy.set_printoptions(legacy="1.25")
-+        ....:     _token = numpy.set_printoptions(legacy="1.25")
-         sage: from numpy import zeros
-         sage: def rosen_der(x):
-         ....:    xm = x[1r:-1r]
-diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index 02442f90ba4..1fe3f0b051a 100644
---- a/src/sage/plot/arrow.py
-+++ b/src/sage/plot/arrow.py
-@@ -55,7 +55,7 @@ class CurveArrow(GraphicPrimitive):
- 
-             sage: import numpy  # to ensure numpy 2.0 compatibility
-             sage: if int(numpy.version.short_version[0]) > 1:
--            ....:     numpy.set_printoptions(legacy="1.25")
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")
-             sage: from sage.plot.arrow import CurveArrow
-             sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
-             ....:                options={})
-diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
-index d2f70b44526..2eaacc6879e 100644
---- a/src/sage/plot/multigraphics.py
-+++ b/src/sage/plot/multigraphics.py
-@@ -766,7 +766,7 @@ class MultiGraphics(WithEqualityById, SageObject):
-             (0.2, 0.3, 0.4, 0.1)
-             sage: import numpy  # to ensure numpy 2.0 compatibility
-             sage: if int(numpy.version.short_version[0]) > 1:
--            ....:     numpy.set_printoptions(legacy="1.25")
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")
-             sage: ax1.get_position().bounds  # tol 1.0e-13
-             (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
-         """
-@@ -1269,7 +1269,7 @@ class GraphicsArray(MultiGraphics):
-             sage: G = graphics_array([g1, g2])
-             sage: import numpy  # to ensure numpy 2.0 compatibility
-             sage: if int(numpy.version.short_version[0]) > 1:
--            ....:     numpy.set_printoptions(legacy="1.25")
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")
-             sage: G.position(0)  # tol 5.0e-3
-             (0.025045451349937315,
-              0.03415488992713045,
-diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index b69a05b37bf..25e404bfc7d 100644
---- a/src/sage/plot/streamline_plot.py
-+++ b/src/sage/plot/streamline_plot.py
-@@ -72,7 +72,7 @@ class StreamlinePlot(GraphicPrimitive):
-             sage: x, y = var('x y')
-             sage: import numpy  # to ensure numpy 2.0 compatibility
-             sage: if int(numpy.version.short_version[0]) > 1:
--            ....:     numpy.set_printoptions(legacy="1.25")
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")
-             sage: d = streamline_plot((.01*x, x+y), (x,10,20), (y,10,20))[0].get_minmax_data()
-             sage: d['xmin']
-             10.0
-diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index 11811b9587f..8ce0f7f2683 100644
---- a/src/sage/rings/integer.pyx
-+++ b/src/sage/rings/integer.pyx
-@@ -595,7 +595,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
-             sage: # needs numpy
-             sage: import numpy
-             sage: if int(numpy.version.short_version[0]) > 1:
--            ....:     numpy.set_printoptions(legacy="1.25")
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")
-             sage: numpy.int8('12') == 12
-             True
-             sage: 12 == numpy.int8('12')
-diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
-index 11953a50ab5..6aafcceed89 100644
---- a/src/sage/rings/real_mpfi.pyx
-+++ b/src/sage/rings/real_mpfi.pyx
-@@ -232,7 +232,7 @@ TESTS::
- 
-     sage: import numpy                                                                  # needs numpy
-     sage: if int(numpy.version.short_version[0]) > 1:                                   # needs numpy
--    ....:     numpy.set_printoptions(legacy="1.25")                                     # needs numpy
-+    ....:     _token = numpy.set_printoptions(legacy="1.25")                            # needs numpy
-     sage: RIF(2) == numpy.int8('2')                                                     # needs numpy
-     True
-     sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
-diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-index 40b92ab23eb..3838bcccb8a 100755
---- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-+++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-@@ -78,7 +78,7 @@ cdef class PeriodicRegion:
- 
-             sage: import numpy as np
-             sage: if int(np.version.short_version[0]) > 1:
--            ....:     np.set_printoptions(legacy="1.25")
-+            ....:     _token = np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
-@@ -296,7 +296,7 @@ cdef class PeriodicRegion:
- 
-             sage: import numpy as np
-             sage: if int(np.version.short_version[0]) > 1:
--            ....:     np.set_printoptions(legacy="1.25")
-+            ....:     _token = np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((10, 10))
-             sage: data[1:4,1:4] = True
-@@ -320,7 +320,7 @@ cdef class PeriodicRegion:
- 
-             sage: import numpy as np
-             sage: if int(np.version.short_version[0]) > 1:
--            ....:     np.set_printoptions(legacy="1.25")
-+            ....:     _token = np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1,1] = True
-@@ -375,7 +375,7 @@ cdef class PeriodicRegion:
- 
-             sage: import numpy as np
-             sage: if int(np.version.short_version[0]) > 1:
--            ....:     np.set_printoptions(legacy="1.25")
-+            ....:     _token = np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
- 
-             sage: data = np.zeros((20, 20))
-@@ -528,7 +528,7 @@ cdef class PeriodicRegion:
- 
-             sage: import numpy as np
-             sage: if int(np.version.short_version[0]) > 1:
--            ....:     np.set_printoptions(legacy="1.25")
-+            ....:     _token = np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1, 1] = True
-diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index 47d890cf0ab..ba7f0cdb0f9 100644
---- a/src/sage/stats/basic_stats.py
-+++ b/src/sage/stats/basic_stats.py
-@@ -222,7 +222,7 @@ def std(v, bias=False):
-         sage: # needs numpy
-         sage: import numpy
-         sage: if int(numpy.version.short_version[0]) > 1:
--        ....:     numpy.set_printoptions(legacy="1.25")
-+        ....:     _token = numpy.set_printoptions(legacy="1.25")
-         sage: x = numpy.array([1,2,3,4,5])
-         sage: std(x, bias=False)
-         1.5811388300841898
-@@ -299,7 +299,7 @@ def variance(v, bias=False):
-         0.4897530450000000?
-         sage: import numpy                                                              # needs numpy
-         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
--        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-+        ....:     _token = numpy.set_printoptions(legacy="1.25")                        # needs numpy
-         sage: x = numpy.array([1,2,3,4,5])                                              # needs numpy
-         sage: variance(x, bias=False)                                                   # needs numpy
-         2.5
-diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
-index cc15eff82e9..e32e7fd28b3 100644
---- a/src/sage/structure/coerce.pyx
-+++ b/src/sage/structure/coerce.pyx
-@@ -521,7 +521,7 @@ cdef class CoercionModel:
- 
-         sage: import numpy                                                              # needs numpy
-         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
--        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-+        ....:     _token = numpy.set_printoptions(legacy="1.25")                        # needs numpy
- 
-         sage: # needs sage.rings.real_mpfr
-         sage: x = polygen(RR)
-diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
-index 362d01ea297..92bce28b032 100644
---- a/src/sage/symbolic/function.pyx
-+++ b/src/sage/symbolic/function.pyx
-@@ -962,7 +962,7 @@ cdef class BuiltinFunction(Function):
- 
-             sage: import numpy                                                          # needs numpy
-             sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
--            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")                    # needs numpy
- 
-             sage: sin(numpy.int32(0))                                                   # needs numpy
-             0.0
-diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 32afe8d3a62..63734e68f63 100644
---- a/src/sage/symbolic/ring.pyx
-+++ b/src/sage/symbolic/ring.pyx
-@@ -1154,7 +1154,7 @@ cdef class NumpyToSRMorphism(Morphism):
- 
-         sage: import numpy                                                              # needs numpy
-         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
--        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-+        ....:     _token = numpy.set_printoptions(legacy="1.25")                        # needs numpy
-         sage: f(x) = x^2
-         sage: f(numpy.int8('2'))                                                        # needs numpy
-         4
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index 709a3ea4262101..4face5e8f7ad84 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,6 +1,6 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.5.beta3
+version=10.5.beta5
 revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=cbf3614c1b9be5f0a0756b0a5480c2ebfa663bd87bd66eefd162a755979bcb3d
+checksum=af4e8215043cd5376adea87f37928b94863561e36cba2171dab48ea984f7f259
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

^ permalink raw reply	[flat|nested] 13+ messages in thread

* Re: [PR PATCH] [Updated] [BETA] sagemath: update to 10.5.beta5
  2024-08-18 17:54 [PR PATCH] [BETA] sagemath: update to 10.5.beta2 tornaria
                   ` (8 preceding siblings ...)
  2024-09-22 12:01 ` [PR PATCH] [Updated] " tornaria
@ 2024-10-15 19:18 ` tornaria
  2024-10-29  0:41 ` [PR PATCH] [Updated] [BETA] sagemath: update to 10.5.beta7 tornaria
  2024-11-18  2:52 ` [PR PATCH] [Updated] [BETA] sagemath: update to 10.5.beta8 tornaria
  11 siblings, 0 replies; 13+ messages in thread
From: tornaria @ 2024-10-15 19:18 UTC (permalink / raw)
  To: ml

[-- Attachment #1: Type: text/plain, Size: 1382 bytes --]

There is an updated pull request by tornaria against master on the void-packages repository

https://github.com/tornaria/void-packages sagemath
https://github.com/void-linux/void-packages/pull/51902

[BETA] sagemath: update to 10.5.beta5
<!-- Uncomment relevant sections and delete options which are not applicable -->

 - python3-Cython: alternative fix for 6122
 - sagemath: enable all cython warnings
 - nauty: update to 2.8.9.

#### Testing the changes
- I tested the changes in this PR: **YES**

@dkwo

<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->

<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration
and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
  - aarch64-musl
  - armv7l
  - armv6l-musl
-->


A patch file from https://github.com/void-linux/void-packages/pull/51902.patch is attached

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-sagemath-51902.patch --]
[-- Type: text/x-diff, Size: 85178 bytes --]

From 9ebf2e52260c14364e8d567088ca1982eaf0e5b1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 11 Aug 2024 22:53:42 -0300
Subject: [PATCH 1/9] python3-Cython: alternative fix for 6122

---
 srcpkgs/python3-Cython/patches/fix-regression.patch | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/srcpkgs/python3-Cython/patches/fix-regression.patch b/srcpkgs/python3-Cython/patches/fix-regression.patch
index f2e761608e373b..f5957cfa59c2f5 100644
--- a/srcpkgs/python3-Cython/patches/fix-regression.patch
+++ b/srcpkgs/python3-Cython/patches/fix-regression.patch
@@ -15,3 +15,11 @@ serious regression, e.g. sagemath FTBS with cython 3.0.11
              warning(self.pos,
                      "Implicit noexcept declaration is deprecated."
                      " Function declaration should contain 'noexcept' keyword.",
+@@ -3128,6 +3126,7 @@ class DefNode(FuncDefNode):
+             if scope is None:
+                 scope = cfunc.scope
+             cfunc_type = cfunc.type
++            has_explicit_exc_clause=True
+             if len(self.args) != len(cfunc_type.args) or cfunc_type.has_varargs:
+                 error(self.pos, "wrong number of arguments")
+                 error(cfunc.pos, "previous declaration here")

From a8eedd114440b0a5b44dd5e4c2af9f967dcb6fc0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 5 Aug 2024 00:21:23 -0300
Subject: [PATCH 2/9] sagemath: update to 10.5.beta2.

---
 .../sagemath/patches/36641-sympy_1.13.patch   |  22 +-
 .../sagemath/patches/37884-gap_4.13.1.patch   |  28 +-
 .../sagemath/patches/38250-numpy_2.0.patch    | 587 ------------------
 .../sagemath/patches/38344-ecm_7.0.6.patch    |  43 --
 srcpkgs/sagemath/patches/get_patches          |   4 +-
 srcpkgs/sagemath/template                     |   6 +-
 6 files changed, 21 insertions(+), 669 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/38250-numpy_2.0.patch
 delete mode 100644 srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch

diff --git a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
index 625c582cdd41b7..01e859ad023f4d 100644
--- a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
+++ b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
@@ -1,8 +1,5 @@
-diff --git a/build/pkgs/sympy/requirements.txt b/build/pkgs/sympy/requirements.txt
-new file mode 100644
-index 00000000000..3ef8f90b550
 diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py
-index 7e9eab2ff2e..43365cd645e 100644
+index 823a0d14a41..de1c8531814 100644
 --- a/src/sage/doctest/forker.py
 +++ b/src/sage/doctest/forker.py
 @@ -150,14 +150,15 @@ def init_sage(controller=None):
@@ -28,7 +25,7 @@ index 7e9eab2ff2e..43365cd645e 100644
      The displayhook sorts dictionary keys to simplify doctesting of
      dictionary output::
 diff --git a/src/sage/functions/hypergeometric.py b/src/sage/functions/hypergeometric.py
-index 010c61febe0..bbccbd20032 100644
+index ade7836b310..eb5c6665c0d 100644
 --- a/src/sage/functions/hypergeometric.py
 +++ b/src/sage/functions/hypergeometric.py
 @@ -124,7 +124,7 @@
@@ -40,21 +37,8 @@ index 010c61febe0..bbccbd20032 100644
      sage: hypergeometric((5, 4), (4, 4), 3)._mathematica_init_()                        # needs sage.symbolic
      'HypergeometricPFQ[{5,4},{4,4},3]'
  
-diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx
-index a92fe241355..f62311423be 100644
---- a/src/sage/symbolic/expression.pyx
-+++ b/src/sage/symbolic/expression.pyx
-@@ -1167,7 +1167,7 @@ cdef class Expression(Expression_abc):
-             sage: unicode_art(SR(13 - I))
-             13 - ⅈ
-             sage: unicode_art(SR(1.3 - I))
--            1.3 - ⅈ
-+            1.3 - 1.0⋅ⅈ
-             sage: unicode_art(cos(I))
-             cosh(1)
- 
 diff --git a/src/sage/typeset/ascii_art.py b/src/sage/typeset/ascii_art.py
-index 28024405d27..458fa8724a3 100644
+index 83d92af8959..e470e2bd88d 100644
 --- a/src/sage/typeset/ascii_art.py
 +++ b/src/sage/typeset/ascii_art.py
 @@ -44,11 +44,12 @@
diff --git a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
index 1550d47e2436c6..321e0a94487da3 100644
--- a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
+++ b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
@@ -1,21 +1,21 @@
 diff --git a/src/sage/algebras/fusion_rings/fusion_double.py b/src/sage/algebras/fusion_rings/fusion_double.py
-index 7ce086f70d0..954513572c3 100644
+index 71277561331..3b681d75d3b 100644
 --- a/src/sage/algebras/fusion_rings/fusion_double.py
 +++ b/src/sage/algebras/fusion_rings/fusion_double.py
 @@ -133,7 +133,7 @@ class FusionDouble(CombinatorialFreeModule):
          sage: G = SmallPermutationGroup(16,9)
-         sage: F = FusionDouble(G, prefix="b",inject_variables=True)
+         sage: F = FusionDouble(G, prefix='b', inject_variables=True)
          sage: b13^2 # long time (4s)
 -        b0 + b2 + b4 + b15 + b16 + b17 + b18 + b24 + b26 + b27
 +        b0 + b3 + b4
- 
      """
      @staticmethod
+     def __classcall_private__(cls, G, prefix='s', inject_variables=False):
 diff --git a/src/sage/categories/simplicial_sets.py b/src/sage/categories/simplicial_sets.py
-index e714a4571c4..a2b87a729d1 100644
+index aabd3cdbb4f..14bebdcd080 100644
 --- a/src/sage/categories/simplicial_sets.py
 +++ b/src/sage/categories/simplicial_sets.py
-@@ -593,9 +593,9 @@ def _canonical_twisting_operator(self):
+@@ -591,9 +591,9 @@ def _canonical_twisting_operator(self):
                      sage: X = simplicial_sets.Torus()
                      sage: d = X._canonical_twisting_operator()
                      sage: d
@@ -27,7 +27,7 @@ index e714a4571c4..a2b87a729d1 100644
                      sage: Y = simplicial_sets.RealProjectiveSpace(2)
                      sage: d2 = Y._canonical_twisting_operator()
                      sage: d2
-@@ -677,10 +677,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
+@@ -674,10 +674,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
                      sage: X = simplicial_sets.Torus()
                      sage: C = X.twisted_chain_complex()
                      sage: C.differential(1)
@@ -41,7 +41,7 @@ index e714a4571c4..a2b87a729d1 100644
                      [      -1       -1]
                      sage: C.differential(3)
                      []
-@@ -848,29 +848,29 @@ def twisted_homology(self, n, reduced=False):
+@@ -844,29 +844,29 @@ def twisted_homology(self, n, reduced=False):
                      sage: # needs sage.graphs
                      sage: Y = simplicial_sets.Torus()
                      sage: Y.twisted_homology(1)
@@ -80,10 +80,10 @@ index e714a4571c4..a2b87a729d1 100644
                      [1 0 0 0 0]
                      [0 1 0 0 0]
 diff --git a/src/sage/combinat/matrices/latin.py b/src/sage/combinat/matrices/latin.py
-index 936edcc6ea4..c06a53d9afd 100644
+index e2d818e9480..84e6c4fcc9b 100644
 --- a/src/sage/combinat/matrices/latin.py
 +++ b/src/sage/combinat/matrices/latin.py
-@@ -2453,7 +2453,7 @@ def p3_group_bitrade_generators(p):
+@@ -2444,7 +2444,7 @@ def p3_group_bitrade_generators(p):
      EXAMPLES::
  
          sage: from sage.combinat.matrices.latin import *
@@ -93,7 +93,7 @@ index 936edcc6ea4..c06a53d9afd 100644
           (1,2,3)(4,7,8)(5,6,9),
           (1,9,2)(3,7,4)(5,8,6),
 diff --git a/src/sage/groups/cubic_braid.py b/src/sage/groups/cubic_braid.py
-index 257b400f1c7..36423c756aa 100644
+index 61db70925e1..521289c7578 100644
 --- a/src/sage/groups/cubic_braid.py
 +++ b/src/sage/groups/cubic_braid.py
 @@ -282,7 +282,7 @@ def _richcmp_(self, other, op):
@@ -106,7 +106,7 @@ index 257b400f1c7..36423c756aa 100644
               c1*c0^-1*c1, c0^-1*c1^-1*c0^-1, c0^-1*c1^-1, c1^-1*c0*c1^-1,
               c0*c1^-1*c0^-1, c0^-1*c1, c0^-1*c1*c0, c0*c1^-1, c1*c0^-1,
 diff --git a/src/sage/groups/finitely_presented.py b/src/sage/groups/finitely_presented.py
-index 4bb52ee4efb..85f572fac6c 100644
+index 4ac2faa783b..7016d08381b 100644
 --- a/src/sage/groups/finitely_presented.py
 +++ b/src/sage/groups/finitely_presented.py
 @@ -1344,8 +1344,8 @@ def abelianization_map(self):
@@ -161,10 +161,10 @@ index 4bb52ee4efb..85f572fac6c 100644
              sage: G.characteristic_varieties(groebner=True)
              {0: [-1 + F1, 1 + F1, 1 - F1 + F1^2, 1 + F1 + F1^2], 1: [1 - F1 + F1^2],  2: []}
 diff --git a/src/sage/groups/perm_gps/permgroup_named.py b/src/sage/groups/perm_gps/permgroup_named.py
-index c1f2683907b..d219e104a2c 100644
+index 5c153b93d4c..bd4afad2942 100644
 --- a/src/sage/groups/perm_gps/permgroup_named.py
 +++ b/src/sage/groups/perm_gps/permgroup_named.py
-@@ -3468,16 +3468,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
+@@ -3465,16 +3465,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
          sage: G = SmallPermutationGroup(12,4); G
          Group of order 12 and GAP Id 4 as a permutation group
          sage: G.gens()
@@ -186,7 +186,7 @@ index c1f2683907b..d219e104a2c 100644
          sage: def numgps(n): return ZZ(libgap.NumberSmallGroups(n))
          sage: all(SmallPermutationGroup(n,k).id() == [n,k]
          ....:     for n in [1..64] for k in [1..numgps(n)])
-@@ -3486,11 +3484,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
+@@ -3483,11 +3481,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
          sage: H.is_abelian()
          False
          sage: [H.centralizer(g) for g in H.conjugacy_classes_representatives()]
diff --git a/srcpkgs/sagemath/patches/38250-numpy_2.0.patch b/srcpkgs/sagemath/patches/38250-numpy_2.0.patch
deleted file mode 100644
index e28fd857afcb75..00000000000000
--- a/srcpkgs/sagemath/patches/38250-numpy_2.0.patch
+++ /dev/null
@@ -1,587 +0,0 @@
-diff --git a/src/sage/arith/misc.py b/src/sage/arith/misc.py
-index 28f81d7b798..d184c52bf19 100644
---- a/src/sage/arith/misc.py
-+++ b/src/sage/arith/misc.py
-@@ -2277,7 +2277,7 @@ def power_mod(a, n, m):
- 
-         sage: from numpy import int32                                                   # needs numpy
-         sage: power_mod(int32(2), int32(390), int32(391))                               # needs numpy
--        285
-+        ...285...
-         sage: from gmpy2 import mpz
-         sage: power_mod(mpz(2), mpz(390), mpz(391))
-         mpz(285)
-diff --git a/src/sage/calculus/interpolators.pyx b/src/sage/calculus/interpolators.pyx
-index 221b52369e2..bb0be7bab0c 100644
---- a/src/sage/calculus/interpolators.pyx
-+++ b/src/sage/calculus/interpolators.pyx
-@@ -27,6 +27,9 @@ Development supported by NSF award No. 0702939.
- import numpy as np
- cimport numpy as np
- 
-+if int(np.version.short_version[0]) > 1:
-+    np.set_printoptions(legacy="1.25")
-+
- from math import pi
- cdef double TWOPI = 2*pi
- 
-diff --git a/src/sage/calculus/riemann.pyx b/src/sage/calculus/riemann.pyx
-index 6ec80d89aa7..c09d93c4260 100644
---- a/src/sage/calculus/riemann.pyx
-+++ b/src/sage/calculus/riemann.pyx
-@@ -44,6 +44,9 @@ from sage.calculus.integration import numerical_integral
- import numpy as np
- cimport numpy as np
- 
-+if int(np.version.short_version[0]) > 1:
-+    np.set_printoptions(legacy="1.25")
-+
- from math import pi
- from math import sin
- from math import cos
-diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index b198fed0c0d..b3ebd206cd2 100644
---- a/src/sage/combinat/fully_packed_loop.py
-+++ b/src/sage/combinat/fully_packed_loop.py
-@@ -66,6 +66,9 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
-     r"""
-     TESTS::
- 
-+        sage: import numpy as np
-+        sage: if int(np.version.short_version[0]) > 1:
-+        ....:     np.set_printoptions(legacy="1.25")
-         sage: from sage.combinat.fully_packed_loop import _make_color_list
-         sage: _make_color_list(5)
-         sage: _make_color_list(5, ['blue', 'red'])
-diff --git a/src/sage/env.py b/src/sage/env.py
-index 722649ab3da..abb9b19f9e3 100644
---- a/src/sage/env.py
-+++ b/src/sage/env.py
-@@ -296,7 +296,7 @@ def sage_include_directories(use_sources=False):
-         sage: import sage.env
-         sage: sage.env.sage_include_directories()
-         ['...',
--         '.../numpy/core/include',
-+         '.../numpy/...core/include',
-          '.../include/python...']
- 
-     To check that C/C++ files are correctly found, we verify that we can
-diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
-index e100ba3ee23..2a03bb68f67 100644
---- a/src/sage/functions/special.py
-+++ b/src/sage/functions/special.py
-@@ -217,6 +217,9 @@ class SphericalHarmonic(BuiltinFunction):
-         sage: spherical_harmonic(1, 1, pi/2, pi).n()  # abs tol 1e-14                   # needs sage.symbolic
-         0.345494149471335
-         sage: from scipy.special import sph_harm  # NB: arguments x and y are swapped   # needs scipy
-+        sage: import numpy as np                                                        # needs scipy
-+        sage: if int(np.version.short_version[0]) > 1:                                  # needs scipy
-+        ....:     np.set_printoptions(legacy="1.25")                                    # needs scipy
-         sage: sph_harm(1, 1, pi.n(), (pi/2).n())  # abs tol 1e-14                       # needs scipy sage.symbolic
-         (0.3454941494713355-4.231083042742082e-17j)
- 
-diff --git a/src/sage/graphs/generators/classical_geometries.py b/src/sage/graphs/generators/classical_geometries.py
-index da04362eef3..957f88d2061 100644
---- a/src/sage/graphs/generators/classical_geometries.py
-+++ b/src/sage/graphs/generators/classical_geometries.py
-@@ -1315,7 +1315,7 @@ def CossidentePenttilaGraph(q):
- 
-     from sage.libs.gap.libgap import libgap
-     adj_list = libgap.function_factory("""function(q)
--        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x;
-+        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x, sqo;
-         LoadPackage("grape");
-         G0:=SO(3,q^2);
-         so:=GeneratorsOfGroup(G0);
-diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
-index 063931ae274..0bafbd00564 100644
---- a/src/sage/graphs/generic_graph.py
-+++ b/src/sage/graphs/generic_graph.py
-@@ -18420,6 +18420,9 @@ def shortest_path_all_pairs(self, by_weight=False, algorithm=None,
-                 M = self.adjacency_matrix(vertices=int_to_vertex)
- 
-             # We call the Floyd-Warshall method from SciPy
-+            import numpy  # to ensure numpy 2.0 compatibility
-+            if int(numpy.version.short_version[0]) > 1:
-+                numpy.set_printoptions(legacy="1.25")
-             from numpy import array as np_array
-             from scipy.sparse.csgraph import floyd_warshall
-             dd, pp = floyd_warshall(np_array(M), directed=self.is_directed(),
-diff --git a/src/sage/graphs/graph_generators_pyx.pyx b/src/sage/graphs/graph_generators_pyx.pyx
-index 033e8b22adc..04b20d3229b 100644
---- a/src/sage/graphs/graph_generators_pyx.pyx
-+++ b/src/sage/graphs/graph_generators_pyx.pyx
-@@ -57,7 +57,7 @@ def RandomGNP(n, p, bint directed=False, bint loops=False, seed=None):
- 
-         sage: from numpy import mean                                                    # needs numpy
-         sage: abs(mean([RandomGNP(200, .2).density() for i in range(30)]) - .2) < .001  # needs numpy
--        True
-+        ...True...
-         sage: RandomGNP(150, .2, loops=True)
-         Traceback (most recent call last):
-         ...
-diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
-index a810418389c..c38df5412f0 100644
---- a/src/sage/matrix/matrix1.pyx
-+++ b/src/sage/matrix/matrix1.pyx
-@@ -705,12 +705,15 @@ cdef class Matrix(Matrix0):
-         Type ``numpy.typecodes`` for a list of the possible
-         typecodes::
- 
--            sage: import numpy                                                          # needs numpy
--            sage: sorted(numpy.typecodes.items())                                       # needs numpy
-+            sage: import numpy                            # needs numpy
-+            sage: numpy.typecodes.items()                 # needs numpy # random
-             [('All', '?bhilqpBHILQPefdgFDGSUVOMm'), ('AllFloat', 'efdgFDG'),
--             ('AllInteger', 'bBhHiIlLqQpP'), ('Character', 'c'), ('Complex', 'FDG'),
--             ('Datetime', 'Mm'), ('Float', 'efdg'), ('Integer', 'bhilqp'),
--             ('UnsignedInteger', 'BHILQP')]
-+            ...
-+
-+        For instance, you can see possibilities for real floating point numbers::
-+
-+            sage: numpy.typecodes['Float']                # needs numpy
-+            'efdg'
- 
-         Alternatively, numpy automatically calls this function (via
-         the magic :meth:`__array__` method) to convert Sage matrices
-diff --git a/src/sage/modules/free_module_element.pyx b/src/sage/modules/free_module_element.pyx
-index d71d22ac1f7..b6f297a3510 100644
---- a/src/sage/modules/free_module_element.pyx
-+++ b/src/sage/modules/free_module_element.pyx
-@@ -555,7 +555,11 @@ def vector(arg0, arg1=None, arg2=None, sparse=None, immutable=False):
-         R = None
- 
-     try:
-+        import numpy
-         from numpy import ndarray
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-+
-     except ImportError:
-         pass
-     else:
-@@ -1188,7 +1192,11 @@ cdef class FreeModuleElement(Vector):   # abstract base class
-             over Rational Field to numpy array of type <... 'float'>:
-             setting an array element with a sequence.
-         """
-+        import numpy
-         from numpy import array
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-+
-         try:
-             return array(self, dtype=dtype)
-         except ValueError as e:
-diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index e3d94d1746e..7ae8ca4966f 100644
---- a/src/sage/numerical/optimize.py
-+++ b/src/sage/numerical/optimize.py
-@@ -155,6 +155,10 @@ def find_root(f, a, b, xtol=10e-13, rtol=2.0**-50, maxiter=100, full_output=Fals
-         b = max(s_1, s_2)
- 
-     import scipy.optimize
-+    import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     g = lambda x: float(f(x))
-     brentqRes = scipy.optimize.brentq(g, a, b,
-                                  full_output=full_output, xtol=xtol, rtol=rtol, maxiter=maxiter)
-@@ -288,6 +292,10 @@ def find_local_minimum(f, a, b, tol=1.48e-08, maxfun=500):
-     a = float(a)
-     b = float(b)
-     import scipy.optimize
-+    import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     xmin, fval, iter, funcalls = scipy.optimize.fminbound(f, a, b, full_output=1, xtol=tol, maxfun=maxfun)
-     return fval, xmin
- 
-@@ -376,6 +384,8 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
-         sage: def rosen(x):  # The Rosenbrock function
-         ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
-         sage: import numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:
-+        ....:     numpy.set_printoptions(legacy="1.25")
-         sage: from numpy import zeros
-         sage: def rosen_der(x):
-         ....:    xm = x[1r:-1r]
-@@ -393,6 +403,9 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
-     from sage.structure.element import Expression
-     from sage.ext.fast_callable import fast_callable
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     from scipy import optimize
-     if isinstance(func, Expression):
-         var_list = func.variables()
-@@ -530,6 +543,8 @@ def minimize_constrained(func,cons,x0,gradient=None,algorithm='default', **args)
-     from sage.structure.element import Expression
-     from sage.ext.fast_callable import fast_callable
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-     from scipy import optimize
-     function_type = type(lambda x,y: x+y)
- 
-@@ -652,6 +667,8 @@ def find_fit(data, model, initial_guess=None, parameters=None, variables=None, s
-     ``lmdif`` and ``lmder`` algorithms.
-     """
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
- 
-     if not isinstance(data, numpy.ndarray):
-         try:
-diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index ac1dc79d802..23e2517ca56 100644
---- a/src/sage/plot/arrow.py
-+++ b/src/sage/plot/arrow.py
-@@ -53,6 +53,9 @@ def get_minmax_data(self):
- 
-         EXAMPLES::
- 
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: from sage.plot.arrow import CurveArrow
-             sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
-             ....:                options={})
-diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx
-index f1f2671a803..4d71414e1c2 100644
---- a/src/sage/plot/complex_plot.pyx
-+++ b/src/sage/plot/complex_plot.pyx
-@@ -1282,15 +1282,13 @@ def rgb_to_hls(rgb):
-         raise ValueError("Last dimension of input array must be 3; "
-                          "shape {} was found.".format(rgb.shape))
-     in_shape = rgb.shape
--    rgb = np.array(
--        rgb, copy=False, dtype=np.dtype(float), ndmin=2
--    )
-+    rgb = np.asarray(rgb, dtype=np.dtype(float))
-     rgb_max = rgb.max(-1)
-     rgb_min = rgb.min(-1)
-     l = (rgb_max + rgb_min)/2.0  # lightness
- 
-     hls = np.zeros_like(rgb)
--    delta = rgb.ptp(-1)
-+    delta = np.ptp(rgb, -1)
-     s = np.zeros_like(delta)
- 
-     ipos = delta > 0
-diff --git a/src/sage/plot/graphics.py b/src/sage/plot/graphics.py
-index a84d162cb56..94f5db09d83 100644
---- a/src/sage/plot/graphics.py
-+++ b/src/sage/plot/graphics.py
-@@ -2754,7 +2754,7 @@ def matplotlib(self, filename=None,
-             sage: xmin, xmax = sub.get_xlim()
-             sage: ymin, ymax = sub.get_ylim()
-             sage: xmin > xmax, ymin > ymax
--            (True, True)
-+            (...True..., ...True...)
-         """
-         if not isinstance(ticks, (list, tuple)):
-             ticks = (ticks, None)
-diff --git a/src/sage/plot/histogram.py b/src/sage/plot/histogram.py
-index fa86a44bd0a..a585cacf9cd 100644
---- a/src/sage/plot/histogram.py
-+++ b/src/sage/plot/histogram.py
-@@ -92,6 +92,8 @@ def get_minmax_data(self):
-             {'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.476190476190..., 'ymin': 0}
-         """
-         import numpy
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
- 
-         # Extract these options (if they are not None) and pass them to
-         # histogram()
-diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
-index b583be32317..6be448f1e04 100644
---- a/src/sage/plot/multigraphics.py
-+++ b/src/sage/plot/multigraphics.py
-@@ -784,6 +784,9 @@ def _add_subplot(self, figure, index, **options):
-             True
-             sage: G.position(1)
-             (0.2, 0.3, 0.4, 0.1)
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: ax1.get_position().bounds  # tol 1.0e-13
-             (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
- 
-@@ -1295,6 +1298,9 @@ def position(self, index):
-             sage: g1 = plot(sin(x), (x, -pi, pi))
-             sage: g2 = circle((0,1), 1.)
-             sage: G = graphics_array([g1, g2])
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: G.position(0)  # tol 5.0e-3
-             (0.025045451349937315,
-              0.03415488992713045,
-diff --git a/src/sage/plot/plot3d/implicit_surface.pyx b/src/sage/plot/plot3d/implicit_surface.pyx
-index ce0da48a4e0..f4d5059b620 100644
---- a/src/sage/plot/plot3d/implicit_surface.pyx
-+++ b/src/sage/plot/plot3d/implicit_surface.pyx
-@@ -468,6 +468,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
-             sage: cube_marcher.y_vertices.tolist()
-             [[[<1.0, 0.5, 0.0>, None]], [[None, None]]]
-             sage: cube_marcher.x_vertices.any() # This shouldn't affect the X vertices.
-+            ...
-         """
-         (self.y_vertices, self.y_vertices_swapped) = \
-             (self.y_vertices_swapped, self.y_vertices)
-@@ -574,6 +575,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
-             sage: cube_marcher.x_vertices.tolist()
-             [[None, None], [None, <1.5, 1.0, 1.0>]]
-             sage: cube_marcher.y_vertices.any() or cube_marcher.z_vertices.any() # This shouldn't affect the Y or Z vertices.
-+            ...
-         """
-         cdef bint has_prev = (_prev is not None)
-         cdef bint has_next = (_next is not None)
-diff --git a/src/sage/plot/scatter_plot.py b/src/sage/plot/scatter_plot.py
-index 4ad418f040b..781854d372c 100644
---- a/src/sage/plot/scatter_plot.py
-+++ b/src/sage/plot/scatter_plot.py
-@@ -63,9 +63,9 @@ def get_minmax_data(self):
-             sage: s = scatter_plot([[0,1],[2,4],[3.2,6]])
-             sage: d = s.get_minmax_data()
-             sage: d['xmin']
--            0.0
-+            ...0.0...
-             sage: d['ymin']
--            1.0
-+            ...1.0...
-         """
-         return {'xmin': self.xdata.min(),
-                 'xmax': self.xdata.max(),
-diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index 663d3aee70b..d2cb11088c7 100644
---- a/src/sage/plot/streamline_plot.py
-+++ b/src/sage/plot/streamline_plot.py
-@@ -71,6 +71,9 @@ def get_minmax_data(self):
-         EXAMPLES::
- 
-             sage: x, y = var('x y')
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: d = streamline_plot((.01*x, x+y), (x,10,20), (y,10,20))[0].get_minmax_data()
-             sage: d['xmin']
-             10.0
-diff --git a/src/sage/probability/probability_distribution.pyx b/src/sage/probability/probability_distribution.pyx
-index e2c71af9c25..59ba4a95ab6 100644
---- a/src/sage/probability/probability_distribution.pyx
-+++ b/src/sage/probability/probability_distribution.pyx
-@@ -140,6 +140,9 @@ cdef class ProbabilityDistribution:
-              1.8,
-              2.0]
-         """
-+        import numpy as np
-+        if int(np.version.short_version[0]) > 1:
-+            np.set_printoptions(legacy="1.25")
-         import pylab
-         ell = [float(self.get_random_element()) for _ in range(num_samples)]
-         S = pylab.hist(ell, bins, density=True)
-diff --git a/src/sage/rings/complex_double.pyx b/src/sage/rings/complex_double.pyx
-index c59a2b46d6f..b4dddebb4dc 100644
---- a/src/sage/rings/complex_double.pyx
-+++ b/src/sage/rings/complex_double.pyx
-@@ -2558,10 +2558,10 @@ cdef class ComplexToCDF(Morphism):
- 
-         sage: # needs numpy
-         sage: import numpy
--        sage: f = CDF.coerce_map_from(numpy.complex_)
--        sage: f(numpy.complex_(I))
-+        sage: f = CDF.coerce_map_from(numpy.complex128)
-+        sage: f(numpy.complex128(I))
-         1.0*I
--        sage: f(numpy.complex_(I)).parent()
-+        sage: f(numpy.complex128(I)).parent()
-         Complex Double Field
-     """
-     def __init__(self, R):
-@@ -2578,7 +2578,7 @@ cdef class ComplexToCDF(Morphism):
-         EXAMPLES::
- 
-             sage: import numpy                                                          # needs numpy
--            sage: CDF(numpy.complex_(I))    # indirect doctest                          # needs numpy
-+            sage: CDF(numpy.complex128(I))    # indirect doctest                          # needs numpy
-             1.0*I
-         """
-         cdef ComplexDoubleElement z = <ComplexDoubleElement>ComplexDoubleElement.__new__(ComplexDoubleElement)
-@@ -2592,7 +2592,7 @@ cdef class ComplexToCDF(Morphism):
-         EXAMPLES::
- 
-             sage: import numpy                                                          # needs numpy
--            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex_)            # needs numpy
-+            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex128)          # needs numpy
-             sage: f._repr_type()                                                        # needs numpy
-             'Native'
-         """
-diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index b4a1fa5039b..38c30f7627b 100644
---- a/src/sage/rings/integer.pyx
-+++ b/src/sage/rings/integer.pyx
-@@ -593,6 +593,8 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
-         Test comparisons with numpy types (see :issue:`13386` and :issue:`18076`)::
- 
-             sage: import numpy                                                          # needs numpy
-+            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
-+            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-             sage: numpy.int8('12') == 12                                                # needs numpy
-             True
-             sage: 12 == numpy.int8('12')                                                # needs numpy
-diff --git a/src/sage/rings/polynomial/polynomial_element.pyx b/src/sage/rings/polynomial/polynomial_element.pyx
-index dcf2af7cdf2..c87eccd44f1 100644
---- a/src/sage/rings/polynomial/polynomial_element.pyx
-+++ b/src/sage/rings/polynomial/polynomial_element.pyx
-@@ -8851,7 +8851,7 @@ cdef class Polynomial(CommutativePolynomial):
-                          'you expect.')
- 
-                 import numpy
--                from numpy.linalg.linalg import LinAlgError
-+                from numpy.linalg import LinAlgError
-                 from sage.rings.complex_double import CDF
- 
-                 numpy_dtype = ('complex' if input_complex else 'double')
-diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
-index 95b472e912c..76fbfedab95 100644
---- a/src/sage/rings/real_mpfi.pyx
-+++ b/src/sage/rings/real_mpfi.pyx
-@@ -231,6 +231,8 @@ specified if given a non-interval and an interval::
- TESTS::
- 
-     sage: import numpy                                                                  # needs numpy
-+    sage: if int(numpy.version.short_version[0]) > 1:                                   # needs numpy
-+    ....:     numpy.set_printoptions(legacy="1.25")                                     # needs numpy
-     sage: RIF(2) == numpy.int8('2')                                                     # needs numpy
-     True
-     sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
-diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-index 8f240627e77..70ce616f92f 100644
---- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-+++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-@@ -77,6 +77,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
-@@ -295,6 +297,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((10, 10))
-             sage: data[1:4,1:4] = True
-@@ -317,6 +321,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1,1] = True
-@@ -370,6 +376,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
- 
-             sage: data = np.zeros((20, 20))
-@@ -520,6 +528,8 @@ cdef class PeriodicRegion:
-         TESTS::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1, 1] = True
-diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index b2e6b301bf7..6937f6cb410 100644
---- a/src/sage/stats/basic_stats.py
-+++ b/src/sage/stats/basic_stats.py
-@@ -227,6 +227,8 @@ def std(v, bias=False):
- 
-         sage: # needs numpy
-         sage: import numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:
-+        ....:     numpy.set_printoptions(legacy="1.25")
-         sage: x = numpy.array([1,2,3,4,5])
-         sage: std(x, bias=False)
-         1.5811388300841898
-@@ -304,6 +306,8 @@ def variance(v, bias=False):
-         sage: variance([RIF(1.0103, 1.0103), RIF(2)])
-         0.4897530450000000?
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-         sage: x = numpy.array([1,2,3,4,5])                                              # needs numpy
-         sage: variance(x, bias=False)                                                   # needs numpy
-         2.5
-diff --git a/src/sage/stats/time_series.pyx b/src/sage/stats/time_series.pyx
-index 2e22ec45c69..23adae84fb4 100644
---- a/src/sage/stats/time_series.pyx
-+++ b/src/sage/stats/time_series.pyx
-@@ -1718,6 +1718,8 @@ cdef class TimeSeries:
-         if len(v0) == 1:
-             return v1[0]/v0[0]
-         import numpy
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-         coeffs = numpy.polyfit(v0,v1,1)
-         return coeffs[0]
- 
-diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
-index dfbd5ff82fa..955a256e9b4 100644
---- a/src/sage/structure/coerce.pyx
-+++ b/src/sage/structure/coerce.pyx
-@@ -520,6 +520,8 @@ cdef class CoercionModel:
-     Check that :issue:`8426` is fixed (see also :issue:`18076`)::
- 
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
- 
-         sage: # needs sage.rings.real_mpfr
-         sage: x = polygen(RR)
-diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
-index 2cb2f09c715..cd89ad2a256 100644
---- a/src/sage/symbolic/function.pyx
-+++ b/src/sage/symbolic/function.pyx
-@@ -964,6 +964,9 @@ cdef class BuiltinFunction(Function):
-             mpc(real='0.83373002513114902', imag='-0.98889770576286506')
- 
-             sage: import numpy                                                          # needs numpy
-+            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
-+            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-+
-             sage: sin(numpy.int32(0))                                                   # needs numpy
-             0.0
-             sage: type(_)                                                               # needs numpy
-diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 501b0920898..5b007d9e5fd 100644
---- a/src/sage/symbolic/ring.pyx
-+++ b/src/sage/symbolic/ring.pyx
-@@ -1162,6 +1162,8 @@ cdef class NumpyToSRMorphism(Morphism):
-     We check that :issue:`8949` and :issue:`9769` are fixed (see also :issue:`18076`)::
- 
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-         sage: f(x) = x^2
-         sage: f(numpy.int8('2'))                                                        # needs numpy
-         4
diff --git a/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch b/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch
deleted file mode 100644
index db0ae9030623b6..00000000000000
--- a/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-diff --git a/src/sage/interfaces/ecm.py b/src/sage/interfaces/ecm.py
-index 99287dec718..98011970404 100644
---- a/src/sage/interfaces/ecm.py
-+++ b/src/sage/interfaces/ecm.py
-@@ -508,7 +508,6 @@ def _find_factor(self, n, factor_digits, B1, **kwds):
-         """
-         n = self._validate(n)
-         kwds.setdefault('c', 1000000000)
--        kwds.setdefault('I', 1)
-         if factor_digits is not None:
-             B1 = self.recommended_B1(factor_digits)
-         kwds['one'] = True
-diff --git a/src/sage/libs/libecm.pyx b/src/sage/libs/libecm.pyx
-index 886a9b816e4..83fb7adaf8d 100644
---- a/src/sage/libs/libecm.pyx
-+++ b/src/sage/libs/libecm.pyx
-@@ -149,11 +149,13 @@ def ecmfactor(number, double B1, verbose=False, sigma=0):
-     Some special cases::
- 
-         sage: ecmfactor(1, 100)
--        (True, 1, ...)
-+        Traceback (most recent call last):
-+        ...
-+        ValueError: Input number (1) must be greater than 1
-         sage: ecmfactor(0, 100)
-         Traceback (most recent call last):
-         ...
--        ValueError: Input number (0) must be positive
-+        ValueError: Input number (0) must be greater than 1
-     """
-     cdef mpz_t n, f
-     cdef int res
-@@ -164,8 +166,8 @@ def ecmfactor(number, double B1, verbose=False, sigma=0):
-     sage_int_number = Integer(number)
-     sage_int_sigma = Integer(sigma)
- 
--    if number <= 0:
--        raise ValueError("Input number (%s) must be positive"%number)
-+    if number <= 1:
-+        raise ValueError("Input number (%s) must be greater than 1"%number)
- 
-     if verbose:
-         print("Performing one curve with B1=%1.0f" % B1)
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 28162dff8a38e1..5cab228f286365 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -19,7 +19,7 @@ get_pr() {
 	echo "curl -sL \"$url\" | filterdiff ... > \"$pr-$desc.patch\""
 	if [ -z "$dry" ]; then
 		curl -sL "$url" |
-			filterdiff -p1 -x src/setup.py -x build/* -x src/doc/* |
+			filterdiff -p1 -x src/setup.py -x environment* -x src/environment* -x build/* -x src/doc/* |
 			cat > "$pr-$desc.patch"
 	fi
 }
@@ -29,8 +29,6 @@ cd $(dirname "$0")
 
 get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
-get_pr 38250 "numpy 2.0"
-get_pr 38344 "ecm 7.0.6"
 
 #get_pr 37645 "fix doctest"
 #get_pr 37885 "cython warnings"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index b116e62bc67a5a..f5e1d8c68cfcbe 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,7 +1,7 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.4
-revision=3
+version=10.5.beta2
+revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
 build_style=python3-pep517
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=f6579e85f33bd9bb6e9b991bfc4c49dab1e649858ed9ee41c7cec75cb92d4c62
+checksum=0fe0c82dd6959951fc07d55737d270290f64947e183a403ca25709e21b751dee
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From 9b392e0823ef62566a738c29c8f53a10fb8f06a8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Wed, 14 Aug 2024 00:12:02 -0300
Subject: [PATCH 3/9] sagemath: enable all cython warnings

---
 srcpkgs/sagemath/patches/37885-cython_warnings.patch | 12 ++++++++++++
 srcpkgs/sagemath/patches/get_patches                 |  2 +-
 2 files changed, 13 insertions(+), 1 deletion(-)
 create mode 100644 srcpkgs/sagemath/patches/37885-cython_warnings.patch

diff --git a/srcpkgs/sagemath/patches/37885-cython_warnings.patch b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
new file mode 100644
index 00000000000000..fa4b648cfc1577
--- /dev/null
+++ b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
@@ -0,0 +1,12 @@
+diff --git a/src/sage_setup/command/sage_build_cython.py b/src/sage_setup/command/sage_build_cython.py
+index f4b1357c543..3435c196d49 100644
+--- a/src/sage_setup/command/sage_build_cython.py
++++ b/src/sage_setup/command/sage_build_cython.py
+@@ -226,6 +226,7 @@ def run(self):
+                 compiler_directives=self.cython_directives,
+                 compile_time_env=self.compile_time_env,
+                 create_extension=self.create_extension,
++                show_all_warnings=True,
+                 # Debugging
+                 gdb_debug=self.debug,
+                 output_dir=os.path.join(self.build_lib, "sage"),
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 5cab228f286365..c182576ea553cd 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -31,4 +31,4 @@ get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
 
 #get_pr 37645 "fix doctest"
-#get_pr 37885 "cython warnings"
+get_pr 37885 "cython warnings"

From 8fa5c8f8cfcab5c183ae720645b43227267d73e9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 20 Aug 2024 17:56:06 -0300
Subject: [PATCH 4/9] sagemath: patch for numpy 2.1

---
 srcpkgs/sagemath/patches/numpy_2.1a.patch |  8 +--
 srcpkgs/sagemath/patches/numpy_2.1b.patch | 70 +++++++++++------------
 2 files changed, 39 insertions(+), 39 deletions(-)

diff --git a/srcpkgs/sagemath/patches/numpy_2.1a.patch b/srcpkgs/sagemath/patches/numpy_2.1a.patch
index 30e2de99d84536..493c75e2f8f8e0 100644
--- a/srcpkgs/sagemath/patches/numpy_2.1a.patch
+++ b/srcpkgs/sagemath/patches/numpy_2.1a.patch
@@ -1,14 +1,14 @@
-commit 241dc39bd0ba1c056f88bee46a0345d59093eaff
+commit d755b32cbed462abf01a1cd782ba57cb92fbf713
 Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
 Date:   Mon Aug 19 23:25:32 2024 -0300
 
     add copy parameter to numpy (needed for v2.1)
 
 diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
-index c38df5412f0..f587cef651a 100644
+index 3edb9ead54d..2c76fd1e557 100644
 --- a/src/sage/matrix/matrix1.pyx
 +++ b/src/sage/matrix/matrix1.pyx
-@@ -671,7 +671,7 @@ cdef class Matrix(Matrix0):
+@@ -670,7 +670,7 @@ cdef class Matrix(Matrix0):
              entries = [[sib(v, 2) for v in row] for row in self.rows()]
              return sib.name('matrix')(self.base_ring(), entries)
  
@@ -17,7 +17,7 @@ index c38df5412f0..f587cef651a 100644
          """
          Return the Numpy matrix associated to this matrix.
  
-@@ -732,7 +732,7 @@ cdef class Matrix(Matrix0):
+@@ -731,7 +731,7 @@ cdef class Matrix(Matrix0):
              (3, 4)
          """
          import numpy
diff --git a/srcpkgs/sagemath/patches/numpy_2.1b.patch b/srcpkgs/sagemath/patches/numpy_2.1b.patch
index b77e28361d2e74..8dc0eec2b5a9d8 100644
--- a/srcpkgs/sagemath/patches/numpy_2.1b.patch
+++ b/srcpkgs/sagemath/patches/numpy_2.1b.patch
@@ -1,11 +1,11 @@
-commit 8b32fdb87725c1d67ffb51dadec1c331c7c35f3c
+commit 8260d18c3cf8e356db3d95fc46f6e68f75b453fd
 Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
 Date:   Tue Aug 20 00:05:33 2024 -0300
 
     silence np.set_printoptions (for numpy 2.1)
 
 diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index b3ebd206cd2..48866824224 100644
+index 74a14fa1ecd..82e6c7eb3c8 100644
 --- a/src/sage/combinat/fully_packed_loop.py
 +++ b/src/sage/combinat/fully_packed_loop.py
 @@ -68,7 +68,7 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
@@ -18,7 +18,7 @@ index b3ebd206cd2..48866824224 100644
          sage: _make_color_list(5)
          sage: _make_color_list(5, ['blue', 'red'])
 diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
-index 2a03bb68f67..30b56722e66 100644
+index 308171af3cd..6f66624ef87 100644
 --- a/src/sage/functions/special.py
 +++ b/src/sage/functions/special.py
 @@ -219,7 +219,7 @@ class SphericalHarmonic(BuiltinFunction):
@@ -31,10 +31,10 @@ index 2a03bb68f67..30b56722e66 100644
          (0.3454941494713355-4.231083042742082e-17j)
  
 diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index 7ae8ca4966f..4cba22efdba 100644
+index b3e42a6a6a2..13ffa4d1789 100644
 --- a/src/sage/numerical/optimize.py
 +++ b/src/sage/numerical/optimize.py
-@@ -385,7 +385,7 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
+@@ -381,7 +381,7 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm='default',
          ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
          sage: import numpy
          sage: if int(numpy.version.short_version[0]) > 1:
@@ -44,7 +44,7 @@ index 7ae8ca4966f..4cba22efdba 100644
          sage: def rosen_der(x):
          ....:    xm = x[1r:-1r]
 diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index 23e2517ca56..7375dcd5d1c 100644
+index 02442f90ba4..1fe3f0b051a 100644
 --- a/src/sage/plot/arrow.py
 +++ b/src/sage/plot/arrow.py
 @@ -55,7 +55,7 @@ class CurveArrow(GraphicPrimitive):
@@ -57,10 +57,10 @@ index 23e2517ca56..7375dcd5d1c 100644
              sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
              ....:                options={})
 diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
-index 6be448f1e04..004594b77c4 100644
+index d2f70b44526..2eaacc6879e 100644
 --- a/src/sage/plot/multigraphics.py
 +++ b/src/sage/plot/multigraphics.py
-@@ -786,7 +786,7 @@ class MultiGraphics(WithEqualityById, SageObject):
+@@ -766,7 +766,7 @@ class MultiGraphics(WithEqualityById, SageObject):
              (0.2, 0.3, 0.4, 0.1)
              sage: import numpy  # to ensure numpy 2.0 compatibility
              sage: if int(numpy.version.short_version[0]) > 1:
@@ -68,8 +68,8 @@ index 6be448f1e04..004594b77c4 100644
 +            ....:     _token = numpy.set_printoptions(legacy="1.25")
              sage: ax1.get_position().bounds  # tol 1.0e-13
              (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
- 
-@@ -1300,7 +1300,7 @@ class GraphicsArray(MultiGraphics):
+         """
+@@ -1269,7 +1269,7 @@ class GraphicsArray(MultiGraphics):
              sage: G = graphics_array([g1, g2])
              sage: import numpy  # to ensure numpy 2.0 compatibility
              sage: if int(numpy.version.short_version[0]) > 1:
@@ -79,10 +79,10 @@ index 6be448f1e04..004594b77c4 100644
              (0.025045451349937315,
               0.03415488992713045,
 diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index d2cb11088c7..6d88517cc15 100644
+index b69a05b37bf..25e404bfc7d 100644
 --- a/src/sage/plot/streamline_plot.py
 +++ b/src/sage/plot/streamline_plot.py
-@@ -73,7 +73,7 @@ class StreamlinePlot(GraphicPrimitive):
+@@ -72,7 +72,7 @@ class StreamlinePlot(GraphicPrimitive):
              sage: x, y = var('x y')
              sage: import numpy  # to ensure numpy 2.0 compatibility
              sage: if int(numpy.version.short_version[0]) > 1:
@@ -92,20 +92,20 @@ index d2cb11088c7..6d88517cc15 100644
              sage: d['xmin']
              10.0
 diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index 38c30f7627b..cfb8a5ff5f7 100644
+index 11811b9587f..8ce0f7f2683 100644
 --- a/src/sage/rings/integer.pyx
 +++ b/src/sage/rings/integer.pyx
-@@ -594,7 +594,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
- 
-             sage: import numpy                                                          # needs numpy
-             sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
--            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")                    # needs numpy
-             sage: numpy.int8('12') == 12                                                # needs numpy
+@@ -595,7 +595,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
+             sage: # needs numpy
+             sage: import numpy
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     _token = numpy.set_printoptions(legacy="1.25")
+             sage: numpy.int8('12') == 12
              True
-             sage: 12 == numpy.int8('12')                                                # needs numpy
+             sage: 12 == numpy.int8('12')
 diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
-index 76fbfedab95..57de30c9d18 100644
+index 11953a50ab5..6aafcceed89 100644
 --- a/src/sage/rings/real_mpfi.pyx
 +++ b/src/sage/rings/real_mpfi.pyx
 @@ -232,7 +232,7 @@ TESTS::
@@ -118,7 +118,7 @@ index 76fbfedab95..57de30c9d18 100644
      True
      sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
 diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-index 70ce616f92f..f604c6d3785 100644
+index 40b92ab23eb..3838bcccb8a 100755
 --- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
 +++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
 @@ -78,7 +78,7 @@ cdef class PeriodicRegion:
@@ -130,7 +130,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
              sage: data = np.zeros((4, 4))
              sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
-@@ -298,7 +298,7 @@ cdef class PeriodicRegion:
+@@ -296,7 +296,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -139,7 +139,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
              sage: data = np.zeros((10, 10))
              sage: data[1:4,1:4] = True
-@@ -322,7 +322,7 @@ cdef class PeriodicRegion:
+@@ -320,7 +320,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -148,7 +148,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
              sage: data = np.zeros((4, 4))
              sage: data[1,1] = True
-@@ -377,7 +377,7 @@ cdef class PeriodicRegion:
+@@ -375,7 +375,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -157,7 +157,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
  
              sage: data = np.zeros((20, 20))
-@@ -529,7 +529,7 @@ cdef class PeriodicRegion:
+@@ -528,7 +528,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -167,10 +167,10 @@ index 70ce616f92f..f604c6d3785 100644
              sage: data = np.zeros((4, 4))
              sage: data[1, 1] = True
 diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index 6937f6cb410..fb296e00fb6 100644
+index 47d890cf0ab..ba7f0cdb0f9 100644
 --- a/src/sage/stats/basic_stats.py
 +++ b/src/sage/stats/basic_stats.py
-@@ -228,7 +228,7 @@ def std(v, bias=False):
+@@ -222,7 +222,7 @@ def std(v, bias=False):
          sage: # needs numpy
          sage: import numpy
          sage: if int(numpy.version.short_version[0]) > 1:
@@ -179,7 +179,7 @@ index 6937f6cb410..fb296e00fb6 100644
          sage: x = numpy.array([1,2,3,4,5])
          sage: std(x, bias=False)
          1.5811388300841898
-@@ -307,7 +307,7 @@ def variance(v, bias=False):
+@@ -299,7 +299,7 @@ def variance(v, bias=False):
          0.4897530450000000?
          sage: import numpy                                                              # needs numpy
          sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
@@ -189,7 +189,7 @@ index 6937f6cb410..fb296e00fb6 100644
          sage: variance(x, bias=False)                                                   # needs numpy
          2.5
 diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
-index 955a256e9b4..e5ed6160b79 100644
+index cc15eff82e9..e32e7fd28b3 100644
 --- a/src/sage/structure/coerce.pyx
 +++ b/src/sage/structure/coerce.pyx
 @@ -521,7 +521,7 @@ cdef class CoercionModel:
@@ -202,10 +202,10 @@ index 955a256e9b4..e5ed6160b79 100644
          sage: # needs sage.rings.real_mpfr
          sage: x = polygen(RR)
 diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
-index cd89ad2a256..6fdf6d8ef23 100644
+index 362d01ea297..92bce28b032 100644
 --- a/src/sage/symbolic/function.pyx
 +++ b/src/sage/symbolic/function.pyx
-@@ -965,7 +965,7 @@ cdef class BuiltinFunction(Function):
+@@ -962,7 +962,7 @@ cdef class BuiltinFunction(Function):
  
              sage: import numpy                                                          # needs numpy
              sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
@@ -215,10 +215,10 @@ index cd89ad2a256..6fdf6d8ef23 100644
              sage: sin(numpy.int32(0))                                                   # needs numpy
              0.0
 diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 5b007d9e5fd..4a096d317e7 100644
+index 32afe8d3a62..63734e68f63 100644
 --- a/src/sage/symbolic/ring.pyx
 +++ b/src/sage/symbolic/ring.pyx
-@@ -1163,7 +1163,7 @@ cdef class NumpyToSRMorphism(Morphism):
+@@ -1154,7 +1154,7 @@ cdef class NumpyToSRMorphism(Morphism):
  
          sage: import numpy                                                              # needs numpy
          sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy

From bc0e48c8fc9bb7cdf3555fc36930f4035d7288f3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 8 Sep 2024 09:35:16 -0300
Subject: [PATCH 5/9] nauty: update to 2.8.9.

---
 srcpkgs/nauty/patches/fix-runalltests.patch | 11 +++++++++++
 srcpkgs/nauty/template                      |  7 ++++---
 2 files changed, 15 insertions(+), 3 deletions(-)
 create mode 100644 srcpkgs/nauty/patches/fix-runalltests.patch

diff --git a/srcpkgs/nauty/patches/fix-runalltests.patch b/srcpkgs/nauty/patches/fix-runalltests.patch
new file mode 100644
index 00000000000000..34e1692cf6e6e3
--- /dev/null
+++ b/srcpkgs/nauty/patches/fix-runalltests.patch
@@ -0,0 +1,11 @@
+--- a/runalltests.in	2024-08-26 00:55:55.000000000 -0300
++++ b/runalltests.in	2024-09-08 09:30:04.032719770 -0300
+@@ -121,7 +121,7 @@
+ runonetest "./geng -q -TD6 10 | ./ransubg -qS765 -P9/10 | ./countg --NN,A,G,GG" "" nautestv.ans
+ runonetest "./genrang -q -P3 -S1234 70 1000 | ./countg --G,GG" "" nautestw.ans
+ runonetest "./genrang -q -P4 -z -S1234 70 500 | ./countg --G,GG" "" nautestx.ans
+-runonetest "./geng -q -bT 12 | ./ranlabg -qS7654 -m5 | uniqg -u" "" nautesty.ans
++runonetest "./geng -q -bT 12 | ./ranlabg -qS7654 -m5 | ./uniqg -u" "" nautesty.ans
+ 
+ echo " "
+ 
diff --git a/srcpkgs/nauty/template b/srcpkgs/nauty/template
index 6f85b1d064d4e5..aea4e4a6eb0294 100644
--- a/srcpkgs/nauty/template
+++ b/srcpkgs/nauty/template
@@ -1,18 +1,18 @@
 # Template file for 'nauty'
 pkgname=nauty
-version=2.8.8
+version=2.8.9
 revision=1
 build_style=gnu-configure
 make_install_args="includedir=/usr/include/nauty
  pkgconfigexecdir=/usr/lib/pkgconfig"
-hostmakedepends="automake"
+hostmakedepends="automake libtool"
 short_desc="Compute the automorphism groups of graphs and digraphs"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="Apache-2.0"
 homepage="https://pallini.di.uniroma1.it/"
 changelog="https://pallini.di.uniroma1.it/changes24-28.txt"
 distfiles="https://pallini.di.uniroma1.it/nauty${version//./_}.tar.gz"
-checksum=159d2156810a6bb240410cd61eb641add85088d9f15c888cdaa37b8681f929ce
+checksum=c97ab42bf48796a86a598bce3e9269047ca2b32c14fc23e07208a244fe52c4ee
 
 build_options="native_build"
 
@@ -21,6 +21,7 @@ if [ -z "$build_option_native_build" ]; then
 fi
 
 pre_configure() {
+	aclocal
 	autoreconf -fi
 }
 

From b00ea1ef12baaa52cd7405775a67696c33cc8688 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sat, 7 Sep 2024 14:32:41 -0300
Subject: [PATCH 6/9] sagemath: update to 10.5.beta3.

---
 .../sagemath/patches/36641-sympy_1.13.patch   | 60 -------------------
 .../sagemath/patches/38572-nauty_2.8.9.patch  | 13 ++++
 srcpkgs/sagemath/patches/get_patches          |  4 +-
 srcpkgs/sagemath/template                     |  4 +-
 4 files changed, 17 insertions(+), 64 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/36641-sympy_1.13.patch
 create mode 100644 srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch

diff --git a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
deleted file mode 100644
index 01e859ad023f4d..00000000000000
--- a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
+++ /dev/null
@@ -1,60 +0,0 @@
-diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py
-index 823a0d14a41..de1c8531814 100644
---- a/src/sage/doctest/forker.py
-+++ b/src/sage/doctest/forker.py
-@@ -150,14 +150,15 @@ def init_sage(controller=None):
-         sage: from sympy.printing.pretty.pretty import PrettyPrinter
-         sage: s = sympify('+x^'.join(str(i) for i in range(30)))
-         sage: print(PrettyPrinter(settings={'wrap_line': True}).doprint(s))
--         29    28    27    26    25    24    23    22    21    20    19    18    17
--        x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   +
-+         29    28    27    26    25    24    23    22    21    20    19    18    17    ↪
-+        x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   +  ↪
-         <BLANKLINE>
--         16    15    14    13    12    11    10    9    8    7    6    5    4    3
--        x   + x   + x   + x   + x   + x   + x   + x  + x  + x  + x  + x  + x  + x  + x
-+        ↪  16    15    14    13    12    11    10    9    8    7    6    5    4    3   ↪
-+        ↪ x   + x   + x   + x   + x   + x   + x   + x  + x  + x  + x  + x  + x  + x  + ↪
-         <BLANKLINE>
--        2
--          + x
-+        ↪   2
-+        ↪  x  + x
-+
- 
-     The displayhook sorts dictionary keys to simplify doctesting of
-     dictionary output::
-diff --git a/src/sage/functions/hypergeometric.py b/src/sage/functions/hypergeometric.py
-index ade7836b310..eb5c6665c0d 100644
---- a/src/sage/functions/hypergeometric.py
-+++ b/src/sage/functions/hypergeometric.py
-@@ -124,7 +124,7 @@
-     sage: maxima(hypergeometric([1, 1, 1], [3, 3, 3], x))                               # needs sage.symbolic
-     hypergeometric([1,1,1],[3,3,3],_SAGE_VAR_x)
-     sage: hypergeometric((5, 4), (4, 4), 3)._sympy_()                                   # needs sympy sage.symbolic
--    hyper((5, 4), (4, 4), 3)
-+    hyper((5,), (4,), 3)
-     sage: hypergeometric((5, 4), (4, 4), 3)._mathematica_init_()                        # needs sage.symbolic
-     'HypergeometricPFQ[{5,4},{4,4},3]'
- 
-diff --git a/src/sage/typeset/ascii_art.py b/src/sage/typeset/ascii_art.py
-index 83d92af8959..e470e2bd88d 100644
---- a/src/sage/typeset/ascii_art.py
-+++ b/src/sage/typeset/ascii_art.py
-@@ -44,11 +44,12 @@
-     sage: shell.run_cell('%display ascii_art')
-     sage: shell.run_cell("i = var('i')")                                                # needs sage.symbolic
-     sage: shell.run_cell('sum(factorial(i)*x^i, i, 0, 10)')                             # needs sage.symbolic
--             10           9          8         7        6        5       4      3
--    3628800*x   + 362880*x  + 40320*x  + 5040*x  + 720*x  + 120*x  + 24*x  + 6*x
-+             10           9          8         7        6        5       4      3  >
-+    3628800*x   + 362880*x  + 40320*x  + 5040*x  + 720*x  + 120*x  + 24*x  + 6*x   >
-     <BLANKLINE>
--         2
--    + 2*x  + x + 1
-+    >      2
-+    > + 2*x  + x + 1
-+
-     sage: shell.run_cell('3/(7*x)')                                                     # needs sage.symbolic
-      3
-     ---
diff --git a/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch b/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
new file mode 100644
index 00000000000000..5f75a8bef5556a
--- /dev/null
+++ b/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
@@ -0,0 +1,13 @@
+diff --git a/src/sage/graphs/generators/families.py b/src/sage/graphs/generators/families.py
+index e6e5312b8a8..aa10d15d4d8 100644
+--- a/src/sage/graphs/generators/families.py
++++ b/src/sage/graphs/generators/families.py
+@@ -3710,7 +3710,7 @@ def nauty_gentreeg(options='', debug=False):
+         ...
+         ValueError: wrong format of parameter options
+         sage: list(graphs.nauty_gentreeg("3 -x", debug=True))
+-        ['>E Usage: ...gentreeg [-D#] [-Z#:#] [-ulps] [-q] n [res/mod] ...
++        ['>E Usage: ...gentreeg [-D#] [-Z#:#] [-ulps] [-q] n... [res/mod] ...
+         sage: list(graphs.nauty_gentreeg("3", debug=True))
+         ['>A ...gentreeg ...\n', Graph on 3 vertices]
+     """
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index c182576ea553cd..8f540dad14bfd1 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -1,6 +1,6 @@
 #! /bin/sh
 
-version=10.4
+version=10.5
 
 URL_BASE_PR="https://github.com/sagemath/sage/pull/"
 URL_BASE_COMPARE="https://github.com/sagemath/sage/compare/${version}..."
@@ -27,8 +27,8 @@ get_pr() {
 # run from patches dir
 cd $(dirname "$0")
 
-get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
+get_pr 38572 "nauty 2.8.9"
 
 #get_pr 37645 "fix doctest"
 get_pr 37885 "cython warnings"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index f5e1d8c68cfcbe..709a3ea4262101 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,6 +1,6 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.5.beta2
+version=10.5.beta3
 revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=0fe0c82dd6959951fc07d55737d270290f64947e183a403ca25709e21b751dee
+checksum=cbf3614c1b9be5f0a0756b0a5480c2ebfa663bd87bd66eefd162a755979bcb3d
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From 2ca21e78126fbd03e10e52452136c5bcc22363b4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 22 Sep 2024 08:19:39 -0300
Subject: [PATCH 7/9] sagemath: update to 10.5.beta5.

---
 .../sagemath/patches/38572-nauty_2.8.9.patch  |  13 -
 srcpkgs/sagemath/patches/numpy_2.1a.patch     |  28 ---
 srcpkgs/sagemath/patches/numpy_2.1b.patch     | 229 ------------------
 srcpkgs/sagemath/template                     |   4 +-
 4 files changed, 2 insertions(+), 272 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
 delete mode 100644 srcpkgs/sagemath/patches/numpy_2.1a.patch
 delete mode 100644 srcpkgs/sagemath/patches/numpy_2.1b.patch

diff --git a/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch b/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
deleted file mode 100644
index 5f75a8bef5556a..00000000000000
--- a/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/src/sage/graphs/generators/families.py b/src/sage/graphs/generators/families.py
-index e6e5312b8a8..aa10d15d4d8 100644
---- a/src/sage/graphs/generators/families.py
-+++ b/src/sage/graphs/generators/families.py
-@@ -3710,7 +3710,7 @@ def nauty_gentreeg(options='', debug=False):
-         ...
-         ValueError: wrong format of parameter options
-         sage: list(graphs.nauty_gentreeg("3 -x", debug=True))
--        ['>E Usage: ...gentreeg [-D#] [-Z#:#] [-ulps] [-q] n [res/mod] ...
-+        ['>E Usage: ...gentreeg [-D#] [-Z#:#] [-ulps] [-q] n... [res/mod] ...
-         sage: list(graphs.nauty_gentreeg("3", debug=True))
-         ['>A ...gentreeg ...\n', Graph on 3 vertices]
-     """
diff --git a/srcpkgs/sagemath/patches/numpy_2.1a.patch b/srcpkgs/sagemath/patches/numpy_2.1a.patch
deleted file mode 100644
index 493c75e2f8f8e0..00000000000000
--- a/srcpkgs/sagemath/patches/numpy_2.1a.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-commit d755b32cbed462abf01a1cd782ba57cb92fbf713
-Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
-Date:   Mon Aug 19 23:25:32 2024 -0300
-
-    add copy parameter to numpy (needed for v2.1)
-
-diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
-index 3edb9ead54d..2c76fd1e557 100644
---- a/src/sage/matrix/matrix1.pyx
-+++ b/src/sage/matrix/matrix1.pyx
-@@ -670,7 +670,7 @@ cdef class Matrix(Matrix0):
-             entries = [[sib(v, 2) for v in row] for row in self.rows()]
-             return sib.name('matrix')(self.base_ring(), entries)
- 
--    def numpy(self, dtype=None):
-+    def numpy(self, dtype=None, copy=True):
-         """
-         Return the Numpy matrix associated to this matrix.
- 
-@@ -731,7 +731,7 @@ cdef class Matrix(Matrix0):
-             (3, 4)
-         """
-         import numpy
--        A = numpy.matrix(self.list(), dtype=dtype)
-+        A = numpy.matrix(self.list(), dtype=dtype, copy=copy)
-         return numpy.resize(A,(self.nrows(), self.ncols()))
- 
-     # Define the magic "__array__" function so that numpy.array(m) can convert
diff --git a/srcpkgs/sagemath/patches/numpy_2.1b.patch b/srcpkgs/sagemath/patches/numpy_2.1b.patch
deleted file mode 100644
index 8dc0eec2b5a9d8..00000000000000
--- a/srcpkgs/sagemath/patches/numpy_2.1b.patch
+++ /dev/null
@@ -1,229 +0,0 @@
-commit 8260d18c3cf8e356db3d95fc46f6e68f75b453fd
-Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
-Date:   Tue Aug 20 00:05:33 2024 -0300
-
-    silence np.set_printoptions (for numpy 2.1)
-
-diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index 74a14fa1ecd..82e6c7eb3c8 100644
---- a/src/sage/combinat/fully_packed_loop.py
-+++ b/src/sage/combinat/fully_packed_loop.py
-@@ -68,7 +68,7 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
- 
-         sage: import numpy as np
-         sage: if int(np.version.short_version[0]) > 1:
--        ....:     np.set_printoptions(legacy="1.25")
-+        ....:     _token = np.set_printoptions(legacy="1.25")
-         sage: from sage.combinat.fully_packed_loop import _make_color_list
-         sage: _make_color_list(5)
-         sage: _make_color_list(5, ['blue', 'red'])
-diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
-index 308171af3cd..6f66624ef87 100644
---- a/src/sage/functions/special.py
-+++ b/src/sage/functions/special.py
-@@ -219,7 +219,7 @@ class SphericalHarmonic(BuiltinFunction):
-         sage: from scipy.special import sph_harm  # NB: arguments x and y are swapped   # needs scipy
-         sage: import numpy as np                                                        # needs scipy
-         sage: if int(np.version.short_version[0]) > 1:                                  # needs scipy
--        ....:     np.set_printoptions(legacy="1.25")                                    # needs scipy
-+        ....:     _token = np.set_printoptions(legacy="1.25")                           # needs scipy
-         sage: sph_harm(1, 1, pi.n(), (pi/2).n())  # abs tol 1e-14                       # needs scipy sage.symbolic
-         (0.3454941494713355-4.231083042742082e-17j)
- 
-diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index b3e42a6a6a2..13ffa4d1789 100644
---- a/src/sage/numerical/optimize.py
-+++ b/src/sage/numerical/optimize.py
-@@ -381,7 +381,7 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm='default',
-         ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
-         sage: import numpy
-         sage: if int(numpy.version.short_version[0]) > 1:
--        ....:     numpy.set_printoptions(legacy="1.25")
-+        ....:     _token = numpy.set_printoptions(legacy="1.25")
-         sage: from numpy import zeros
-         sage: def rosen_der(x):
-         ....:    xm = x[1r:-1r]
-diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index 02442f90ba4..1fe3f0b051a 100644
---- a/src/sage/plot/arrow.py
-+++ b/src/sage/plot/arrow.py
-@@ -55,7 +55,7 @@ class CurveArrow(GraphicPrimitive):
- 
-             sage: import numpy  # to ensure numpy 2.0 compatibility
-             sage: if int(numpy.version.short_version[0]) > 1:
--            ....:     numpy.set_printoptions(legacy="1.25")
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")
-             sage: from sage.plot.arrow import CurveArrow
-             sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
-             ....:                options={})
-diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
-index d2f70b44526..2eaacc6879e 100644
---- a/src/sage/plot/multigraphics.py
-+++ b/src/sage/plot/multigraphics.py
-@@ -766,7 +766,7 @@ class MultiGraphics(WithEqualityById, SageObject):
-             (0.2, 0.3, 0.4, 0.1)
-             sage: import numpy  # to ensure numpy 2.0 compatibility
-             sage: if int(numpy.version.short_version[0]) > 1:
--            ....:     numpy.set_printoptions(legacy="1.25")
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")
-             sage: ax1.get_position().bounds  # tol 1.0e-13
-             (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
-         """
-@@ -1269,7 +1269,7 @@ class GraphicsArray(MultiGraphics):
-             sage: G = graphics_array([g1, g2])
-             sage: import numpy  # to ensure numpy 2.0 compatibility
-             sage: if int(numpy.version.short_version[0]) > 1:
--            ....:     numpy.set_printoptions(legacy="1.25")
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")
-             sage: G.position(0)  # tol 5.0e-3
-             (0.025045451349937315,
-              0.03415488992713045,
-diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index b69a05b37bf..25e404bfc7d 100644
---- a/src/sage/plot/streamline_plot.py
-+++ b/src/sage/plot/streamline_plot.py
-@@ -72,7 +72,7 @@ class StreamlinePlot(GraphicPrimitive):
-             sage: x, y = var('x y')
-             sage: import numpy  # to ensure numpy 2.0 compatibility
-             sage: if int(numpy.version.short_version[0]) > 1:
--            ....:     numpy.set_printoptions(legacy="1.25")
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")
-             sage: d = streamline_plot((.01*x, x+y), (x,10,20), (y,10,20))[0].get_minmax_data()
-             sage: d['xmin']
-             10.0
-diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index 11811b9587f..8ce0f7f2683 100644
---- a/src/sage/rings/integer.pyx
-+++ b/src/sage/rings/integer.pyx
-@@ -595,7 +595,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
-             sage: # needs numpy
-             sage: import numpy
-             sage: if int(numpy.version.short_version[0]) > 1:
--            ....:     numpy.set_printoptions(legacy="1.25")
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")
-             sage: numpy.int8('12') == 12
-             True
-             sage: 12 == numpy.int8('12')
-diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
-index 11953a50ab5..6aafcceed89 100644
---- a/src/sage/rings/real_mpfi.pyx
-+++ b/src/sage/rings/real_mpfi.pyx
-@@ -232,7 +232,7 @@ TESTS::
- 
-     sage: import numpy                                                                  # needs numpy
-     sage: if int(numpy.version.short_version[0]) > 1:                                   # needs numpy
--    ....:     numpy.set_printoptions(legacy="1.25")                                     # needs numpy
-+    ....:     _token = numpy.set_printoptions(legacy="1.25")                            # needs numpy
-     sage: RIF(2) == numpy.int8('2')                                                     # needs numpy
-     True
-     sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
-diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-index 40b92ab23eb..3838bcccb8a 100755
---- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-+++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-@@ -78,7 +78,7 @@ cdef class PeriodicRegion:
- 
-             sage: import numpy as np
-             sage: if int(np.version.short_version[0]) > 1:
--            ....:     np.set_printoptions(legacy="1.25")
-+            ....:     _token = np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
-@@ -296,7 +296,7 @@ cdef class PeriodicRegion:
- 
-             sage: import numpy as np
-             sage: if int(np.version.short_version[0]) > 1:
--            ....:     np.set_printoptions(legacy="1.25")
-+            ....:     _token = np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((10, 10))
-             sage: data[1:4,1:4] = True
-@@ -320,7 +320,7 @@ cdef class PeriodicRegion:
- 
-             sage: import numpy as np
-             sage: if int(np.version.short_version[0]) > 1:
--            ....:     np.set_printoptions(legacy="1.25")
-+            ....:     _token = np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1,1] = True
-@@ -375,7 +375,7 @@ cdef class PeriodicRegion:
- 
-             sage: import numpy as np
-             sage: if int(np.version.short_version[0]) > 1:
--            ....:     np.set_printoptions(legacy="1.25")
-+            ....:     _token = np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
- 
-             sage: data = np.zeros((20, 20))
-@@ -528,7 +528,7 @@ cdef class PeriodicRegion:
- 
-             sage: import numpy as np
-             sage: if int(np.version.short_version[0]) > 1:
--            ....:     np.set_printoptions(legacy="1.25")
-+            ....:     _token = np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1, 1] = True
-diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index 47d890cf0ab..ba7f0cdb0f9 100644
---- a/src/sage/stats/basic_stats.py
-+++ b/src/sage/stats/basic_stats.py
-@@ -222,7 +222,7 @@ def std(v, bias=False):
-         sage: # needs numpy
-         sage: import numpy
-         sage: if int(numpy.version.short_version[0]) > 1:
--        ....:     numpy.set_printoptions(legacy="1.25")
-+        ....:     _token = numpy.set_printoptions(legacy="1.25")
-         sage: x = numpy.array([1,2,3,4,5])
-         sage: std(x, bias=False)
-         1.5811388300841898
-@@ -299,7 +299,7 @@ def variance(v, bias=False):
-         0.4897530450000000?
-         sage: import numpy                                                              # needs numpy
-         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
--        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-+        ....:     _token = numpy.set_printoptions(legacy="1.25")                        # needs numpy
-         sage: x = numpy.array([1,2,3,4,5])                                              # needs numpy
-         sage: variance(x, bias=False)                                                   # needs numpy
-         2.5
-diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
-index cc15eff82e9..e32e7fd28b3 100644
---- a/src/sage/structure/coerce.pyx
-+++ b/src/sage/structure/coerce.pyx
-@@ -521,7 +521,7 @@ cdef class CoercionModel:
- 
-         sage: import numpy                                                              # needs numpy
-         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
--        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-+        ....:     _token = numpy.set_printoptions(legacy="1.25")                        # needs numpy
- 
-         sage: # needs sage.rings.real_mpfr
-         sage: x = polygen(RR)
-diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
-index 362d01ea297..92bce28b032 100644
---- a/src/sage/symbolic/function.pyx
-+++ b/src/sage/symbolic/function.pyx
-@@ -962,7 +962,7 @@ cdef class BuiltinFunction(Function):
- 
-             sage: import numpy                                                          # needs numpy
-             sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
--            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")                    # needs numpy
- 
-             sage: sin(numpy.int32(0))                                                   # needs numpy
-             0.0
-diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 32afe8d3a62..63734e68f63 100644
---- a/src/sage/symbolic/ring.pyx
-+++ b/src/sage/symbolic/ring.pyx
-@@ -1154,7 +1154,7 @@ cdef class NumpyToSRMorphism(Morphism):
- 
-         sage: import numpy                                                              # needs numpy
-         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
--        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-+        ....:     _token = numpy.set_printoptions(legacy="1.25")                        # needs numpy
-         sage: f(x) = x^2
-         sage: f(numpy.int8('2'))                                                        # needs numpy
-         4
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index 709a3ea4262101..4face5e8f7ad84 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,6 +1,6 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.5.beta3
+version=10.5.beta5
 revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=cbf3614c1b9be5f0a0756b0a5480c2ebfa663bd87bd66eefd162a755979bcb3d
+checksum=af4e8215043cd5376adea87f37928b94863561e36cba2171dab48ea984f7f259
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From 68be4598fbb9fbf28755943079c18b59c5507759 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 29 Sep 2024 22:24:40 -0300
Subject: [PATCH 8/9] sagemath: update to 10.5.beta6.

---
 srcpkgs/sagemath/patches/get_patches | 2 +-
 srcpkgs/sagemath/template            | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 8f540dad14bfd1..381c307a3e962a 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -28,7 +28,7 @@ get_pr() {
 cd $(dirname "$0")
 
 get_pr 37884 "gap 4.13.1"
-get_pr 38572 "nauty 2.8.9"
+#get_pr 38572 "nauty 2.8.9"
 
 #get_pr 37645 "fix doctest"
 get_pr 37885 "cython warnings"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index 4face5e8f7ad84..fb806ca641d378 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,6 +1,6 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.5.beta5
+version=10.5.beta6
 revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=af4e8215043cd5376adea87f37928b94863561e36cba2171dab48ea984f7f259
+checksum=f95f196142d7abf091185e31d8023091c5746a9e3d2321d906161c65f944fa40
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From 7a6c952594bb82744d992d6f07775fec78804740 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 15 Oct 2024 15:30:11 -0300
Subject: [PATCH 9/9] sagemath: update to 10.5.beta7.

---
 srcpkgs/sagemath/template | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index fb806ca641d378..d19d4ac007f9ba 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,6 +1,6 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.5.beta6
+version=10.5.beta7
 revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=f95f196142d7abf091185e31d8023091c5746a9e3d2321d906161c65f944fa40
+checksum=b98a883aab3b6f551243bc3cffb6825c92f6faf86604e9a9cc8f38cfb9af2f32
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

^ permalink raw reply	[flat|nested] 13+ messages in thread

* Re: [PR PATCH] [Updated] [BETA] sagemath: update to 10.5.beta7
  2024-08-18 17:54 [PR PATCH] [BETA] sagemath: update to 10.5.beta2 tornaria
                   ` (9 preceding siblings ...)
  2024-10-15 19:18 ` [PR PATCH] [Updated] [BETA] sagemath: update to 10.5.beta5 tornaria
@ 2024-10-29  0:41 ` tornaria
  2024-11-18  2:52 ` [PR PATCH] [Updated] [BETA] sagemath: update to 10.5.beta8 tornaria
  11 siblings, 0 replies; 13+ messages in thread
From: tornaria @ 2024-10-29  0:41 UTC (permalink / raw)
  To: ml

[-- Attachment #1: Type: text/plain, Size: 1382 bytes --]

There is an updated pull request by tornaria against master on the void-packages repository

https://github.com/tornaria/void-packages sagemath
https://github.com/void-linux/void-packages/pull/51902

[BETA] sagemath: update to 10.5.beta7
<!-- Uncomment relevant sections and delete options which are not applicable -->

 - python3-Cython: alternative fix for 6122
 - sagemath: enable all cython warnings
 - nauty: update to 2.8.9.

#### Testing the changes
- I tested the changes in this PR: **YES**

@dkwo

<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->

<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration
and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
  - aarch64-musl
  - armv7l
  - armv6l-musl
-->


A patch file from https://github.com/void-linux/void-packages/pull/51902.patch is attached

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-sagemath-51902.patch --]
[-- Type: text/x-diff, Size: 106116 bytes --]

From a872bc6a4cc1dbc4a24fda78b9cac9b9fff1152e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 11 Aug 2024 22:53:42 -0300
Subject: [PATCH 01/11] python3-Cython: alternative fix for 6122

---
 srcpkgs/python3-Cython/patches/fix-regression.patch | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/srcpkgs/python3-Cython/patches/fix-regression.patch b/srcpkgs/python3-Cython/patches/fix-regression.patch
index f2e761608e373b..f5957cfa59c2f5 100644
--- a/srcpkgs/python3-Cython/patches/fix-regression.patch
+++ b/srcpkgs/python3-Cython/patches/fix-regression.patch
@@ -15,3 +15,11 @@ serious regression, e.g. sagemath FTBS with cython 3.0.11
              warning(self.pos,
                      "Implicit noexcept declaration is deprecated."
                      " Function declaration should contain 'noexcept' keyword.",
+@@ -3128,6 +3126,7 @@ class DefNode(FuncDefNode):
+             if scope is None:
+                 scope = cfunc.scope
+             cfunc_type = cfunc.type
++            has_explicit_exc_clause=True
+             if len(self.args) != len(cfunc_type.args) or cfunc_type.has_varargs:
+                 error(self.pos, "wrong number of arguments")
+                 error(cfunc.pos, "previous declaration here")

From be48e3a2ac455db986466ef8be8429d8e68f5e0f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 5 Aug 2024 00:21:23 -0300
Subject: [PATCH 02/11] sagemath: update to 10.5.beta2.

---
 .../sagemath/patches/36641-sympy_1.13.patch   |  22 +-
 .../sagemath/patches/37884-gap_4.13.1.patch   |  28 +-
 .../sagemath/patches/38250-numpy_2.0.patch    | 587 ------------------
 .../sagemath/patches/38344-ecm_7.0.6.patch    |  43 --
 srcpkgs/sagemath/patches/get_patches          |   4 +-
 srcpkgs/sagemath/template                     |   6 +-
 6 files changed, 21 insertions(+), 669 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/38250-numpy_2.0.patch
 delete mode 100644 srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch

diff --git a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
index 625c582cdd41b7..01e859ad023f4d 100644
--- a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
+++ b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
@@ -1,8 +1,5 @@
-diff --git a/build/pkgs/sympy/requirements.txt b/build/pkgs/sympy/requirements.txt
-new file mode 100644
-index 00000000000..3ef8f90b550
 diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py
-index 7e9eab2ff2e..43365cd645e 100644
+index 823a0d14a41..de1c8531814 100644
 --- a/src/sage/doctest/forker.py
 +++ b/src/sage/doctest/forker.py
 @@ -150,14 +150,15 @@ def init_sage(controller=None):
@@ -28,7 +25,7 @@ index 7e9eab2ff2e..43365cd645e 100644
      The displayhook sorts dictionary keys to simplify doctesting of
      dictionary output::
 diff --git a/src/sage/functions/hypergeometric.py b/src/sage/functions/hypergeometric.py
-index 010c61febe0..bbccbd20032 100644
+index ade7836b310..eb5c6665c0d 100644
 --- a/src/sage/functions/hypergeometric.py
 +++ b/src/sage/functions/hypergeometric.py
 @@ -124,7 +124,7 @@
@@ -40,21 +37,8 @@ index 010c61febe0..bbccbd20032 100644
      sage: hypergeometric((5, 4), (4, 4), 3)._mathematica_init_()                        # needs sage.symbolic
      'HypergeometricPFQ[{5,4},{4,4},3]'
  
-diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx
-index a92fe241355..f62311423be 100644
---- a/src/sage/symbolic/expression.pyx
-+++ b/src/sage/symbolic/expression.pyx
-@@ -1167,7 +1167,7 @@ cdef class Expression(Expression_abc):
-             sage: unicode_art(SR(13 - I))
-             13 - ⅈ
-             sage: unicode_art(SR(1.3 - I))
--            1.3 - ⅈ
-+            1.3 - 1.0⋅ⅈ
-             sage: unicode_art(cos(I))
-             cosh(1)
- 
 diff --git a/src/sage/typeset/ascii_art.py b/src/sage/typeset/ascii_art.py
-index 28024405d27..458fa8724a3 100644
+index 83d92af8959..e470e2bd88d 100644
 --- a/src/sage/typeset/ascii_art.py
 +++ b/src/sage/typeset/ascii_art.py
 @@ -44,11 +44,12 @@
diff --git a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
index 1550d47e2436c6..321e0a94487da3 100644
--- a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
+++ b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
@@ -1,21 +1,21 @@
 diff --git a/src/sage/algebras/fusion_rings/fusion_double.py b/src/sage/algebras/fusion_rings/fusion_double.py
-index 7ce086f70d0..954513572c3 100644
+index 71277561331..3b681d75d3b 100644
 --- a/src/sage/algebras/fusion_rings/fusion_double.py
 +++ b/src/sage/algebras/fusion_rings/fusion_double.py
 @@ -133,7 +133,7 @@ class FusionDouble(CombinatorialFreeModule):
          sage: G = SmallPermutationGroup(16,9)
-         sage: F = FusionDouble(G, prefix="b",inject_variables=True)
+         sage: F = FusionDouble(G, prefix='b', inject_variables=True)
          sage: b13^2 # long time (4s)
 -        b0 + b2 + b4 + b15 + b16 + b17 + b18 + b24 + b26 + b27
 +        b0 + b3 + b4
- 
      """
      @staticmethod
+     def __classcall_private__(cls, G, prefix='s', inject_variables=False):
 diff --git a/src/sage/categories/simplicial_sets.py b/src/sage/categories/simplicial_sets.py
-index e714a4571c4..a2b87a729d1 100644
+index aabd3cdbb4f..14bebdcd080 100644
 --- a/src/sage/categories/simplicial_sets.py
 +++ b/src/sage/categories/simplicial_sets.py
-@@ -593,9 +593,9 @@ def _canonical_twisting_operator(self):
+@@ -591,9 +591,9 @@ def _canonical_twisting_operator(self):
                      sage: X = simplicial_sets.Torus()
                      sage: d = X._canonical_twisting_operator()
                      sage: d
@@ -27,7 +27,7 @@ index e714a4571c4..a2b87a729d1 100644
                      sage: Y = simplicial_sets.RealProjectiveSpace(2)
                      sage: d2 = Y._canonical_twisting_operator()
                      sage: d2
-@@ -677,10 +677,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
+@@ -674,10 +674,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
                      sage: X = simplicial_sets.Torus()
                      sage: C = X.twisted_chain_complex()
                      sage: C.differential(1)
@@ -41,7 +41,7 @@ index e714a4571c4..a2b87a729d1 100644
                      [      -1       -1]
                      sage: C.differential(3)
                      []
-@@ -848,29 +848,29 @@ def twisted_homology(self, n, reduced=False):
+@@ -844,29 +844,29 @@ def twisted_homology(self, n, reduced=False):
                      sage: # needs sage.graphs
                      sage: Y = simplicial_sets.Torus()
                      sage: Y.twisted_homology(1)
@@ -80,10 +80,10 @@ index e714a4571c4..a2b87a729d1 100644
                      [1 0 0 0 0]
                      [0 1 0 0 0]
 diff --git a/src/sage/combinat/matrices/latin.py b/src/sage/combinat/matrices/latin.py
-index 936edcc6ea4..c06a53d9afd 100644
+index e2d818e9480..84e6c4fcc9b 100644
 --- a/src/sage/combinat/matrices/latin.py
 +++ b/src/sage/combinat/matrices/latin.py
-@@ -2453,7 +2453,7 @@ def p3_group_bitrade_generators(p):
+@@ -2444,7 +2444,7 @@ def p3_group_bitrade_generators(p):
      EXAMPLES::
  
          sage: from sage.combinat.matrices.latin import *
@@ -93,7 +93,7 @@ index 936edcc6ea4..c06a53d9afd 100644
           (1,2,3)(4,7,8)(5,6,9),
           (1,9,2)(3,7,4)(5,8,6),
 diff --git a/src/sage/groups/cubic_braid.py b/src/sage/groups/cubic_braid.py
-index 257b400f1c7..36423c756aa 100644
+index 61db70925e1..521289c7578 100644
 --- a/src/sage/groups/cubic_braid.py
 +++ b/src/sage/groups/cubic_braid.py
 @@ -282,7 +282,7 @@ def _richcmp_(self, other, op):
@@ -106,7 +106,7 @@ index 257b400f1c7..36423c756aa 100644
               c1*c0^-1*c1, c0^-1*c1^-1*c0^-1, c0^-1*c1^-1, c1^-1*c0*c1^-1,
               c0*c1^-1*c0^-1, c0^-1*c1, c0^-1*c1*c0, c0*c1^-1, c1*c0^-1,
 diff --git a/src/sage/groups/finitely_presented.py b/src/sage/groups/finitely_presented.py
-index 4bb52ee4efb..85f572fac6c 100644
+index 4ac2faa783b..7016d08381b 100644
 --- a/src/sage/groups/finitely_presented.py
 +++ b/src/sage/groups/finitely_presented.py
 @@ -1344,8 +1344,8 @@ def abelianization_map(self):
@@ -161,10 +161,10 @@ index 4bb52ee4efb..85f572fac6c 100644
              sage: G.characteristic_varieties(groebner=True)
              {0: [-1 + F1, 1 + F1, 1 - F1 + F1^2, 1 + F1 + F1^2], 1: [1 - F1 + F1^2],  2: []}
 diff --git a/src/sage/groups/perm_gps/permgroup_named.py b/src/sage/groups/perm_gps/permgroup_named.py
-index c1f2683907b..d219e104a2c 100644
+index 5c153b93d4c..bd4afad2942 100644
 --- a/src/sage/groups/perm_gps/permgroup_named.py
 +++ b/src/sage/groups/perm_gps/permgroup_named.py
-@@ -3468,16 +3468,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
+@@ -3465,16 +3465,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
          sage: G = SmallPermutationGroup(12,4); G
          Group of order 12 and GAP Id 4 as a permutation group
          sage: G.gens()
@@ -186,7 +186,7 @@ index c1f2683907b..d219e104a2c 100644
          sage: def numgps(n): return ZZ(libgap.NumberSmallGroups(n))
          sage: all(SmallPermutationGroup(n,k).id() == [n,k]
          ....:     for n in [1..64] for k in [1..numgps(n)])
-@@ -3486,11 +3484,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
+@@ -3483,11 +3481,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
          sage: H.is_abelian()
          False
          sage: [H.centralizer(g) for g in H.conjugacy_classes_representatives()]
diff --git a/srcpkgs/sagemath/patches/38250-numpy_2.0.patch b/srcpkgs/sagemath/patches/38250-numpy_2.0.patch
deleted file mode 100644
index e28fd857afcb75..00000000000000
--- a/srcpkgs/sagemath/patches/38250-numpy_2.0.patch
+++ /dev/null
@@ -1,587 +0,0 @@
-diff --git a/src/sage/arith/misc.py b/src/sage/arith/misc.py
-index 28f81d7b798..d184c52bf19 100644
---- a/src/sage/arith/misc.py
-+++ b/src/sage/arith/misc.py
-@@ -2277,7 +2277,7 @@ def power_mod(a, n, m):
- 
-         sage: from numpy import int32                                                   # needs numpy
-         sage: power_mod(int32(2), int32(390), int32(391))                               # needs numpy
--        285
-+        ...285...
-         sage: from gmpy2 import mpz
-         sage: power_mod(mpz(2), mpz(390), mpz(391))
-         mpz(285)
-diff --git a/src/sage/calculus/interpolators.pyx b/src/sage/calculus/interpolators.pyx
-index 221b52369e2..bb0be7bab0c 100644
---- a/src/sage/calculus/interpolators.pyx
-+++ b/src/sage/calculus/interpolators.pyx
-@@ -27,6 +27,9 @@ Development supported by NSF award No. 0702939.
- import numpy as np
- cimport numpy as np
- 
-+if int(np.version.short_version[0]) > 1:
-+    np.set_printoptions(legacy="1.25")
-+
- from math import pi
- cdef double TWOPI = 2*pi
- 
-diff --git a/src/sage/calculus/riemann.pyx b/src/sage/calculus/riemann.pyx
-index 6ec80d89aa7..c09d93c4260 100644
---- a/src/sage/calculus/riemann.pyx
-+++ b/src/sage/calculus/riemann.pyx
-@@ -44,6 +44,9 @@ from sage.calculus.integration import numerical_integral
- import numpy as np
- cimport numpy as np
- 
-+if int(np.version.short_version[0]) > 1:
-+    np.set_printoptions(legacy="1.25")
-+
- from math import pi
- from math import sin
- from math import cos
-diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index b198fed0c0d..b3ebd206cd2 100644
---- a/src/sage/combinat/fully_packed_loop.py
-+++ b/src/sage/combinat/fully_packed_loop.py
-@@ -66,6 +66,9 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
-     r"""
-     TESTS::
- 
-+        sage: import numpy as np
-+        sage: if int(np.version.short_version[0]) > 1:
-+        ....:     np.set_printoptions(legacy="1.25")
-         sage: from sage.combinat.fully_packed_loop import _make_color_list
-         sage: _make_color_list(5)
-         sage: _make_color_list(5, ['blue', 'red'])
-diff --git a/src/sage/env.py b/src/sage/env.py
-index 722649ab3da..abb9b19f9e3 100644
---- a/src/sage/env.py
-+++ b/src/sage/env.py
-@@ -296,7 +296,7 @@ def sage_include_directories(use_sources=False):
-         sage: import sage.env
-         sage: sage.env.sage_include_directories()
-         ['...',
--         '.../numpy/core/include',
-+         '.../numpy/...core/include',
-          '.../include/python...']
- 
-     To check that C/C++ files are correctly found, we verify that we can
-diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
-index e100ba3ee23..2a03bb68f67 100644
---- a/src/sage/functions/special.py
-+++ b/src/sage/functions/special.py
-@@ -217,6 +217,9 @@ class SphericalHarmonic(BuiltinFunction):
-         sage: spherical_harmonic(1, 1, pi/2, pi).n()  # abs tol 1e-14                   # needs sage.symbolic
-         0.345494149471335
-         sage: from scipy.special import sph_harm  # NB: arguments x and y are swapped   # needs scipy
-+        sage: import numpy as np                                                        # needs scipy
-+        sage: if int(np.version.short_version[0]) > 1:                                  # needs scipy
-+        ....:     np.set_printoptions(legacy="1.25")                                    # needs scipy
-         sage: sph_harm(1, 1, pi.n(), (pi/2).n())  # abs tol 1e-14                       # needs scipy sage.symbolic
-         (0.3454941494713355-4.231083042742082e-17j)
- 
-diff --git a/src/sage/graphs/generators/classical_geometries.py b/src/sage/graphs/generators/classical_geometries.py
-index da04362eef3..957f88d2061 100644
---- a/src/sage/graphs/generators/classical_geometries.py
-+++ b/src/sage/graphs/generators/classical_geometries.py
-@@ -1315,7 +1315,7 @@ def CossidentePenttilaGraph(q):
- 
-     from sage.libs.gap.libgap import libgap
-     adj_list = libgap.function_factory("""function(q)
--        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x;
-+        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x, sqo;
-         LoadPackage("grape");
-         G0:=SO(3,q^2);
-         so:=GeneratorsOfGroup(G0);
-diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
-index 063931ae274..0bafbd00564 100644
---- a/src/sage/graphs/generic_graph.py
-+++ b/src/sage/graphs/generic_graph.py
-@@ -18420,6 +18420,9 @@ def shortest_path_all_pairs(self, by_weight=False, algorithm=None,
-                 M = self.adjacency_matrix(vertices=int_to_vertex)
- 
-             # We call the Floyd-Warshall method from SciPy
-+            import numpy  # to ensure numpy 2.0 compatibility
-+            if int(numpy.version.short_version[0]) > 1:
-+                numpy.set_printoptions(legacy="1.25")
-             from numpy import array as np_array
-             from scipy.sparse.csgraph import floyd_warshall
-             dd, pp = floyd_warshall(np_array(M), directed=self.is_directed(),
-diff --git a/src/sage/graphs/graph_generators_pyx.pyx b/src/sage/graphs/graph_generators_pyx.pyx
-index 033e8b22adc..04b20d3229b 100644
---- a/src/sage/graphs/graph_generators_pyx.pyx
-+++ b/src/sage/graphs/graph_generators_pyx.pyx
-@@ -57,7 +57,7 @@ def RandomGNP(n, p, bint directed=False, bint loops=False, seed=None):
- 
-         sage: from numpy import mean                                                    # needs numpy
-         sage: abs(mean([RandomGNP(200, .2).density() for i in range(30)]) - .2) < .001  # needs numpy
--        True
-+        ...True...
-         sage: RandomGNP(150, .2, loops=True)
-         Traceback (most recent call last):
-         ...
-diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
-index a810418389c..c38df5412f0 100644
---- a/src/sage/matrix/matrix1.pyx
-+++ b/src/sage/matrix/matrix1.pyx
-@@ -705,12 +705,15 @@ cdef class Matrix(Matrix0):
-         Type ``numpy.typecodes`` for a list of the possible
-         typecodes::
- 
--            sage: import numpy                                                          # needs numpy
--            sage: sorted(numpy.typecodes.items())                                       # needs numpy
-+            sage: import numpy                            # needs numpy
-+            sage: numpy.typecodes.items()                 # needs numpy # random
-             [('All', '?bhilqpBHILQPefdgFDGSUVOMm'), ('AllFloat', 'efdgFDG'),
--             ('AllInteger', 'bBhHiIlLqQpP'), ('Character', 'c'), ('Complex', 'FDG'),
--             ('Datetime', 'Mm'), ('Float', 'efdg'), ('Integer', 'bhilqp'),
--             ('UnsignedInteger', 'BHILQP')]
-+            ...
-+
-+        For instance, you can see possibilities for real floating point numbers::
-+
-+            sage: numpy.typecodes['Float']                # needs numpy
-+            'efdg'
- 
-         Alternatively, numpy automatically calls this function (via
-         the magic :meth:`__array__` method) to convert Sage matrices
-diff --git a/src/sage/modules/free_module_element.pyx b/src/sage/modules/free_module_element.pyx
-index d71d22ac1f7..b6f297a3510 100644
---- a/src/sage/modules/free_module_element.pyx
-+++ b/src/sage/modules/free_module_element.pyx
-@@ -555,7 +555,11 @@ def vector(arg0, arg1=None, arg2=None, sparse=None, immutable=False):
-         R = None
- 
-     try:
-+        import numpy
-         from numpy import ndarray
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-+
-     except ImportError:
-         pass
-     else:
-@@ -1188,7 +1192,11 @@ cdef class FreeModuleElement(Vector):   # abstract base class
-             over Rational Field to numpy array of type <... 'float'>:
-             setting an array element with a sequence.
-         """
-+        import numpy
-         from numpy import array
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-+
-         try:
-             return array(self, dtype=dtype)
-         except ValueError as e:
-diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index e3d94d1746e..7ae8ca4966f 100644
---- a/src/sage/numerical/optimize.py
-+++ b/src/sage/numerical/optimize.py
-@@ -155,6 +155,10 @@ def find_root(f, a, b, xtol=10e-13, rtol=2.0**-50, maxiter=100, full_output=Fals
-         b = max(s_1, s_2)
- 
-     import scipy.optimize
-+    import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     g = lambda x: float(f(x))
-     brentqRes = scipy.optimize.brentq(g, a, b,
-                                  full_output=full_output, xtol=xtol, rtol=rtol, maxiter=maxiter)
-@@ -288,6 +292,10 @@ def find_local_minimum(f, a, b, tol=1.48e-08, maxfun=500):
-     a = float(a)
-     b = float(b)
-     import scipy.optimize
-+    import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     xmin, fval, iter, funcalls = scipy.optimize.fminbound(f, a, b, full_output=1, xtol=tol, maxfun=maxfun)
-     return fval, xmin
- 
-@@ -376,6 +384,8 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
-         sage: def rosen(x):  # The Rosenbrock function
-         ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
-         sage: import numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:
-+        ....:     numpy.set_printoptions(legacy="1.25")
-         sage: from numpy import zeros
-         sage: def rosen_der(x):
-         ....:    xm = x[1r:-1r]
-@@ -393,6 +403,9 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
-     from sage.structure.element import Expression
-     from sage.ext.fast_callable import fast_callable
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     from scipy import optimize
-     if isinstance(func, Expression):
-         var_list = func.variables()
-@@ -530,6 +543,8 @@ def minimize_constrained(func,cons,x0,gradient=None,algorithm='default', **args)
-     from sage.structure.element import Expression
-     from sage.ext.fast_callable import fast_callable
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-     from scipy import optimize
-     function_type = type(lambda x,y: x+y)
- 
-@@ -652,6 +667,8 @@ def find_fit(data, model, initial_guess=None, parameters=None, variables=None, s
-     ``lmdif`` and ``lmder`` algorithms.
-     """
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
- 
-     if not isinstance(data, numpy.ndarray):
-         try:
-diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index ac1dc79d802..23e2517ca56 100644
---- a/src/sage/plot/arrow.py
-+++ b/src/sage/plot/arrow.py
-@@ -53,6 +53,9 @@ def get_minmax_data(self):
- 
-         EXAMPLES::
- 
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: from sage.plot.arrow import CurveArrow
-             sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
-             ....:                options={})
-diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx
-index f1f2671a803..4d71414e1c2 100644
---- a/src/sage/plot/complex_plot.pyx
-+++ b/src/sage/plot/complex_plot.pyx
-@@ -1282,15 +1282,13 @@ def rgb_to_hls(rgb):
-         raise ValueError("Last dimension of input array must be 3; "
-                          "shape {} was found.".format(rgb.shape))
-     in_shape = rgb.shape
--    rgb = np.array(
--        rgb, copy=False, dtype=np.dtype(float), ndmin=2
--    )
-+    rgb = np.asarray(rgb, dtype=np.dtype(float))
-     rgb_max = rgb.max(-1)
-     rgb_min = rgb.min(-1)
-     l = (rgb_max + rgb_min)/2.0  # lightness
- 
-     hls = np.zeros_like(rgb)
--    delta = rgb.ptp(-1)
-+    delta = np.ptp(rgb, -1)
-     s = np.zeros_like(delta)
- 
-     ipos = delta > 0
-diff --git a/src/sage/plot/graphics.py b/src/sage/plot/graphics.py
-index a84d162cb56..94f5db09d83 100644
---- a/src/sage/plot/graphics.py
-+++ b/src/sage/plot/graphics.py
-@@ -2754,7 +2754,7 @@ def matplotlib(self, filename=None,
-             sage: xmin, xmax = sub.get_xlim()
-             sage: ymin, ymax = sub.get_ylim()
-             sage: xmin > xmax, ymin > ymax
--            (True, True)
-+            (...True..., ...True...)
-         """
-         if not isinstance(ticks, (list, tuple)):
-             ticks = (ticks, None)
-diff --git a/src/sage/plot/histogram.py b/src/sage/plot/histogram.py
-index fa86a44bd0a..a585cacf9cd 100644
---- a/src/sage/plot/histogram.py
-+++ b/src/sage/plot/histogram.py
-@@ -92,6 +92,8 @@ def get_minmax_data(self):
-             {'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.476190476190..., 'ymin': 0}
-         """
-         import numpy
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
- 
-         # Extract these options (if they are not None) and pass them to
-         # histogram()
-diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
-index b583be32317..6be448f1e04 100644
---- a/src/sage/plot/multigraphics.py
-+++ b/src/sage/plot/multigraphics.py
-@@ -784,6 +784,9 @@ def _add_subplot(self, figure, index, **options):
-             True
-             sage: G.position(1)
-             (0.2, 0.3, 0.4, 0.1)
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: ax1.get_position().bounds  # tol 1.0e-13
-             (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
- 
-@@ -1295,6 +1298,9 @@ def position(self, index):
-             sage: g1 = plot(sin(x), (x, -pi, pi))
-             sage: g2 = circle((0,1), 1.)
-             sage: G = graphics_array([g1, g2])
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: G.position(0)  # tol 5.0e-3
-             (0.025045451349937315,
-              0.03415488992713045,
-diff --git a/src/sage/plot/plot3d/implicit_surface.pyx b/src/sage/plot/plot3d/implicit_surface.pyx
-index ce0da48a4e0..f4d5059b620 100644
---- a/src/sage/plot/plot3d/implicit_surface.pyx
-+++ b/src/sage/plot/plot3d/implicit_surface.pyx
-@@ -468,6 +468,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
-             sage: cube_marcher.y_vertices.tolist()
-             [[[<1.0, 0.5, 0.0>, None]], [[None, None]]]
-             sage: cube_marcher.x_vertices.any() # This shouldn't affect the X vertices.
-+            ...
-         """
-         (self.y_vertices, self.y_vertices_swapped) = \
-             (self.y_vertices_swapped, self.y_vertices)
-@@ -574,6 +575,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
-             sage: cube_marcher.x_vertices.tolist()
-             [[None, None], [None, <1.5, 1.0, 1.0>]]
-             sage: cube_marcher.y_vertices.any() or cube_marcher.z_vertices.any() # This shouldn't affect the Y or Z vertices.
-+            ...
-         """
-         cdef bint has_prev = (_prev is not None)
-         cdef bint has_next = (_next is not None)
-diff --git a/src/sage/plot/scatter_plot.py b/src/sage/plot/scatter_plot.py
-index 4ad418f040b..781854d372c 100644
---- a/src/sage/plot/scatter_plot.py
-+++ b/src/sage/plot/scatter_plot.py
-@@ -63,9 +63,9 @@ def get_minmax_data(self):
-             sage: s = scatter_plot([[0,1],[2,4],[3.2,6]])
-             sage: d = s.get_minmax_data()
-             sage: d['xmin']
--            0.0
-+            ...0.0...
-             sage: d['ymin']
--            1.0
-+            ...1.0...
-         """
-         return {'xmin': self.xdata.min(),
-                 'xmax': self.xdata.max(),
-diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index 663d3aee70b..d2cb11088c7 100644
---- a/src/sage/plot/streamline_plot.py
-+++ b/src/sage/plot/streamline_plot.py
-@@ -71,6 +71,9 @@ def get_minmax_data(self):
-         EXAMPLES::
- 
-             sage: x, y = var('x y')
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: d = streamline_plot((.01*x, x+y), (x,10,20), (y,10,20))[0].get_minmax_data()
-             sage: d['xmin']
-             10.0
-diff --git a/src/sage/probability/probability_distribution.pyx b/src/sage/probability/probability_distribution.pyx
-index e2c71af9c25..59ba4a95ab6 100644
---- a/src/sage/probability/probability_distribution.pyx
-+++ b/src/sage/probability/probability_distribution.pyx
-@@ -140,6 +140,9 @@ cdef class ProbabilityDistribution:
-              1.8,
-              2.0]
-         """
-+        import numpy as np
-+        if int(np.version.short_version[0]) > 1:
-+            np.set_printoptions(legacy="1.25")
-         import pylab
-         ell = [float(self.get_random_element()) for _ in range(num_samples)]
-         S = pylab.hist(ell, bins, density=True)
-diff --git a/src/sage/rings/complex_double.pyx b/src/sage/rings/complex_double.pyx
-index c59a2b46d6f..b4dddebb4dc 100644
---- a/src/sage/rings/complex_double.pyx
-+++ b/src/sage/rings/complex_double.pyx
-@@ -2558,10 +2558,10 @@ cdef class ComplexToCDF(Morphism):
- 
-         sage: # needs numpy
-         sage: import numpy
--        sage: f = CDF.coerce_map_from(numpy.complex_)
--        sage: f(numpy.complex_(I))
-+        sage: f = CDF.coerce_map_from(numpy.complex128)
-+        sage: f(numpy.complex128(I))
-         1.0*I
--        sage: f(numpy.complex_(I)).parent()
-+        sage: f(numpy.complex128(I)).parent()
-         Complex Double Field
-     """
-     def __init__(self, R):
-@@ -2578,7 +2578,7 @@ cdef class ComplexToCDF(Morphism):
-         EXAMPLES::
- 
-             sage: import numpy                                                          # needs numpy
--            sage: CDF(numpy.complex_(I))    # indirect doctest                          # needs numpy
-+            sage: CDF(numpy.complex128(I))    # indirect doctest                          # needs numpy
-             1.0*I
-         """
-         cdef ComplexDoubleElement z = <ComplexDoubleElement>ComplexDoubleElement.__new__(ComplexDoubleElement)
-@@ -2592,7 +2592,7 @@ cdef class ComplexToCDF(Morphism):
-         EXAMPLES::
- 
-             sage: import numpy                                                          # needs numpy
--            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex_)            # needs numpy
-+            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex128)          # needs numpy
-             sage: f._repr_type()                                                        # needs numpy
-             'Native'
-         """
-diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index b4a1fa5039b..38c30f7627b 100644
---- a/src/sage/rings/integer.pyx
-+++ b/src/sage/rings/integer.pyx
-@@ -593,6 +593,8 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
-         Test comparisons with numpy types (see :issue:`13386` and :issue:`18076`)::
- 
-             sage: import numpy                                                          # needs numpy
-+            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
-+            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-             sage: numpy.int8('12') == 12                                                # needs numpy
-             True
-             sage: 12 == numpy.int8('12')                                                # needs numpy
-diff --git a/src/sage/rings/polynomial/polynomial_element.pyx b/src/sage/rings/polynomial/polynomial_element.pyx
-index dcf2af7cdf2..c87eccd44f1 100644
---- a/src/sage/rings/polynomial/polynomial_element.pyx
-+++ b/src/sage/rings/polynomial/polynomial_element.pyx
-@@ -8851,7 +8851,7 @@ cdef class Polynomial(CommutativePolynomial):
-                          'you expect.')
- 
-                 import numpy
--                from numpy.linalg.linalg import LinAlgError
-+                from numpy.linalg import LinAlgError
-                 from sage.rings.complex_double import CDF
- 
-                 numpy_dtype = ('complex' if input_complex else 'double')
-diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
-index 95b472e912c..76fbfedab95 100644
---- a/src/sage/rings/real_mpfi.pyx
-+++ b/src/sage/rings/real_mpfi.pyx
-@@ -231,6 +231,8 @@ specified if given a non-interval and an interval::
- TESTS::
- 
-     sage: import numpy                                                                  # needs numpy
-+    sage: if int(numpy.version.short_version[0]) > 1:                                   # needs numpy
-+    ....:     numpy.set_printoptions(legacy="1.25")                                     # needs numpy
-     sage: RIF(2) == numpy.int8('2')                                                     # needs numpy
-     True
-     sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
-diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-index 8f240627e77..70ce616f92f 100644
---- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-+++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-@@ -77,6 +77,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
-@@ -295,6 +297,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((10, 10))
-             sage: data[1:4,1:4] = True
-@@ -317,6 +321,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1,1] = True
-@@ -370,6 +376,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
- 
-             sage: data = np.zeros((20, 20))
-@@ -520,6 +528,8 @@ cdef class PeriodicRegion:
-         TESTS::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1, 1] = True
-diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index b2e6b301bf7..6937f6cb410 100644
---- a/src/sage/stats/basic_stats.py
-+++ b/src/sage/stats/basic_stats.py
-@@ -227,6 +227,8 @@ def std(v, bias=False):
- 
-         sage: # needs numpy
-         sage: import numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:
-+        ....:     numpy.set_printoptions(legacy="1.25")
-         sage: x = numpy.array([1,2,3,4,5])
-         sage: std(x, bias=False)
-         1.5811388300841898
-@@ -304,6 +306,8 @@ def variance(v, bias=False):
-         sage: variance([RIF(1.0103, 1.0103), RIF(2)])
-         0.4897530450000000?
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-         sage: x = numpy.array([1,2,3,4,5])                                              # needs numpy
-         sage: variance(x, bias=False)                                                   # needs numpy
-         2.5
-diff --git a/src/sage/stats/time_series.pyx b/src/sage/stats/time_series.pyx
-index 2e22ec45c69..23adae84fb4 100644
---- a/src/sage/stats/time_series.pyx
-+++ b/src/sage/stats/time_series.pyx
-@@ -1718,6 +1718,8 @@ cdef class TimeSeries:
-         if len(v0) == 1:
-             return v1[0]/v0[0]
-         import numpy
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-         coeffs = numpy.polyfit(v0,v1,1)
-         return coeffs[0]
- 
-diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
-index dfbd5ff82fa..955a256e9b4 100644
---- a/src/sage/structure/coerce.pyx
-+++ b/src/sage/structure/coerce.pyx
-@@ -520,6 +520,8 @@ cdef class CoercionModel:
-     Check that :issue:`8426` is fixed (see also :issue:`18076`)::
- 
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
- 
-         sage: # needs sage.rings.real_mpfr
-         sage: x = polygen(RR)
-diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
-index 2cb2f09c715..cd89ad2a256 100644
---- a/src/sage/symbolic/function.pyx
-+++ b/src/sage/symbolic/function.pyx
-@@ -964,6 +964,9 @@ cdef class BuiltinFunction(Function):
-             mpc(real='0.83373002513114902', imag='-0.98889770576286506')
- 
-             sage: import numpy                                                          # needs numpy
-+            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
-+            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-+
-             sage: sin(numpy.int32(0))                                                   # needs numpy
-             0.0
-             sage: type(_)                                                               # needs numpy
-diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 501b0920898..5b007d9e5fd 100644
---- a/src/sage/symbolic/ring.pyx
-+++ b/src/sage/symbolic/ring.pyx
-@@ -1162,6 +1162,8 @@ cdef class NumpyToSRMorphism(Morphism):
-     We check that :issue:`8949` and :issue:`9769` are fixed (see also :issue:`18076`)::
- 
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-         sage: f(x) = x^2
-         sage: f(numpy.int8('2'))                                                        # needs numpy
-         4
diff --git a/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch b/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch
deleted file mode 100644
index db0ae9030623b6..00000000000000
--- a/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-diff --git a/src/sage/interfaces/ecm.py b/src/sage/interfaces/ecm.py
-index 99287dec718..98011970404 100644
---- a/src/sage/interfaces/ecm.py
-+++ b/src/sage/interfaces/ecm.py
-@@ -508,7 +508,6 @@ def _find_factor(self, n, factor_digits, B1, **kwds):
-         """
-         n = self._validate(n)
-         kwds.setdefault('c', 1000000000)
--        kwds.setdefault('I', 1)
-         if factor_digits is not None:
-             B1 = self.recommended_B1(factor_digits)
-         kwds['one'] = True
-diff --git a/src/sage/libs/libecm.pyx b/src/sage/libs/libecm.pyx
-index 886a9b816e4..83fb7adaf8d 100644
---- a/src/sage/libs/libecm.pyx
-+++ b/src/sage/libs/libecm.pyx
-@@ -149,11 +149,13 @@ def ecmfactor(number, double B1, verbose=False, sigma=0):
-     Some special cases::
- 
-         sage: ecmfactor(1, 100)
--        (True, 1, ...)
-+        Traceback (most recent call last):
-+        ...
-+        ValueError: Input number (1) must be greater than 1
-         sage: ecmfactor(0, 100)
-         Traceback (most recent call last):
-         ...
--        ValueError: Input number (0) must be positive
-+        ValueError: Input number (0) must be greater than 1
-     """
-     cdef mpz_t n, f
-     cdef int res
-@@ -164,8 +166,8 @@ def ecmfactor(number, double B1, verbose=False, sigma=0):
-     sage_int_number = Integer(number)
-     sage_int_sigma = Integer(sigma)
- 
--    if number <= 0:
--        raise ValueError("Input number (%s) must be positive"%number)
-+    if number <= 1:
-+        raise ValueError("Input number (%s) must be greater than 1"%number)
- 
-     if verbose:
-         print("Performing one curve with B1=%1.0f" % B1)
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 28162dff8a38e1..5cab228f286365 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -19,7 +19,7 @@ get_pr() {
 	echo "curl -sL \"$url\" | filterdiff ... > \"$pr-$desc.patch\""
 	if [ -z "$dry" ]; then
 		curl -sL "$url" |
-			filterdiff -p1 -x src/setup.py -x build/* -x src/doc/* |
+			filterdiff -p1 -x src/setup.py -x environment* -x src/environment* -x build/* -x src/doc/* |
 			cat > "$pr-$desc.patch"
 	fi
 }
@@ -29,8 +29,6 @@ cd $(dirname "$0")
 
 get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
-get_pr 38250 "numpy 2.0"
-get_pr 38344 "ecm 7.0.6"
 
 #get_pr 37645 "fix doctest"
 #get_pr 37885 "cython warnings"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index b116e62bc67a5a..f5e1d8c68cfcbe 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,7 +1,7 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.4
-revision=3
+version=10.5.beta2
+revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
 build_style=python3-pep517
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=f6579e85f33bd9bb6e9b991bfc4c49dab1e649858ed9ee41c7cec75cb92d4c62
+checksum=0fe0c82dd6959951fc07d55737d270290f64947e183a403ca25709e21b751dee
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From 7d53b5dc0d8be8db96aedf9d34edaba3d540a106 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Wed, 14 Aug 2024 00:12:02 -0300
Subject: [PATCH 03/11] sagemath: enable all cython warnings

---
 srcpkgs/sagemath/patches/37885-cython_warnings.patch | 12 ++++++++++++
 srcpkgs/sagemath/patches/get_patches                 |  2 +-
 2 files changed, 13 insertions(+), 1 deletion(-)
 create mode 100644 srcpkgs/sagemath/patches/37885-cython_warnings.patch

diff --git a/srcpkgs/sagemath/patches/37885-cython_warnings.patch b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
new file mode 100644
index 00000000000000..fa4b648cfc1577
--- /dev/null
+++ b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
@@ -0,0 +1,12 @@
+diff --git a/src/sage_setup/command/sage_build_cython.py b/src/sage_setup/command/sage_build_cython.py
+index f4b1357c543..3435c196d49 100644
+--- a/src/sage_setup/command/sage_build_cython.py
++++ b/src/sage_setup/command/sage_build_cython.py
+@@ -226,6 +226,7 @@ def run(self):
+                 compiler_directives=self.cython_directives,
+                 compile_time_env=self.compile_time_env,
+                 create_extension=self.create_extension,
++                show_all_warnings=True,
+                 # Debugging
+                 gdb_debug=self.debug,
+                 output_dir=os.path.join(self.build_lib, "sage"),
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 5cab228f286365..c182576ea553cd 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -31,4 +31,4 @@ get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
 
 #get_pr 37645 "fix doctest"
-#get_pr 37885 "cython warnings"
+get_pr 37885 "cython warnings"

From 96d94d062bbc96ffc2110bc7057d27235214f579 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 20 Aug 2024 17:56:06 -0300
Subject: [PATCH 04/11] sagemath: patch for numpy 2.1

---
 srcpkgs/sagemath/patches/numpy_2.1a.patch |  8 +--
 srcpkgs/sagemath/patches/numpy_2.1b.patch | 70 +++++++++++------------
 2 files changed, 39 insertions(+), 39 deletions(-)

diff --git a/srcpkgs/sagemath/patches/numpy_2.1a.patch b/srcpkgs/sagemath/patches/numpy_2.1a.patch
index 30e2de99d84536..493c75e2f8f8e0 100644
--- a/srcpkgs/sagemath/patches/numpy_2.1a.patch
+++ b/srcpkgs/sagemath/patches/numpy_2.1a.patch
@@ -1,14 +1,14 @@
-commit 241dc39bd0ba1c056f88bee46a0345d59093eaff
+commit d755b32cbed462abf01a1cd782ba57cb92fbf713
 Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
 Date:   Mon Aug 19 23:25:32 2024 -0300
 
     add copy parameter to numpy (needed for v2.1)
 
 diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
-index c38df5412f0..f587cef651a 100644
+index 3edb9ead54d..2c76fd1e557 100644
 --- a/src/sage/matrix/matrix1.pyx
 +++ b/src/sage/matrix/matrix1.pyx
-@@ -671,7 +671,7 @@ cdef class Matrix(Matrix0):
+@@ -670,7 +670,7 @@ cdef class Matrix(Matrix0):
              entries = [[sib(v, 2) for v in row] for row in self.rows()]
              return sib.name('matrix')(self.base_ring(), entries)
  
@@ -17,7 +17,7 @@ index c38df5412f0..f587cef651a 100644
          """
          Return the Numpy matrix associated to this matrix.
  
-@@ -732,7 +732,7 @@ cdef class Matrix(Matrix0):
+@@ -731,7 +731,7 @@ cdef class Matrix(Matrix0):
              (3, 4)
          """
          import numpy
diff --git a/srcpkgs/sagemath/patches/numpy_2.1b.patch b/srcpkgs/sagemath/patches/numpy_2.1b.patch
index b77e28361d2e74..8dc0eec2b5a9d8 100644
--- a/srcpkgs/sagemath/patches/numpy_2.1b.patch
+++ b/srcpkgs/sagemath/patches/numpy_2.1b.patch
@@ -1,11 +1,11 @@
-commit 8b32fdb87725c1d67ffb51dadec1c331c7c35f3c
+commit 8260d18c3cf8e356db3d95fc46f6e68f75b453fd
 Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
 Date:   Tue Aug 20 00:05:33 2024 -0300
 
     silence np.set_printoptions (for numpy 2.1)
 
 diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index b3ebd206cd2..48866824224 100644
+index 74a14fa1ecd..82e6c7eb3c8 100644
 --- a/src/sage/combinat/fully_packed_loop.py
 +++ b/src/sage/combinat/fully_packed_loop.py
 @@ -68,7 +68,7 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
@@ -18,7 +18,7 @@ index b3ebd206cd2..48866824224 100644
          sage: _make_color_list(5)
          sage: _make_color_list(5, ['blue', 'red'])
 diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
-index 2a03bb68f67..30b56722e66 100644
+index 308171af3cd..6f66624ef87 100644
 --- a/src/sage/functions/special.py
 +++ b/src/sage/functions/special.py
 @@ -219,7 +219,7 @@ class SphericalHarmonic(BuiltinFunction):
@@ -31,10 +31,10 @@ index 2a03bb68f67..30b56722e66 100644
          (0.3454941494713355-4.231083042742082e-17j)
  
 diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index 7ae8ca4966f..4cba22efdba 100644
+index b3e42a6a6a2..13ffa4d1789 100644
 --- a/src/sage/numerical/optimize.py
 +++ b/src/sage/numerical/optimize.py
-@@ -385,7 +385,7 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
+@@ -381,7 +381,7 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm='default',
          ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
          sage: import numpy
          sage: if int(numpy.version.short_version[0]) > 1:
@@ -44,7 +44,7 @@ index 7ae8ca4966f..4cba22efdba 100644
          sage: def rosen_der(x):
          ....:    xm = x[1r:-1r]
 diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index 23e2517ca56..7375dcd5d1c 100644
+index 02442f90ba4..1fe3f0b051a 100644
 --- a/src/sage/plot/arrow.py
 +++ b/src/sage/plot/arrow.py
 @@ -55,7 +55,7 @@ class CurveArrow(GraphicPrimitive):
@@ -57,10 +57,10 @@ index 23e2517ca56..7375dcd5d1c 100644
              sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
              ....:                options={})
 diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
-index 6be448f1e04..004594b77c4 100644
+index d2f70b44526..2eaacc6879e 100644
 --- a/src/sage/plot/multigraphics.py
 +++ b/src/sage/plot/multigraphics.py
-@@ -786,7 +786,7 @@ class MultiGraphics(WithEqualityById, SageObject):
+@@ -766,7 +766,7 @@ class MultiGraphics(WithEqualityById, SageObject):
              (0.2, 0.3, 0.4, 0.1)
              sage: import numpy  # to ensure numpy 2.0 compatibility
              sage: if int(numpy.version.short_version[0]) > 1:
@@ -68,8 +68,8 @@ index 6be448f1e04..004594b77c4 100644
 +            ....:     _token = numpy.set_printoptions(legacy="1.25")
              sage: ax1.get_position().bounds  # tol 1.0e-13
              (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
- 
-@@ -1300,7 +1300,7 @@ class GraphicsArray(MultiGraphics):
+         """
+@@ -1269,7 +1269,7 @@ class GraphicsArray(MultiGraphics):
              sage: G = graphics_array([g1, g2])
              sage: import numpy  # to ensure numpy 2.0 compatibility
              sage: if int(numpy.version.short_version[0]) > 1:
@@ -79,10 +79,10 @@ index 6be448f1e04..004594b77c4 100644
              (0.025045451349937315,
               0.03415488992713045,
 diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index d2cb11088c7..6d88517cc15 100644
+index b69a05b37bf..25e404bfc7d 100644
 --- a/src/sage/plot/streamline_plot.py
 +++ b/src/sage/plot/streamline_plot.py
-@@ -73,7 +73,7 @@ class StreamlinePlot(GraphicPrimitive):
+@@ -72,7 +72,7 @@ class StreamlinePlot(GraphicPrimitive):
              sage: x, y = var('x y')
              sage: import numpy  # to ensure numpy 2.0 compatibility
              sage: if int(numpy.version.short_version[0]) > 1:
@@ -92,20 +92,20 @@ index d2cb11088c7..6d88517cc15 100644
              sage: d['xmin']
              10.0
 diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index 38c30f7627b..cfb8a5ff5f7 100644
+index 11811b9587f..8ce0f7f2683 100644
 --- a/src/sage/rings/integer.pyx
 +++ b/src/sage/rings/integer.pyx
-@@ -594,7 +594,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
- 
-             sage: import numpy                                                          # needs numpy
-             sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
--            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")                    # needs numpy
-             sage: numpy.int8('12') == 12                                                # needs numpy
+@@ -595,7 +595,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
+             sage: # needs numpy
+             sage: import numpy
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     _token = numpy.set_printoptions(legacy="1.25")
+             sage: numpy.int8('12') == 12
              True
-             sage: 12 == numpy.int8('12')                                                # needs numpy
+             sage: 12 == numpy.int8('12')
 diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
-index 76fbfedab95..57de30c9d18 100644
+index 11953a50ab5..6aafcceed89 100644
 --- a/src/sage/rings/real_mpfi.pyx
 +++ b/src/sage/rings/real_mpfi.pyx
 @@ -232,7 +232,7 @@ TESTS::
@@ -118,7 +118,7 @@ index 76fbfedab95..57de30c9d18 100644
      True
      sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
 diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-index 70ce616f92f..f604c6d3785 100644
+index 40b92ab23eb..3838bcccb8a 100755
 --- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
 +++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
 @@ -78,7 +78,7 @@ cdef class PeriodicRegion:
@@ -130,7 +130,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
              sage: data = np.zeros((4, 4))
              sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
-@@ -298,7 +298,7 @@ cdef class PeriodicRegion:
+@@ -296,7 +296,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -139,7 +139,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
              sage: data = np.zeros((10, 10))
              sage: data[1:4,1:4] = True
-@@ -322,7 +322,7 @@ cdef class PeriodicRegion:
+@@ -320,7 +320,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -148,7 +148,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
              sage: data = np.zeros((4, 4))
              sage: data[1,1] = True
-@@ -377,7 +377,7 @@ cdef class PeriodicRegion:
+@@ -375,7 +375,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -157,7 +157,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
  
              sage: data = np.zeros((20, 20))
-@@ -529,7 +529,7 @@ cdef class PeriodicRegion:
+@@ -528,7 +528,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -167,10 +167,10 @@ index 70ce616f92f..f604c6d3785 100644
              sage: data = np.zeros((4, 4))
              sage: data[1, 1] = True
 diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index 6937f6cb410..fb296e00fb6 100644
+index 47d890cf0ab..ba7f0cdb0f9 100644
 --- a/src/sage/stats/basic_stats.py
 +++ b/src/sage/stats/basic_stats.py
-@@ -228,7 +228,7 @@ def std(v, bias=False):
+@@ -222,7 +222,7 @@ def std(v, bias=False):
          sage: # needs numpy
          sage: import numpy
          sage: if int(numpy.version.short_version[0]) > 1:
@@ -179,7 +179,7 @@ index 6937f6cb410..fb296e00fb6 100644
          sage: x = numpy.array([1,2,3,4,5])
          sage: std(x, bias=False)
          1.5811388300841898
-@@ -307,7 +307,7 @@ def variance(v, bias=False):
+@@ -299,7 +299,7 @@ def variance(v, bias=False):
          0.4897530450000000?
          sage: import numpy                                                              # needs numpy
          sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
@@ -189,7 +189,7 @@ index 6937f6cb410..fb296e00fb6 100644
          sage: variance(x, bias=False)                                                   # needs numpy
          2.5
 diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
-index 955a256e9b4..e5ed6160b79 100644
+index cc15eff82e9..e32e7fd28b3 100644
 --- a/src/sage/structure/coerce.pyx
 +++ b/src/sage/structure/coerce.pyx
 @@ -521,7 +521,7 @@ cdef class CoercionModel:
@@ -202,10 +202,10 @@ index 955a256e9b4..e5ed6160b79 100644
          sage: # needs sage.rings.real_mpfr
          sage: x = polygen(RR)
 diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
-index cd89ad2a256..6fdf6d8ef23 100644
+index 362d01ea297..92bce28b032 100644
 --- a/src/sage/symbolic/function.pyx
 +++ b/src/sage/symbolic/function.pyx
-@@ -965,7 +965,7 @@ cdef class BuiltinFunction(Function):
+@@ -962,7 +962,7 @@ cdef class BuiltinFunction(Function):
  
              sage: import numpy                                                          # needs numpy
              sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
@@ -215,10 +215,10 @@ index cd89ad2a256..6fdf6d8ef23 100644
              sage: sin(numpy.int32(0))                                                   # needs numpy
              0.0
 diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 5b007d9e5fd..4a096d317e7 100644
+index 32afe8d3a62..63734e68f63 100644
 --- a/src/sage/symbolic/ring.pyx
 +++ b/src/sage/symbolic/ring.pyx
-@@ -1163,7 +1163,7 @@ cdef class NumpyToSRMorphism(Morphism):
+@@ -1154,7 +1154,7 @@ cdef class NumpyToSRMorphism(Morphism):
  
          sage: import numpy                                                              # needs numpy
          sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy

From 957cb88a6e2398a873a2d900d5faba44f5c8ceaf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 8 Sep 2024 09:35:16 -0300
Subject: [PATCH 05/11] nauty: update to 2.8.9.

---
 srcpkgs/nauty/patches/fix-runalltests.patch | 11 +++++++++++
 srcpkgs/nauty/template                      |  7 ++++---
 2 files changed, 15 insertions(+), 3 deletions(-)
 create mode 100644 srcpkgs/nauty/patches/fix-runalltests.patch

diff --git a/srcpkgs/nauty/patches/fix-runalltests.patch b/srcpkgs/nauty/patches/fix-runalltests.patch
new file mode 100644
index 00000000000000..34e1692cf6e6e3
--- /dev/null
+++ b/srcpkgs/nauty/patches/fix-runalltests.patch
@@ -0,0 +1,11 @@
+--- a/runalltests.in	2024-08-26 00:55:55.000000000 -0300
++++ b/runalltests.in	2024-09-08 09:30:04.032719770 -0300
+@@ -121,7 +121,7 @@
+ runonetest "./geng -q -TD6 10 | ./ransubg -qS765 -P9/10 | ./countg --NN,A,G,GG" "" nautestv.ans
+ runonetest "./genrang -q -P3 -S1234 70 1000 | ./countg --G,GG" "" nautestw.ans
+ runonetest "./genrang -q -P4 -z -S1234 70 500 | ./countg --G,GG" "" nautestx.ans
+-runonetest "./geng -q -bT 12 | ./ranlabg -qS7654 -m5 | uniqg -u" "" nautesty.ans
++runonetest "./geng -q -bT 12 | ./ranlabg -qS7654 -m5 | ./uniqg -u" "" nautesty.ans
+ 
+ echo " "
+ 
diff --git a/srcpkgs/nauty/template b/srcpkgs/nauty/template
index 6f85b1d064d4e5..aea4e4a6eb0294 100644
--- a/srcpkgs/nauty/template
+++ b/srcpkgs/nauty/template
@@ -1,18 +1,18 @@
 # Template file for 'nauty'
 pkgname=nauty
-version=2.8.8
+version=2.8.9
 revision=1
 build_style=gnu-configure
 make_install_args="includedir=/usr/include/nauty
  pkgconfigexecdir=/usr/lib/pkgconfig"
-hostmakedepends="automake"
+hostmakedepends="automake libtool"
 short_desc="Compute the automorphism groups of graphs and digraphs"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="Apache-2.0"
 homepage="https://pallini.di.uniroma1.it/"
 changelog="https://pallini.di.uniroma1.it/changes24-28.txt"
 distfiles="https://pallini.di.uniroma1.it/nauty${version//./_}.tar.gz"
-checksum=159d2156810a6bb240410cd61eb641add85088d9f15c888cdaa37b8681f929ce
+checksum=c97ab42bf48796a86a598bce3e9269047ca2b32c14fc23e07208a244fe52c4ee
 
 build_options="native_build"
 
@@ -21,6 +21,7 @@ if [ -z "$build_option_native_build" ]; then
 fi
 
 pre_configure() {
+	aclocal
 	autoreconf -fi
 }
 

From 1c1032e91f22c617773f3aa8c1ac9135831624c4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sat, 7 Sep 2024 14:32:41 -0300
Subject: [PATCH 06/11] sagemath: update to 10.5.beta3.

---
 .../sagemath/patches/36641-sympy_1.13.patch   | 60 -------------------
 .../sagemath/patches/38572-nauty_2.8.9.patch  | 13 ++++
 srcpkgs/sagemath/patches/get_patches          |  4 +-
 srcpkgs/sagemath/template                     |  4 +-
 4 files changed, 17 insertions(+), 64 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/36641-sympy_1.13.patch
 create mode 100644 srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch

diff --git a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
deleted file mode 100644
index 01e859ad023f4d..00000000000000
--- a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
+++ /dev/null
@@ -1,60 +0,0 @@
-diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py
-index 823a0d14a41..de1c8531814 100644
---- a/src/sage/doctest/forker.py
-+++ b/src/sage/doctest/forker.py
-@@ -150,14 +150,15 @@ def init_sage(controller=None):
-         sage: from sympy.printing.pretty.pretty import PrettyPrinter
-         sage: s = sympify('+x^'.join(str(i) for i in range(30)))
-         sage: print(PrettyPrinter(settings={'wrap_line': True}).doprint(s))
--         29    28    27    26    25    24    23    22    21    20    19    18    17
--        x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   +
-+         29    28    27    26    25    24    23    22    21    20    19    18    17    ↪
-+        x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   +  ↪
-         <BLANKLINE>
--         16    15    14    13    12    11    10    9    8    7    6    5    4    3
--        x   + x   + x   + x   + x   + x   + x   + x  + x  + x  + x  + x  + x  + x  + x
-+        ↪  16    15    14    13    12    11    10    9    8    7    6    5    4    3   ↪
-+        ↪ x   + x   + x   + x   + x   + x   + x   + x  + x  + x  + x  + x  + x  + x  + ↪
-         <BLANKLINE>
--        2
--          + x
-+        ↪   2
-+        ↪  x  + x
-+
- 
-     The displayhook sorts dictionary keys to simplify doctesting of
-     dictionary output::
-diff --git a/src/sage/functions/hypergeometric.py b/src/sage/functions/hypergeometric.py
-index ade7836b310..eb5c6665c0d 100644
---- a/src/sage/functions/hypergeometric.py
-+++ b/src/sage/functions/hypergeometric.py
-@@ -124,7 +124,7 @@
-     sage: maxima(hypergeometric([1, 1, 1], [3, 3, 3], x))                               # needs sage.symbolic
-     hypergeometric([1,1,1],[3,3,3],_SAGE_VAR_x)
-     sage: hypergeometric((5, 4), (4, 4), 3)._sympy_()                                   # needs sympy sage.symbolic
--    hyper((5, 4), (4, 4), 3)
-+    hyper((5,), (4,), 3)
-     sage: hypergeometric((5, 4), (4, 4), 3)._mathematica_init_()                        # needs sage.symbolic
-     'HypergeometricPFQ[{5,4},{4,4},3]'
- 
-diff --git a/src/sage/typeset/ascii_art.py b/src/sage/typeset/ascii_art.py
-index 83d92af8959..e470e2bd88d 100644
---- a/src/sage/typeset/ascii_art.py
-+++ b/src/sage/typeset/ascii_art.py
-@@ -44,11 +44,12 @@
-     sage: shell.run_cell('%display ascii_art')
-     sage: shell.run_cell("i = var('i')")                                                # needs sage.symbolic
-     sage: shell.run_cell('sum(factorial(i)*x^i, i, 0, 10)')                             # needs sage.symbolic
--             10           9          8         7        6        5       4      3
--    3628800*x   + 362880*x  + 40320*x  + 5040*x  + 720*x  + 120*x  + 24*x  + 6*x
-+             10           9          8         7        6        5       4      3  >
-+    3628800*x   + 362880*x  + 40320*x  + 5040*x  + 720*x  + 120*x  + 24*x  + 6*x   >
-     <BLANKLINE>
--         2
--    + 2*x  + x + 1
-+    >      2
-+    > + 2*x  + x + 1
-+
-     sage: shell.run_cell('3/(7*x)')                                                     # needs sage.symbolic
-      3
-     ---
diff --git a/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch b/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
new file mode 100644
index 00000000000000..5f75a8bef5556a
--- /dev/null
+++ b/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
@@ -0,0 +1,13 @@
+diff --git a/src/sage/graphs/generators/families.py b/src/sage/graphs/generators/families.py
+index e6e5312b8a8..aa10d15d4d8 100644
+--- a/src/sage/graphs/generators/families.py
++++ b/src/sage/graphs/generators/families.py
+@@ -3710,7 +3710,7 @@ def nauty_gentreeg(options='', debug=False):
+         ...
+         ValueError: wrong format of parameter options
+         sage: list(graphs.nauty_gentreeg("3 -x", debug=True))
+-        ['>E Usage: ...gentreeg [-D#] [-Z#:#] [-ulps] [-q] n [res/mod] ...
++        ['>E Usage: ...gentreeg [-D#] [-Z#:#] [-ulps] [-q] n... [res/mod] ...
+         sage: list(graphs.nauty_gentreeg("3", debug=True))
+         ['>A ...gentreeg ...\n', Graph on 3 vertices]
+     """
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index c182576ea553cd..8f540dad14bfd1 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -1,6 +1,6 @@
 #! /bin/sh
 
-version=10.4
+version=10.5
 
 URL_BASE_PR="https://github.com/sagemath/sage/pull/"
 URL_BASE_COMPARE="https://github.com/sagemath/sage/compare/${version}..."
@@ -27,8 +27,8 @@ get_pr() {
 # run from patches dir
 cd $(dirname "$0")
 
-get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
+get_pr 38572 "nauty 2.8.9"
 
 #get_pr 37645 "fix doctest"
 get_pr 37885 "cython warnings"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index f5e1d8c68cfcbe..709a3ea4262101 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,6 +1,6 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.5.beta2
+version=10.5.beta3
 revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=0fe0c82dd6959951fc07d55737d270290f64947e183a403ca25709e21b751dee
+checksum=cbf3614c1b9be5f0a0756b0a5480c2ebfa663bd87bd66eefd162a755979bcb3d
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From 91e2bbb98c7707f436c090192396a097909510d6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 22 Sep 2024 08:19:39 -0300
Subject: [PATCH 07/11] sagemath: update to 10.5.beta5.

---
 .../sagemath/patches/38572-nauty_2.8.9.patch  |  13 -
 srcpkgs/sagemath/patches/numpy_2.1a.patch     |  28 ---
 srcpkgs/sagemath/patches/numpy_2.1b.patch     | 229 ------------------
 srcpkgs/sagemath/template                     |   4 +-
 4 files changed, 2 insertions(+), 272 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
 delete mode 100644 srcpkgs/sagemath/patches/numpy_2.1a.patch
 delete mode 100644 srcpkgs/sagemath/patches/numpy_2.1b.patch

diff --git a/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch b/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
deleted file mode 100644
index 5f75a8bef5556a..00000000000000
--- a/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/src/sage/graphs/generators/families.py b/src/sage/graphs/generators/families.py
-index e6e5312b8a8..aa10d15d4d8 100644
---- a/src/sage/graphs/generators/families.py
-+++ b/src/sage/graphs/generators/families.py
-@@ -3710,7 +3710,7 @@ def nauty_gentreeg(options='', debug=False):
-         ...
-         ValueError: wrong format of parameter options
-         sage: list(graphs.nauty_gentreeg("3 -x", debug=True))
--        ['>E Usage: ...gentreeg [-D#] [-Z#:#] [-ulps] [-q] n [res/mod] ...
-+        ['>E Usage: ...gentreeg [-D#] [-Z#:#] [-ulps] [-q] n... [res/mod] ...
-         sage: list(graphs.nauty_gentreeg("3", debug=True))
-         ['>A ...gentreeg ...\n', Graph on 3 vertices]
-     """
diff --git a/srcpkgs/sagemath/patches/numpy_2.1a.patch b/srcpkgs/sagemath/patches/numpy_2.1a.patch
deleted file mode 100644
index 493c75e2f8f8e0..00000000000000
--- a/srcpkgs/sagemath/patches/numpy_2.1a.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-commit d755b32cbed462abf01a1cd782ba57cb92fbf713
-Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
-Date:   Mon Aug 19 23:25:32 2024 -0300
-
-    add copy parameter to numpy (needed for v2.1)
-
-diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
-index 3edb9ead54d..2c76fd1e557 100644
---- a/src/sage/matrix/matrix1.pyx
-+++ b/src/sage/matrix/matrix1.pyx
-@@ -670,7 +670,7 @@ cdef class Matrix(Matrix0):
-             entries = [[sib(v, 2) for v in row] for row in self.rows()]
-             return sib.name('matrix')(self.base_ring(), entries)
- 
--    def numpy(self, dtype=None):
-+    def numpy(self, dtype=None, copy=True):
-         """
-         Return the Numpy matrix associated to this matrix.
- 
-@@ -731,7 +731,7 @@ cdef class Matrix(Matrix0):
-             (3, 4)
-         """
-         import numpy
--        A = numpy.matrix(self.list(), dtype=dtype)
-+        A = numpy.matrix(self.list(), dtype=dtype, copy=copy)
-         return numpy.resize(A,(self.nrows(), self.ncols()))
- 
-     # Define the magic "__array__" function so that numpy.array(m) can convert
diff --git a/srcpkgs/sagemath/patches/numpy_2.1b.patch b/srcpkgs/sagemath/patches/numpy_2.1b.patch
deleted file mode 100644
index 8dc0eec2b5a9d8..00000000000000
--- a/srcpkgs/sagemath/patches/numpy_2.1b.patch
+++ /dev/null
@@ -1,229 +0,0 @@
-commit 8260d18c3cf8e356db3d95fc46f6e68f75b453fd
-Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
-Date:   Tue Aug 20 00:05:33 2024 -0300
-
-    silence np.set_printoptions (for numpy 2.1)
-
-diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index 74a14fa1ecd..82e6c7eb3c8 100644
---- a/src/sage/combinat/fully_packed_loop.py
-+++ b/src/sage/combinat/fully_packed_loop.py
-@@ -68,7 +68,7 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
- 
-         sage: import numpy as np
-         sage: if int(np.version.short_version[0]) > 1:
--        ....:     np.set_printoptions(legacy="1.25")
-+        ....:     _token = np.set_printoptions(legacy="1.25")
-         sage: from sage.combinat.fully_packed_loop import _make_color_list
-         sage: _make_color_list(5)
-         sage: _make_color_list(5, ['blue', 'red'])
-diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
-index 308171af3cd..6f66624ef87 100644
---- a/src/sage/functions/special.py
-+++ b/src/sage/functions/special.py
-@@ -219,7 +219,7 @@ class SphericalHarmonic(BuiltinFunction):
-         sage: from scipy.special import sph_harm  # NB: arguments x and y are swapped   # needs scipy
-         sage: import numpy as np                                                        # needs scipy
-         sage: if int(np.version.short_version[0]) > 1:                                  # needs scipy
--        ....:     np.set_printoptions(legacy="1.25")                                    # needs scipy
-+        ....:     _token = np.set_printoptions(legacy="1.25")                           # needs scipy
-         sage: sph_harm(1, 1, pi.n(), (pi/2).n())  # abs tol 1e-14                       # needs scipy sage.symbolic
-         (0.3454941494713355-4.231083042742082e-17j)
- 
-diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index b3e42a6a6a2..13ffa4d1789 100644
---- a/src/sage/numerical/optimize.py
-+++ b/src/sage/numerical/optimize.py
-@@ -381,7 +381,7 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm='default',
-         ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
-         sage: import numpy
-         sage: if int(numpy.version.short_version[0]) > 1:
--        ....:     numpy.set_printoptions(legacy="1.25")
-+        ....:     _token = numpy.set_printoptions(legacy="1.25")
-         sage: from numpy import zeros
-         sage: def rosen_der(x):
-         ....:    xm = x[1r:-1r]
-diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index 02442f90ba4..1fe3f0b051a 100644
---- a/src/sage/plot/arrow.py
-+++ b/src/sage/plot/arrow.py
-@@ -55,7 +55,7 @@ class CurveArrow(GraphicPrimitive):
- 
-             sage: import numpy  # to ensure numpy 2.0 compatibility
-             sage: if int(numpy.version.short_version[0]) > 1:
--            ....:     numpy.set_printoptions(legacy="1.25")
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")
-             sage: from sage.plot.arrow import CurveArrow
-             sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
-             ....:                options={})
-diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
-index d2f70b44526..2eaacc6879e 100644
---- a/src/sage/plot/multigraphics.py
-+++ b/src/sage/plot/multigraphics.py
-@@ -766,7 +766,7 @@ class MultiGraphics(WithEqualityById, SageObject):
-             (0.2, 0.3, 0.4, 0.1)
-             sage: import numpy  # to ensure numpy 2.0 compatibility
-             sage: if int(numpy.version.short_version[0]) > 1:
--            ....:     numpy.set_printoptions(legacy="1.25")
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")
-             sage: ax1.get_position().bounds  # tol 1.0e-13
-             (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
-         """
-@@ -1269,7 +1269,7 @@ class GraphicsArray(MultiGraphics):
-             sage: G = graphics_array([g1, g2])
-             sage: import numpy  # to ensure numpy 2.0 compatibility
-             sage: if int(numpy.version.short_version[0]) > 1:
--            ....:     numpy.set_printoptions(legacy="1.25")
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")
-             sage: G.position(0)  # tol 5.0e-3
-             (0.025045451349937315,
-              0.03415488992713045,
-diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index b69a05b37bf..25e404bfc7d 100644
---- a/src/sage/plot/streamline_plot.py
-+++ b/src/sage/plot/streamline_plot.py
-@@ -72,7 +72,7 @@ class StreamlinePlot(GraphicPrimitive):
-             sage: x, y = var('x y')
-             sage: import numpy  # to ensure numpy 2.0 compatibility
-             sage: if int(numpy.version.short_version[0]) > 1:
--            ....:     numpy.set_printoptions(legacy="1.25")
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")
-             sage: d = streamline_plot((.01*x, x+y), (x,10,20), (y,10,20))[0].get_minmax_data()
-             sage: d['xmin']
-             10.0
-diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index 11811b9587f..8ce0f7f2683 100644
---- a/src/sage/rings/integer.pyx
-+++ b/src/sage/rings/integer.pyx
-@@ -595,7 +595,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
-             sage: # needs numpy
-             sage: import numpy
-             sage: if int(numpy.version.short_version[0]) > 1:
--            ....:     numpy.set_printoptions(legacy="1.25")
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")
-             sage: numpy.int8('12') == 12
-             True
-             sage: 12 == numpy.int8('12')
-diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
-index 11953a50ab5..6aafcceed89 100644
---- a/src/sage/rings/real_mpfi.pyx
-+++ b/src/sage/rings/real_mpfi.pyx
-@@ -232,7 +232,7 @@ TESTS::
- 
-     sage: import numpy                                                                  # needs numpy
-     sage: if int(numpy.version.short_version[0]) > 1:                                   # needs numpy
--    ....:     numpy.set_printoptions(legacy="1.25")                                     # needs numpy
-+    ....:     _token = numpy.set_printoptions(legacy="1.25")                            # needs numpy
-     sage: RIF(2) == numpy.int8('2')                                                     # needs numpy
-     True
-     sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
-diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-index 40b92ab23eb..3838bcccb8a 100755
---- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-+++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-@@ -78,7 +78,7 @@ cdef class PeriodicRegion:
- 
-             sage: import numpy as np
-             sage: if int(np.version.short_version[0]) > 1:
--            ....:     np.set_printoptions(legacy="1.25")
-+            ....:     _token = np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
-@@ -296,7 +296,7 @@ cdef class PeriodicRegion:
- 
-             sage: import numpy as np
-             sage: if int(np.version.short_version[0]) > 1:
--            ....:     np.set_printoptions(legacy="1.25")
-+            ....:     _token = np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((10, 10))
-             sage: data[1:4,1:4] = True
-@@ -320,7 +320,7 @@ cdef class PeriodicRegion:
- 
-             sage: import numpy as np
-             sage: if int(np.version.short_version[0]) > 1:
--            ....:     np.set_printoptions(legacy="1.25")
-+            ....:     _token = np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1,1] = True
-@@ -375,7 +375,7 @@ cdef class PeriodicRegion:
- 
-             sage: import numpy as np
-             sage: if int(np.version.short_version[0]) > 1:
--            ....:     np.set_printoptions(legacy="1.25")
-+            ....:     _token = np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
- 
-             sage: data = np.zeros((20, 20))
-@@ -528,7 +528,7 @@ cdef class PeriodicRegion:
- 
-             sage: import numpy as np
-             sage: if int(np.version.short_version[0]) > 1:
--            ....:     np.set_printoptions(legacy="1.25")
-+            ....:     _token = np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1, 1] = True
-diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index 47d890cf0ab..ba7f0cdb0f9 100644
---- a/src/sage/stats/basic_stats.py
-+++ b/src/sage/stats/basic_stats.py
-@@ -222,7 +222,7 @@ def std(v, bias=False):
-         sage: # needs numpy
-         sage: import numpy
-         sage: if int(numpy.version.short_version[0]) > 1:
--        ....:     numpy.set_printoptions(legacy="1.25")
-+        ....:     _token = numpy.set_printoptions(legacy="1.25")
-         sage: x = numpy.array([1,2,3,4,5])
-         sage: std(x, bias=False)
-         1.5811388300841898
-@@ -299,7 +299,7 @@ def variance(v, bias=False):
-         0.4897530450000000?
-         sage: import numpy                                                              # needs numpy
-         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
--        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-+        ....:     _token = numpy.set_printoptions(legacy="1.25")                        # needs numpy
-         sage: x = numpy.array([1,2,3,4,5])                                              # needs numpy
-         sage: variance(x, bias=False)                                                   # needs numpy
-         2.5
-diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
-index cc15eff82e9..e32e7fd28b3 100644
---- a/src/sage/structure/coerce.pyx
-+++ b/src/sage/structure/coerce.pyx
-@@ -521,7 +521,7 @@ cdef class CoercionModel:
- 
-         sage: import numpy                                                              # needs numpy
-         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
--        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-+        ....:     _token = numpy.set_printoptions(legacy="1.25")                        # needs numpy
- 
-         sage: # needs sage.rings.real_mpfr
-         sage: x = polygen(RR)
-diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
-index 362d01ea297..92bce28b032 100644
---- a/src/sage/symbolic/function.pyx
-+++ b/src/sage/symbolic/function.pyx
-@@ -962,7 +962,7 @@ cdef class BuiltinFunction(Function):
- 
-             sage: import numpy                                                          # needs numpy
-             sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
--            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")                    # needs numpy
- 
-             sage: sin(numpy.int32(0))                                                   # needs numpy
-             0.0
-diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 32afe8d3a62..63734e68f63 100644
---- a/src/sage/symbolic/ring.pyx
-+++ b/src/sage/symbolic/ring.pyx
-@@ -1154,7 +1154,7 @@ cdef class NumpyToSRMorphism(Morphism):
- 
-         sage: import numpy                                                              # needs numpy
-         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
--        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-+        ....:     _token = numpy.set_printoptions(legacy="1.25")                        # needs numpy
-         sage: f(x) = x^2
-         sage: f(numpy.int8('2'))                                                        # needs numpy
-         4
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index 709a3ea4262101..4face5e8f7ad84 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,6 +1,6 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.5.beta3
+version=10.5.beta5
 revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=cbf3614c1b9be5f0a0756b0a5480c2ebfa663bd87bd66eefd162a755979bcb3d
+checksum=af4e8215043cd5376adea87f37928b94863561e36cba2171dab48ea984f7f259
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From 296ec0fdc151e67a541387e4954be1d4a73a513b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 29 Sep 2024 22:24:40 -0300
Subject: [PATCH 08/11] sagemath: update to 10.5.beta6.

---
 srcpkgs/sagemath/patches/get_patches | 2 +-
 srcpkgs/sagemath/template            | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 8f540dad14bfd1..381c307a3e962a 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -28,7 +28,7 @@ get_pr() {
 cd $(dirname "$0")
 
 get_pr 37884 "gap 4.13.1"
-get_pr 38572 "nauty 2.8.9"
+#get_pr 38572 "nauty 2.8.9"
 
 #get_pr 37645 "fix doctest"
 get_pr 37885 "cython warnings"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index 4face5e8f7ad84..fb806ca641d378 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,6 +1,6 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.5.beta5
+version=10.5.beta6
 revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=af4e8215043cd5376adea87f37928b94863561e36cba2171dab48ea984f7f259
+checksum=f95f196142d7abf091185e31d8023091c5746a9e3d2321d906161c65f944fa40
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From 76f44bc40fb4c8a13545656de73a73337336bef0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 15 Oct 2024 15:30:11 -0300
Subject: [PATCH 09/11] sagemath: update to 10.5.beta7.

---
 srcpkgs/sagemath/template | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index fb806ca641d378..d19d4ac007f9ba 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,6 +1,6 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.5.beta6
+version=10.5.beta7
 revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=f95f196142d7abf091185e31d8023091c5746a9e3d2321d906161c65f944fa40
+checksum=b98a883aab3b6f551243bc3cffb6825c92f6faf86604e9a9cc8f38cfb9af2f32
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From 041826e8f89a9b6c92985182eb6e79b12d19ed81 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sat, 26 Oct 2024 19:06:21 -0300
Subject: [PATCH 10/11] python3-Cython: new alternative fix for 6122, taken
 from 6430

---
 srcpkgs/python3-Cython/patches/fix-regression.patch | 12 +++++++++---
 srcpkgs/python3-Cython/template                     |  2 +-
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/srcpkgs/python3-Cython/patches/fix-regression.patch b/srcpkgs/python3-Cython/patches/fix-regression.patch
index f5957cfa59c2f5..5a29e6a5143ed9 100644
--- a/srcpkgs/python3-Cython/patches/fix-regression.patch
+++ b/srcpkgs/python3-Cython/patches/fix-regression.patch
@@ -1,9 +1,11 @@
 Revert https://github.com/cython/cython/pull/6124 which causes a
 serious regression, e.g. sagemath FTBS with cython 3.0.11
 
+Source: https://github.com/cython/cython/pull/6430
+
 --- a/Cython/Compiler/Nodes.py
 +++ b/Cython/Compiler/Nodes.py
-@@ -710,10 +710,8 @@ class CFuncDeclaratorNode(CDeclaratorNode):
+@@ -717,10 +717,8 @@ def analyse(self, return_type, env, nonempty=0, directive_locals=None, visibilit
                  and not self.has_explicit_exc_clause
                  and self.exception_check
                  and visibility != 'extern'):
@@ -15,11 +17,15 @@ serious regression, e.g. sagemath FTBS with cython 3.0.11
              warning(self.pos,
                      "Implicit noexcept declaration is deprecated."
                      " Function declaration should contain 'noexcept' keyword.",
-@@ -3128,6 +3126,7 @@ class DefNode(FuncDefNode):
+@@ -3128,6 +3126,11 @@ def as_cfunction(self, cfunc=None, scope=None, overridable=True, returns=None, e
              if scope is None:
                  scope = cfunc.scope
              cfunc_type = cfunc.type
-+            has_explicit_exc_clause=True
++            if cfunc_type.exception_check:
++                # this ensures `legacy_implicit_noexcept` does not trigger
++                # as it would result in a mismatch
++                # (declaration with except, definition with implicit noexcept)
++                has_explicit_exc_clause = True
              if len(self.args) != len(cfunc_type.args) or cfunc_type.has_varargs:
                  error(self.pos, "wrong number of arguments")
                  error(cfunc.pos, "previous declaration here")
diff --git a/srcpkgs/python3-Cython/template b/srcpkgs/python3-Cython/template
index faec5722ae171a..a01702f0747d10 100644
--- a/srcpkgs/python3-Cython/template
+++ b/srcpkgs/python3-Cython/template
@@ -1,7 +1,7 @@
 # Template file for 'python3-Cython'
 pkgname=python3-Cython
 version=3.0.11
-revision=2
+revision=3
 build_style=python3-module
 hostmakedepends="python3-setuptools"
 makedepends="python3-devel"

From 06c01ba6cef7e3216a6d041a12a6af349b63c008 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sat, 26 Oct 2024 18:59:52 -0300
Subject: [PATCH 11/11] sagemath: update to 10.5.beta8.

---
 .../sagemath/patches/37884-gap_4.13.1.patch   | 203 ------------------
 .../sagemath/patches/38873-fix_doctest.patch  |  25 +++
 srcpkgs/sagemath/patches/get_patches          |   3 +-
 srcpkgs/sagemath/patches/revert-38826.patch   |  26 +++
 srcpkgs/sagemath/template                     |   4 +-
 5 files changed, 55 insertions(+), 206 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
 create mode 100644 srcpkgs/sagemath/patches/38873-fix_doctest.patch
 create mode 100644 srcpkgs/sagemath/patches/revert-38826.patch

diff --git a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
deleted file mode 100644
index 321e0a94487da3..00000000000000
--- a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
+++ /dev/null
@@ -1,203 +0,0 @@
-diff --git a/src/sage/algebras/fusion_rings/fusion_double.py b/src/sage/algebras/fusion_rings/fusion_double.py
-index 71277561331..3b681d75d3b 100644
---- a/src/sage/algebras/fusion_rings/fusion_double.py
-+++ b/src/sage/algebras/fusion_rings/fusion_double.py
-@@ -133,7 +133,7 @@ class FusionDouble(CombinatorialFreeModule):
-         sage: G = SmallPermutationGroup(16,9)
-         sage: F = FusionDouble(G, prefix='b', inject_variables=True)
-         sage: b13^2 # long time (4s)
--        b0 + b2 + b4 + b15 + b16 + b17 + b18 + b24 + b26 + b27
-+        b0 + b3 + b4
-     """
-     @staticmethod
-     def __classcall_private__(cls, G, prefix='s', inject_variables=False):
-diff --git a/src/sage/categories/simplicial_sets.py b/src/sage/categories/simplicial_sets.py
-index aabd3cdbb4f..14bebdcd080 100644
---- a/src/sage/categories/simplicial_sets.py
-+++ b/src/sage/categories/simplicial_sets.py
-@@ -591,9 +591,9 @@ def _canonical_twisting_operator(self):
-                     sage: X = simplicial_sets.Torus()
-                     sage: d = X._canonical_twisting_operator()
-                     sage: d
--                    {(s_0 v_0, sigma_1): f3, (sigma_1, s_0 v_0): f2*f3^-1, (sigma_1, sigma_1): f2}
-+                    {(s_0 v_0, sigma_1): f2, (sigma_1, s_0 v_0): f1*f2^-1, (sigma_1, sigma_1): f1}
-                     sage: list(d.values())[0].parent()
--                    Multivariate Laurent Polynomial Ring in f2, f3 over Integer Ring
-+                    Multivariate Laurent Polynomial Ring in f1, f2 over Integer Ring
-                     sage: Y = simplicial_sets.RealProjectiveSpace(2)
-                     sage: d2 = Y._canonical_twisting_operator()
-                     sage: d2
-@@ -674,10 +674,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
-                     sage: X = simplicial_sets.Torus()
-                     sage: C = X.twisted_chain_complex()
-                     sage: C.differential(1)
--                    [      f3 - 1 f2*f3^-1 - 1       f2 - 1]
-+                    [      f2 - 1 f1*f2^-1 - 1       f1 - 1]
-                     sage: C.differential(2)
--                    [       1 f2*f3^-1]
--                    [      f3        1]
-+                    [       1 f1*f2^-1]
-+                    [      f2        1]
-                     [      -1       -1]
-                     sage: C.differential(3)
-                     []
-@@ -844,29 +844,29 @@ def twisted_homology(self, n, reduced=False):
-                     sage: # needs sage.graphs
-                     sage: Y = simplicial_sets.Torus()
-                     sage: Y.twisted_homology(1)
--                    Quotient module by Submodule of Ambient free module of rank 5 over the integral domain Multivariate Polynomial Ring in f2, f2inv, f3, f3inv over Integer Ring
-+                    Quotient module by Submodule of Ambient free module of rank 5 over the integral domain Multivariate Polynomial Ring in f1, f1inv, f2, f2inv over Integer Ring
-                     Generated by the rows of the matrix:
-                     [           1            0            0            0            0]
-                     [           0            1            0            0            0]
-                     [           0            0            1            0            0]
-                     [           0            0            0            1            0]
-                     [           0            0            0            0            1]
-+                    [f1*f1inv - 1            0            0            0            0]
-+                    [           0 f1*f1inv - 1            0            0            0]
-+                    [           0            0 f1*f1inv - 1            0            0]
-+                    [           0            0            0 f1*f1inv - 1            0]
-+                    [           0            0            0            0 f1*f1inv - 1]
-                     [f2*f2inv - 1            0            0            0            0]
-                     [           0 f2*f2inv - 1            0            0            0]
-                     [           0            0 f2*f2inv - 1            0            0]
-                     [           0            0            0 f2*f2inv - 1            0]
-                     [           0            0            0            0 f2*f2inv - 1]
--                    [f3*f3inv - 1            0            0            0            0]
--                    [           0 f3*f3inv - 1            0            0            0]
--                    [           0            0 f3*f3inv - 1            0            0]
--                    [           0            0            0 f3*f3inv - 1            0]
--                    [           0            0            0            0 f3*f3inv - 1]
-                     sage: Y.twisted_homology(2)
--                    Quotient module by Submodule of Ambient free module of rank 0 over the integral domain Multivariate Polynomial Ring in f2, f2inv, f3, f3inv over Integer Ring
-+                    Quotient module by Submodule of Ambient free module of rank 0 over the integral domain Multivariate Polynomial Ring in f1, f1inv, f2, f2inv over Integer Ring
-                     Generated by the rows of the matrix:
-                     []
-                     sage: Y.twisted_homology(1, reduced=True)
--                    Quotient module by Submodule of Ambient free module of rank 5 over the integral domain Multivariate Polynomial Ring in f2, f2inv, f3, f3inv over Integer Ring
-+                    Quotient module by Submodule of Ambient free module of rank 5 over the integral domain Multivariate Polynomial Ring in f1, f1inv, f2, f2inv over Integer Ring
-                     Generated by the rows of the matrix:
-                     [1 0 0 0 0]
-                     [0 1 0 0 0]
-diff --git a/src/sage/combinat/matrices/latin.py b/src/sage/combinat/matrices/latin.py
-index e2d818e9480..84e6c4fcc9b 100644
---- a/src/sage/combinat/matrices/latin.py
-+++ b/src/sage/combinat/matrices/latin.py
-@@ -2444,7 +2444,7 @@ def p3_group_bitrade_generators(p):
-     EXAMPLES::
- 
-         sage: from sage.combinat.matrices.latin import *
--        sage: p3_group_bitrade_generators(3)
-+        sage: p3_group_bitrade_generators(3)  # random output
-         ((2,6,7)(3,8,9),
-          (1,2,3)(4,7,8)(5,6,9),
-          (1,9,2)(3,7,4)(5,8,6),
-diff --git a/src/sage/groups/cubic_braid.py b/src/sage/groups/cubic_braid.py
-index 61db70925e1..521289c7578 100644
---- a/src/sage/groups/cubic_braid.py
-+++ b/src/sage/groups/cubic_braid.py
-@@ -282,7 +282,7 @@ def _richcmp_(self, other, op):
-         EXAMPLES::
- 
-             sage: CBG3 = CubicBraidGroup(3)
--            sage: sorted(CBG3)    # indirect doctest
-+            sage: sorted(CBG3)    # indirect doctest, random output
-             [(c0*c1^-1)^2, c0*c1^-1*c0, c0^-1*c1*c0^-1, c0^-1*c1^-1*c0,
-              c1*c0^-1*c1, c0^-1*c1^-1*c0^-1, c0^-1*c1^-1, c1^-1*c0*c1^-1,
-              c0*c1^-1*c0^-1, c0^-1*c1, c0^-1*c1*c0, c0*c1^-1, c1*c0^-1,
-diff --git a/src/sage/groups/finitely_presented.py b/src/sage/groups/finitely_presented.py
-index 4ac2faa783b..7016d08381b 100644
---- a/src/sage/groups/finitely_presented.py
-+++ b/src/sage/groups/finitely_presented.py
-@@ -1344,8 +1344,8 @@ def abelianization_map(self):
-             sage: H = G.quotient([g1^2, g2*g1*g2^(-1)*g1^(-1), g1*g3^(-2), g0^4])
-             sage: H.abelianization_map()
-             Group morphism:
--                From: Finitely presented group  < g0, g1, g2, g3 | g1^2, g2*g1*g2^-1*g1^-1, g1*g3^-2, g0^4 >
--                To:   Finitely presented group  < f2, f3, f4 | f2^-1*f3^-1*f2*f3, f2^-1*f4^-1*f2*f4, f3^-1*f4^-1*f3*f4, f2^4, f3^4 >
-+              From: Finitely presented group < g0, g1, g2, g3 | g1^2, g2*g1*g2^-1*g1^-1, g1*g3^-2, g0^4 >
-+              To:   Finitely presented group < f1, f2, f3 | f1^4, f2^-1*f1^-1*f2*f1, f2^4, f3^-1*f1^-1*f3*f1, f3^-1*f2^-1*f3*f2 >
-             sage: g = FreeGroup(0) / []
-             sage: g.abelianization_map()
-             Group endomorphism of Finitely presented group  <  |  >
-@@ -1394,10 +1394,10 @@ def abelianization_to_algebra(self, ring=QQ):
-             Defining g0, g1, g2, g3
-             sage: H = G.quotient([g1^2, g2*g1*g2^(-1)*g1^(-1), g1*g3^(-2), g0^4])
-             sage: H.abelianization_to_algebra()
--            (Finitely presented group  < f2, f3, f4 | f2^-1*f3^-1*f2*f3, f2^-1*f4^-1*f2*f4,
--                                                      f3^-1*f4^-1*f3*f4, f2^4, f3^4 >,
--             Multivariate Laurent Polynomial Ring in f2, f3, f4 over Rational Field,
--             [f2^4 - 1, f3^4 - 1], [f2^-1*f3^-2, f3^-2, f4, f3])
-+            (Finitely presented group < f1, f2, f3 | f1^4, f2^-1*f1^-1*f2*f1, f2^4, f3^-1*f1^-1*f3*f1, f3^-1*f2^-1*f3*f2 >,
-+             Multivariate Laurent Polynomial Ring in f1, f2, f3 over Rational Field,
-+             [f1^4 - 1, f2^4 - 1],
-+             [f1^3*f2^2, f2^2, f3, f2])
-             sage: g=FreeGroup(0) / []
-             sage: g.abelianization_to_algebra()
-             (Finitely presented group  <  |  >, Rational Field, [], [])
-@@ -1673,7 +1673,7 @@ def abelian_alexander_matrix(self, ring=QQ, simplified=True):
-             []
-             sage: G = FreeGroup(3)/[(2, 1, 1), (1, 2, 2, 3, 3)]
-             sage: A, ideal = G.abelian_alexander_matrix(simplified=True); A
--            [-f3^2 - f3^4 - f3^6         f3^3 + f3^6]
-+            [-f1^2 - f1^4 - f1^6         f1^3 + f1^6]
-             sage: g = FreeGroup(1) / []
-             sage: g.abelian_alexander_matrix()
-             ([], [])
-@@ -1773,11 +1773,11 @@ def characteristic_varieties(self, ring=QQ, matrix_ideal=None, groebner=False):
-              3: Ideal (1) of Multivariate Laurent Polynomial Ring in f1, f2 over Integer Ring}
-             sage: G = FreeGroup(2)/[(1,2,1,-2,-1,-2)]
-             sage: G.characteristic_varieties()
--            {0: Ideal (0) of Univariate Laurent Polynomial Ring in f2 over Rational Field,
--             1: Ideal (-1 + 2*f2 - 2*f2^2 + f2^3) of Univariate Laurent Polynomial Ring in f2 over Rational Field,
--             2: Ideal (1) of Univariate Laurent Polynomial Ring in f2 over Rational Field}
-+            {0: Ideal (0) of Univariate Laurent Polynomial Ring in f1 over Rational Field,
-+             1: Ideal (-1 + 2*f1 - 2*f1^2 + f1^3) of Univariate Laurent Polynomial Ring in f1 over Rational Field,
-+             2: Ideal (1) of Univariate Laurent Polynomial Ring in f1 over Rational Field}
-             sage: G.characteristic_varieties(groebner=True)
--            {0: [0], 1: [-1 + f2, 1 - f2 + f2^2], 2: []}
-+            {0: [0], 1: [-1 + f1, 1 - f1 + f1^2], 2: []}
-             sage: G = FreeGroup(2)/[3 * (1, ), 2 * (2, )]
-             sage: G.characteristic_varieties(groebner=True)
-             {0: [-1 + F1, 1 + F1, 1 - F1 + F1^2, 1 + F1 + F1^2], 1: [1 - F1 + F1^2],  2: []}
-diff --git a/src/sage/groups/perm_gps/permgroup_named.py b/src/sage/groups/perm_gps/permgroup_named.py
-index 5c153b93d4c..bd4afad2942 100644
---- a/src/sage/groups/perm_gps/permgroup_named.py
-+++ b/src/sage/groups/perm_gps/permgroup_named.py
-@@ -3465,16 +3465,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
-         sage: G = SmallPermutationGroup(12,4); G
-         Group of order 12 and GAP Id 4 as a permutation group
-         sage: G.gens()
--        ((1,2)(3,5)(4,10)(6,8)(7,12)(9,11),
--         (1,3)(2,5)(4,7)(6,9)(8,11)(10,12),
--         (1,4,8)(2,6,10)(3,7,11)(5,9,12))
-+        ((4,5), (1,2), (3,4,5))
-         sage: G.character_table()                                                       # needs sage.rings.number_field
-         [ 1  1  1  1  1  1]
--        [ 1 -1 -1  1  1 -1]
-+        [ 1 -1  1 -1  1 -1]
-         [ 1 -1  1  1 -1  1]
--        [ 1  1 -1  1 -1 -1]
--        [ 2  0 -2 -1  0  1]
--        [ 2  0  2 -1  0 -1]
-+        [ 1  1  1 -1 -1 -1]
-+        [ 2  0 -1 -2  0  1]
-+        [ 2  0 -1  2  0 -1]
-         sage: def numgps(n): return ZZ(libgap.NumberSmallGroups(n))
-         sage: all(SmallPermutationGroup(n,k).id() == [n,k]
-         ....:     for n in [1..64] for k in [1..numgps(n)])
-@@ -3483,11 +3481,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
-         sage: H.is_abelian()
-         False
-         sage: [H.centralizer(g) for g in H.conjugacy_classes_representatives()]
--        [Subgroup generated by [(1,2)(3,6)(4,5), (1,3,5)(2,4,6)] of
-+        [Subgroup generated by [(1,3), (2,3)] of
-           (Group of order 6 and GAP Id 1 as a permutation group),
--         Subgroup generated by [(1,2)(3,6)(4,5)] of
-+         Subgroup generated by [(2,3)] of
-           (Group of order 6 and GAP Id 1 as a permutation group),
--         Subgroup generated by [(1,3,5)(2,4,6), (1,5,3)(2,6,4)] of
-+         Subgroup generated by [(1,2,3)] of
-           (Group of order 6 and GAP Id 1 as a permutation group)]
-     """
- 
diff --git a/srcpkgs/sagemath/patches/38873-fix_doctest.patch b/srcpkgs/sagemath/patches/38873-fix_doctest.patch
new file mode 100644
index 00000000000000..f42a8a570ca0cb
--- /dev/null
+++ b/srcpkgs/sagemath/patches/38873-fix_doctest.patch
@@ -0,0 +1,25 @@
+diff --git a/src/sage/parallel/map_reduce.py b/src/sage/parallel/map_reduce.py
+index 303f7405416..a182a136a2f 100644
+--- a/src/sage/parallel/map_reduce.py
++++ b/src/sage/parallel/map_reduce.py
+@@ -1133,18 +1133,16 @@ def start_workers(self):
+ 
+         TESTS::
+ 
++            sage: # long time
+             sage: from sage.parallel.map_reduce import RESetMapReduce
+             sage: def children(x):
+             ....:     print(f"Starting: {x}", flush=True)
+             ....:     return []
+             sage: S = RESetMapReduce(roots=[1, 2], children=children)
+             sage: S.setup_workers(2)
+-            sage: S.start_workers(); sleep(float(5))  # long time
++            sage: S.start_workers(); sleep(float(5))
+             Starting: ...
+             Starting: ...
+-
+-        Cleanup::
+-
+             sage: S.finish()
+         """
+         if self._nprocess == 0:
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 381c307a3e962a..39fb67ef79aa7d 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -27,8 +27,9 @@ get_pr() {
 # run from patches dir
 cd $(dirname "$0")
 
-get_pr 37884 "gap 4.13.1"
+#get_pr 37884 "gap 4.13.1"
 #get_pr 38572 "nauty 2.8.9"
 
 #get_pr 37645 "fix doctest"
 get_pr 37885 "cython warnings"
+get_pr 38873 "fix doctest"
diff --git a/srcpkgs/sagemath/patches/revert-38826.patch b/srcpkgs/sagemath/patches/revert-38826.patch
new file mode 100644
index 00000000000000..6a97d896db44f7
--- /dev/null
+++ b/srcpkgs/sagemath/patches/revert-38826.patch
@@ -0,0 +1,26 @@
+Revert "src/sage/env.py: canonicalize paths in a test"
+
+This reverts commit 53a6d3133ea7782c7498ea6ab6bd3041815bd6a6.
+
+See: https://github.com/sagemath/sage/pull/38826#issuecomment-2439757935
+
+--- a/src/sage/env.py
++++ b/src/sage/env.py
+@@ -8,14 +8,10 @@ environment variables, and has the same ``SAGE_ROOT`` and ``SAGE_LOCAL``
+ 
+     sage: env = {k:v for (k,v) in os.environ.items() if not k.startswith("SAGE_")}
+     sage: from subprocess import check_output
+-    sage: module_name = "sage.all"   # hide .all import from the linter
+-    sage: cmd  = f"from {module_name} import SAGE_ROOT, SAGE_LOCAL;"
+-    sage: cmd +=  "from os.path import samefile;"
+-    sage: cmd += f"s1 = samefile(SAGE_ROOT, '{SAGE_ROOT}');"
+-    sage: cmd += f"s2 = samefile(SAGE_LOCAL, '{SAGE_LOCAL}');"
+-    sage: cmd += "print(s1 and s2);"
++    sage: environment = "sage.all"
++    sage: cmd = f"from {environment} import SAGE_ROOT, SAGE_LOCAL; print((SAGE_ROOT, SAGE_LOCAL))"
+     sage: out = check_output([sys.executable, "-c", cmd], env=env).decode().strip()   # long time
+-    sage: out == "True"                                                               # long time
++    sage: out == repr((SAGE_ROOT, SAGE_LOCAL))                                        # long time
+     True
+ 
+ AUTHORS:
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index d19d4ac007f9ba..0fa1fb968249f6 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,6 +1,6 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.5.beta7
+version=10.5.beta8
 revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=b98a883aab3b6f551243bc3cffb6825c92f6faf86604e9a9cc8f38cfb9af2f32
+checksum=0c386e88524a91ad97db4f3f8ee7408d8678072596b3ab5e9ffaea2cb6be13fd
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

^ permalink raw reply	[flat|nested] 13+ messages in thread

* Re: [PR PATCH] [Updated] [BETA] sagemath: update to 10.5.beta8
  2024-08-18 17:54 [PR PATCH] [BETA] sagemath: update to 10.5.beta2 tornaria
                   ` (10 preceding siblings ...)
  2024-10-29  0:41 ` [PR PATCH] [Updated] [BETA] sagemath: update to 10.5.beta7 tornaria
@ 2024-11-18  2:52 ` tornaria
  11 siblings, 0 replies; 13+ messages in thread
From: tornaria @ 2024-11-18  2:52 UTC (permalink / raw)
  To: ml

[-- Attachment #1: Type: text/plain, Size: 1382 bytes --]

There is an updated pull request by tornaria against master on the void-packages repository

https://github.com/tornaria/void-packages sagemath
https://github.com/void-linux/void-packages/pull/51902

[BETA] sagemath: update to 10.5.beta8
<!-- Uncomment relevant sections and delete options which are not applicable -->

 - python3-Cython: alternative fix for 6122
 - sagemath: enable all cython warnings
 - nauty: update to 2.8.9.

#### Testing the changes
- I tested the changes in this PR: **YES**

@dkwo

<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->

<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration
and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
  - aarch64-musl
  - armv7l
  - armv6l-musl
-->


A patch file from https://github.com/void-linux/void-packages/pull/51902.patch is attached

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-sagemath-51902.patch --]
[-- Type: text/x-diff, Size: 336789 bytes --]

From 31a98e235afa24e1e3e8196e52bd7c46dbc1863d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 1 Oct 2024 23:21:35 -0300
Subject: [PATCH 01/21] pari: update to 2.17.0.

---
 common/shlibs                                 |  2 +-
 ...1f63771186bf01bbb2a1f3351688c3269fe4.patch | 21 +++++++++++++++++++
 srcpkgs/pari/template                         |  4 ++--
 3 files changed, 24 insertions(+), 3 deletions(-)
 create mode 100644 srcpkgs/pari/patches/1ac81f63771186bf01bbb2a1f3351688c3269fe4.patch

diff --git a/common/shlibs b/common/shlibs
index e4f09f58695930..60946e5198feec 100644
--- a/common/shlibs
+++ b/common/shlibs
@@ -4196,7 +4196,7 @@ libsimavrparts.so.1 simavr-1.6_2
 libsword-1.8.1.so libsword-1.8.1_6
 libgivaro.so.9 givaro-4.1.1_1
 liblinbox.so.0 linbox-1.6.3_1
-libpari-gmp-tls.so.8 pari-2.15.0_1
+libpari-gmp-tls.so.9 pari-2.17.0_1
 libtree-sitter.so.0.24 tree-sitter-0.24.3_1
 libplanarity.so.0 planarity-3.0.1.1_1
 libgap.so.9 gap-4.13.0_1
diff --git a/srcpkgs/pari/patches/1ac81f63771186bf01bbb2a1f3351688c3269fe4.patch b/srcpkgs/pari/patches/1ac81f63771186bf01bbb2a1f3351688c3269fe4.patch
new file mode 100644
index 00000000000000..30506cdf9dcdf0
--- /dev/null
+++ b/srcpkgs/pari/patches/1ac81f63771186bf01bbb2a1f3351688c3269fe4.patch
@@ -0,0 +1,21 @@
+From: Bill Allombert <Bill.Allombert@math.u-bordeaux.fr>
+Date: Tue, 1 Oct 2024 21:54:34 +0000 (+0200)
+Subject: qfcvp: fix prototype code [#2575]
+X-Git-Url: https://pari.math.u-bordeaux.fr/cgi-bin/sgitweb.cgi?p=pari.git;a=commitdiff_plain;h=1ac81f63771186bf01bbb2a1f3351688c3269fe4
+
+qfcvp: fix prototype code [#2575]
+---
+
+diff --git a/src/functions/linear_algebra/qfcvp b/src/functions/linear_algebra/qfcvp
+index 5ee883390a..7be5fa9570 100644
+--- a/src/functions/linear_algebra/qfcvp
++++ b/src/functions/linear_algebra/qfcvp
+@@ -1,7 +1,7 @@
+ Function: qfcvp
+ Section: linear_algebra
+ C-Name: qfcvp0
+-Prototype: GGDGDGD0,L,p
++Prototype: GGDGDGD0,L,
+ Help: qfcvp(x,t,{B},{m},{flag=0}): x being a square and symmetric
+  matrix representing a positive definite quadratic form, and t a vector of
+  the same dimension, this function deals with the vectors of whose squared
diff --git a/srcpkgs/pari/template b/srcpkgs/pari/template
index 6b2c5c00a1b7b2..116995aa672741 100644
--- a/srcpkgs/pari/template
+++ b/srcpkgs/pari/template
@@ -1,6 +1,6 @@
 # Template file for 'pari'
 pkgname=pari
-version=2.15.5
+version=2.17.0
 revision=1
 build_style=configure
 build_helper=qemu
@@ -19,7 +19,7 @@ license="GPL-2.0-or-later"
 homepage="https://pari.math.u-bordeaux.fr"
 changelog="https://pari.math.u-bordeaux.fr/cgi-bin/gitweb.cgi?p=pari.git;a=blob_plain;f=CHANGES;hb=refs/heads/pari-${version%.*}"
 distfiles="https://pari.math.u-bordeaux.fr/pub/pari/unix/pari-${version}.tar.gz"
-checksum=0efdda7515d9d954f63324c34b34c560e60f73a81c3924a71260a2cc91d5f981
+checksum=e723e7cef18d08c6ece2283af9a9b4d56077c22b4fce998faaa588d389b1aea8
 
 build_options="x11 pthreads"
 build_options_default="x11 pthreads"

From 7a2b5da39833d90827c8aae43433585cc368cf18 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 1 Oct 2024 23:33:00 -0300
Subject: [PATCH 02/21] eclib: revbump for pari-2.17.0_1

---
 srcpkgs/eclib/template | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/srcpkgs/eclib/template b/srcpkgs/eclib/template
index dd22d4e6de6f31..37a878b35b3e57 100644
--- a/srcpkgs/eclib/template
+++ b/srcpkgs/eclib/template
@@ -1,7 +1,7 @@
 # Template file for 'eclib'
 pkgname=eclib
 version=20240408
-revision=1
+revision=2
 build_style=gnu-configure
 configure_args="--with-flint --with-boost"
 makedepends="pari-devel ntl-devel flintlib-devel boost-devel"

From 447c0456b78f9c46cfc7b95b65eef8935929b2ae Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Wed, 30 Oct 2024 20:45:09 -0300
Subject: [PATCH 03/21] giac: revbump for pari-2.17.0_1

---
 srcpkgs/giac/template | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/srcpkgs/giac/template b/srcpkgs/giac/template
index 82a3381723d8d3..c3737e0ef946de 100644
--- a/srcpkgs/giac/template
+++ b/srcpkgs/giac/template
@@ -1,7 +1,7 @@
 # Template file for 'giac'
 pkgname=giac
 version=1.9.0.995
-revision=1
+revision=2
 build_style=gnu-configure
 configure_args="--disable-micropy --disable-quickjs"
 hostmakedepends="automake gettext-devel libtool"

From 02df2fc4bc86ebda7c96ec3a255902e0856661af Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 1 Oct 2024 23:33:01 -0300
Subject: [PATCH 04/21] lcalc: revbump for pari-2.17.0_1

---
 srcpkgs/lcalc/template | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/srcpkgs/lcalc/template b/srcpkgs/lcalc/template
index 3c6be5fcbc2828..aaab6d14ead440 100644
--- a/srcpkgs/lcalc/template
+++ b/srcpkgs/lcalc/template
@@ -1,7 +1,7 @@
 # Template file for 'lcalc'
 pkgname=lcalc
 version=2.0.5
-revision=2
+revision=3
 build_style=gnu-configure
 configure_args="--with-pari"
 hostmakedepends="automake libtool pkg-config gengetopt"

From d0c15a15974b25144f396f860f988be46c290d3c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 1 Oct 2024 23:33:01 -0300
Subject: [PATCH 05/21] python3-cysignals: revbump for pari-2.17.0_1

---
 srcpkgs/python3-cysignals/template | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/srcpkgs/python3-cysignals/template b/srcpkgs/python3-cysignals/template
index 6cd461880c9d6f..cf39b51cedeafc 100644
--- a/srcpkgs/python3-cysignals/template
+++ b/srcpkgs/python3-cysignals/template
@@ -1,7 +1,7 @@
 # Template file for 'python3-cysignals'
 pkgname=python3-cysignals
 version=1.11.4
-revision=1
+revision=2
 # need gnu-configure build style to support cross build
 build_style=gnu-configure
 build_helper=python3

From 1c057b01589a348b4c65c7b350809a1cd03e7b95 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 1 Oct 2024 23:33:01 -0300
Subject: [PATCH 06/21] python3-cypari2: revbump and patch for pari-2.17.0_1

---
 srcpkgs/python3-cypari2/patches/165.patch  |  38 ++
 srcpkgs/python3-cypari2/patches/166.diff   | 442 +++++++++++++++++++++
 srcpkgs/python3-cypari2/patches/166a.patch |  65 +++
 srcpkgs/python3-cypari2/patches/167.patch  |  31 ++
 srcpkgs/python3-cypari2/template           |   2 +-
 5 files changed, 577 insertions(+), 1 deletion(-)
 create mode 100644 srcpkgs/python3-cypari2/patches/165.patch
 create mode 100644 srcpkgs/python3-cypari2/patches/166.diff
 create mode 100644 srcpkgs/python3-cypari2/patches/166a.patch
 create mode 100644 srcpkgs/python3-cypari2/patches/167.patch

diff --git a/srcpkgs/python3-cypari2/patches/165.patch b/srcpkgs/python3-cypari2/patches/165.patch
new file mode 100644
index 00000000000000..e7e01b71c06fcb
--- /dev/null
+++ b/srcpkgs/python3-cypari2/patches/165.patch
@@ -0,0 +1,38 @@
+See: https://github.com/sagemath/cypari2/pull/165
+and https://github.com/sagemath/sage/pull/38749
+
+From 0a5a7b42e53d065f8d78bdaa8181d6afa20d1f4f Mon Sep 17 00:00:00 2001
+From: Antonio Rojas <arojas@archlinux.org>
+Date: Tue, 1 Oct 2024 18:54:19 +0200
+Subject: [PATCH] Add pari_PRIMES declaration
+
+Needed to port sagemath to work with pari 2.17
+---
+ cypari2/paridecl.pxd | 1 +
+ cypari2/types.pxd    | 1 +
+ 2 files changed, 2 insertions(+)
+
+diff --git a/cypari2/paridecl.pxd b/cypari2/paridecl.pxd
+index 29cb8ef..9ccf336 100644
+--- a/cypari2/paridecl.pxd
++++ b/cypari2/paridecl.pxd
+@@ -118,6 +118,7 @@ cdef extern from *:     # PARI headers already included by types.pxd
+     extern PariOUT* pariOut
+     extern PariOUT* pariErr
+     extern byteptr diffptr
++    extern pari_prime* pari_PRIMES
+ 
+     ###############################################
+     #                                             #
+diff --git a/cypari2/types.pxd b/cypari2/types.pxd
+index 9ee4fe6..7f00b52 100644
+--- a/cypari2/types.pxd
++++ b/cypari2/types.pxd
+@@ -24,6 +24,7 @@ cdef extern from "pari/pari.h":
+     ctypedef long* GEN
+     ctypedef char* byteptr
+     ctypedef unsigned long pari_sp
++    ctypedef unsigned long pari_prime
+ 
+     # PARI types
+     enum:
diff --git a/srcpkgs/python3-cypari2/patches/166.diff b/srcpkgs/python3-cypari2/patches/166.diff
new file mode 100644
index 00000000000000..c5a6f9a617d98b
--- /dev/null
+++ b/srcpkgs/python3-cypari2/patches/166.diff
@@ -0,0 +1,442 @@
+diff --git a/autogen/args.py b/autogen/args.py
+index cd84008..02c57b9 100644
+--- a/autogen/args.py
++++ b/autogen/args.py
+@@ -304,11 +304,11 @@ def _typerepr(self):
+     def ctype(self):
+         return "long"
+     def always_default(self):
+-        return "0"
++        return "DEFAULT_BITPREC"
+     def get_argument_name(self, namesiter):
+         return "precision"
+     def c_convert_code(self):
+-        s = "        {name} = prec_bits_to_words({name})\n"
++        s = "        {name} = nbits2prec({name})\n"
+         return s.format(name=self.name)
+ 
+ class PariArgumentBitprec(PariArgumentClass):
+@@ -317,13 +317,9 @@ def _typerepr(self):
+     def ctype(self):
+         return "long"
+     def always_default(self):
+-        return "0"
++        return "DEFAULT_BITPREC"
+     def get_argument_name(self, namesiter):
+         return "precision"
+-    def c_convert_code(self):
+-        s  = "        if not {name}:\n"
+-        s += "            {name} = default_bitprec()\n"
+-        return s.format(name=self.name)
+ 
+ class PariArgumentSeriesPrec(PariArgumentClass):
+     def _typerepr(self):
+diff --git a/autogen/doc.py b/autogen/doc.py
+index 711827b..c71e7c6 100644
+--- a/autogen/doc.py
++++ b/autogen/doc.py
+@@ -289,7 +289,7 @@ def get_rest_doc(function):
+         >>> from autogen.doc import get_rest_doc
+         >>> print(get_rest_doc("teichmuller"))
+         Teichmüller character of the :math:`p`-adic number :math:`x`, i.e. the unique
+-        :math:`(p-1)`-th root of unity congruent to :math:`x / p^{v_p(x)}` modulo :math:`p`...
++        :math:`(p-1)`-th root of unity congruent to :math:`x / p^{v_...(x)}` modulo :math:`p`...
+ 
+     ::
+ 
+@@ -300,24 +300,24 @@ def get_rest_doc(function):
+         .. MATH::
+         <BLANKLINE>
+             f(x) = \exp (-i\pi/24).\eta ((x+1)/2)/\eta (x) {such that}
+-            j = (f^{24}-16)^3/f^{24},
++            j = (f^{24}-16)^.../f^{24},
+         <BLANKLINE>
+         where :math:`j` is the elliptic :math:`j`-invariant (see the function :literal:`ellj`).
+         If :math:`flag = 1`, returns
+         <BLANKLINE>
+         .. MATH::
+         <BLANKLINE>
+-            f_1(x) = \eta (x/2)/\eta (x) {such that}
+-            j = (f_1^{24}+16)^3/f_1^{24}.
++            f_...(x) = \eta (x/2)/\eta (x) {such that}
++            j = (f_...^{24}+16)^.../f_...^{24}.
+         <BLANKLINE>
+         Finally, if :math:`flag = 2`, returns
+         <BLANKLINE>
+         .. MATH::
+         <BLANKLINE>
+-            f_2(x) = \sqrt{2}\eta (2x)/\eta (x) {such that}
+-            j = (f_2^{24}+16)^3/f_2^{24}.
++            f_...(x) = \sqrt{2}\eta (2x)/\eta (x) {such that}
++            j = (f_...^{24}+16)^.../f_...^{24}.
+         <BLANKLINE>
+-        Note the identities :math:`f^8 = f_1^8+f_2^8` and :math:`ff_1f_2 = \sqrt2`.
++        Note the identities :math:`f^... = f_...^...+f_...^...` and :math:`ff_...f_... = \sqrt2`.
+ 
+ 
+     ::
+@@ -333,7 +333,7 @@ def get_rest_doc(function):
+         .. MATH::
+         <BLANKLINE>
+             \sum
+-            (x_i or y_i) 2^i
++            (x_... or y_...) 2^...
+         <BLANKLINE>
+         See ``bitand`` (in the PARI manual) for the behavior for negative arguments.
+     """
+diff --git a/autogen/generator.py b/autogen/generator.py
+index 048adce..4154723 100644
+--- a/autogen/generator.py
++++ b/autogen/generator.py
+@@ -139,7 +139,7 @@ def handle_pari_function(self, function, cname, prototype="", help="", obsolete=
+             ...     help=r"bnfinit(P,{flag=0},{tech=[]}): compute...",
+             ...     **{"class":"basic", "section":"number_fields"})
+                 GEN bnfinit0(GEN, long, GEN, long)
+-                def bnfinit(P, long flag=0, tech=None, long precision=0):
++                def bnfinit(P, long flag=0, tech=None, long precision=DEFAULT_BITPREC):
+                     ...
+                     cdef bint _have_tech = (tech is not None)
+                     if _have_tech:
+@@ -149,7 +149,7 @@ def bnfinit(P, long flag=0, tech=None, long precision=0):
+                     cdef GEN _tech = NULL
+                     if _have_tech:
+                         _tech = (<Gen>tech).g
+-                    precision = prec_bits_to_words(precision)
++                    precision = nbits2prec(precision)
+                     cdef GEN _ret = bnfinit0(_P, flag, _tech, precision)
+                     return new_gen(_ret)
+             <BLANKLINE>
+diff --git a/autogen/parser.py b/autogen/parser.py
+index d910946..a7fe02f 100644
+--- a/autogen/parser.py
++++ b/autogen/parser.py
+@@ -109,7 +109,7 @@ def parse_prototype(proto, help, initial_args=[]):
+         >>> parse_prototype(proto, help)
+         ([GEN x, GEN* r=NULL], GEN)
+         >>> parse_prototype("lp", "foo()", [str("TEST")])
+-        (['TEST', prec precision=0], long)
++        (['TEST', prec precision=DEFAULT_BITPREC], long)
+     """
+     # Use the help string just for the argument names.
+     # "names" should be an iterator over the argument names.
+diff --git a/cypari2/gen.pyx b/cypari2/gen.pyx
+index a109244..d910ae5 100644
+--- a/cypari2/gen.pyx
++++ b/cypari2/gen.pyx
+@@ -66,8 +66,7 @@ from .types cimport *
+ from .string_utils cimport to_string, to_bytes
+ from .paripriv cimport *
+ from .convert cimport PyObject_AsGEN, gen_to_integer
+-from .pari_instance cimport (prec_bits_to_words,
+-                             default_bitprec, get_var)
++from .pari_instance cimport DEFAULT_BITPREC, get_var
+ from .stack cimport (new_gen, new_gens2, new_gen_noclear,
+                      clone_gen, clear_stack, reset_avma,
+                      remove_from_pari_stack, move_gens_to_heap)
+@@ -647,7 +646,7 @@ cdef class Gen(Gen_base):
+         if m is not None:
+             t0 = t0.Mod(m)
+         sig_on()
+-        return new_gen(gpow(t0.g, t1.g, prec_bits_to_words(0)))
++        return new_gen(gpow(t0.g, t1.g, nbits2prec(DEFAULT_BITPREC)))
+ 
+     def __neg__(self):
+         sig_on()
+@@ -902,6 +901,7 @@ cdef class Gen(Gen_base):
+ 
+         >>> x = pari('x')
+ 
++        >>> pari.setrand(1)
+         >>> (x**2 - 65).bnfinit().bnf_get_fu()
+         [Mod(x - 8, x^2 - 65)]
+         >>> (x**4 - x**2 + 1).bnfinit().bnf_get_fu()
+@@ -951,6 +951,7 @@ cdef class Gen(Gen_base):
+         >>> import warnings
+         >>> with warnings.catch_warnings(record=True) as w:
+         ...     warnings.simplefilter('always')
++        ...     pari.setrand(1)
+         ...     funits = (x**2 - 65).bnfinit().bnfunit()
+         ...     assert len(w) == 1
+         ...     assert issubclass(w[0].category, DeprecationWarning)
+@@ -2911,7 +2912,7 @@ cdef class Gen(Gen_base):
+         sig_on()
+         return new_gen(bernfrac(self))
+ 
+-    def bernreal(self, unsigned long precision=0):
++    def bernreal(self, unsigned long precision=DEFAULT_BITPREC):
+         r"""
+         The Bernoulli number `B_x`, as for the function bernfrac,
+         but `B_x` is returned as a real number (with the current
+@@ -2926,9 +2927,9 @@ cdef class Gen(Gen_base):
+         54.9711779448622
+         """
+         sig_on()
+-        return new_gen(bernreal(self, prec_bits_to_words(precision)))
++        return new_gen(bernreal(self, nbits2prec(precision)))
+ 
+-    def besselk(nu, x, unsigned long precision=0):
++    def besselk(nu, x, unsigned long precision=DEFAULT_BITPREC):
+         """
+         nu.besselk(x): K-Bessel function (modified Bessel function
+         of the second kind) of index nu, which can be complex, and argument
+@@ -2963,9 +2964,9 @@ cdef class Gen(Gen_base):
+         """
+         cdef Gen t0 = objtogen(x)
+         sig_on()
+-        return new_gen(kbessel(nu.g, t0.g, prec_bits_to_words(precision)))
++        return new_gen(kbessel(nu.g, t0.g, nbits2prec(precision)))
+ 
+-    def eint1(x, long n=0, unsigned long precision=0):
++    def eint1(x, long n=0, unsigned long precision=DEFAULT_BITPREC):
+         r"""
+         x.eint1(n): exponential integral E1(x):
+ 
+@@ -2991,13 +2992,14 @@ cdef class Gen(Gen_base):
+         """
+         sig_on()
+         if n <= 0:
+-            return new_gen(eint1(x.g, prec_bits_to_words(precision)))
++            return new_gen(eint1(x.g, nbits2prec(precision)))
+         else:
+-            return new_gen(veceint1(x.g, stoi(n), prec_bits_to_words(precision)))
++            return new_gen(veceint1(x.g, stoi(n), nbits2prec(precision)))
+ 
+     log_gamma = Gen_base.lngamma
+ 
+-    def polylog(x, long m, long flag=0, unsigned long precision=0):
++    def polylog(x, long m, long flag=0,
++                unsigned long precision=DEFAULT_BITPREC):
+         """
+         x.polylog(m,flag=0): m-th polylogarithm of x. flag is optional, and
+         can be 0: default, 1: D_m -modified m-th polylog of x, 2:
+@@ -3026,9 +3028,9 @@ cdef class Gen(Gen_base):
+         -0.400459056163451
+         """
+         sig_on()
+-        return new_gen(polylog0(m, x.g, flag, prec_bits_to_words(precision)))
++        return new_gen(polylog0(m, x.g, flag, nbits2prec(precision)))
+ 
+-    def sqrtn(x, n, unsigned long precision=0):
++    def sqrtn(x, n, unsigned long precision=DEFAULT_BITPREC):
+         r"""
+         x.sqrtn(n): return the principal branch of the n-th root of x,
+         i.e., the one such that
+@@ -3090,7 +3092,7 @@ cdef class Gen(Gen_base):
+         cdef GEN ans, zetan
+         cdef Gen t0 = objtogen(n)
+         sig_on()
+-        ans = gsqrtn(x.g, t0.g, &zetan, prec_bits_to_words(precision))
++        ans = gsqrtn(x.g, t0.g, &zetan, nbits2prec(precision))
+         return new_gens2(ans, zetan)
+ 
+     def ffprimroot(self):
+@@ -4531,7 +4533,8 @@ cdef class Gen(Gen_base):
+         g = polint(self.g, t0.g, t1.g, &dy)
+         return new_gens2(g, dy)
+ 
+-    def ellwp(self, z='z', long n=20, long flag=0, unsigned long precision=0):
++    def ellwp(self, z='z', long n=20, long flag=0,
++              unsigned long precision=DEFAULT_BITPREC):
+         """
+         Return the value or the series expansion of the Weierstrass
+         `P`-function at `z` on the lattice `self` (or the lattice
+@@ -4609,7 +4612,7 @@ cdef class Gen(Gen_base):
+         elif typ(g0) == t_RFRAC:
+             g0 = rfrac_to_ser(g0, n+4)
+ 
+-        cdef GEN r = ellwp0(self.g, g0, flag, prec_bits_to_words(precision))
++        cdef GEN r = ellwp0(self.g, g0, flag, nbits2prec(precision))
+         if flag == 1 and have_ellwp_flag1_bug():
+             # Work around ellwp() bug: double the second element
+             set_gel(r, 2, gmulgs(gel(r, 2), 2))
+diff --git a/cypari2/pari_instance.pxd b/cypari2/pari_instance.pxd
+index f239487..d56f2c2 100644
+--- a/cypari2/pari_instance.pxd
++++ b/cypari2/pari_instance.pxd
+@@ -3,10 +3,14 @@ cimport cython
+ 
+ from .gen cimport Gen
+ 
+-cpdef long prec_bits_to_words(unsigned long prec_in_bits) noexcept
+-cpdef long prec_words_to_bits(long prec_in_words) noexcept
+ cpdef long default_bitprec() noexcept
+ 
++cdef extern from *:
++    """
++    #define DEFAULT_BITPREC prec2nbits(DEFAULTPREC)
++    """
++    long DEFAULT_BITPREC
++
+ cdef class Pari_auto:
+     pass
+ 
+diff --git a/cypari2/pari_instance.pyx b/cypari2/pari_instance.pyx
+index 65d705a..cfb8ecc 100644
+--- a/cypari2/pari_instance.pyx
++++ b/cypari2/pari_instance.pyx
+@@ -235,9 +235,9 @@ Verify that ``nfroots()`` (which has an unusual signature with a
+ non-default argument following a default argument) works:
+ 
+ >>> pari.nfroots(x='x^4 - 1')
+-[-1, 1]
++[-1, 1]...
+ >>> pari.nfroots(pari.nfinit('t^2 + 1'), "x^4 - 1")
+-[-1, 1, Mod(-t, t^2 + 1), Mod(t, t^2 + 1)]
++[-1, 1, Mod(-t, t^2 + 1), Mod(t, t^2 + 1)]...
+ 
+ Reset default precision for the following tests:
+ 
+@@ -299,10 +299,6 @@ from .stack cimport (new_gen, new_gen_noclear, clear_stack,
+ from .handle_error cimport _pari_init_error_handling
+ from .closure cimport _pari_init_closure
+ 
+-# Default precision (in PARI words) for the PARI library interface,
+-# when no explicit precision is given and the inputs are exact.
+-cdef long prec = prec_bits_to_words(53)
+-
+ 
+ #################################################################
+ # conversions between various real precision models
+@@ -341,57 +337,6 @@ def prec_dec_to_bits(long prec_in_dec):
+     return int(prec_in_dec*log_10 + 1.0)  # Add one to round up
+ 
+ 
+-cpdef long prec_bits_to_words(unsigned long prec_in_bits) noexcept:
+-    r"""
+-    Convert from precision expressed in bits to pari real precision
+-    expressed in words. Note: this rounds up to the nearest word,
+-    adjusts for the two codewords of a pari real, and is
+-    architecture-dependent.
+-
+-    Examples:
+-
+-    >>> from cypari2.pari_instance import prec_bits_to_words
+-    >>> import sys
+-    >>> bitness = '64' if sys.maxsize > (1 << 32) else '32'
+-    >>> prec_bits_to_words(70) == (5 if bitness == '32' else 4)
+-    True
+-
+-    >>> ans32 = [(32, 3), (64, 4), (96, 5), (128, 6), (160, 7), (192, 8), (224, 9), (256, 10)]
+-    >>> ans64 = [(32, 3), (64, 3), (96, 4), (128, 4), (160, 5), (192, 5), (224, 6), (256, 6)]
+-    >>> [(32*n, prec_bits_to_words(32*n)) for n in range(1, 9)] == (ans32 if bitness == '32' else ans64)
+-    True
+-    """
+-    if not prec_in_bits:
+-        return prec
+-    cdef unsigned long wordsize = BITS_IN_LONG
+-
+-    # This equals ceil(prec_in_bits/wordsize) + 2
+-    return (prec_in_bits - 1)//wordsize + 3
+-
+-
+-cpdef long prec_words_to_bits(long prec_in_words) noexcept:
+-    r"""
+-    Convert from pari real precision expressed in words to precision
+-    expressed in bits. Note: this adjusts for the two codewords of a
+-    pari real, and is architecture-dependent.
+-
+-    Examples:
+-
+-    >>> from cypari2.pari_instance import prec_words_to_bits
+-    >>> import sys
+-    >>> bitness = '64' if sys.maxsize > (1 << 32) else '32'
+-    >>> prec_words_to_bits(10) == (256 if bitness == '32' else 512)
+-    True
+-
+-    >>> ans32 = [(3, 32), (4, 64), (5, 96), (6, 128), (7, 160), (8, 192), (9, 224)]
+-    >>> ans64 = [(3, 64), (4, 128), (5, 192), (6, 256), (7, 320), (8, 384), (9, 448)] # 64-bit
+-    >>> [(n, prec_words_to_bits(n)) for n in range(3, 10)] == (ans32 if bitness == '32' else ans64)
+-    True
+-    """
+-    # see user's guide to the pari library, page 10
+-    return (prec_in_words - 2) * BITS_IN_LONG
+-
+-
+ cpdef long default_bitprec() noexcept:
+     r"""
+     Return the default precision in bits.
+@@ -402,51 +347,7 @@ cpdef long default_bitprec() noexcept:
+     >>> default_bitprec()
+     64
+     """
+-    return (prec - 2) * BITS_IN_LONG
+-
+-
+-def prec_dec_to_words(long prec_in_dec):
+-    r"""
+-    Convert from precision expressed in decimal to precision expressed
+-    in words. Note: this rounds up to the nearest word, adjusts for the
+-    two codewords of a pari real, and is architecture-dependent.
+-
+-    Examples:
+-
+-    >>> from cypari2.pari_instance import prec_dec_to_words
+-    >>> import sys
+-    >>> bitness = '64' if sys.maxsize > (1 << 32) else '32'
+-    >>> prec_dec_to_words(38) == (6 if bitness == '32' else 4)
+-    True
+-
+-    >>> ans32 = [(10, 4), (20, 5), (30, 6), (40, 7), (50, 8), (60, 9), (70, 10), (80, 11)]
+-    >>> ans64 = [(10, 3), (20, 4), (30, 4), (40, 5), (50, 5), (60, 6), (70, 6), (80, 7)] # 64-bit
+-    >>> [(n, prec_dec_to_words(n)) for n in range(10, 90, 10)] == (ans32 if bitness == '32' else ans64)
+-    True
+-    """
+-    return prec_bits_to_words(prec_dec_to_bits(prec_in_dec))
+-
+-
+-def prec_words_to_dec(long prec_in_words):
+-    r"""
+-    Convert from precision expressed in words to precision expressed in
+-    decimal. Note: this adjusts for the two codewords of a pari real,
+-    and is architecture-dependent.
+-
+-    Examples:
+-
+-    >>> from cypari2.pari_instance import prec_words_to_dec
+-    >>> import sys
+-    >>> bitness = '64' if sys.maxsize > (1 << 32) else '32'
+-    >>> prec_words_to_dec(5) == (28 if bitness == '32' else 57)
+-    True
+-
+-    >>> ans32 = [(3, 9), (4, 19), (5, 28), (6, 38), (7, 48), (8, 57), (9, 67)]
+-    >>> ans64 = [(3, 19), (4, 38), (5, 57), (6, 77), (7, 96), (8, 115), (9, 134)]
+-    >>> [(n, prec_words_to_dec(n)) for n in range(3, 10)] == (ans32 if bitness == '32' else ans64)
+-    True
+-    """
+-    return prec_bits_to_dec(prec_words_to_bits(prec_in_words))
++    return DEFAULT_BITPREC
+ 
+ 
+ # Callbacks from PARI to print stuff using sys.stdout.write() instead
+diff --git a/cypari2/paridecl.pxd b/cypari2/paridecl.pxd
+index 9ccf336..7b8d12d 100644
+--- a/cypari2/paridecl.pxd
++++ b/cypari2/paridecl.pxd
+@@ -5107,6 +5107,7 @@ cdef extern from *:     # PARI headers already included by types.pxd
+     void   killblock(GEN x)
+     GEN    leading_coeff(GEN x)
+     void   lg_increase(GEN x)
++    long   lg2prec(long x)
+     long   lgcols(GEN x)
+     long   lgpol(GEN x)
+     GEN    matpascal(long n)
+@@ -5196,6 +5197,7 @@ cdef extern from *:     # PARI headers already included by types.pxd
+     GEN    polx_zx(long sv)
+     GEN    powii(GEN x, GEN n)
+     GEN    powIs(long n)
++    long   prec2lg(long x)
+     long   prec2nbits(long x)
+     double prec2nbits_mul(long x, double y)
+     long   prec2ndec(long x)
+diff --git a/cypari2/types.pxd b/cypari2/types.pxd
+index 7f00b52..2c6487d 100644
+--- a/cypari2/types.pxd
++++ b/cypari2/types.pxd
+@@ -53,6 +53,7 @@ cdef extern from "pari/pari.h":
+         t_INFINITY
+ 
+     int BITS_IN_LONG
++    int LOWDEFAULTPREC
+     long DEFAULTPREC       # 64 bits precision
+     long MEDDEFAULTPREC    # 128 bits precision
+     long BIGDEFAULTPREC    # 192 bits precision
diff --git a/srcpkgs/python3-cypari2/patches/166a.patch b/srcpkgs/python3-cypari2/patches/166a.patch
new file mode 100644
index 00000000000000..1abdb6d6146108
--- /dev/null
+++ b/srcpkgs/python3-cypari2/patches/166a.patch
@@ -0,0 +1,65 @@
+From 137caa8d45e39f103c19a7d29f85a8d158ecdbde Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
+Date: Sat, 2 Nov 2024 12:55:54 -0300
+Subject: [PATCH] Restore prec_words_to_bits as deprecated function
+
+This is needed to support sagemath < 10.5.
+---
+ cypari2/pari_instance.pxd |  2 ++
+ cypari2/pari_instance.pyx | 30 ++++++++++++++++++++++++++++++
+ 2 files changed, 32 insertions(+)
+
+diff --git a/cypari2/pari_instance.pxd b/cypari2/pari_instance.pxd
+index d56f2c2..d6a75a7 100644
+--- a/cypari2/pari_instance.pxd
++++ b/cypari2/pari_instance.pxd
+@@ -3,6 +3,8 @@ cimport cython
+ 
+ from .gen cimport Gen
+ 
++# DEPRECATED INTERNAL FUNCTION used (incorrectly) in sagemath < 10.5
++cpdef long prec_words_to_bits(long prec_in_words) noexcept
+ cpdef long default_bitprec() noexcept
+ 
+ cdef extern from *:
+diff --git a/cypari2/pari_instance.pyx b/cypari2/pari_instance.pyx
+index cfb8ecc..3e21a7d 100644
+--- a/cypari2/pari_instance.pyx
++++ b/cypari2/pari_instance.pyx
+@@ -337,6 +337,36 @@ def prec_dec_to_bits(long prec_in_dec):
+     return int(prec_in_dec*log_10 + 1.0)  # Add one to round up
+ 
+ 
++cpdef long prec_words_to_bits(long prec_in_words) noexcept:
++    r"""
++    Deprecated internal function. Used (incorrectly) in sagemath < 10.5.
++
++    Convert from pari real precision expressed in words to precision
++    expressed in bits. Note: this adjusts for the two codewords of a
++    pari real, and is architecture-dependent.
++
++    Examples:
++
++    >>> from cypari2.pari_instance import prec_words_to_bits
++    >>> import sys
++    >>> import warnings
++    >>> warnings.simplefilter("ignore")
++    >>> bitness = '64' if sys.maxsize > (1 << 32) else '32'
++    >>> prec_words_to_bits(10) == (256 if bitness == '32' else 512)
++    True
++
++    >>> ans32 = [(3, 32), (4, 64), (5, 96), (6, 128), (7, 160), (8, 192), (9, 224)]
++    >>> ans64 = [(3, 64), (4, 128), (5, 192), (6, 256), (7, 320), (8, 384), (9, 448)] # 64-bit
++    >>> [(n, prec_words_to_bits(n)) for n in range(3, 10)] == (ans32 if bitness == '32' else ans64)
++    True
++    """
++    from warnings import warn
++    warn("'prec_words_to_bits` in cypari2 is internal and deprecated",
++         DeprecationWarning)
++    # see user's guide to the pari library, page 10
++    return (prec_in_words - 2) * BITS_IN_LONG
++
++
+ cpdef long default_bitprec() noexcept:
+     r"""
+     Return the default precision in bits.
diff --git a/srcpkgs/python3-cypari2/patches/167.patch b/srcpkgs/python3-cypari2/patches/167.patch
new file mode 100644
index 00000000000000..6b9678cb2ffe8c
--- /dev/null
+++ b/srcpkgs/python3-cypari2/patches/167.patch
@@ -0,0 +1,31 @@
+From 796b90d19442d2f704fd2916457601cf6c65f0d9 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
+Date: Wed, 30 Oct 2024 17:52:04 -0300
+Subject: [PATCH] fix implicit noexcept warnings
+
+---
+ cypari2/custom_block.pyx | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/cypari2/custom_block.pyx b/cypari2/custom_block.pyx
+index ddbb829..67419f8 100644
+--- a/cypari2/custom_block.pyx
++++ b/cypari2/custom_block.pyx
+@@ -12,14 +12,14 @@ from cysignals.signals cimport add_custom_signals
+ cdef extern from "pari/pari.h":
+     int     PARI_SIGINT_block, PARI_SIGINT_pending
+ 
+-cdef int custom_signal_is_blocked():
++cdef int custom_signal_is_blocked() noexcept:
+     return PARI_SIGINT_block
+ 
+-cdef void custom_signal_unblock():
++cdef void custom_signal_unblock() noexcept:
+     global PARI_SIGINT_block
+     PARI_SIGINT_block = 0
+ 
+-cdef void custom_set_pending_signal(int sig):
++cdef void custom_set_pending_signal(int sig) noexcept:
+     global PARI_SIGINT_pending
+     PARI_SIGINT_pending = sig
+ 
diff --git a/srcpkgs/python3-cypari2/template b/srcpkgs/python3-cypari2/template
index 2a6b284f2f0ab1..e6f2dbb7e4ee5b 100644
--- a/srcpkgs/python3-cypari2/template
+++ b/srcpkgs/python3-cypari2/template
@@ -1,7 +1,7 @@
 # Template file for 'python3-cypari2'
 pkgname=python3-cypari2
 version=2.2.0
-revision=1
+revision=2
 build_style=python3-pep517
 hostmakedepends="python3-setuptools python3-wheel python3-Cython
  python3-cysignals pari perl"

From be4ffae3b64cb4ebba0459bb34435bcda44f7694 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 1 Oct 2024 23:33:02 -0300
Subject: [PATCH 07/21] sagemath: revbump and patch for pari-2.17.0_1

---
 .../patches/38749-00-prepare_backport.patch   |   89 +
 .../sagemath/patches/38749-pari_2.17.patch    | 2056 +++++++++++++++++
 .../patches/38749-zz-fixup_backport.patch     |   95 +
 srcpkgs/sagemath/patches/get_patches          |    2 +
 srcpkgs/sagemath/template                     |    2 +-
 5 files changed, 2243 insertions(+), 1 deletion(-)
 create mode 100644 srcpkgs/sagemath/patches/38749-00-prepare_backport.patch
 create mode 100644 srcpkgs/sagemath/patches/38749-pari_2.17.patch
 create mode 100644 srcpkgs/sagemath/patches/38749-zz-fixup_backport.patch

diff --git a/srcpkgs/sagemath/patches/38749-00-prepare_backport.patch b/srcpkgs/sagemath/patches/38749-00-prepare_backport.patch
new file mode 100644
index 00000000000000..01e6e0bc150141
--- /dev/null
+++ b/srcpkgs/sagemath/patches/38749-00-prepare_backport.patch
@@ -0,0 +1,89 @@
+commit 95d7f3070d46c971fe1ea1fceb3cc6d8039c1d66
+Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
+Date:   Sun Nov 3 13:09:51 2024 -0300
+
+    prepare for backport of #38749
+
+diff --git a/src/sage/modular/dirichlet.py b/src/sage/modular/dirichlet.py
+index e579c5090e3..efc533c51f0 100644
+--- a/src/sage/modular/dirichlet.py
++++ b/src/sage/modular/dirichlet.py
+@@ -2388,7 +2388,8 @@ class DirichletGroupFactory(UniqueFactory):
+ 
+     ::
+ 
+-        sage: r4 = CyclotomicField(4).ring_of_integers()
++        sage: K = CyclotomicField(4)
++        sage: r4 = K.ring_of_integers()
+         sage: G = DirichletGroup(60, r4)
+         sage: G.gens()
+         (Dirichlet character modulo 60 of conductor 4
+@@ -2401,8 +2402,7 @@ class DirichletGroupFactory(UniqueFactory):
+         zeta4
+         sage: parent(val)
+         Gaussian Integers generated by zeta4 in Cyclotomic Field of order 4 and degree 2
+-        sage: r4_29_0 = r4.residue_field(r4.ideal(29).factor()[0][0]); r4_29_0(val)
+-        doctest:warning ... DeprecationWarning: ...
++        sage: r4_29_0 = r4.residue_field(K(29).factor()[0][0]); r4_29_0(val)
+         17
+         sage: r4_29_0(val) * GF(29)(3)
+         22
+diff --git a/src/sage/rings/number_field/selmer_group.py b/src/sage/rings/number_field/selmer_group.py
+index 49b4030b2e9..2a650138291 100644
+--- a/src/sage/rings/number_field/selmer_group.py
++++ b/src/sage/rings/number_field/selmer_group.py
+@@ -73,7 +73,6 @@ def _ideal_generator(I):
+         sage: K.<a> = QuadraticField(-11)
+         sage: [_ideal_generator(K.prime_above(p)) for p in primes(25)]
+         [2, 1/2*a - 1/2, -1/2*a - 3/2, 7, -a, 13, 17, 19, 1/2*a + 9/2]
+-
+     """
+     try:
+         return I.gens_reduced()[0]
+diff --git a/src/sage/schemes/elliptic_curves/gp_simon.py b/src/sage/schemes/elliptic_curves/gp_simon.py
+index 39a60361ec6..f258961f685 100644
+--- a/src/sage/schemes/elliptic_curves/gp_simon.py
++++ b/src/sage/schemes/elliptic_curves/gp_simon.py
+@@ -57,6 +57,9 @@ def simon_two_descent(E, verbose=0, lim1=None, lim3=None, limtriv=None,
+         sage: import sage.schemes.elliptic_curves.gp_simon
+         sage: E = EllipticCurve('389a1')
+         sage: sage.schemes.elliptic_curves.gp_simon.simon_two_descent(E)
++        doctest:warning...:
++        DeprecationWarning: please use the 2-descent algorithm over QQ inside pari
++        See https://github.com/sagemath/sage/issues/38461 for details.
+         (2, 2, [(5/4 : 5/8 : 1), (-3/4 : 7/8 : 1)])
+ 
+     TESTS::
+diff --git a/src/sage/schemes/plane_conics/con_number_field.py b/src/sage/schemes/plane_conics/con_number_field.py
+index 393b77bc1ff..af946d05fb7 100644
+--- a/src/sage/schemes/plane_conics/con_number_field.py
++++ b/src/sage/schemes/plane_conics/con_number_field.py
+@@ -123,9 +123,9 @@ class ProjectiveConic_number_field(ProjectiveConic_field):
+             sage: C = Conic(K, [1, 3, -5])
+             sage: C.has_rational_point(point=True, obstruction=True)
+             (False, Fractional ideal (-i - 2))
+-            sage: C.has_rational_point(algorithm="rnfisnorm")
++            sage: C.has_rational_point(algorithm='rnfisnorm')
+             False
+-            sage: C.has_rational_point(algorithm="rnfisnorm", obstruction=True,
++            sage: C.has_rational_point(algorithm='rnfisnorm', obstruction=True,
+             ....:                      read_cache=False)
+             Traceback (most recent call last):
+             ...
+diff --git a/src/sage/schemes/projective/projective_morphism.py b/src/sage/schemes/projective/projective_morphism.py
+index 339406cd9d6..2baab7e5cda 100644
+--- a/src/sage/schemes/projective/projective_morphism.py
++++ b/src/sage/schemes/projective/projective_morphism.py
+@@ -1764,10 +1764,10 @@ class SchemeMorphism_polynomial_projective_space_field(SchemeMorphism_polynomial
+             Scheme morphism:
+               From: Projective Space of dimension 1 over Number Field in a
+                     with defining polynomial y^4 + 3*y^2 + 1
+-                    with a = 0.?e-151 + 0.618033988749895?*I
++                    with a = 0.?e-113 + 0.618033988749895?*I
+               To:   Projective Space of dimension 2 over Number Field in a
+                     with defining polynomial y^4 + 3*y^2 + 1
+-                    with a = 0.?e-151 + 0.618033988749895?*I
++                    with a = 0.?e-113 + 0.618033988749895?*I
+               Defn: Defined on coordinates by sending (x : y) to
+                     (x^2 + (a^3 + 2*a)*x*y + 3*y^2 : y^2 : (2*a^2 + 3)*x*y)
+ 
diff --git a/srcpkgs/sagemath/patches/38749-pari_2.17.patch b/srcpkgs/sagemath/patches/38749-pari_2.17.patch
new file mode 100644
index 00000000000000..4fbdd7358c0025
--- /dev/null
+++ b/srcpkgs/sagemath/patches/38749-pari_2.17.patch
@@ -0,0 +1,2056 @@
+diff --git a/src/sage/arith/misc.py b/src/sage/arith/misc.py
+index 745d5fcbbe7..86409ab3243 100644
+--- a/src/sage/arith/misc.py
++++ b/src/sage/arith/misc.py
+@@ -2691,9 +2691,14 @@ def factor(n, proof=None, int_=False, algorithm='pari', verbose=0, **kwds):
+ 
+     Any object which has a factor method can be factored like this::
+ 
+-        sage: K.<i> = QuadraticField(-1)                                                # needs sage.rings.number_field
+-        sage: factor(122 - 454*i)                                                       # needs sage.rings.number_field
+-        (-i) * (-i - 2)^3 * (i + 1)^3 * (-2*i + 3) * (i + 4)
++        sage: # needs sage.rings.number_field
++        sage: K.<i> = QuadraticField(-1)
++        sage: f = factor(122 - 454*i); f                                                # random
++        (i) * (i - 1)^3 * (i + 2)^3 * (3*i + 2) * (i + 4)
++        sage: len(f)
++        4
++        sage: product(p[0]^p[1] for p in f) * f.unit()
++        -454*i + 122
+ 
+     To access the data in a factorization::
+ 
+@@ -2775,8 +2780,10 @@ def radical(n, *args, **kwds):
+         ...
+         ArithmeticError: radical of 0 is not defined
+         sage: K.<i> = QuadraticField(-1)                                                # needs sage.rings.number_field
+-        sage: radical(K(2))                                                             # needs sage.rings.number_field
+-        i + 1
++        sage: r = radical(K(2)); r                                                      # random, needs sage.rings.number_field
++        i - 1
++        sage: r.norm()                                                                  # needs sage.rings.number_field
++        2
+ 
+     Tests with numpy and gmpy2 numbers::
+ 
+@@ -3031,7 +3038,7 @@ def is_squarefree(n):
+         sage: is_squarefree(O(2))
+         False
+         sage: O(2).factor()
+-        (-I) * (I + 1)^2
++        (...) * (...)^2
+ 
+     This method fails on domains which are not Unique Factorization Domains::
+ 
+diff --git a/src/sage/categories/quotient_fields.py b/src/sage/categories/quotient_fields.py
+index 76f0570a819..0e4d13ef889 100644
+--- a/src/sage/categories/quotient_fields.py
++++ b/src/sage/categories/quotient_fields.py
+@@ -100,7 +100,7 @@ def gcd(self, other):
+                 sage: R = ZZ.extension(x^2 + 1, names='i')
+                 sage: i = R.1
+                 sage: gcd(5, 3 + 4*i)
+-                -i - 2
++                2*i - 1
+                 sage: P.<t> = R[]
+                 sage: gcd(t, i)
+                 Traceback (most recent call last):
+diff --git a/src/sage/dynamics/arithmetic_dynamics/berkovich_ds.py b/src/sage/dynamics/arithmetic_dynamics/berkovich_ds.py
+index 6995f61f463..457b0ba2253 100644
+--- a/src/sage/dynamics/arithmetic_dynamics/berkovich_ds.py
++++ b/src/sage/dynamics/arithmetic_dynamics/berkovich_ds.py
+@@ -690,10 +690,10 @@ def conjugate(self, M, adjugate=False, new_ideal=None):
+ 
+             sage: # needs sage.rings.number_field
+             sage: ideal = A.ideal(5).factor()[1][0]; ideal
+-            Fractional ideal (2*a + 1)
++            Fractional ideal (-a + 2)
+             sage: g = f.conjugate(conj, new_ideal=ideal)
+             sage: g.domain().ideal()
+-            Fractional ideal (2*a + 1)
++            Fractional ideal (-a + 2)
+         """
+         if self.domain().is_padic_base():
+             return DynamicalSystem_Berkovich(self._system.conjugate(M, adjugate=adjugate))
+diff --git a/src/sage/dynamics/arithmetic_dynamics/projective_ds.py b/src/sage/dynamics/arithmetic_dynamics/projective_ds.py
+index a74efd9129a..151f9e71335 100644
+--- a/src/sage/dynamics/arithmetic_dynamics/projective_ds.py
++++ b/src/sage/dynamics/arithmetic_dynamics/projective_ds.py
+@@ -1790,7 +1790,7 @@ def primes_of_bad_reduction(self, check=True):
+             sage: P.<x,y> = ProjectiveSpace(K,1)
+             sage: f = DynamicalSystem_projective([1/3*x^2+1/a*y^2, y^2])
+             sage: f.primes_of_bad_reduction()                                           # needs sage.rings.function_field
+-            [Fractional ideal (a), Fractional ideal (3)]
++            [Fractional ideal (-a), Fractional ideal (3)]
+ 
+         This is an example where ``check=False`` returns extra primes::
+ 
+diff --git a/src/sage/libs/pari/convert_sage.pyx b/src/sage/libs/pari/convert_sage.pyx
+index 64386bcf632..db6725f39a5 100644
+--- a/src/sage/libs/pari/convert_sage.pyx
++++ b/src/sage/libs/pari/convert_sage.pyx
+@@ -573,17 +573,16 @@ cpdef list pari_prime_range(long c_start, long c_stop, bint py_ints=False):
+         sage: pari_prime_range(2, 19)
+         [2, 3, 5, 7, 11, 13, 17]
+     """
+-    cdef long p = 0
+-    cdef byteptr pari_prime_ptr = diffptr
++    cdef ulong i = 1
+     res = []
+-    while p < c_start:
+-        NEXT_PRIME_VIADIFF(p, pari_prime_ptr)
+-    while p < c_stop:
++    while pari_PRIMES[i] < c_start:
++        i+=1
++    while pari_PRIMES[i] < c_stop:
+         if py_ints:
+-            res.append(p)
++            res.append(pari_PRIMES[i])
+         else:
+             z = <Integer>PY_NEW(Integer)
+-            mpz_set_ui(z.value, p)
++            mpz_set_ui(z.value, pari_PRIMES[i])
+             res.append(z)
+-        NEXT_PRIME_VIADIFF(p, pari_prime_ptr)
++        i+=1
+     return res
+diff --git a/src/sage/libs/pari/convert_sage_real_mpfr.pyx b/src/sage/libs/pari/convert_sage_real_mpfr.pyx
+index 98db6023dc9..5fd7fba1c47 100644
+--- a/src/sage/libs/pari/convert_sage_real_mpfr.pyx
++++ b/src/sage/libs/pari/convert_sage_real_mpfr.pyx
+@@ -28,7 +28,7 @@ cpdef Gen new_gen_from_real_mpfr_element(RealNumber self):
+ 
+     # We round up the precision to the nearest multiple of wordsize.
+     cdef int rounded_prec
+-    rounded_prec = (self.prec() + wordsize - 1) & ~(wordsize - 1)
++    rounded_prec = nbits2prec(self.prec())
+ 
+     # Yes, assigning to self works fine, even in Cython.
+     if rounded_prec > prec:
+@@ -48,7 +48,7 @@ cpdef Gen new_gen_from_real_mpfr_element(RealNumber self):
+         exponent = mpfr_get_z_exp(mantissa, self.value)
+ 
+         # Create a PARI REAL
+-        pari_float = cgetr(2 + rounded_prec / wordsize)
++        pari_float = cgetr(rounded_prec)
+         pari_float[1] = evalexpo(exponent + rounded_prec - 1) + evalsigne(mpfr_sgn(self.value))
+         mpz_export(&pari_float[2], NULL, 1, wordsize // 8, 0, 0, mantissa)
+         mpz_clear(mantissa)
+diff --git a/src/sage/libs/pari/tests.py b/src/sage/libs/pari/tests.py
+index 1ed571cd4b9..bd8dc9641d2 100644
+--- a/src/sage/libs/pari/tests.py
++++ b/src/sage/libs/pari/tests.py
+@@ -1502,7 +1502,7 @@
+     sage: pari(-104).quadclassunit()
+     [6, [6], [Qfb(5, -4, 6)], 1]
+     sage: pari(109).quadclassunit()
+-    [1, [], [], 5.56453508676047]
++    [1, [], [], 5.56453508676047, -1]
+     sage: pari(10001).quadclassunit() # random generators
+     [16, [16], [Qfb(10, 99, -5, 0.E-38)], 5.29834236561059]
+     sage: pari(10001).quadclassunit()[0]
+@@ -1749,13 +1749,13 @@
+     sage: y = QQ['yy'].0; _ = pari(y) # pari has variable ordering rules
+     sage: x = QQ['zz'].0; nf = pari(x^2 + 2).nfinit()
+     sage: nf.nfroots(y^2 + 2)
+-    [Mod(-zz, zz^2 + 2), Mod(zz, zz^2 + 2)]
++    [Mod(-zz, zz^2 + 2), Mod(zz, zz^2 + 2)]~
+     sage: nf = pari(x^3 + 2).nfinit()
+     sage: nf.nfroots(y^3 + 2)
+-    [Mod(zz, zz^3 + 2)]
++    [Mod(zz, zz^3 + 2)]~
+     sage: nf = pari(x^4 + 2).nfinit()
+     sage: nf.nfroots(y^4 + 2)
+-    [Mod(-zz, zz^4 + 2), Mod(zz, zz^4 + 2)]
++    [Mod(-zz, zz^4 + 2), Mod(zz, zz^4 + 2)]~
+ 
+     sage: nf = pari('x^2 + 1').nfinit()
+     sage: nf.nfrootsof1()
+diff --git a/src/sage/matrix/matrix2.pyx b/src/sage/matrix/matrix2.pyx
+index 0c257cfaf33..780cae7fbf2 100644
+--- a/src/sage/matrix/matrix2.pyx
++++ b/src/sage/matrix/matrix2.pyx
+@@ -16583,7 +16583,7 @@ cdef class Matrix(Matrix1):
+             ....:   -2*a^2 + 4*a - 2, -2*a^2 + 1, 2*a, a^2 - 6, 3*a^2 - a ])
+             sage: r,s,p = m._echelon_form_PID()
+             sage: s[2]
+-            (0, 0, -3*a^2 - 18*a + 34, -68*a^2 + 134*a - 53, -111*a^2 + 275*a - 90)
++            (0, 0, 3*a^2 + 18*a - 34, 68*a^2 - 134*a + 53, 111*a^2 - 275*a + 90)
+             sage: r * m == s and r.det() == 1
+             True
+ 
+diff --git a/src/sage/modular/cusps_nf.py b/src/sage/modular/cusps_nf.py
+index 4d120c075da..f3a3ff7e65b 100644
+--- a/src/sage/modular/cusps_nf.py
++++ b/src/sage/modular/cusps_nf.py
+@@ -1184,9 +1184,9 @@ def NFCusps_ideal_reps_for_levelN(N, nlists=1):
+         sage: from sage.modular.cusps_nf import NFCusps_ideal_reps_for_levelN
+         sage: NFCusps_ideal_reps_for_levelN(N)
+         [(Fractional ideal (1),
+-          Fractional ideal (67, a + 17),
+-          Fractional ideal (127, a + 48),
+-          Fractional ideal (157, a - 19))]
++          Fractional ideal (67, -4/7*a^3 + 13/7*a^2 + 39/7*a - 43),
++          Fractional ideal (127, -4/7*a^3 + 13/7*a^2 + 39/7*a - 42),
++          Fractional ideal (157, -4/7*a^3 + 13/7*a^2 + 39/7*a + 48))]
+         sage: L = NFCusps_ideal_reps_for_levelN(N, 5)
+         sage: all(len(L[i]) == k.class_number() for i in range(len(L)))
+         True
+@@ -1244,7 +1244,7 @@ def units_mod_ideal(I):
+         sage: I = k.ideal(5, a + 1)
+         sage: units_mod_ideal(I)
+         [1,
+-        -2*a^2 - 4*a + 1,
++        2*a^2 + 4*a - 1,
+         ...]
+ 
+     ::
+diff --git a/src/sage/modular/dirichlet.py b/src/sage/modular/dirichlet.py
+index 1f6a7a94444..1cf3ccdb611 100644
+--- a/src/sage/modular/dirichlet.py
++++ b/src/sage/modular/dirichlet.py
+@@ -2395,13 +2395,13 @@ class DirichletGroupFactory(UniqueFactory):
+         sage: parent(val)
+         Gaussian Integers generated by zeta4 in Cyclotomic Field of order 4 and degree 2
+         sage: r4_29_0 = r4.residue_field(K(29).factor()[0][0]); r4_29_0(val)
+-        17
++        12
+         sage: r4_29_0(val) * GF(29)(3)
+-        22
++        7
+         sage: r4_29_0(G.gens()[2].values_on_gens()[2]) * 3
+-        22
++        7
+         sage: parent(r4_29_0(G.gens()[2].values_on_gens()[2]) * 3)
+-        Residue field of Fractional ideal (-2*zeta4 + 5)
++        Residue field of Fractional ideal (-2*zeta4 - 5)
+ 
+     ::
+ 
+diff --git a/src/sage/modular/modsym/p1list_nf.py b/src/sage/modular/modsym/p1list_nf.py
+index 86d33071974..00bb0979ea4 100644
+--- a/src/sage/modular/modsym/p1list_nf.py
++++ b/src/sage/modular/modsym/p1list_nf.py
+@@ -61,7 +61,7 @@
+ 
+     sage: alpha = MSymbol(N, a + 2, 3*a^2)
+     sage: alpha.lift_to_sl2_Ok()
+-    [-1, 4*a^2 - 13*a + 23, a + 2, 5*a^2 + 3*a - 3]
++    [-a - 1, 15*a^2 - 38*a + 86, a + 2, -a^2 + 9*a - 19]
+     sage: Ok = k.ring_of_integers()
+     sage: M = Matrix(Ok, 2, alpha.lift_to_sl2_Ok())
+     sage: det(M)
+@@ -977,11 +977,11 @@ def apply_J_epsilon(self, i, e1, e2=1):
+             sage: N = k.ideal(5, a + 1)
+             sage: P = P1NFList(N)
+             sage: u = k.unit_group().gens_values(); u
+-            [-1, -2*a^2 - 4*a + 1]
++            [-1, 2*a^2 + 4*a - 1]
+             sage: P.apply_J_epsilon(4, -1)
+             2
+             sage: P.apply_J_epsilon(4, u[0], u[1])
+-            5
++            1
+ 
+         ::
+ 
+@@ -1122,7 +1122,7 @@ def lift_to_sl2_Ok(N, c, d):
+         sage: M = Matrix(Ok, 2, lift_to_sl2_Ok(N, 0, 7))
+         Traceback (most recent call last):
+         ...
+-        ValueError: <0> + <7> and the Fractional ideal (7, a) are not coprime.
++        ValueError: <0> + <7> and the Fractional ideal (7, -4/7*a^3 + 13/7*a^2 + 39/7*a - 19) are not coprime.
+     """
+     k = N.number_field()
+     # check the input
+diff --git a/src/sage/quadratic_forms/binary_qf.py b/src/sage/quadratic_forms/binary_qf.py
+index 1a75f415b64..c89759288b9 100755
+--- a/src/sage/quadratic_forms/binary_qf.py
++++ b/src/sage/quadratic_forms/binary_qf.py
+@@ -1646,7 +1646,7 @@ def solve_integer(self, n, *, algorithm='general', _flag=2):
+             sage: Q = BinaryQF([1, 0, 12345])
+             sage: n = 2^99 + 5273
+             sage: Q.solve_integer(n)                                                    # needs sage.libs.pari
+-            (-67446480057659, 7139620553488)
++            (67446480057659, 7139620553488)
+             sage: Q.solve_integer(n, algorithm='cornacchia')                            # needs sage.libs.pari
+             (67446480057659, 7139620553488)
+             sage: timeit('Q.solve_integer(n)')                          # not tested
+@@ -1661,7 +1661,7 @@ def solve_integer(self, n, *, algorithm='general', _flag=2):
+             sage: Qs
+             [x^2 + x*y + 6*y^2, 2*x^2 - x*y + 3*y^2, 2*x^2 + x*y + 3*y^2]
+             sage: [Q.solve_integer(3) for Q in Qs]
+-            [None, (0, -1), (0, -1)]
++            [None, (0, 1), (0, 1)]
+             sage: [Q.solve_integer(5) for Q in Qs]
+             [None, None, None]
+             sage: [Q.solve_integer(6) for Q in Qs]
+@@ -1741,11 +1741,11 @@ def solve_integer(self, n, *, algorithm='general', _flag=2):
+             sage: # needs sage.libs.pari
+             sage: Q = BinaryQF([1, 0, 5])
+             sage: Q.solve_integer(126, _flag=1)
+-            [(11, -1), (-1, -5), (-1, 5), (-11, -1)]
++            [(-11, -1), (-1, -5), (-1, 5), (11, -1)]
+             sage: Q.solve_integer(126, _flag=2)
+             (11, -1)
+             sage: Q.solve_integer(126, _flag=3)
+-            [(11, -1), (-1, -5), (-1, 5), (-11, -1), (-9, -3), (9, -3)]
++            [(-11, -1), (-9, -3), (-1, -5), (-1, 5), (9, -3), (11, -1)]
+         """
+         if self.is_negative_definite():  # not supported by PARI
+             return (-self).solve_integer(-n)
+diff --git a/src/sage/rings/finite_rings/finite_field_prime_modn.py b/src/sage/rings/finite_rings/finite_field_prime_modn.py
+index d94b0a4335a..0978c7328fe 100644
+--- a/src/sage/rings/finite_rings/finite_field_prime_modn.py
++++ b/src/sage/rings/finite_rings/finite_field_prime_modn.py
+@@ -114,9 +114,9 @@ def _coerce_map_from_(self, S):
+             sage: RF13 = K.residue_field(pp)
+             sage: RF13.hom([GF(13)(1)])
+             Ring morphism:
+-             From: Residue field of Fractional ideal (-w - 18)
+-             To:   Finite Field of size 13
+-             Defn: 1 |--> 1
++              From: Residue field of Fractional ideal (w + 18)
++              To:   Finite Field of size 13
++              Defn: 1 |--> 1
+ 
+         Check that :issue:`19573` is resolved::
+ 
+diff --git a/src/sage/rings/finite_rings/residue_field.pyx b/src/sage/rings/finite_rings/residue_field.pyx
+index 3146f7fd764..a8e77e48b76 100644
+--- a/src/sage/rings/finite_rings/residue_field.pyx
++++ b/src/sage/rings/finite_rings/residue_field.pyx
+@@ -22,14 +22,13 @@ monogenic (i.e., 2 is an essential discriminant divisor)::
+     sage: # needs sage.rings.number_field
+     sage: K.<a> = NumberField(x^3 + x^2 - 2*x + 8)
+     sage: F = K.factor(2); F
+-    (Fractional ideal (-1/2*a^2 + 1/2*a - 1)) * (Fractional ideal (-a^2 + 2*a - 3))
+-    * (Fractional ideal (3/2*a^2 - 5/2*a + 4))
++    (Fractional ideal (-1/2*a^2 + 1/2*a - 1)) * (Fractional ideal (a^2 - 2*a + 3)) * (Fractional ideal (-3/2*a^2 + 5/2*a - 4))
+     sage: F[0][0].residue_field()
+     Residue field of Fractional ideal (-1/2*a^2 + 1/2*a - 1)
+     sage: F[1][0].residue_field()
+-    Residue field of Fractional ideal (-a^2 + 2*a - 3)
++    Residue field of Fractional ideal (a^2 - 2*a + 3)
+     sage: F[2][0].residue_field()
+-    Residue field of Fractional ideal (3/2*a^2 - 5/2*a + 4)
++    Residue field of Fractional ideal (-3/2*a^2 + 5/2*a - 4)
+ 
+ We can also form residue fields from `\ZZ`::
+ 
+@@ -126,10 +125,10 @@ First over a small non-prime field::
+     sage: I = ideal([ubar*X + Y]); I
+     Ideal (ubar*X + Y) of Multivariate Polynomial Ring in X, Y over
+      Residue field in ubar of Fractional ideal
+-      (47, 517/55860*u^5 + 235/3724*u^4 + 9829/13965*u^3
+-            + 54106/13965*u^2 + 64517/27930*u + 755696/13965)
++      (47, 4841/93100*u^5 + 34451/139650*u^4 + 303697/69825*u^3
++            + 297893/27930*u^2 + 1649764/23275*u + 2633506/69825)
+     sage: I.groebner_basis()                                                            # needs sage.libs.singular
+-    [X + (-19*ubar^2 - 5*ubar - 17)*Y]
++    [X + (-15*ubar^2 + 3*ubar - 2)*Y]
+ 
+ And now over a large prime field::
+ 
+@@ -496,9 +495,9 @@ class ResidueField_generic(Field):
+ 
+         sage: # needs sage.rings.number_field
+         sage: I = QQ[i].factor(2)[0][0]; I
+-        Fractional ideal (I + 1)
++        Fractional ideal (-I - 1)
+         sage: k = I.residue_field(); k
+-        Residue field of Fractional ideal (I + 1)
++        Residue field of Fractional ideal (-I - 1)
+         sage: type(k)
+         <class 'sage.rings.finite_rings.residue_field.ResidueFiniteField_prime_modn_with_category'>
+ 
+@@ -1008,7 +1007,7 @@ cdef class ReductionMap(Map):
+             sage: cr
+             Partially defined reduction map:
+               From: Number Field in a with defining polynomial x^2 + 1
+-              To:   Residue field of Fractional ideal (a + 1)
++              To:   Residue field of Fractional ideal (-a + 1)
+             sage: cr == r                       # not implemented
+             True
+             sage: r(2 + a) == cr(2 + a)
+@@ -1039,7 +1038,7 @@ cdef class ReductionMap(Map):
+             sage: cr
+             Partially defined reduction map:
+               From: Number Field in a with defining polynomial x^2 + 1
+-              To:   Residue field of Fractional ideal (a + 1)
++              To:   Residue field of Fractional ideal (-a + 1)
+             sage: cr == r                       # not implemented
+             True
+             sage: r(2 + a) == cr(2 + a)
+@@ -1071,7 +1070,7 @@ cdef class ReductionMap(Map):
+             sage: r = F.reduction_map(); r
+             Partially defined reduction map:
+               From: Number Field in a with defining polynomial x^2 + 1
+-              To:   Residue field of Fractional ideal (a + 1)
++              To:   Residue field of Fractional ideal (-a + 1)
+ 
+         We test that calling the function also works after copying::
+ 
+@@ -1083,7 +1082,7 @@ cdef class ReductionMap(Map):
+             Traceback (most recent call last):
+             ...
+             ZeroDivisionError: Cannot reduce field element 1/2*a
+-            modulo Fractional ideal (a + 1): it has negative valuation
++            modulo Fractional ideal (-a + 1): it has negative valuation
+ 
+             sage: # needs sage.rings.finite_rings
+             sage: R.<t> = GF(2)[]; h = t^5 + t^2 + 1
+@@ -1105,11 +1104,11 @@ cdef class ReductionMap(Map):
+             sage: # needs sage.rings.number_field
+             sage: K.<i> = NumberField(x^2 + 1)
+             sage: P1, P2 = [g[0] for g in K.factor(5)]; P1, P2
+-            (Fractional ideal (-i - 2), Fractional ideal (2*i + 1))
++            (Fractional ideal (2*i - 1), Fractional ideal (-2*i - 1))
+             sage: a = 1/(1+2*i)
+             sage: F1, F2 = [g.residue_field() for g in [P1,P2]]; F1, F2
+-            (Residue field of Fractional ideal (-i - 2),
+-             Residue field of Fractional ideal (2*i + 1))
++            (Residue field of Fractional ideal (2*i - 1),
++             Residue field of Fractional ideal (-2*i - 1))
+             sage: a.valuation(P1)
+             0
+             sage: F1(i/7)
+@@ -1122,7 +1121,7 @@ cdef class ReductionMap(Map):
+             Traceback (most recent call last):
+             ...
+             ZeroDivisionError: Cannot reduce field element -2/5*i + 1/5
+-            modulo Fractional ideal (2*i + 1): it has negative valuation
++            modulo Fractional ideal (-2*i - 1): it has negative valuation
+         """
+         # The reduction map is just x |--> F(to_vs(x) * (PB**(-1))) if
+         # either x is integral or the denominator of x is coprime to
+@@ -1188,8 +1187,7 @@ cdef class ReductionMap(Map):
+             sage: f = k.convert_map_from(K)
+             sage: s = f.section(); s
+             Lifting map:
+-              From: Residue field in abar of
+-                    Fractional ideal (-14*a^4 + 24*a^3 + 26*a^2 - 58*a + 15)
++              From: Residue field in abar of Fractional ideal (14*a^4 - 24*a^3 - 26*a^2 + 58*a - 15)
+               To:   Number Field in a with defining polynomial x^5 - 5*x + 2
+             sage: s(k.gen())
+             a
+@@ -1424,8 +1422,7 @@ cdef class ResidueFieldHomomorphism_global(RingHomomorphism):
+             sage: f = k.coerce_map_from(K.ring_of_integers())
+             sage: s = f.section(); s
+             Lifting map:
+-              From: Residue field in abar of
+-                    Fractional ideal (-14*a^4 + 24*a^3 + 26*a^2 - 58*a + 15)
++              From: Residue field in abar of Fractional ideal (14*a^4 - 24*a^3 - 26*a^2 + 58*a - 15)
+               To:   Maximal Order generated by a in Number Field in a with defining polynomial x^5 - 5*x + 2
+             sage: s(k.gen())
+             a
+@@ -1678,7 +1675,7 @@ cdef class LiftingMap(Section):
+             sage: F.<tmod> = K.factor(7)[0][0].residue_field()
+             sage: F.lift_map() #indirect doctest
+             Lifting map:
+-              From: Residue field in tmod of Fractional ideal (theta_12^2 + 2)
++              From: Residue field in tmod of Fractional ideal (2*theta_12^3 + theta_12)
+               To:   Maximal Order generated by theta_12 in Cyclotomic Field of order 12 and degree 4
+         """
+         return "Lifting"
+diff --git a/src/sage/rings/finite_rings/residue_field_pari_ffelt.pyx b/src/sage/rings/finite_rings/residue_field_pari_ffelt.pyx
+index e9962c3ccde..90a68c619f6 100644
+--- a/src/sage/rings/finite_rings/residue_field_pari_ffelt.pyx
++++ b/src/sage/rings/finite_rings/residue_field_pari_ffelt.pyx
+@@ -103,7 +103,7 @@ class ResidueFiniteField_pari_ffelt(ResidueField_generic, FiniteField_pari_ffelt
+             sage: P.residue_class_degree()
+             2
+             sage: ff.<alpha> = P.residue_field(); ff
+-            Residue field in alpha of Fractional ideal (-12*aa^2 + 189*aa - 475)
++            Residue field in alpha of Fractional ideal (12*aa^2 - 189*aa + 475)
+             sage: type(ff)
+             <class 'sage.rings.finite_rings.residue_field_pari_ffelt.ResidueFiniteField_pari_ffelt_with_category'>
+             sage: ff(alpha^2 + 1)
+diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
+index 9616e7946bc..bcc45e703a2 100644
+--- a/src/sage/rings/integer.pyx
++++ b/src/sage/rings/integer.pyx
+@@ -5585,7 +5585,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
+             sage: 5.is_norm(K)
+             False
+             sage: n.is_norm(K, element=True)
+-            (True, -4*beta + 6)
++            (True, 4*beta + 6)
+             sage: n.is_norm(K, element=True)[1].norm()
+             4
+             sage: n = 5
+diff --git a/src/sage/rings/number_field/S_unit_solver.py b/src/sage/rings/number_field/S_unit_solver.py
+index 0ffac369720..1260650ef77 100644
+--- a/src/sage/rings/number_field/S_unit_solver.py
++++ b/src/sage/rings/number_field/S_unit_solver.py
+@@ -12,10 +12,10 @@
+     sage: x = polygen(ZZ, 'x')
+     sage: K.<xi> = NumberField(x^2 + x + 1)
+     sage: S = K.primes_above(3)
+-    sage: expected = [((0, 1), (4, 0), xi + 2, -xi - 1),
+-    ....:             ((1, -1), (0, -1), 1/3*xi + 2/3, -1/3*xi + 1/3),
++    sage: expected = [((4, 1), (4, 0), xi + 2, -xi - 1),
++    ....:             ((3, -1), (2, -1), 1/3*xi + 2/3, -1/3*xi + 1/3),
+     ....:             ((1, 0), (5, 0), xi + 1, -xi),
+-    ....:             ((2, 0), (5, 1), xi, -xi + 1)]
++    ....:             ((2, 0), (3, 1), xi, -xi + 1)]
+     sage: sols = solve_S_unit_equation(K, S, 200)
+     sage: eq_up_to_order(sols, expected)
+     True
+@@ -1448,7 +1448,7 @@ def embedding_to_Kp(a, prime, prec):
+         sage: from sage.rings.number_field.S_unit_solver import embedding_to_Kp
+         sage: K.<a> = QuadraticField(17)
+         sage: p = K.prime_above(13); p
+-        Fractional ideal (-a + 2)
++        Fractional ideal (a - 2)
+         sage: embedding_to_Kp(a-3, p, 15)
+         -20542890112375827
+ 
+@@ -1791,10 +1791,10 @@ def sieve_ordering(SUK, q):
+          Residue field of Fractional ideal (2*xi + 1))
+ 
+         sage: sieve_data[2]
+-        ([18, 12, 16, 8], [18, 16, 10, 4], [18, 10, 12, 10])
++        ([18, 9, 16, 8], [18, 7, 10, 4], [18, 3, 12, 10])
+ 
+         sage: sieve_data[3]
+-        (648, 2916, 3888)
++        (972, 972, 3888)
+     """
+ 
+     K = SUK.number_field()
+@@ -2170,23 +2170,23 @@ def construct_complement_dictionaries(split_primes_list, SUK, verbose=False):
+         sage: SUK = K.S_unit_group(S=K.primes_above(H))
+         sage: split_primes_list = [3, 7]
+         sage: actual = construct_complement_dictionaries(split_primes_list, SUK)
+-        sage: expected = {3: {(0, 1, 0): [(1, 0, 0), (0, 1, 0)],
+-        ....:                 (1, 0, 0): [(1, 0, 0), (0, 1, 0)]},
+-        ....:             7: {(0, 1, 0): [(1, 0, 0), (1, 4, 4), (1, 2, 2)],
+-        ....:                 (0, 1, 2): [(0, 1, 2), (0, 3, 4), (0, 5, 0)],
+-        ....:                 (0, 3, 2): [(1, 0, 0), (1, 4, 4), (1, 2, 2)],
+-        ....:                 (0, 3, 4): [(0, 1, 2), (0, 3, 4), (0, 5, 0)],
+-        ....:                 (0, 5, 0): [(0, 1, 2), (0, 3, 4), (0, 5, 0)],
+-        ....:                 (0, 5, 4): [(1, 0, 0), (1, 4, 4), (1, 2, 2)],
+-        ....:                 (1, 0, 0): [(0, 5, 4), (0, 3, 2), (0, 1, 0)],
+-        ....:                 (1, 0, 2): [(1, 0, 4), (1, 4, 2), (1, 2, 0)],
++        sage: expected = {3: {(1, 1, 0): [(1, 0, 0), (1, 1, 0)],
++        ....:                 (1, 0, 0): [(1, 0, 0), (1, 1, 0)]},
++        ....:             7: {(1, 1, 0): [(1, 0, 0), (1, 4, 4), (1, 2, 2)],
++        ....:                 (1, 3, 2): [(1, 0, 0), (1, 4, 4), (1, 2, 2)],
++        ....:                 (1, 5, 4): [(1, 0, 0), (1, 4, 4), (1, 2, 2)],
+         ....:                 (1, 0, 4): [(1, 2, 4), (1, 4, 0), (1, 0, 2)],
+         ....:                 (1, 2, 0): [(1, 2, 4), (1, 4, 0), (1, 0, 2)],
+-        ....:                 (1, 2, 2): [(0, 5, 4), (0, 3, 2), (0, 1, 0)],
++        ....:                 (1, 4, 2): [(1, 2, 4), (1, 4, 0), (1, 0, 2)],
++        ....:                 (1, 1, 2): [(1, 1, 2), (1, 3, 4), (1, 5, 0)],
++        ....:                 (1, 3, 4): [(1, 1, 2), (1, 3, 4), (1, 5, 0)],
++        ....:                 (1, 5, 0): [(1, 1, 2), (1, 3, 4), (1, 5, 0)],
++        ....:                 (1, 0, 2): [(1, 0, 4), (1, 4, 2), (1, 2, 0)],
+         ....:                 (1, 2, 4): [(1, 0, 4), (1, 4, 2), (1, 2, 0)],
+         ....:                 (1, 4, 0): [(1, 0, 4), (1, 4, 2), (1, 2, 0)],
+-        ....:                 (1, 4, 2): [(1, 2, 4), (1, 4, 0), (1, 0, 2)],
+-        ....:                 (1, 4, 4): [(0, 5, 4), (0, 3, 2), (0, 1, 0)]}}
++        ....:                 (1, 0, 0): [(1, 5, 4), (1, 3, 2), (1, 1, 0)],
++        ....:                 (1, 2, 2): [(1, 5, 4), (1, 3, 2), (1, 1, 0)],
++        ....:                 (1, 4, 4): [(1, 5, 4), (1, 3, 2), (1, 1, 0)]}}
+         sage: all(set(actual[p][vec]) == set(expected[p][vec])
+         ....:     for p in [3, 7] for vec in expected[p])
+         True
+@@ -2693,9 +2693,9 @@ def sieve_below_bound(K, S, bound=10, bump=10, split_primes_list=[], verbose=Fal
+         sage: SUK = UnitGroup(K, S=tuple(K.primes_above(3)))
+         sage: S = SUK.primes()
+         sage: sols = sieve_below_bound(K, S, 10)
+-        sage: expected = [((1, -1), (0, -1), 1/3*xi + 2/3, -1/3*xi + 1/3),
+-        ....:             ((0, 1), (4, 0), xi + 2, -xi - 1),
+-        ....:             ((2, 0), (5, 1), xi, -xi + 1),
++        sage: expected = [((3, -1), (2, -1), 1/3*xi + 2/3, -1/3*xi + 1/3),
++        ....:             ((4, 1), (4, 0), xi + 2, -xi - 1),
++        ....:             ((2, 0), (3, 1), xi, -xi + 1),
+         ....:             ((1, 0), (5, 0), xi + 1, -xi)]
+         sage: eq_up_to_order(sols, expected)
+         True
+@@ -2758,10 +2758,10 @@ def solve_S_unit_equation(K, S, prec=106, include_exponents=True, include_bound=
+         sage: K.<xi> = NumberField(x^2 + x + 1)
+         sage: S = K.primes_above(3)
+         sage: sols = solve_S_unit_equation(K, S, 200)
+-        sage: expected = [((0, 1), (4, 0), xi + 2, -xi - 1),
+-        ....:             ((1, -1), (0, -1), 1/3*xi + 2/3, -1/3*xi + 1/3),
++        sage: expected = [((4, 1), (4, 0), xi + 2, -xi - 1),
++        ....:             ((3, -1), (2, -1), 1/3*xi + 2/3, -1/3*xi + 1/3),
+         ....:             ((1, 0), (5, 0), xi + 1, -xi),
+-        ....:             ((2, 0), (5, 1), xi, -xi + 1)]
++        ....:             ((2, 0), (3, 1), xi, -xi + 1)]
+         sage: eq_up_to_order(sols, expected)
+         True
+ 
+@@ -2769,7 +2769,7 @@ def solve_S_unit_equation(K, S, prec=106, include_exponents=True, include_bound=
+ 
+         sage: solutions, bound = solve_S_unit_equation(K, S, 100, include_bound=True)
+         sage: bound
+-        7
++        6
+ 
+     You can omit the exponent vectors::
+ 
+diff --git a/src/sage/rings/number_field/galois_group.py b/src/sage/rings/number_field/galois_group.py
+index c974c3df6ff..ee53ca6d674 100644
+--- a/src/sage/rings/number_field/galois_group.py
++++ b/src/sage/rings/number_field/galois_group.py
+@@ -995,8 +995,8 @@ def artin_symbol(self, P):
+             sage: K.<b> = NumberField(x^4 - 2*x^2 + 2, 'a').galois_closure()
+             sage: G = K.galois_group()
+             sage: [G.artin_symbol(P) for P in K.primes_above(7)]
+-            [(1,4)(2,3)(5,8)(6,7), (1,4)(2,3)(5,8)(6,7),
+-             (1,5)(2,6)(3,7)(4,8), (1,5)(2,6)(3,7)(4,8)]
++            [(1,5)(2,6)(3,7)(4,8), (1,5)(2,6)(3,7)(4,8),
++             (1,4)(2,3)(5,8)(6,7), (1,4)(2,3)(5,8)(6,7)]
+             sage: G.artin_symbol(17)
+             Traceback (most recent call last):
+             ...
+diff --git a/src/sage/rings/number_field/number_field.py b/src/sage/rings/number_field/number_field.py
+index bb16476980e..3a98a997962 100644
+--- a/src/sage/rings/number_field/number_field.py
++++ b/src/sage/rings/number_field/number_field.py
+@@ -3627,7 +3627,7 @@ def fractional_ideal(self, *gens, **kwds):
+             sage: L.<b> = K.extension(x^2 - 3, x^2 + 1)
+             sage: M.<c> = L.extension(x^2 + 1)
+             sage: L.ideal(K.ideal(2, a))
+-            Fractional ideal (a)
++            Fractional ideal (-a)
+             sage: M.ideal(K.ideal(2, a)) == M.ideal(a*(b - c)/2)
+             True
+ 
+@@ -3665,40 +3665,29 @@ def ideals_of_bdd_norm(self, bound):
+ 
+             sage: x = polygen(QQ, 'x')
+             sage: K.<a> = NumberField(x^2 + 23)
+-            sage: d = K.ideals_of_bdd_norm(10)
+-            sage: for n in d:
+-            ....:     print(n)
+-            ....:     for I in sorted(d[n]):
+-            ....:         print(I)
+-            1
+-            Fractional ideal (1)
+-            2
+-            Fractional ideal (2, 1/2*a - 1/2)
+-            Fractional ideal (2, 1/2*a + 1/2)
+-            3
+-            Fractional ideal (3, 1/2*a - 1/2)
+-            Fractional ideal (3, 1/2*a + 1/2)
+-            4
+-            Fractional ideal (2)
+-            Fractional ideal (4, 1/2*a + 3/2)
+-            Fractional ideal (4, 1/2*a + 5/2)
+-            5
+-            6
+-            Fractional ideal (1/2*a - 1/2)
+-            Fractional ideal (1/2*a + 1/2)
+-            Fractional ideal (6, 1/2*a + 5/2)
+-            Fractional ideal (6, 1/2*a + 7/2)
+-            7
+-            8
+-            Fractional ideal (4, a - 1)
+-            Fractional ideal (4, a + 1)
+-            Fractional ideal (1/2*a + 3/2)
+-            Fractional ideal (1/2*a - 3/2)
+-            9
+-            Fractional ideal (3)
+-            Fractional ideal (9, 1/2*a + 7/2)
+-            Fractional ideal (9, 1/2*a + 11/2)
+-            10
++            sage: d = K.ideals_of_bdd_norm(10); d # random
++                {1: [Fractional ideal (1)],
++                2: [Fractional ideal (2, 1/2*a - 1/2), Fractional ideal (2, 1/2*a + 1/2)],
++                3: [Fractional ideal (3, 1/2*a + 1/2), Fractional ideal (3, 1/2*a - 1/2)],
++                4: [Fractional ideal (4, 1/2*a + 3/2),
++                 Fractional ideal (2),
++                 Fractional ideal (4, 1/2*a + 5/2)],
++                5: [],
++                6: [Fractional ideal (6, 1/2*a + 7/2),
++                 Fractional ideal (-1/2*a - 1/2),
++                 Fractional ideal (-1/2*a + 1/2),
++                 Fractional ideal (6, 1/2*a + 5/2)],
++                7: [],
++                8: [Fractional ideal (1/2*a + 3/2),
++                 Fractional ideal (4, a - 1),
++                 Fractional ideal (4, a + 1),
++                 Fractional ideal (-1/2*a + 3/2)],
++                9: [Fractional ideal (9, 1/2*a + 7/2),
++                 Fractional ideal (3),
++                 Fractional ideal (9, 1/2*a + 11/2)],
++                10: []}
++            sage: [[I.norm() for I in sorted(d[n])] for n in d]
++                [[1], [2, 2], [3, 3], [4, 4, 4], [], [6, 6, 6, 6], [], [8, 8, 8, 8], [9, 9, 9], []]
+         """
+         hnf_ideals = self.pari_nf().ideallist(bound)
+         d = {}
+@@ -3925,9 +3914,13 @@ def primes_of_bounded_norm(self, B):
+         EXAMPLES::
+ 
+             sage: K.<i> = QuadraticField(-1)
+-            sage: K.primes_of_bounded_norm(10)
+-            [Fractional ideal (i + 1), Fractional ideal (-i - 2),
+-             Fractional ideal (2*i + 1), Fractional ideal (3)]
++            sage: P = K.primes_of_bounded_norm(10); P # random
++            [Fractional ideal (i + 1),
++             Fractional ideal (i + 2),
++             Fractional ideal (-i + 2),
++             Fractional ideal (3)]
++            sage: [p.norm() for p in P]
++            [2, 5, 5, 9]
+             sage: K.primes_of_bounded_norm(1)
+             []
+             sage: x = polygen(QQ, 'x')
+@@ -3936,10 +3929,10 @@ def primes_of_bounded_norm(self, B):
+             sage: P
+             [Fractional ideal (a),
+              Fractional ideal (a + 1),
+-             Fractional ideal (-a^2 - 1),
++             Fractional ideal (a^2 + 1),
+              Fractional ideal (a^2 + a - 1),
+              Fractional ideal (2*a + 1),
+-             Fractional ideal (-2*a^2 - a - 1),
++             Fractional ideal (2*a^2 + a + 1),
+              Fractional ideal (a^2 - 2*a - 1),
+              Fractional ideal (a + 3)]
+             sage: [p.norm() for p in P]
+@@ -3988,11 +3981,13 @@ def primes_of_bounded_norm_iter(self, B):
+ 
+             sage: K.<i> = QuadraticField(-1)
+             sage: it = K.primes_of_bounded_norm_iter(10)
+-            sage: list(it)
++            sage: l = list(it); l # random
+             [Fractional ideal (i + 1),
+              Fractional ideal (3),
+-             Fractional ideal (-i - 2),
+-             Fractional ideal (2*i + 1)]
++             Fractional ideal (i + 2),
++             Fractional ideal (-i + 2)]
++            sage: [I.norm() for I in l]
++            [2, 9, 5, 5]
+             sage: list(K.primes_of_bounded_norm_iter(1))
+             []
+         """
+@@ -4317,7 +4312,7 @@ def pari_nf(self, important=True):
+             sage: k.<a> = NumberField(x^4 - 3/2*x + 5/3); k
+             Number Field in a with defining polynomial x^4 - 3/2*x + 5/3
+             sage: k.pari_nf()
+-            [y^4 - 324*y + 2160, [0, 2], 48918708, 216, ..., [36, 36*y, y^3 + 6*y^2 - 252, 6*y^2], [1, 0, 0, 252; 0, 1, 0, 0; 0, 0, 0, 36; 0, 0, 6, -36], [1, 0, 0, 0, 0, 0, -18, 42, 0, -18, -46, -60, 0, 42, -60, -60; 0, 1, 0, 0, 1, 0, 2, 0, 0, 2, -11, -1, 0, 0, -1, 9; 0, 0, 1, 0, 0, 0, 6, 6, 1, 6, -5, 0, 0, 6, 0, 0; 0, 0, 0, 1, 0, 6, -6, -6, 0, -6, -1, 2, 1, -6, 2, 0]]
++            [y^4 - 324*y + 2160, [0, 2], 48918708, 216, ..., [36, 36*y, y^3 + 6*y^2 - 252, -6*y^2], [1, 0, 0, 252; 0, 1, 0, 0; 0, 0, 0, 36; 0, 0, -6, 36], [1, 0, 0, 0, 0, 0, -18, -42, 0, -18, -46, 60, 0, -42, 60, -60; 0, 1, 0, 0, 1, 0, 2, 0, 0, 2, -11, 1, 0, 0, 1, 9; 0, 0, 1, 0, 0, 0, 6, -6, 1, 6, -5, 0, 0, -6, 0, 0; 0, 0, 0, 1, 0, -6, 6, -6, 0, 6, 1, 2, 1, -6, 2, 0]]
+             sage: pari(k)
+             [y^4 - 324*y + 2160, [0, 2], 48918708, 216, ...]
+             sage: gp(k)
+@@ -4807,7 +4802,7 @@ def _S_class_group_and_units(self, S, proof=True):
+              1/13*a^2 + 7/13*a - 332/13,
+              -1/13*a^2 + 6/13*a + 345/13,
+              -1,
+-             -2/13*a^2 - 1/13*a + 755/13]
++             1/13*a^2 - 19/13*a - 7/13]
+             sage: units[5] in (1/13*a^2 - 19/13*a - 7/13, 1/13*a^2 + 20/13*a - 7/13)
+             True
+             sage: len(units) == 6
+@@ -4818,7 +4813,7 @@ def _S_class_group_and_units(self, S, proof=True):
+ 
+             sage: K.<a> = NumberField(2*x^2 - 1/3)
+             sage: K._S_class_group_and_units(tuple(K.primes_above(2) + K.primes_above(3)))
+-            ([6*a + 2, 6*a + 3, -1, -12*a + 5], [])
++            ([...6*a...2, ...6*a...3, -1, ...12*a...5], [])
+         """
+         K_pari = self.pari_bnf(proof=proof)
+         S_pari = [p.pari_prime() for p in sorted(set(S))]
+@@ -4996,7 +4991,7 @@ def selmer_generators(self, S, m, proof=True, orders=False):
+              1/13*a^2 + 7/13*a - 332/13,
+              -1/13*a^2 + 6/13*a + 345/13,
+              -1,
+-             -2/13*a^2 - 1/13*a + 755/13]
++             1/13*a^2 - 19/13*a - 7/13]
+             sage: gens[5] in (1/13*a^2 - 19/13*a - 7/13, 1/13*a^2 + 20/13*a - 7/13)
+             True
+             sage: gens[6] in (-1/13*a^2 + 45/13*a - 97/13, 1/13*a^2 - 45/13*a + 97/13)
+@@ -5153,16 +5148,20 @@ def selmer_space(self, S, p, proof=None):
+             sage: KS2, gens, fromKS2, toKS2 = K.selmer_space([P2, P3, P5], 2)
+             sage: KS2
+             Vector space of dimension 4 over Finite Field of size 2
+-            sage: gens
+-            [a + 1, a, 2, -1]
++            sage: gens  # random
++            [-a - 1, a, 2, -1]
++            sage: gens in ([-a - 1, a, 2, -1], [a + 1, a, 2, -1])
++            True
+ 
+         Each generator must have even valuation at primes not in `S`::
+ 
+-            sage: [K.ideal(g).factor() for g in gens]
++            sage: facgens = [K.ideal(g).factor() for g in gens]; facgens # random
+             [(Fractional ideal (2, a + 1)) * (Fractional ideal (3, a + 1)),
+              Fractional ideal (a),
+              (Fractional ideal (2, a + 1))^2,
+              1]
++            sage: facgens[2][0][1]
++            2
+ 
+             sage: toKS2(10)
+             (0, 0, 1, 1)
+@@ -5174,8 +5173,10 @@ def selmer_space(self, S, p, proof=None):
+             sage: KS3, gens, fromKS3, toKS3 = K.selmer_space([P2, P3, P5], 3)
+             sage: KS3
+             Vector space of dimension 3 over Finite Field of size 3
+-            sage: gens
+-            [1/2, 1/4*a + 1/4, a]
++            sage: gens # random
++            [1/2, -1/4*a - 1/4, a]
++            sage: gens in ([1/2, -1/4*a - 1/4, a], [1/2, 1/4*a + 1/4, a])
++            True
+ 
+         An example to show that the group `K(S,2)` may be strictly
+         larger than the group of elements giving extensions unramified
+@@ -5640,7 +5641,7 @@ def different(self):
+             sage: k.<a> = NumberField(x^2 + 23)
+             sage: d = k.different()
+             sage: d
+-            Fractional ideal (-a)
++            Fractional ideal (a)
+             sage: d.norm()
+             23
+             sage: k.disc()
+@@ -5760,7 +5761,7 @@ def elements_of_norm(self, n, proof=None) -> list:
+             sage: K.elements_of_norm(3)
+             []
+             sage: K.elements_of_norm(50)
+-            [-a - 7, 5*a - 5, 7*a + 1]
++            [7*a - 1, 5*a - 5, -7*a - 1]
+ 
+         TESTS:
+ 
+@@ -5871,11 +5872,16 @@ def factor(self, n):
+             sage: K.<a> = NumberField(x^2 + 1)
+             sage: K.factor(1/3)
+             (Fractional ideal (3))^-1
+-            sage: K.factor(1+a)
+-            Fractional ideal (a + 1)
+-            sage: K.factor(1+a/5)
+-            (Fractional ideal (a + 1)) * (Fractional ideal (-a - 2))^-1
+-              * (Fractional ideal (2*a + 1))^-1 * (Fractional ideal (-2*a + 3))
++            sage: fac = K.factor(1+a); fac # random
++            Fractional ideal (-a - 1)
++            sage: len(fac)
++            1
++            sage: fac = K.factor(1+a/5); fac # random
++            (Fractional ideal (-a - 1)) * (Fractional ideal (2*a - 1))^-1 * (Fractional ideal (-2*a - 1))^-1 * (Fractional ideal (3*a + 2))
++            sage: len(fac)
++            4
++            sage: product(I[0]^I[1] for I in list(fac))
++            Fractional ideal (1/5*a + 1)
+ 
+         An example over a relative number field::
+ 
+@@ -5908,9 +5914,9 @@ def factor(self, n):
+             sage: (fi, fj) = f[::]
+             sage: (fi[1], fj[1])
+             (1, 1)
+-            sage: fi[0] == L.fractional_ideal(1/2*a*b - a + 1/2)
++            sage: fi[0] == L.fractional_ideal(-1/2*a*b - a + 1/2)
+             True
+-            sage: fj[0] == L.fractional_ideal(-1/2*a*b - a + 1/2)
++            sage: fj[0] == L.fractional_ideal(1/2*a*b - a + 1/2)
+             True
+         """
+         return self.ideal(n).factor()
+@@ -6507,12 +6513,12 @@ def reduced_basis(self, prec=None):
+             sage: k.<a> = NumberField(x^6 + 2218926655879913714112*x^4 - 32507675650290949030789018433536*x^3 + 4923635504174417014460581055002374467948544*x^2 - 36066074010564497464129951249279114076897746988630016*x + 264187244046129768986806800244258952598300346857154900812365824)
+             sage: new_basis = k.reduced_basis(prec=120)
+             sage: [c.minpoly() for c in new_basis]
+-            [x - 1,
+-             x^2 + x + 1,
+-             x^6 + 3*x^5 - 102*x^4 - 103*x^3 + 10572*x^2 - 59919*x + 127657,
+-             x^6 + 3*x^5 - 102*x^4 - 103*x^3 + 10572*x^2 - 59919*x + 127657,
+-             x^3 - 171*x + 848,
+-             x^6 + 171*x^4 + 1696*x^3 + 29241*x^2 + 145008*x + 719104]
++            [x^2 + x + 1,
++             x - 1,
++             x^6 + 3*x^5 - 102*x^4 - 315*x^3 + 10254*x^2 + 80955*x + 198147,
++             x^6 + 213*x^4 + 12567*x^2 + 198147,
++             x^6 + 171*x^4 - 1696*x^3 + 29241*x^2 - 145008*x + 719104,
++             x^6 + 171*x^4 - 1696*x^3 + 29241*x^2 - 145008*x + 719104]
+             sage: R = k.order(new_basis)
+             sage: R.discriminant()==k.discriminant()
+             True
+@@ -7107,14 +7113,14 @@ def units(self, proof=None):
+             sage: K.units(proof=True)  # takes forever, not tested
+             ...
+             sage: K.units(proof=False)  # result not independently verified
+-            (-a^9 - a + 1,
++            (a^9 + a - 1,
++             -a^15 + a^12 - a^10 + a^9 + 2*a^8 - 3*a^7 - a^6 + 3*a^5 - a^4 - 4*a^3 + 3*a^2 + 2*a - 2,
++             a^15 + a^14 + a^13 + a^12 + a^10 - a^7 - a^6 - a^2 - 1,
++             2*a^16 - 3*a^15 + 3*a^14 - 3*a^13 + 3*a^12 - a^11 + a^9 - 3*a^8 + 4*a^7 - 5*a^6 + 6*a^5 - 4*a^4 + 3*a^3 - 2*a^2 - 2*a + 4,
+              -a^16 + a^15 - a^14 + a^12 - a^11 + a^10 + a^8 - a^7 + 2*a^6 - a^4 + 3*a^3 - 2*a^2 + 2*a - 1,
+-             2*a^16 - a^14 - a^13 + 3*a^12 - 2*a^10 + a^9 + 3*a^8 - 3*a^6 + 3*a^5 + 3*a^4 - 2*a^3 - 2*a^2 + 3*a + 4,
+-             a^15 + a^14 + 2*a^11 + a^10 - a^9 + a^8 + 2*a^7 - a^5 + 2*a^3 - a^2 - 3*a + 1,
+-             -a^16 - a^15 - a^14 - a^13 - a^12 - a^11 - a^10 - a^9 - a^8 - a^7 - a^6 - a^5 - a^4 - a^3 - a^2 + 2,
+-             -2*a^16 + 3*a^15 - 3*a^14 + 3*a^13 - 3*a^12 + a^11 - a^9 + 3*a^8 - 4*a^7 + 5*a^6 - 6*a^5 + 4*a^4 - 3*a^3 + 2*a^2 + 2*a - 4,
+-             a^15 - a^12 + a^10 - a^9 - 2*a^8 + 3*a^7 + a^6 - 3*a^5 + a^4 + 4*a^3 - 3*a^2 - 2*a + 2,
+-             2*a^16 + a^15 - a^11 - 3*a^10 - 4*a^9 - 4*a^8 - 4*a^7 - 5*a^6 - 7*a^5 - 8*a^4 - 6*a^3 - 5*a^2 - 6*a - 7)
++             a^16 - 2*a^15 - 2*a^13 - a^12 - a^11 - 2*a^10 + a^9 - 2*a^8 + 2*a^7 - 3*a^6 - 3*a^4 - 2*a^3 - a^2 - 4*a + 2,
++             -a^15 - a^14 - 2*a^11 - a^10 + a^9 - a^8 - 2*a^7 + a^5 - 2*a^3 + a^2 + 3*a - 1,
++             -3*a^16 - 3*a^15 - 3*a^14 - 3*a^13 - 3*a^12 - 2*a^11 - 2*a^10 - 2*a^9 - a^8 + a^7 + 2*a^6 + 3*a^5 + 3*a^4 + 4*a^3 + 6*a^2 + 8*a + 8)
+ 
+         TESTS:
+ 
+@@ -7123,7 +7129,7 @@ def units(self, proof=None):
+ 
+             sage: K.<a> = NumberField(1/2*x^2 - 1/6)
+             sage: K.units()
+-            (3*a - 2,)
++            (-3*a + 2,)
+         """
+         proof = proof_flag(proof)
+ 
+@@ -7205,14 +7211,14 @@ def unit_group(self, proof=None):
+             (u0, u1, u2, u3, u4, u5, u6, u7, u8)
+             sage: U.gens_values()  # result not independently verified
+             [-1,
+-             -a^9 - a + 1,
++             a^9 + a - 1,
++             -a^15 + a^12 - a^10 + a^9 + 2*a^8 - 3*a^7 - a^6 + 3*a^5 - a^4 - 4*a^3 + 3*a^2 + 2*a - 2,
++             a^15 + a^14 + a^13 + a^12 + a^10 - a^7 - a^6 - a^2 - 1,
++             2*a^16 - 3*a^15 + 3*a^14 - 3*a^13 + 3*a^12 - a^11 + a^9 - 3*a^8 + 4*a^7 - 5*a^6 + 6*a^5 - 4*a^4 + 3*a^3 - 2*a^2 - 2*a + 4,
+              -a^16 + a^15 - a^14 + a^12 - a^11 + a^10 + a^8 - a^7 + 2*a^6 - a^4 + 3*a^3 - 2*a^2 + 2*a - 1,
+-             2*a^16 - a^14 - a^13 + 3*a^12 - 2*a^10 + a^9 + 3*a^8 - 3*a^6 + 3*a^5 + 3*a^4 - 2*a^3 - 2*a^2 + 3*a + 4,
+-             a^15 + a^14 + 2*a^11 + a^10 - a^9 + a^8 + 2*a^7 - a^5 + 2*a^3 - a^2 - 3*a + 1,
+-             -a^16 - a^15 - a^14 - a^13 - a^12 - a^11 - a^10 - a^9 - a^8 - a^7 - a^6 - a^5 - a^4 - a^3 - a^2 + 2,
+-             -2*a^16 + 3*a^15 - 3*a^14 + 3*a^13 - 3*a^12 + a^11 - a^9 + 3*a^8 - 4*a^7 + 5*a^6 - 6*a^5 + 4*a^4 - 3*a^3 + 2*a^2 + 2*a - 4,
+-             a^15 - a^12 + a^10 - a^9 - 2*a^8 + 3*a^7 + a^6 - 3*a^5 + a^4 + 4*a^3 - 3*a^2 - 2*a + 2,
+-             2*a^16 + a^15 - a^11 - 3*a^10 - 4*a^9 - 4*a^8 - 4*a^7 - 5*a^6 - 7*a^5 - 8*a^4 - 6*a^3 - 5*a^2 - 6*a - 7]
++             a^16 - 2*a^15 - 2*a^13 - a^12 - a^11 - 2*a^10 + a^9 - 2*a^8 + 2*a^7 - 3*a^6 - 3*a^4 - 2*a^3 - a^2 - 4*a + 2,
++             -a^15 - a^14 - 2*a^11 - a^10 + a^9 - a^8 - 2*a^7 + a^5 - 2*a^3 + a^2 + 3*a - 1,
++             -3*a^16 - 3*a^15 - 3*a^14 - 3*a^13 - 3*a^12 - 2*a^11 - 2*a^10 - 2*a^9 - a^8 + a^7 + 2*a^6 + 3*a^5 + 3*a^4 + 4*a^3 + 6*a^2 + 8*a + 8]
+         """
+         proof = proof_flag(proof)
+ 
+@@ -7261,8 +7267,8 @@ def S_unit_group(self, proof=None, S=None):
+             sage: U = K.S_unit_group(S=a); U
+             S-unit group with structure C10 x Z x Z x Z of
+              Number Field in a with defining polynomial x^4 - 10*x^3 + 100*x^2 - 375*x + 1375
+-             with S = (Fractional ideal (5, 1/275*a^3 + 4/55*a^2 - 5/11*a + 5),
+-                       Fractional ideal (11, 1/275*a^3 + 4/55*a^2 - 5/11*a + 9))
++             with S = (Fractional ideal (5, -7/275*a^3 + 1/11*a^2 - 9/11*a),
++                       Fractional ideal (11, -7/275*a^3 + 1/11*a^2 - 9/11*a + 3))
+             sage: U.gens()
+             (u0, u1, u2, u3)
+             sage: U.gens_values()  # random
+@@ -7273,8 +7279,8 @@ def S_unit_group(self, proof=None, S=None):
+             sage: [u.multiplicative_order() for u in U.gens()]
+             [10, +Infinity, +Infinity, +Infinity]
+             sage: U.primes()
+-            (Fractional ideal (5, 1/275*a^3 + 4/55*a^2 - 5/11*a + 5),
+-             Fractional ideal (11, 1/275*a^3 + 4/55*a^2 - 5/11*a + 9))
++            (Fractional ideal (5, -7/275*a^3 + 1/11*a^2 - 9/11*a),
++             Fractional ideal (11, -7/275*a^3 + 1/11*a^2 - 9/11*a + 3))
+ 
+         With the default value of `S`, the S-unit group is the same as
+         the global unit group::
+@@ -7426,8 +7432,8 @@ def S_unit_solutions(self, S=[], prec=106, include_exponents=False, include_boun
+ 
+             sage: # needs sage.rings.padics
+             sage: solutions, bound = K.S_unit_solutions(S, prec=100, include_bound=True)
+-            sage: bound
+-            7
++            sage: bound in (6, 7)
++            True
+         """
+         from .S_unit_solver import solve_S_unit_equation
+         return solve_S_unit_equation(self, S, prec, include_exponents, include_bound, proof)
+@@ -8782,7 +8788,7 @@ def subfields(self, degree=0, name=None):
+             (Number Field in a1 with defining polynomial x^2 - 2, Ring morphism:
+               From: Number Field in a1 with defining polynomial x^2 - 2
+               To:   Number Field in a with defining polynomial 2*x^4 + 6*x^2 + 1/2
+-              Defn: a1 |--> a^2 + 3/2, None),
++              Defn: a1 |--> -a^2 - 3/2, None),
+             (Number Field in a2 with defining polynomial x^2 + 4, Ring morphism:
+               From: Number Field in a2 with defining polynomial x^2 + 4
+               To:   Number Field in a with defining polynomial 2*x^4 + 6*x^2 + 1/2
+@@ -8790,14 +8796,14 @@ def subfields(self, degree=0, name=None):
+             (Number Field in a3 with defining polynomial x^2 + 2, Ring morphism:
+               From: Number Field in a3 with defining polynomial x^2 + 2
+               To:   Number Field in a with defining polynomial 2*x^4 + 6*x^2 + 1/2
+-              Defn: a3 |--> 2*a^3 + 5*a, None),
++              Defn: a3 |--> -2*a^3 - 5*a, None),
+             (Number Field in a4 with defining polynomial x^4 + 1, Ring morphism:
+               From: Number Field in a4 with defining polynomial x^4 + 1
+               To:   Number Field in a with defining polynomial 2*x^4 + 6*x^2 + 1/2
+-              Defn: a4 |--> a^3 + 1/2*a^2 + 5/2*a + 3/4, Ring morphism:
++              Defn: a4 |--> -a^3 - 1/2*a^2 - 5/2*a - 3/4, Ring morphism:
+               From: Number Field in a with defining polynomial 2*x^4 + 6*x^2 + 1/2
+               To:   Number Field in a4 with defining polynomial x^4 + 1
+-              Defn: a |--> -1/2*a4^3 + a4^2 - 1/2*a4)
++              Defn: a |--> 1/2*a4^3 + a4^2 + 1/2*a4)
+             ]
+         """
+         return self._subfields_helper(degree=degree, name=name,
+@@ -12694,12 +12700,12 @@ def _splitting_classes_gens_(K, m, d):
+         sage: L = K.subfields(20)[0][0]
+         sage: L.conductor()                                                             # needs sage.groups
+         101
+-        sage: _splitting_classes_gens_(L,101,20)                                        # needs sage.libs.gap  # optional - gap_package_polycyclic
++        sage: _splitting_classes_gens_(L,101,20)        # optional - gap_package_polycyclic, needs sage.libs.gap
+         [95]
+ 
+         sage: K = CyclotomicField(44)
+         sage: L = K.subfields(4)[0][0]
+-        sage: _splitting_classes_gens_(L,44,4)                                          # needs sage.libs.gap  # optional - gap_package_polycyclic
++        sage: _splitting_classes_gens_(L,44,4)  # optional - gap_package_polycyclic, needs sage.libs.gap
+         [37]
+ 
+         sage: K = CyclotomicField(44)
+@@ -12711,7 +12717,7 @@ def _splitting_classes_gens_(K, m, d):
+          with zeta44_0 = 3.837971894457990?
+         sage: L.conductor()                                                             # needs sage.groups
+         11
+-        sage: _splitting_classes_gens_(L,11,5)                                          # needs sage.libs.gap  # optional - gap_package_polycyclic
++        sage: _splitting_classes_gens_(L,11,5)  # optional - gap_package_polycyclic, needs sage.libs.gap
+         [10]
+     """
+     from sage.groups.abelian_gps.abelian_group import AbelianGroup
+diff --git a/src/sage/rings/number_field/number_field_element.pyx b/src/sage/rings/number_field/number_field_element.pyx
+index 27432813b2b..1a676ee087b 100644
+--- a/src/sage/rings/number_field/number_field_element.pyx
++++ b/src/sage/rings/number_field/number_field_element.pyx
+@@ -1954,14 +1954,14 @@ cdef class NumberFieldElement(NumberFieldElement_base):
+             sage: x = polygen(ZZ, 'x')
+             sage: K.<i> = NumberField(x^2 + 1)
+             sage: (6*i + 6).factor()
+-            (-i) * (i + 1)^3 * 3
++            (i) * (-i - 1)^3 * 3
+ 
+         In the following example, the class number is 2.  If a factorization
+         in prime elements exists, we will find it::
+ 
+             sage: K.<a> = NumberField(x^2 - 10)
+             sage: factor(169*a + 531)
+-            (-6*a - 19) * (-3*a - 1) * (-2*a + 9)
++            (-6*a - 19) * (2*a - 9) * (3*a + 1)
+             sage: factor(K(3))
+             Traceback (most recent call last):
+             ...
+@@ -4238,7 +4238,7 @@ cdef class NumberFieldElement(NumberFieldElement_base):
+ 
+             sage: P5s = F(5).support()
+             sage: P5s
+-            [Fractional ideal (-t^2 - 1), Fractional ideal (t^2 - 2*t - 1)]
++            [Fractional ideal (t^2 + 1), Fractional ideal (t^2 - 2*t - 1)]
+             sage: all(5 in P5 for P5 in P5s)
+             True
+             sage: all(P5.is_prime() for P5 in P5s)
+@@ -4487,7 +4487,7 @@ cdef class NumberFieldElement(NumberFieldElement_base):
+             sage: f = Qi.embeddings(K)[0]
+             sage: a = f(2+3*i) * (2-zeta)^2
+             sage: a.descend_mod_power(Qi,2)
+-            [-2*i + 3, 3*i + 2]
++            [3*i + 2, 2*i - 3]
+ 
+         An absolute example::
+ 
+diff --git a/src/sage/rings/number_field/number_field_ideal.py b/src/sage/rings/number_field/number_field_ideal.py
+index 3686840ccba..b269045cf96 100644
+--- a/src/sage/rings/number_field/number_field_ideal.py
++++ b/src/sage/rings/number_field/number_field_ideal.py
+@@ -75,7 +75,7 @@ class NumberFieldIdeal(Ideal_generic):
+         Fractional ideal (3)
+         sage: F = pari(K).idealprimedec(5)
+         sage: K.ideal(F[0])
+-        Fractional ideal (2*i + 1)
++        Fractional ideal (-2*i - 1)
+ 
+     TESTS:
+ 
+@@ -236,7 +236,7 @@ def _richcmp_(self, other, op):
+             sage: K.<a> = NumberField(x^2 + 3); K
+             Number Field in a with defining polynomial x^2 + 3
+             sage: f = K.factor(15); f
+-            (Fractional ideal (1/2*a + 3/2))^2 * (Fractional ideal (5))
++            (Fractional ideal (-a))^2 * (Fractional ideal (5))
+             sage: (f[0][0] < f[1][0])
+             True
+             sage: (f[0][0] == f[0][0])
+@@ -273,7 +273,7 @@ def _mul_(self, other):
+             sage: A = K.ideal([5, 2 + I])
+             sage: B = K.ideal([13, 5 + 12*I])
+             sage: A*B
+-            Fractional ideal (4*I - 7)
++            Fractional ideal (-4*I + 7)
+             sage: (K.ideal(3 + I) * K.ideal(7 + I)).gens()
+             (10*I + 20,)
+ 
+@@ -683,17 +683,17 @@ def free_module(self):
+             sage: I.free_module()
+             Free module of degree 4 and rank 4 over Integer Ring
+             User basis matrix:
+-            [  4   0   0   0]
+-            [ -3   7  -1   1]
+-            [  3   7   1   1]
+-            [  0 -10   0  -2]
++            [ 4  0  0  0]
++            [ 3  7  1  1]
++            [ 0 10  0  2]
++            [ 3 -7  1 -1]
+             sage: J = I^(-1); J.free_module()
+             Free module of degree 4 and rank 4 over Integer Ring
+             User basis matrix:
+             [  1/4     0     0     0]
+-            [-3/16  7/16 -1/16  1/16]
+             [ 3/16  7/16  1/16  1/16]
+-            [    0  -5/8     0  -1/8]
++            [    0   5/8     0   1/8]
++            [ 3/16 -7/16  1/16 -1/16]
+ 
+         An example of intersecting ideals by intersecting free modules.::
+ 
+@@ -790,7 +790,7 @@ def gens_reduced(self, proof=None):
+             sage: J.is_principal()
+             False
+             sage: J.gens_reduced()
+-            (5, a)
++            (5, -a)
+             sage: all(j.parent() is K for j in J.gens())
+             True
+             sage: all(j.parent() is K for j in J.gens_reduced())
+@@ -2069,7 +2069,7 @@ def ramification_index(self):
+             sage: K.<a> = NumberField(x^2 + 2); K
+             Number Field in a with defining polynomial x^2 + 2
+             sage: f = K.factor(2); f
+-            (Fractional ideal (a))^2
++            (Fractional ideal (...a))^2
+             sage: f[0][0].ramification_index()
+             2
+             sage: K.ideal(13).ramification_index()
+@@ -2416,9 +2416,9 @@ def denominator(self):
+             sage: I = K.ideal((3+4*i)/5); I
+             Fractional ideal (4/5*i + 3/5)
+             sage: I.denominator()
+-            Fractional ideal (2*i + 1)
++            Fractional ideal (-2*i - 1)
+             sage: I.numerator()
+-            Fractional ideal (-i - 2)
++            Fractional ideal (2*i - 1)
+             sage: I.numerator().is_integral() and I.denominator().is_integral()
+             True
+             sage: I.numerator() + I.denominator() == K.unit_ideal()
+@@ -2447,9 +2447,9 @@ def numerator(self):
+             sage: I = K.ideal((3+4*i)/5); I
+             Fractional ideal (4/5*i + 3/5)
+             sage: I.denominator()
+-            Fractional ideal (2*i + 1)
++            Fractional ideal (-2*i - 1)
+             sage: I.numerator()
+-            Fractional ideal (-i - 2)
++            Fractional ideal (2*i - 1)
+             sage: I.numerator().is_integral() and I.denominator().is_integral()
+             True
+             sage: I.numerator() + I.denominator() == K.unit_ideal()
+@@ -3164,11 +3164,11 @@ def _p_quotient(self, p):
+             Partially defined quotient map
+              from Number Field in i with defining polynomial x^2 + 1
+                to an explicit vector space representation for the quotient of
+-                  the ring of integers by (p,I) for the ideal I=Fractional ideal (-i - 2).
++                  the ring of integers by (p,I) for the ideal I=Fractional ideal (2*i - 1).
+             sage: lift
+             Lifting map
+                to Gaussian Integers generated by i in Number Field in i with defining polynomial x^2 + 1
+-               from quotient of integers by Fractional ideal (-i - 2)
++               from quotient of integers by Fractional ideal (2*i - 1)
+         """
+         return quotient_char_p(self, p)
+ 
+@@ -3213,11 +3213,11 @@ def residue_field(self, names=None):
+ 
+             sage: K.<i> = NumberField(x^2 + 1)
+             sage: P1, P2 = [g[0] for g in K.factor(5)]; P1, P2
+-            (Fractional ideal (-i - 2), Fractional ideal (2*i + 1))
++            (Fractional ideal (2*i - 1), Fractional ideal (-2*i - 1))
+             sage: a = 1/(1+2*i)
+             sage: F1, F2 = [g.residue_field() for g in [P1, P2]]; F1, F2
+-            (Residue field of Fractional ideal (-i - 2),
+-             Residue field of Fractional ideal (2*i + 1))
++            (Residue field of Fractional ideal (2*i - 1),
++             Residue field of Fractional ideal (-2*i - 1))
+             sage: a.valuation(P1)
+             0
+             sage: F1(i/7)
+@@ -3230,7 +3230,7 @@ def residue_field(self, names=None):
+             Traceback (most recent call last):
+             ...
+             ZeroDivisionError: Cannot reduce field element -2/5*i + 1/5
+-            modulo Fractional ideal (2*i + 1): it has negative valuation
++            modulo Fractional ideal (-2*i - 1): it has negative valuation
+ 
+         An example with a relative number field::
+ 
+@@ -3491,7 +3491,7 @@ def quotient_char_p(I, p):
+         []
+ 
+         sage: I = K.factor(13)[0][0]; I
+-        Fractional ideal (-2*i + 3)
++        Fractional ideal (3*i + 2)
+         sage: I.residue_class_degree()
+         1
+         sage: quotient_char_p(I, 13)[0]
+diff --git a/src/sage/rings/number_field/number_field_ideal_rel.py b/src/sage/rings/number_field/number_field_ideal_rel.py
+index 7f6cfd9b1b7..eb39f6f4d12 100644
+--- a/src/sage/rings/number_field/number_field_ideal_rel.py
++++ b/src/sage/rings/number_field/number_field_ideal_rel.py
+@@ -11,7 +11,7 @@
+     sage: G = [from_A(z) for z in I.gens()]; G
+     [7, -2*b*a - 1]
+     sage: K.fractional_ideal(G)
+-    Fractional ideal ((1/2*b + 2)*a - 1/2*b + 2)
++    Fractional ideal ((-1/2*b + 2)*a - 1/2*b - 2)
+     sage: K.fractional_ideal(G).absolute_norm().factor()
+     7^2
+ 
+@@ -277,7 +277,7 @@ def gens_reduced(self):
+             sage: L.<b> = K.extension(5*x^2 + 1)
+             sage: P = L.primes_above(2)[0]
+             sage: P.gens_reduced()
+-            (2, -15*a*b + 3*a + 1)
++            (2, -15*a*b - 3*a + 1)
+         """
+         try:
+             # Compute the single generator, if it exists
+@@ -385,7 +385,7 @@ def relative_norm(self):
+             sage: K.<a> = NumberField(x^2 + 6)
+             sage: L.<b> = K.extension(K['x'].gen()^4 + a)
+             sage: N = L.ideal(b).relative_norm(); N
+-            Fractional ideal (-a)
++            Fractional ideal (a)
+             sage: N.parent()
+             Monoid of ideals of Number Field in a with defining polynomial x^2 + 6
+             sage: N.ring()
+@@ -409,8 +409,10 @@ def relative_norm(self):
+             sage: K.<a> = NumberField(2*x^2 - 1/3)
+             sage: L.<b> = K.extension(5*x^2 + 1)
+             sage: P = L.primes_above(2)[0]
+-            sage: P.relative_norm()
+-            Fractional ideal (6*a + 2)
++            sage: rn = P.relative_norm(); rn # random
++            Fractional ideal (6*a - 2)
++            sage: rn in [K.ideal(6*a - 2), K.ideal(-6*a -2)]
++            True
+         """
+         L = self.number_field()
+         K = L.base_field()
+@@ -528,8 +530,10 @@ def ideal_below(self):
+             sage: K.<a> = NumberField(2*x^2 - 1/3)
+             sage: L.<b> = K.extension(5*x^2 + 1)
+             sage: P = L.primes_above(2)[0]
+-            sage: P.ideal_below()
+-            Fractional ideal (6*a + 2)
++            sage: ib = P.ideal_below(); ib # random
++            Fractional ideal (6*a - 2)
++            sage: ib in [K.ideal(6*a - 2), K.ideal(-6*a -2)]
++            True
+         """
+         L = self.number_field()
+         K = L.base_field()
+@@ -548,14 +552,12 @@ def factor(self):
+             sage: x = polygen(ZZ, 'x')
+             sage: K.<a, b> = QQ.extension([x^2 + 11, x^2 - 5])
+             sage: K.factor(5)
+-            (Fractional ideal (5, (-1/4*b - 1/4)*a + 1/4*b - 3/4))^2
+-             * (Fractional ideal (5, (-1/4*b - 1/4)*a + 1/4*b - 7/4))^2
++            (Fractional ideal (5, (1/4*b - 1/4)*a + 1/4*b + 3/4))^2 * (Fractional ideal (5, (1/4*b - 1/4)*a + 1/4*b + 7/4))^2
+             sage: K.ideal(5).factor()
+-            (Fractional ideal (5, (-1/4*b - 1/4)*a + 1/4*b - 3/4))^2
+-             * (Fractional ideal (5, (-1/4*b - 1/4)*a + 1/4*b - 7/4))^2
++            (Fractional ideal (5, (1/4*b - 1/4)*a + 1/4*b + 3/4))^2 * (Fractional ideal (5, (1/4*b - 1/4)*a + 1/4*b + 7/4))^2
+             sage: K.ideal(5).prime_factors()
+-            [Fractional ideal (5, (-1/4*b - 1/4)*a + 1/4*b - 3/4),
+-             Fractional ideal (5, (-1/4*b - 1/4)*a + 1/4*b - 7/4)]
++            [Fractional ideal (5, (1/4*b - 1/4)*a + 1/4*b + 3/4),
++             Fractional ideal (5, (1/4*b - 1/4)*a + 1/4*b + 7/4)]
+ 
+             sage: PQ.<X> = QQ[]
+             sage: F.<a, b> = NumberFieldTower([X^2 - 2, X^2 - 3])
+@@ -914,7 +916,7 @@ def is_NumberFieldFractionalIdeal_rel(x):
+         sage: is_NumberFieldFractionalIdeal_rel(I)
+         True
+         sage: N = I.relative_norm(); N
+-        Fractional ideal (-a)
++        Fractional ideal (a)
+         sage: is_NumberFieldFractionalIdeal_rel(N)
+         False
+     """
+diff --git a/src/sage/rings/number_field/number_field_rel.py b/src/sage/rings/number_field/number_field_rel.py
+index 9ab6fd4c261..6e9bf71baf4 100644
+--- a/src/sage/rings/number_field/number_field_rel.py
++++ b/src/sage/rings/number_field/number_field_rel.py
+@@ -233,21 +233,21 @@ def __init__(self, base, polynomial, name,
+             sage: l.<b> = k.extension(5*x^2 + 3); l
+             Number Field in b with defining polynomial 5*x^2 + 3 over its base field
+             sage: l.pari_rnf()
+-            [x^2 + (-y^3 + 1/2*y^2 - 6*y + 3/2)*x + (-3/4*y^3 - 1/4*y^2 - 17/4*y - 19/4), ..., y^4 + 6*y^2 + 1, x^2 + (-y^3 + 1/2*y^2 - 6*y + 3/2)*x + (-3/4*y^3 - 1/4*y^2 - 17/4*y - 19/4)], [0, 0]]
++            [x^2 + (5/4*y^3 - 1/4*y^2 + 27/4*y - 3/4)*x + (-9/4*y^3 - 1/4*y^2 - 47/4*y - 7/4), ..., y^4 + 6*y^2 + 1, x^2 + (5/4*y^3 - 1/4*y^2 + 27/4*y - 3/4)*x + (-9/4*y^3 - 1/4*y^2 - 47/4*y - 7/4)], [0, 0]]
+             sage: b
+             b
+ 
+             sage: l.<b> = k.extension(x^2 + 3/5); l
+             Number Field in b with defining polynomial x^2 + 3/5 over its base field
+             sage: l.pari_rnf()
+-            [x^2 + (-y^3 + 1/2*y^2 - 6*y + 3/2)*x + (-3/4*y^3 - 1/4*y^2 - 17/4*y - 19/4), ..., y^4 + 6*y^2 + 1, x^2 + (-y^3 + 1/2*y^2 - 6*y + 3/2)*x + (-3/4*y^3 - 1/4*y^2 - 17/4*y - 19/4)], [0, 0]]
++            [x^2 + (5/4*y^3 - 1/4*y^2 + 27/4*y - 3/4)*x + (-9/4*y^3 - 1/4*y^2 - 47/4*y - 7/4), ..., y^4 + 6*y^2 + 1, x^2 + (5/4*y^3 - 1/4*y^2 + 27/4*y - 3/4)*x + (-9/4*y^3 - 1/4*y^2 - 47/4*y - 7/4)], [0, 0]]
+             sage: b
+             b
+ 
+             sage: l.<b> = k.extension(x - 1/a0); l
+             Number Field in b with defining polynomial x + 1/2*a0 over its base field
+             sage: l.pari_rnf()
+-            [x, [4, -x^3 - x^2 - 7*x - 3, -x^3 + x^2 - 7*x + 3, 2*x^3 + 10*x], ..., [x^4 + 6*x^2 + 1, -x, -1, y^4 + 6*y^2 + 1, x], [0, 0]]
++            [x, [4, -x^3 + x^2 - 7*x + 3, -2*x^3 - 10*x, x^3 + x^2 + 7*x + 3], ..., [x^4 + 6*x^2 + 1, -x, -1, y^4 + 6*y^2 + 1, x], [0, 0]]
+             sage: b
+             -1/2*a0
+ 
+@@ -1635,9 +1635,9 @@ def _pari_relative_structure(self):
+             sage: K.<a> = NumberField(x^2 + 1)
+             sage: L.<b> = K.extension(x^2 - 1/2)
+             sage: L._pari_relative_structure()
+-            (x^2 + Mod(-y, y^2 + 1),
+-             Mod(Mod(1/2*y - 1/2, y^2 + 1)*x, x^2 + Mod(-y, y^2 + 1)),
+-             Mod(Mod(-y - 1, y^2 + 1)*x, Mod(1, y^2 + 1)*x^2 + Mod(-1/2, y^2 + 1)))
++            (x^2 + Mod(y, y^2 + 1),
++             Mod(Mod(-1/2*y - 1/2, y^2 + 1)*x, x^2 + Mod(y, y^2 + 1)),
++             Mod(Mod(y - 1, y^2 + 1)*x, x^2 + Mod(-1/2, y^2 + 1)))
+ 
+         An example where both fields are defined by non-integral or
+         non-monic polynomials::
+@@ -1937,7 +1937,7 @@ def absolute_polynomial(self):
+             sage: k.relative_polynomial()
+             x^2 + 1/3
+             sage: k.pari_relative_polynomial()
+-            x^2 + Mod(y, y^2 + 1)*x - 1
++            x^2 + Mod(-y, y^2 + 1)*x - 1
+         """
+         return QQ['x'](self._pari_rnfeq()[0])
+ 
+@@ -2721,7 +2721,7 @@ def uniformizer(self, P, others='positive'):
+             sage: x = polygen(ZZ, 'x')
+             sage: K.<a, b> = NumberField([x^2 + 23, x^2 - 3])
+             sage: P = K.prime_factors(5)[0]; P
+-            Fractional ideal (5, 1/2*a + b - 5/2)
++            Fractional ideal (5, -1/2*a + b + 5/2)
+             sage: u = K.uniformizer(P)
+             sage: u.valuation(P)
+             1
+diff --git a/src/sage/rings/number_field/order.py b/src/sage/rings/number_field/order.py
+index 55db3bbbcbf..8b69baf5464 100644
+--- a/src/sage/rings/number_field/order.py
++++ b/src/sage/rings/number_field/order.py
+@@ -495,7 +495,7 @@ def fractional_ideal(self, *args, **kwds):
+             sage: K.<a> = NumberField(x^2 + 2)
+             sage: R = K.maximal_order()
+             sage: R.fractional_ideal(2/3 + 7*a, a)
+-            Fractional ideal (1/3*a)
++            Fractional ideal (-1/3*a)
+         """
+         return self.number_field().fractional_ideal(*args, **kwds)
+ 
+@@ -569,7 +569,7 @@ def __mul__(self, right):
+             sage: k.<a> = NumberField(x^2 + 5077); G = k.class_group(); G
+             Class group of order 22 with structure C22 of Number Field in a with defining polynomial x^2 + 5077
+             sage: G.0 ^ -9
+-            Fractional ideal class (43, a + 13)
++            Fractional ideal class (67, a + 45)
+             sage: Ok = k.maximal_order(); Ok
+             Maximal Order generated by a in Number Field in a with defining polynomial x^2 + 5077
+             sage: Ok * (11, a + 7)
+@@ -2918,7 +2918,7 @@ def GaussianIntegers(names='I', latex_name='i'):
+         sage: ZZI
+         Gaussian Integers generated by I in Number Field in I with defining polynomial x^2 + 1 with I = 1*I
+         sage: factor(3 + I)
+-        (-I) * (I + 1) * (2*I + 1)
++        (-I) * (I - 2) * (-I + 1)
+         sage: CC(I)
+         1.00000000000000*I
+         sage: I.minpoly()
+@@ -2949,7 +2949,7 @@ def EisensteinIntegers(names='omega'):
+          with defining polynomial x^2 + x + 1
+          with omega = -0.50000000000000000? + 0.866025403784439?*I
+         sage: factor(3 + omega)
+-        (-1) * (-omega - 3)
++        (omega + 1) * (-2*omega + 1)
+         sage: CC(omega)
+         -0.500000000000000 + 0.866025403784439*I
+         sage: omega.minpoly()
+diff --git a/src/sage/rings/number_field/selmer_group.py b/src/sage/rings/number_field/selmer_group.py
+index acdf2954fdf..7da6b58a209 100644
+--- a/src/sage/rings/number_field/selmer_group.py
++++ b/src/sage/rings/number_field/selmer_group.py
+@@ -71,7 +71,7 @@ def _ideal_generator(I):
+ 
+         sage: K.<a> = QuadraticField(-11)
+         sage: [_ideal_generator(K.prime_above(p)) for p in primes(25)]
+-        [2, 1/2*a - 1/2, -1/2*a - 3/2, 7, -a, 13, 17, 19, 1/2*a + 9/2]
++        [2, 1/2*a - 1/2, -1/2*a - 3/2, 7, a, 13, 17, 19, 1/2*a + 9/2]
+     """
+     try:
+         return I.gens_reduced()[0]
+diff --git a/src/sage/rings/polynomial/polynomial_quotient_ring.py b/src/sage/rings/polynomial/polynomial_quotient_ring.py
+index e12977e8464..c5bf39a1c73 100644
+--- a/src/sage/rings/polynomial/polynomial_quotient_ring.py
++++ b/src/sage/rings/polynomial/polynomial_quotient_ring.py
+@@ -1429,13 +1429,13 @@ def S_class_group(self, S, proof=True):
+             sage: R.<x> = K[]
+             sage: S.<xbar> = R.quotient(x^2 + 23)
+             sage: S.S_class_group([])
+-            [((2, -a + 1, 1/2*xbar + 1/2, -1/2*a*xbar + 1/2*a + 1), 6)]
++            [((2, a + 1, -1/2*xbar + 3/2, 1/2*a*xbar - 1/2*a + 1), 6)]
+             sage: S.S_class_group([K.ideal(3, a-1)])
+             []
+             sage: S.S_class_group([K.ideal(2, a+1)])
+             []
+             sage: S.S_class_group([K.ideal(a)])
+-            [((2, -a + 1, 1/2*xbar + 1/2, -1/2*a*xbar + 1/2*a + 1), 6)]
++            [((2, a + 1, -1/2*xbar + 3/2, 1/2*a*xbar - 1/2*a + 1), 6)]
+ 
+         Now we take an example over a nontrivial base with two factors, each
+         contributing to the class group::
+@@ -1495,14 +1495,14 @@ def S_class_group(self, S, proof=True):
+             sage: C = S.S_class_group([])
+             sage: C[:2]
+             [((1/4*xbar^2 + 31/4,
+-               (-1/8*a + 1/8)*xbar^2 - 31/8*a + 31/8,
+-               1/16*xbar^3 + 1/16*xbar^2 + 31/16*xbar + 31/16,
+-               -1/16*a*xbar^3 + (1/16*a + 1/8)*xbar^2 - 31/16*a*xbar + 31/16*a + 31/8),
++               (1/8*a + 1/8)*xbar^2 + 31/8*a + 31/8,
++               -1/16*xbar^3 + 3/16*xbar^2 - 31/16*xbar + 93/16,
++               1/16*a*xbar^3 + (-1/16*a + 1/8)*xbar^2 + 31/16*a*xbar - 31/16*a + 31/8),
+               6),
+              ((-1/4*xbar^2 - 23/4,
+-               (1/8*a - 1/8)*xbar^2 + 23/8*a - 23/8,
+-               -1/16*xbar^3 - 1/16*xbar^2 - 23/16*xbar - 23/16,
+-               1/16*a*xbar^3 + (-1/16*a - 1/8)*xbar^2 + 23/16*a*xbar - 23/16*a - 23/8),
++               (-1/8*a - 1/8)*xbar^2 - 23/8*a - 23/8,
++               1/16*xbar^3 + 1/16*xbar^2 + 23/16*xbar + 23/16,
++               -1/16*a*xbar^3 + (1/16*a - 1/8)*xbar^2 - 23/16*a*xbar + 23/16*a - 23/8),
+               6)]
+             sage: C[2][1]
+             2
+@@ -1514,11 +1514,11 @@ def S_class_group(self, S, proof=True):
+             ....:     1/16*a*xbar^3 - 1/16*a*xbar^2 + 23/16*a*xbar - 23/16*a)
+             sage: gens[0] == expected_gens[0]
+             True
+-            sage: gens[1] in (expected_gens[1], expected_gens[1]/2 + expected_gens[0]/2)
++            sage: gens[1] in (expected_gens[1], expected_gens[1]/2 + expected_gens[0]/2, -expected_gens[1]/2 + expected_gens[0]/2)
+             True
+-            sage: gens[2] in (expected_gens[2], expected_gens[2] + expected_gens[0]/2)
++            sage: gens[2] in (expected_gens[2], expected_gens[2] + expected_gens[0]/2, -expected_gens[2] + expected_gens[0]/2)
+             True
+-            sage: gens[3] in (expected_gens[3], expected_gens[3] + expected_gens[0]/2)
++            sage: gens[3] in (expected_gens[3], expected_gens[3] + expected_gens[0]/2, -expected_gens[3] + expected_gens[0]/2)
+             True
+         """
+         fields, isos, iso_classes = self._S_decomposition(tuple(S))
+@@ -1611,7 +1611,7 @@ def class_group(self, proof=True):
+             sage: R.<x> = K[]
+             sage: S.<xbar> = R.quotient(x^2 + 23)
+             sage: S.class_group()
+-            [((2, -a + 1, 1/2*xbar + 1/2, -1/2*a*xbar + 1/2*a + 1), 6)]
++            [((2, a + 1, -1/2*xbar + 3/2, 1/2*a*xbar - 1/2*a + 1), 6)]
+ 
+         Here is an example of a product of number fields, both of which
+         contribute to the class group::
+@@ -1711,19 +1711,19 @@ def S_units(self, S, proof=True):
+              with defining polynomial x^2 + 3 with a = 1.732050807568878?*I
+              with modulus y^3 + 5
+             sage: [u for u, o in L.S_units([]) if o is Infinity]
+-            [(-1/3*a - 1)*b^2 - 4/3*a*b - 5/6*a + 7/2,
+-             2/3*a*b^2 + (2/3*a - 2)*b - 5/6*a - 7/2]
++            [(-1/3*a - 1)*b^2 - 4/3*a*b - 4/3*a + 3,
++             (-1/3*a - 1)*b^2 + (2/3*a - 2)*b + 13/6*a - 1/2]
+             sage: [u for u, o in L.S_units([K.ideal(1/2*a - 3/2)])
+             ....:  if o is Infinity]
+             [(-1/6*a - 1/2)*b^2 + (1/3*a - 1)*b + 4/3*a,
+-             (-1/3*a - 1)*b^2 - 4/3*a*b - 5/6*a + 7/2,
+-             2/3*a*b^2 + (2/3*a - 2)*b - 5/6*a - 7/2]
++             (-1/3*a - 1)*b^2 - 4/3*a*b - 4/3*a + 3,
++             (-1/3*a - 1)*b^2 + (2/3*a - 2)*b + 13/6*a - 1/2]
+             sage: [u for u, o in L.S_units([K.ideal(2)]) if o is Infinity]
+             [(1/2*a - 1/2)*b^2 + (a + 1)*b + 3,
+-             (1/6*a + 1/2)*b^2 + (-1/3*a + 1)*b - 5/6*a + 1/2,
+              (1/6*a + 1/2)*b^2 + (-1/3*a + 1)*b - 5/6*a - 1/2,
+-             (-1/3*a - 1)*b^2 - 4/3*a*b - 5/6*a + 7/2,
+-             2/3*a*b^2 + (2/3*a - 2)*b - 5/6*a - 7/2]
++             1/3*a*b^2 + (1/3*a + 1)*b - 1/6*a + 3/2,
++             (-1/3*a - 1)*b^2 - 4/3*a*b - 4/3*a + 3,
++             (-1/3*a - 1)*b^2 + (2/3*a - 2)*b + 13/6*a - 1/2]
+ 
+         Note that all the returned values live where we expect them to::
+ 
+@@ -1808,8 +1808,8 @@ def units(self, proof=True):
+              with defining polynomial x^2 + 3 with a = 1.732050807568878?*I
+              with modulus y^3 + 5
+             sage: [u for u, o in L.units() if o is Infinity]
+-            [(-1/3*a - 1)*b^2 - 4/3*a*b - 5/6*a + 7/2,
+-             2/3*a*b^2 + (2/3*a - 2)*b - 5/6*a - 7/2]
++            [(-1/3*a - 1)*b^2 - 4/3*a*b - 4/3*a + 3,
++             (-1/3*a - 1)*b^2 + (2/3*a - 2)*b + 13/6*a - 1/2]
+             sage: L.<b> = K.extension(y^3 + 5)
+             sage: L.unit_group()
+             Unit group with structure C6 x Z x Z of
+@@ -1817,8 +1817,8 @@ def units(self, proof=True):
+             sage: L.unit_group().gens()    # abstract generators
+             (u0, u1, u2)
+             sage: L.unit_group().gens_values()[1:]
+-            [(-1/3*a - 1)*b^2 - 4/3*a*b - 5/6*a + 7/2,
+-             2/3*a*b^2 + (2/3*a - 2)*b - 5/6*a - 7/2]
++            [(-1/3*a - 1)*b^2 - 4/3*a*b - 4/3*a + 3,
++             (-1/3*a - 1)*b^2 + (2/3*a - 2)*b + 13/6*a - 1/2]
+ 
+         Note that all the returned values live where we expect them to::
+ 
+diff --git a/src/sage/rings/qqbar.py b/src/sage/rings/qqbar.py
+index 300d64b8279..08c04e6e234 100644
+--- a/src/sage/rings/qqbar.py
++++ b/src/sage/rings/qqbar.py
+@@ -2776,11 +2776,12 @@ def number_field_elements_from_algebraics(numbers, minimal=False,
+             To:   Algebraic Real Field
+             Defn: a |--> 1.732050807568878?)
+         sage: number_field_elements_from_algebraics((rt2,qqI))                          # needs sage.symbolic
+-        (Number Field in a with defining polynomial y^4 + 1, [-a^3 + a, a^2],
++        (Number Field in a with defining polynomial y^4 + 1,
++         [a^3 - a, a^2],
+          Ring morphism:
+-            From: Number Field in a with defining polynomial y^4 + 1
+-            To:   Algebraic Field
+-            Defn: a |--> 0.7071067811865475? + 0.7071067811865475?*I)
++           From: Number Field in a with defining polynomial y^4 + 1
++           To:   Algebraic Field
++           Defn: a |--> -0.7071067811865475? - 0.7071067811865475?*I)
+ 
+     Note that for the first example, where \sage does not realize that
+     the number is real, we get a homomorphism to ``QQbar``::
+@@ -4590,8 +4591,7 @@ def _exact_field(self):
+             Number Field in a with defining polynomial y^4 - 20*y^2 + 81
+              with a in -3.789313782671036?
+             sage: (QQbar(7)^(3/5))._exact_field()
+-            Number Field in a with defining polynomial
+-             y^5 - 2*y^4 - 18*y^3 + 38*y^2 + 82*y - 181 with a in 2.554256611698490?
++            Number Field in a with defining polynomial y^5 - 7 with a in 1.475773161594552?
+         """
+         sd = self._descr
+         if isinstance(sd, (ANRational, ANExtensionElement)):
+@@ -4611,7 +4611,7 @@ def _exact_value(self):
+             sage: (sqrt(QQbar(2)) + sqrt(QQbar(19)))._exact_value()
+             -1/9*a^3 + a^2 + 11/9*a - 10 where a^4 - 20*a^2 + 81 = 0 and a in -3.789313782671036?
+             sage: (QQbar(7)^(3/5))._exact_value()
+-            2*a^4 + 2*a^3 - 34*a^2 - 17*a + 150 where a^5 - 2*a^4 - 18*a^3 + 38*a^2 + 82*a - 181 = 0 and a in 2.554256611698490?
++            a^3 where a^5 - 7 = 0 and a in 1.475773161594552?
+         """
+         sd = self._descr
+         if isinstance(sd, (ANRational, ANExtensionElement)):
+@@ -7839,8 +7839,8 @@ def handle_sage_input(self, sib, coerce, is_qqbar):
+             sage: sage_input(v, verify=True)
+             # Verified
+             R.<y> = QQ[]
+-            v = QQbar.polynomial_root(AA.common_polynomial(y^8 - y^7 + y^5 - y^4 + y^3 - y + 1), CIF(RIF(RR(0.91354545764260087), RR(0.91354545764260098)), RIF(RR(0.40673664307580015), RR(0.40673664307580021))))
+-            v^5 + v^3
++            v = QQbar.polynomial_root(AA.common_polynomial(y^8 - y^7 + y^5 - y^4 + y^3 - y + 1), CIF(RIF(RR(0.66913060635885813), RR(0.66913060635885824)), RIF(-RR(0.74314482547739424), -RR(0.74314482547739413))))
++            v^6 + v^5
+             sage: v = QQbar(sqrt(AA(2)))
+             sage: v.exactify()
+             sage: sage_input(v, verify=True)
+diff --git a/src/sage/rings/rational.pyx b/src/sage/rings/rational.pyx
+index 272650abeef..0dbe3453dd2 100644
+--- a/src/sage/rings/rational.pyx
++++ b/src/sage/rings/rational.pyx
+@@ -1446,7 +1446,7 @@ cdef class Rational(sage.structure.element.FieldElement):
+             sage: 0.is_norm(K)
+             True
+             sage: (1/7).is_norm(K, element=True)
+-            (True, 1/7*beta + 3/7)
++            (True, -3/7*beta + 5/7)
+             sage: (1/10).is_norm(K, element=True)
+             (False, None)
+             sage: (1/691).is_norm(QQ, element=True)
+@@ -1558,7 +1558,7 @@ cdef class Rational(sage.structure.element.FieldElement):
+         EXAMPLES::
+ 
+             sage: QQ(2)._bnfisnorm(QuadraticField(-1, 'i'))                             # needs sage.rings.number_field
+-            (i + 1, 1)
++            (-i + 1, 1)
+             sage: x = polygen(QQ, 'x')
+             sage: 7._bnfisnorm(NumberField(x^3 - 2, 'b'))                               # needs sage.rings.number_field
+             (1, 7)
+diff --git a/src/sage/schemes/affine/affine_morphism.py b/src/sage/schemes/affine/affine_morphism.py
+index 0eba4c662ec..2208cefca1d 100755
+--- a/src/sage/schemes/affine/affine_morphism.py
++++ b/src/sage/schemes/affine/affine_morphism.py
+@@ -1158,13 +1158,11 @@ def reduce_base_field(self):
+             sage: H = End(A)
+             sage: f = H([QQbar(3^(1/3))*x^2 + QQbar(sqrt(-2))])                         # needs sage.symbolic
+             sage: f.reduce_base_field()                                                 # needs sage.symbolic
+-            Scheme endomorphism of Affine Space of dimension 1 over Number
+-            Field in a with defining polynomial y^6 + 6*y^4 - 6*y^3 + 12*y^2 + 36*y + 17
+-             with a = 1.442249570307409? + 1.414213562373095?*I
++            Scheme endomorphism of Affine Space of dimension 1 over Number Field in a with defining polynomial y^6 + 6*y^4 - 6*y^3 + 12*y^2 + 36*y + 17 with a = 1.442249570307409? - 1.414213562373095?*I
+               Defn: Defined on coordinates by sending (x) to
+                     ((-48/269*a^5 + 27/269*a^4 - 320/269*a^3 + 468/269*a^2 - 772/269*a
+-                    - 1092/269)*x^2 + (48/269*a^5 - 27/269*a^4 + 320/269*a^3 - 468/269*a^2
+-                    + 1041/269*a + 1092/269))
++                    - 1092/269)*x^2 + (-48/269*a^5 + 27/269*a^4 - 320/269*a^3 + 468/269*a^2
++                    - 1041/269*a - 1092/269))
+ 
+         ::
+ 
+diff --git a/src/sage/schemes/elliptic_curves/ell_field.py b/src/sage/schemes/elliptic_curves/ell_field.py
+index a63dbf57809..84a719adfbb 100755
+--- a/src/sage/schemes/elliptic_curves/ell_field.py
++++ b/src/sage/schemes/elliptic_curves/ell_field.py
+@@ -902,7 +902,7 @@ def division_field(self, n, names='t', map=False, **kwds):
+              by y^2 = x^3 + 5*a0*x^2 + (-200*a0^2)*x + (-42000*a0^2+42000*a0+126000)
+              over Number Field in a0 with defining polynomial x^3 - 3*x^2 + 3*x + 9
+             sage: K.<b> = E.division_field(3, simplify_all=True); K
+-            Number Field in b with defining polynomial x^12 - 25*x^10 + 130*x^8 + 645*x^6 + 1050*x^4 + 675*x^2 + 225
++            Number Field in b with defining polynomial x^12 + 5*x^10 + 40*x^8 + 315*x^6 + 750*x^4 + 675*x^2 + 2025
+ 
+         Some higher-degree examples::
+ 
+diff --git a/src/sage/schemes/elliptic_curves/ell_local_data.py b/src/sage/schemes/elliptic_curves/ell_local_data.py
+index 7434659b5a2..df076ed62b6 100755
+--- a/src/sage/schemes/elliptic_curves/ell_local_data.py
++++ b/src/sage/schemes/elliptic_curves/ell_local_data.py
+@@ -1161,7 +1161,7 @@ def check_prime(K, P):
+         sage: check_prime(K, a + 1)
+         Fractional ideal (a + 1)
+         sage: [check_prime(K, P) for P in K.primes_above(31)]
+-        [Fractional ideal (5/2*a + 1/2), Fractional ideal (5/2*a - 1/2)]
++        [Fractional ideal (-5/2*a - 1/2), Fractional ideal (-5/2*a + 1/2)]
+         sage: L.<b> = NumberField(x^2 + 3)
+         sage: check_prime(K, L.ideal(5))
+         Traceback (most recent call last):
+diff --git a/src/sage/schemes/elliptic_curves/ell_number_field.py b/src/sage/schemes/elliptic_curves/ell_number_field.py
+index eea2e5cc243..cceab500959 100755
+--- a/src/sage/schemes/elliptic_curves/ell_number_field.py
++++ b/src/sage/schemes/elliptic_curves/ell_number_field.py
+@@ -229,9 +229,9 @@ def simon_two_descent(self, verbose=0, lim1=2, lim3=4, limtriv=2,
+             sage: E == loads(dumps(E))
+             True
+             sage: E.simon_two_descent()
+-            (2, 2, [(0 : 0 : 1), (1/18*a + 7/18 : -5/54*a - 17/54 : 1)])
++            (2, 2, [(0 : 0 : 1), (1/8*a + 5/8 : -3/16*a - 7/16 : 1)])
+             sage: E.simon_two_descent(lim1=5, lim3=5, limtriv=10, maxprob=7, limbigprime=10)
+-            (2, 2, [(-1 : 0 : 1), (-2 : -1/2*a - 1/2 : 1)])
++            (2, 2, [(-1 : 0 : 1), (1/2*a - 5/2 : -1/2*a - 13/2 : 1)])
+ 
+         ::
+ 
+@@ -277,7 +277,7 @@ def simon_two_descent(self, verbose=0, lim1=2, lim3=4, limtriv=2,
+             sage: E.simon_two_descent()  # long time (4s on sage.math, 2013)
+             (3,
+              3,
+-             [(1/8*zeta43_0^2 - 3/8*zeta43_0 - 1/4 : -5/16*zeta43_0^2 + 7/16*zeta43_0 + 1/8 : 1),
++             [(-1/2*zeta43_0^2 - 1/2*zeta43_0 + 7 : -3/2*zeta43_0^2 - 5/2*zeta43_0 + 18 : 1),
+               (0 : 0 : 1)])
+         """
+         verbose = int(verbose)
+@@ -872,7 +872,7 @@ def local_data(self, P=None, proof=None, algorithm='pari', globally=False):
+             sage: K.<i> = NumberField(x^2 + 1)
+             sage: E = EllipticCurve([1 + i, 0, 1, 0, 0])
+             sage: E.local_data()
+-            [Local data at Fractional ideal (2*i + 1):
++            [Local data at Fractional ideal (-2*i - 1):
+                Reduction type: bad non-split multiplicative
+                Local minimal model: Elliptic Curve defined by y^2 + (i+1)*x*y + y = x^3
+                                     over Number Field in i with defining polynomial x^2 + 1
+@@ -880,7 +880,7 @@ def local_data(self, P=None, proof=None, algorithm='pari', globally=False):
+                Conductor exponent: 1
+                Kodaira Symbol: I1
+                Tamagawa Number: 1,
+-             Local data at Fractional ideal (-2*i + 3):
++             Local data at Fractional ideal (3*i + 2):
+                Reduction type: bad split multiplicative
+                Local minimal model: Elliptic Curve defined by y^2 + (i+1)*x*y + y = x^3
+                                     over Number Field in i with defining polynomial x^2 + 1
+@@ -898,7 +898,7 @@ def local_data(self, P=None, proof=None, algorithm='pari', globally=False):
+               Kodaira Symbol: I0
+               Tamagawa Number: 1
+             sage: E.local_data(2*i + 1)
+-            Local data at Fractional ideal (2*i + 1):
++            Local data at Fractional ideal (-2*i - 1):
+               Reduction type: bad non-split multiplicative
+               Local minimal model: Elliptic Curve defined by y^2 + (i+1)*x*y + y = x^3
+                                    over Number Field in i with defining polynomial x^2 + 1
+@@ -1456,8 +1456,10 @@ def kodaira_symbol(self, P, proof=None):
+             sage: K.<a> = NumberField(x^2 - 5)
+             sage: E = EllipticCurve([20, 225, 750, 625*a + 6875, 31250*a + 46875])
+             sage: bad_primes = E.discriminant().support(); bad_primes
+-            [Fractional ideal (-a), Fractional ideal (7/2*a - 81/2),
+-             Fractional ideal (-a - 52), Fractional ideal (2)]
++            [Fractional ideal (-a),
++             Fractional ideal (-7/2*a + 81/2),
++             Fractional ideal (-a - 52),
++             Fractional ideal (2)]
+             sage: [E.kodaira_symbol(P) for P in bad_primes]
+             [I0, I1, I1, II]
+             sage: K.<a> = QuadraticField(-11)
+@@ -1483,10 +1485,12 @@ def conductor(self):
+ 
+             sage: K.<i> = NumberField(x^2 + 1)
+             sage: EllipticCurve([i, i - 1, i + 1, 24*i + 15, 14*i + 35]).conductor()
+-            Fractional ideal (21*i - 3)
++            Fractional ideal (3*i + 21)
+             sage: K.<a> = NumberField(x^2 - x + 3)
+-            sage: EllipticCurve([1 + a, -1 + a, 1 + a, -11 + a, 5 - 9*a]).conductor()
+-            Fractional ideal (-6*a)
++            sage: cond = EllipticCurve([1 + a, -1 + a, 1 + a, -11 + a, 5 - 9*a]).conductor(); cond # random
++            Fractional ideal (6*a)
++            sage: cond == K.ideal(6*a)
++            True
+ 
+         A not so well known curve with everywhere good reduction::
+ 
+@@ -2584,8 +2588,8 @@ def isogeny_class(self, reducible_primes=None, algorithm='Billerey', minimal_mod
+             sage: [E1.ainvs() for E1 in C]
+             [(0, 0, 0, 0, -27),
+             (0, 0, 0, 0, 1),
+-            (i + 1, i, i + 1, -i + 3, 4*i),
+-            (i + 1, i, i + 1, -i + 33, -58*i)]
++            (i + 1, i, 0, 3, -i),
++            (i + 1, i, 0, 33, 91*i)]
+ 
+         The matrix of degrees of cyclic isogenies between curves::
+ 
+@@ -2616,13 +2620,13 @@ class :class:`EllipticCurveIsogeny` allowed composition.  In
+             sage: [((i,j), isogs[i][j].x_rational_map())
+             ....:  for i in range(4) for j in range(4) if isogs[i][j] != 0]
+             [((0, 1), (1/9*x^3 - 12)/x^2),
+-             ((0, 3), (-1/2*i*x^2 + i*x - 12*i)/(x - 3)),
++             ((0, 3), (1/2*i*x^2 - 2*i*x + 15*i)/(x - 3)),
+              ((1, 0), (x^3 + 4)/x^2),
+-             ((1, 2), (-1/2*i*x^2 - i*x - 2*i)/(x + 1)),
+-             ((2, 1), (1/2*i*x^2 - x)/(x + 3/2*i)),
+-             ((2, 3), (x^3 + 4*i*x^2 - 10*x - 10*i)/(x^2 + 4*i*x - 4)),
+-             ((3, 0), (1/2*i*x^2 + x + 4*i)/(x - 5/2*i)),
+-             ((3, 2), (1/9*x^3 - 4/3*i*x^2 - 34/3*x + 226/9*i)/(x^2 - 8*i*x - 16))]
++             ((1, 2), (1/2*i*x^2 + i)/(x + 1)),
++             ((2, 1), (-1/2*i*x^2 - 1/2*i)/(x - 1/2*i)),
++             ((2, 3), (x^3 - 2*i*x^2 - 7*x + 4*i)/(x^2 - 2*i*x - 1)),
++             ((3, 0), (-1/2*i*x^2 + 2*x - 5/2*i)/(x + 7/2*i)),
++             ((3, 2), (1/9*x^3 + 2/3*i*x^2 - 13/3*x - 116/9*i)/(x^2 + 10*i*x - 25))]
+ 
+         The isogeny class may be visualized by obtaining its graph and
+         plotting it::
+@@ -3103,10 +3107,10 @@ def is_isogenous(self, other, proof=True, maxnorm=100):
+             sage: K.<i> = QuadraticField(-1)
+             sage: E1 = EllipticCurve([i + 1, 0, 1, -240*i - 400, -2869*i - 2627])
+             sage: E1.conductor()
+-            Fractional ideal (-4*i - 7)
++            Fractional ideal (4*i + 7)
+             sage: E2 = EllipticCurve([1+i,0,1,0,0])
+             sage: E2.conductor()
+-            Fractional ideal (-4*i - 7)
++            Fractional ideal (4*i + 7)
+             sage: E1.is_isogenous(E2) # long time
+             True
+             sage: E1.is_isogenous(E2, proof=False) # faster  (~170ms)
+@@ -3433,8 +3437,8 @@ def lll_reduce(self, points, height_matrix=None, precision=None):
+             sage: Q = E(0,-1)
+             sage: E.lll_reduce([P,Q])
+             (
+-                                                     [0 1]
+-            [(0 : -1 : 1), (-2 : -1/2*a - 1/2 : 1)], [1 0]
++                                                    [ 0 -1]
++            [(0 : -1 : 1), (-2 : 1/2*a - 1/2 : 1)], [ 1  0]
+             )
+ 
+         ::
+@@ -3445,9 +3449,10 @@ def lll_reduce(self, points, height_matrix=None, precision=None):
+             ....:           E.point([-17/18*a - 1/9, -109/108*a - 277/108])]
+             sage: E.lll_reduce(points)
+             (
+-            [(-a + 4 : -3*a + 7 : 1), (-17/18*a - 1/9 : 109/108*a + 277/108 : 1)],
+-            [ 1  0]
+-            [ 1 -1]
++            [(-a + 4 : -3*a + 7 : 1), (-17/18*a - 1/9 : -109/108*a - 277/108 : 1)],
++            <BLANKLINE>
++            [1 0]
++            [1 1]
+             )
+         """
+         r = len(points)
+diff --git a/src/sage/schemes/elliptic_curves/ell_point.py b/src/sage/schemes/elliptic_curves/ell_point.py
+index 0da080ffdbe..61b016ca08e 100755
+--- a/src/sage/schemes/elliptic_curves/ell_point.py
++++ b/src/sage/schemes/elliptic_curves/ell_point.py
+@@ -142,7 +142,6 @@
+ 
+ try:
+     from sage.libs.pari.all import pari, PariError
+-    from cypari2.pari_instance import prec_words_to_bits
+ except ImportError:
+     PariError = ()
+ 
+@@ -2672,10 +2671,10 @@ def has_good_reduction(self, P=None):
+             sage: K.<i> = NumberField(x^2 + 1)
+             sage: E = EllipticCurve(K, [0,1,0,-160,308])
+             sage: P = E(26, -120)
+-            sage: E.discriminant().support()
+-            [Fractional ideal (i + 1),
+-             Fractional ideal (-i - 2),
+-             Fractional ideal (2*i + 1),
++            sage: E.discriminant().support() # random
++            [Fractional ideal (-i - 1),
++             Fractional ideal (2*i - 1),
++             Fractional ideal (-2*i - 1),
+              Fractional ideal (3)]
+             sage: [E.tamagawa_exponent(p) for p in E.discriminant().support()]
+             [1, 4, 4, 4]
+@@ -3705,7 +3704,7 @@ def elliptic_logarithm(self, embedding=None, precision=100,
+         E_pari = E_work.pari_curve()
+         log_pari = E_pari.ellpointtoz(pt_pari, precision=working_prec)
+ 
+-        while prec_words_to_bits(log_pari.precision()) < precision:
++        while log_pari.bitprecision() < precision:
+             # result is not precise enough, re-compute with double
+             # precision. if the base field is not QQ, this
+             # requires modifying the precision of the embedding,
+diff --git a/src/sage/schemes/elliptic_curves/ell_rational_field.py b/src/sage/schemes/elliptic_curves/ell_rational_field.py
+index 0bc71b09d42..feb584fdf72 100755
+--- a/src/sage/schemes/elliptic_curves/ell_rational_field.py
++++ b/src/sage/schemes/elliptic_curves/ell_rational_field.py
+@@ -1848,7 +1848,7 @@ def simon_two_descent(self, verbose=0, lim1=5, lim3=50, limtriv=3,
+             sage: E = EllipticCurve('389a1')
+             sage: E._known_points = []  # clear cached points
+             sage: E.simon_two_descent()
+-            (2, 2, [(5/4 : 5/8 : 1), (-3/4 : 7/8 : 1)])
++            (2, 2, [(-3/4 : 7/8 : 1), (5/4 : 5/8 : 1)])
+             sage: E = EllipticCurve('5077a1')
+             sage: E.simon_two_descent()
+             (3, 3, [(1 : 0 : 1), (2 : 0 : 1), (0 : 2 : 1)])
+diff --git a/src/sage/schemes/elliptic_curves/gal_reps_number_field.py b/src/sage/schemes/elliptic_curves/gal_reps_number_field.py
+index a4eb66a6df7..8b597e41595 100755
+--- a/src/sage/schemes/elliptic_curves/gal_reps_number_field.py
++++ b/src/sage/schemes/elliptic_curves/gal_reps_number_field.py
+@@ -800,17 +800,17 @@ def deg_one_primes_iter(K, principal_only=False):
+         [Fractional ideal (2, a + 1),
+          Fractional ideal (3, a + 1),
+          Fractional ideal (3, a + 2),
+-         Fractional ideal (a),
++         Fractional ideal (-a),
+          Fractional ideal (7, a + 3),
+          Fractional ideal (7, a + 4)]
+         sage: it = deg_one_primes_iter(K, True)
+         sage: [next(it) for _ in range(6)]
+-        [Fractional ideal (a),
+-         Fractional ideal (-2*a + 3),
+-         Fractional ideal (2*a + 3),
++        [Fractional ideal (-a),
++         Fractional ideal (2*a - 3),
++         Fractional ideal (-2*a - 3),
+          Fractional ideal (a + 6),
+          Fractional ideal (a - 6),
+-         Fractional ideal (-3*a + 4)]
++         Fractional ideal (3*a - 4)]
+     """
+     # imaginary quadratic fields have no principal primes of norm < disc / 4
+     start = K.discriminant().abs() // 4 if principal_only and K.signature() == (0,1) else 2
+diff --git a/src/sage/schemes/elliptic_curves/gp_simon.py b/src/sage/schemes/elliptic_curves/gp_simon.py
+index 6be377e2f74..4134ae1b7a6 100644
+--- a/src/sage/schemes/elliptic_curves/gp_simon.py
++++ b/src/sage/schemes/elliptic_curves/gp_simon.py
+@@ -49,7 +49,7 @@ def simon_two_descent(E, verbose=0, lim1=None, lim3=None, limtriv=None,
+         doctest:warning...:
+         DeprecationWarning: please use the 2-descent algorithm over QQ inside pari
+         See https://github.com/sagemath/sage/issues/38461 for details.
+-        (2, 2, [(5/4 : 5/8 : 1), (-3/4 : 7/8 : 1)])
++        (2, 2, [(-3/4 : 7/8 : 1), (5/4 : 5/8 : 1)])
+ 
+     TESTS::
+ 
+diff --git a/src/sage/schemes/elliptic_curves/isogeny_class.py b/src/sage/schemes/elliptic_curves/isogeny_class.py
+index 13edc68a022..a83fd8705ac 100755
+--- a/src/sage/schemes/elliptic_curves/isogeny_class.py
++++ b/src/sage/schemes/elliptic_curves/isogeny_class.py
+@@ -223,8 +223,8 @@ def _repr_(self):
+             sage: C.curves
+             [Elliptic Curve defined by y^2 = x^3 + (-27) over Number Field in i with defining polynomial x^2 + 1 with i = 1*I,
+              Elliptic Curve defined by y^2 = x^3 + 1 over Number Field in i with defining polynomial x^2 + 1 with i = 1*I,
+-             Elliptic Curve defined by y^2 + (i+1)*x*y + (i+1)*y = x^3 + i*x^2 + (-i+3)*x + 4*i over Number Field in i with defining polynomial x^2 + 1 with i = 1*I,
+-             Elliptic Curve defined by y^2 + (i+1)*x*y + (i+1)*y = x^3 + i*x^2 + (-i+33)*x + (-58*i) over Number Field in i with defining polynomial x^2 + 1 with i = 1*I]
++             Elliptic Curve defined by y^2 + (i+1)*x*y = x^3 + i*x^2 + 3*x + (-i) over Number Field in i with defining polynomial x^2 + 1 with i = 1*I,
++             Elliptic Curve defined by y^2 + (i+1)*x*y = x^3 + i*x^2 + 33*x + 91*i over Number Field in i with defining polynomial x^2 + 1 with i = 1*I]
+         """
+         if self._label:
+             return "Elliptic curve isogeny class %s" % (self._label)
+@@ -615,8 +615,8 @@ def __init__(self, E, reducible_primes=None, algorithm='Billerey', minimal_model
+             sage: [E1.ainvs() for E1 in C]
+             [(0, 0, 0, 0, -27),
+              (0, 0, 0, 0, 1),
+-             (i + 1, i, i + 1, -i + 3, 4*i),
+-             (i + 1, i, i + 1, -i + 33, -58*i)]
++             (i + 1, i, 0, 3, -i),
++             (i + 1, i, 0, 33, 91*i)]
+ 
+         The matrix of degrees of cyclic isogenies between curves::
+ 
+@@ -647,13 +647,13 @@ class :class:`EllipticCurveIsogeny` allowed composition.  In
+             sage: [((i,j), isogs[i][j].x_rational_map())
+             ....:  for i in range(4) for j in range(4) if isogs[i][j] != 0]
+             [((0, 1), (1/9*x^3 - 12)/x^2),
+-             ((0, 3), (-1/2*i*x^2 + i*x - 12*i)/(x - 3)),
++             ((0, 3), (1/2*i*x^2 - 2*i*x + 15*i)/(x - 3)),
+              ((1, 0), (x^3 + 4)/x^2),
+-             ((1, 2), (-1/2*i*x^2 - i*x - 2*i)/(x + 1)),
+-             ((2, 1), (1/2*i*x^2 - x)/(x + 3/2*i)),
+-             ((2, 3), (x^3 + 4*i*x^2 - 10*x - 10*i)/(x^2 + 4*i*x - 4)),
+-             ((3, 0), (1/2*i*x^2 + x + 4*i)/(x - 5/2*i)),
+-             ((3, 2), (1/9*x^3 - 4/3*i*x^2 - 34/3*x + 226/9*i)/(x^2 - 8*i*x - 16))]
++             ((1, 2), (1/2*i*x^2 + i)/(x + 1)),
++             ((2, 1), (-1/2*i*x^2 - 1/2*i)/(x - 1/2*i)),
++             ((2, 3), (x^3 - 2*i*x^2 - 7*x + 4*i)/(x^2 - 2*i*x - 1)),
++             ((3, 0), (-1/2*i*x^2 + 2*x - 5/2*i)/(x + 7/2*i)),
++             ((3, 2), (1/9*x^3 + 2/3*i*x^2 - 13/3*x - 116/9*i)/(x^2 + 10*i*x - 25))]
+ 
+             sage: K.<i> = QuadraticField(-1)
+             sage: E = EllipticCurve([1+i, -i, i, 1, 0])
+diff --git a/src/sage/schemes/elliptic_curves/isogeny_small_degree.py b/src/sage/schemes/elliptic_curves/isogeny_small_degree.py
+index 6a0194fb0f9..90f7382a94e 100755
+--- a/src/sage/schemes/elliptic_curves/isogeny_small_degree.py
++++ b/src/sage/schemes/elliptic_curves/isogeny_small_degree.py
+@@ -886,15 +886,15 @@ def isogenies_5_0(E, minimal_models=True):
+           from Elliptic Curve defined by y^2 + y = x^3
+                over Number Field in a with defining polynomial x^6 - 320*x^3 - 320
+             to Elliptic Curve defined by
+-               y^2 + y = x^3 + (241565/32*a^5-362149/48*a^4+180281/24*a^3-9693307/4*a^2+14524871/6*a-7254985/3)*x
+-                          + (1660391123/192*a^5-829315373/96*a^4+77680504/9*a^3-66622345345/24*a^2+33276655441/12*a-24931615912/9)
++               y^2 + y = x^3 + (643/8*a^5-15779/48*a^4-32939/24*a^3-71989/2*a^2+214321/6*a-112115/3)*x
++                          + (2901961/96*a^5+4045805/48*a^4+12594215/18*a^3-30029635/6*a^2+15341626/3*a-38944312/9)
+                over Number Field in a with defining polynomial x^6 - 320*x^3 - 320,
+          Isogeny of degree 5
+           from Elliptic Curve defined by y^2 + y = x^3
+                over Number Field in a with defining polynomial x^6 - 320*x^3 - 320
+             to Elliptic Curve defined by
+-               y^2 + y = x^3 + (47519/32*a^5-72103/48*a^4+32939/24*a^3-1909753/4*a^2+2861549/6*a-1429675/3)*x
+-                          + (-131678717/192*a^5+65520419/96*a^4-12594215/18*a^3+5280985135/24*a^2-2637787519/12*a+1976130088/9)
++               y^2 + y = x^3 + (-1109/8*a^5-53873/48*a^4-180281/24*a^3-14491/2*a^2+35899/6*a-43745/3)*x
++                          + (-17790679/96*a^5-60439571/48*a^4-77680504/9*a^3+1286245/6*a^2-4961854/3*a-73854632/9)
+                over Number Field in a with defining polynomial x^6 - 320*x^3 - 320]
+     """
+     F = E.base_field()
+diff --git a/src/sage/schemes/plane_conics/con_number_field.py b/src/sage/schemes/plane_conics/con_number_field.py
+index e09a1f60262..69fe9960c3d 100755
+--- a/src/sage/schemes/plane_conics/con_number_field.py
++++ b/src/sage/schemes/plane_conics/con_number_field.py
+@@ -121,7 +121,7 @@ def has_rational_point(self, point=False, obstruction=False,
+             sage: K.<i> = QuadraticField(-1)
+             sage: C = Conic(K, [1, 3, -5])
+             sage: C.has_rational_point(point=True, obstruction=True)
+-            (False, Fractional ideal (-i - 2))
++            (False, Fractional ideal (i + 2))
+             sage: C.has_rational_point(algorithm='rnfisnorm')
+             False
+             sage: C.has_rational_point(algorithm='rnfisnorm', obstruction=True,
+@@ -135,7 +135,7 @@ def has_rational_point(self, point=False, obstruction=False,
+             sage: L.<b> = NumberField(x^3 - 5)
+             sage: C = Conic(L, [1, 2, -3])
+             sage: C.has_rational_point(point=True, algorithm='rnfisnorm')
+-            (True, (5/3 : -1/3 : 1))
++            (True, (-5/3 : 1/3 : 1))
+ 
+             sage: K.<a> = NumberField(x^4+2)
+             sage: Conic(QQ, [4,5,6]).has_rational_point()
+diff --git a/src/sage/schemes/projective/projective_morphism.py b/src/sage/schemes/projective/projective_morphism.py
+index 20031e81a41..fcbb0c01e82 100755
+--- a/src/sage/schemes/projective/projective_morphism.py
++++ b/src/sage/schemes/projective/projective_morphism.py
+@@ -928,7 +928,7 @@ def normalize_coordinates(self, **kwds):
+             Dynamical System of Projective Space of dimension 1 over
+             Number Field in a with defining polynomial 3*x^2 + 1
+             Defn: Defined on coordinates by sending (z : w) to
+-                ((-3/2*a + 1/2)*z^2 + (-3/2*a + 1/2)*w^2 : (-3/2*a - 3/2)*z*w)
++                ((3/2*a + 1/2)*z^2 + (3/2*a + 1/2)*w^2 : (-3/2*a + 3/2)*z*w)
+ 
+         ::
+ 
+@@ -1728,11 +1728,11 @@ def _number_field_from_algebraics(self):
+             sage: f._number_field_from_algebraics()                                     # needs sage.symbolic
+             Scheme endomorphism of Projective Space of dimension 1 over Number
+              Field in a with defining polynomial y^6 + 6*y^4 - 6*y^3 + 12*y^2 + 36*y + 17
+-             with a = 1.442249570307409? + 1.414213562373095?*I
++             with a = 1.442249570307409? - 1.414213562373095?*I
+               Defn: Defined on coordinates by sending (x : y) to
+                     ((-48/269*a^5 + 27/269*a^4 - 320/269*a^3 + 468/269*a^2 - 772/269*a
+-                    - 1092/269)*x^2 + (48/269*a^5 - 27/269*a^4 + 320/269*a^3 - 468/269*a^2
+-                    + 1041/269*a + 1092/269)*y^2 : y^2)
++                    - 1092/269)*x^2 + (-48/269*a^5 + 27/269*a^4 - 320/269*a^3 + 468/269*a^2
++                    - 1041/269*a - 1092/269)*y^2 : y^2)
+ 
+         ::
+ 
+@@ -1745,12 +1745,12 @@ def _number_field_from_algebraics(self):
+             Scheme morphism:
+               From: Projective Space of dimension 1 over Number Field in a
+                     with defining polynomial y^4 + 3*y^2 + 1
+-                    with a = 0.?e-113 + 0.618033988749895?*I
++                    with a = 0.?e-166 + 1.618033988749895?*I
+               To:   Projective Space of dimension 2 over Number Field in a
+                     with defining polynomial y^4 + 3*y^2 + 1
+-                    with a = 0.?e-113 + 0.618033988749895?*I
++                    with a = 0.?e-166 + 1.618033988749895?*I
+               Defn: Defined on coordinates by sending (x : y) to
+-                    (x^2 + (a^3 + 2*a)*x*y + 3*y^2 : y^2 : (2*a^2 + 3)*x*y)
++                    (x^2 + (-a^3 - 2*a)*x*y + 3*y^2 : y^2 : (-2*a^2 - 3)*x*y)
+ 
+         The following was fixed in :issue:`23808`::
+ 
+diff --git a/src/sage/schemes/projective/projective_point.py b/src/sage/schemes/projective/projective_point.py
+index 7f941ec6726..b0f443acb4e 100755
+--- a/src/sage/schemes/projective/projective_point.py
++++ b/src/sage/schemes/projective/projective_point.py
+@@ -1238,10 +1238,10 @@ def _number_field_from_algebraics(self):
+             sage: P.<x,y> = ProjectiveSpace(QQbar, 1)
+             sage: Q = P([-1/2*QQbar(sqrt(2)) + QQbar(I), 1])
+             sage: S = Q._number_field_from_algebraics(); S
+-            (1/2*a^3 + a^2 - 1/2*a : 1)
++            (-1/2*a^3 + a^2 + 1/2*a : 1)
+             sage: S.codomain()
+             Projective Space of dimension 1 over Number Field in a with defining
+-             polynomial y^4 + 1 with a = 0.7071067811865475? + 0.7071067811865475?*I
++             polynomial y^4 + 1 with a = -0.7071067811865475? - 0.7071067811865475?*I
+ 
+         The following was fixed in :issue:`23808`::
+ 
+@@ -1251,7 +1251,7 @@ def _number_field_from_algebraics(self):
+             sage: Q = P([-1/2*QQbar(sqrt(2)) + QQbar(I), 1]);Q
+             (-0.7071067811865475? + 1*I : 1)
+             sage: S = Q._number_field_from_algebraics(); S
+-            (1/2*a^3 + a^2 - 1/2*a : 1)
++            (-1/2*a^3 + a^2 + 1/2*a : 1)
+             sage: T = S.change_ring(QQbar)  # Used to fail
+             sage: T
+             (-0.7071067811865475? + 1.000000000000000?*I : 1)
+diff --git a/src/sage/structure/factorization.py b/src/sage/structure/factorization.py
+index ab3fa717031..b16822791dc 100644
+--- a/src/sage/structure/factorization.py
++++ b/src/sage/structure/factorization.py
+@@ -143,17 +143,17 @@
+     sage: K.<a> = NumberField(x^2 + 3); K
+     Number Field in a with defining polynomial x^2 + 3
+     sage: f = K.factor(15); f
+-    (Fractional ideal (1/2*a + 3/2))^2 * (Fractional ideal (5))
++    (Fractional ideal (-a))^2 * (Fractional ideal (5))
+     sage: f.universe()
+     Monoid of ideals of Number Field in a with defining polynomial x^2 + 3
+     sage: f.unit()
+     Fractional ideal (1)
+     sage: g = K.factor(9); g
+-    (Fractional ideal (1/2*a + 3/2))^4
++    (Fractional ideal (-a))^4
+     sage: f.lcm(g)
+-    (Fractional ideal (1/2*a + 3/2))^4 * (Fractional ideal (5))
++    (Fractional ideal (-a))^4 * (Fractional ideal (5))
+     sage: f.gcd(g)
+-    (Fractional ideal (1/2*a + 3/2))^2
++    (Fractional ideal (-a))^2
+     sage: f.is_integral()
+     True
+ 
diff --git a/srcpkgs/sagemath/patches/38749-zz-fixup_backport.patch b/srcpkgs/sagemath/patches/38749-zz-fixup_backport.patch
new file mode 100644
index 00000000000000..4a5550140eab6a
--- /dev/null
+++ b/srcpkgs/sagemath/patches/38749-zz-fixup_backport.patch
@@ -0,0 +1,95 @@
+commit 031e32abfded6902eeb5974b51026bec05e6a3c5
+Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
+Date:   Sun Nov 3 18:23:36 2024 -0300
+
+    fixup backport of #38749
+
+diff --git a/src/sage/rings/number_field/number_field_ideal_rel.py b/src/sage/rings/number_field/number_field_ideal_rel.py
+index 75b2ecc69d8..4f52eba6279 100644
+--- a/src/sage/rings/number_field/number_field_ideal_rel.py
++++ b/src/sage/rings/number_field/number_field_ideal_rel.py
+@@ -380,6 +380,7 @@ class NumberFieldFractionalIdeal_rel(NumberFieldFractionalIdeal):
+ 
+         EXAMPLES::
+ 
++            sage: pari.setrand(3)
+             sage: R.<x> = QQ[]
+             sage: K.<a> = NumberField(x^2 + 6)
+             sage: L.<b> = K.extension(K['x'].gen()^4 + a)
+diff --git a/src/sage/rings/number_field/order.py b/src/sage/rings/number_field/order.py
+index c499bc2812c..c28e3b0a7a9 100644
+--- a/src/sage/rings/number_field/order.py
++++ b/src/sage/rings/number_field/order.py
+@@ -590,7 +590,7 @@ class Order(IntegralDomain, sage.rings.abc.Order):
+             sage: k.<a> = NumberField(x^2 + 5077); G = k.class_group(); G
+             Class group of order 22 with structure C22 of Number Field in a with defining polynomial x^2 + 5077
+             sage: G.0 ^ -9
+-            Fractional ideal class (67, a + 45)
++            Fractional ideal class (43, a + 13)
+             sage: Ok = k.maximal_order(); Ok
+             Maximal Order generated by a in Number Field in a with defining polynomial x^2 + 5077
+             sage: Ok * (11, a + 7)
+@@ -2994,7 +2994,7 @@ def EisensteinIntegers(names="omega"):
+          with defining polynomial x^2 + x + 1
+          with omega = -0.50000000000000000? + 0.866025403784439?*I
+         sage: factor(3 + omega)
+-        (omega + 1) * (-2*omega + 1)
++        (-omega - 1) * (2*omega - 1)
+         sage: CC(omega)
+         -0.500000000000000 + 0.866025403784439*I
+         sage: omega.minpoly()
+diff --git a/src/sage/schemes/elliptic_curves/ell_number_field.py b/src/sage/schemes/elliptic_curves/ell_number_field.py
+index 0e60ef0f6a2..4c615e75ac9 100644
+--- a/src/sage/schemes/elliptic_curves/ell_number_field.py
++++ b/src/sage/schemes/elliptic_curves/ell_number_field.py
+@@ -2603,6 +2603,7 @@ class EllipticCurve_number_field(EllipticCurve_field):
+ 
+         EXAMPLES::
+ 
++            sage: pari.setrand(1)
+             sage: K.<i> = QuadraticField(-1)
+             sage: E = EllipticCurve(K, [0,0,0,0,1])
+             sage: C = E.isogeny_class(); C
+diff --git a/src/sage/schemes/elliptic_curves/gal_reps_number_field.py b/src/sage/schemes/elliptic_curves/gal_reps_number_field.py
+index 3fe8260947d..cf905787257 100644
+--- a/src/sage/schemes/elliptic_curves/gal_reps_number_field.py
++++ b/src/sage/schemes/elliptic_curves/gal_reps_number_field.py
+@@ -795,6 +795,7 @@ def deg_one_primes_iter(K, principal_only=False):
+ 
+     EXAMPLES::
+ 
++        sage: pari.setrand(1)
+         sage: K.<a> = QuadraticField(-5)
+         sage: from sage.schemes.elliptic_curves.gal_reps_number_field import deg_one_primes_iter
+         sage: it = deg_one_primes_iter(K)
+diff --git a/src/sage/schemes/elliptic_curves/gp_simon.py b/src/sage/schemes/elliptic_curves/gp_simon.py
+index fdf6f0852e8..046b635cca8 100644
+--- a/src/sage/schemes/elliptic_curves/gp_simon.py
++++ b/src/sage/schemes/elliptic_curves/gp_simon.py
+@@ -57,9 +57,6 @@ def simon_two_descent(E, verbose=0, lim1=None, lim3=None, limtriv=None,
+         sage: import sage.schemes.elliptic_curves.gp_simon
+         sage: E = EllipticCurve('389a1')
+         sage: sage.schemes.elliptic_curves.gp_simon.simon_two_descent(E)
+-        doctest:warning...:
+-        DeprecationWarning: please use the 2-descent algorithm over QQ inside pari
+-        See https://github.com/sagemath/sage/issues/38461 for details.
+         (2, 2, [(-3/4 : 7/8 : 1), (5/4 : 5/8 : 1)])
+ 
+     TESTS::
+diff --git a/src/sage/schemes/projective/projective_morphism.py b/src/sage/schemes/projective/projective_morphism.py
+index 5f4512f5be6..2c1c6aef618 100644
+--- a/src/sage/schemes/projective/projective_morphism.py
++++ b/src/sage/schemes/projective/projective_morphism.py
+@@ -1764,10 +1764,10 @@ class SchemeMorphism_polynomial_projective_space_field(SchemeMorphism_polynomial
+             Scheme morphism:
+               From: Projective Space of dimension 1 over Number Field in a
+                     with defining polynomial y^4 + 3*y^2 + 1
+-                    with a = 0.?e-166 + 1.618033988749895?*I
++                    with a = 0.?e-165 + 1.618033988749895?*I
+               To:   Projective Space of dimension 2 over Number Field in a
+                     with defining polynomial y^4 + 3*y^2 + 1
+-                    with a = 0.?e-166 + 1.618033988749895?*I
++                    with a = 0.?e-165 + 1.618033988749895?*I
+               Defn: Defined on coordinates by sending (x : y) to
+                     (x^2 + (-a^3 - 2*a)*x*y + 3*y^2 : y^2 : (-2*a^2 - 3)*x*y)
+ 
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 28162dff8a38e1..3232a1c60954a3 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -34,3 +34,5 @@ get_pr 38344 "ecm 7.0.6"
 
 #get_pr 37645 "fix doctest"
 #get_pr 37885 "cython warnings"
+
+get_pr 38749 "pari 2.17"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index b116e62bc67a5a..b3835fb2276dcb 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,7 +1,7 @@
 # Template file for 'sagemath'
 pkgname=sagemath
 version=10.4
-revision=3
+revision=4
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
 build_style=python3-pep517

From b6d6280ae4f2b8d3b5e8ce3e8b9da174b83e9bcc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 11 Aug 2024 22:53:42 -0300
Subject: [PATCH 08/21] python3-Cython: alternative fix for 6122

---
 srcpkgs/python3-Cython/patches/fix-regression.patch | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/srcpkgs/python3-Cython/patches/fix-regression.patch b/srcpkgs/python3-Cython/patches/fix-regression.patch
index f2e761608e373b..f5957cfa59c2f5 100644
--- a/srcpkgs/python3-Cython/patches/fix-regression.patch
+++ b/srcpkgs/python3-Cython/patches/fix-regression.patch
@@ -15,3 +15,11 @@ serious regression, e.g. sagemath FTBS with cython 3.0.11
              warning(self.pos,
                      "Implicit noexcept declaration is deprecated."
                      " Function declaration should contain 'noexcept' keyword.",
+@@ -3128,6 +3126,7 @@ class DefNode(FuncDefNode):
+             if scope is None:
+                 scope = cfunc.scope
+             cfunc_type = cfunc.type
++            has_explicit_exc_clause=True
+             if len(self.args) != len(cfunc_type.args) or cfunc_type.has_varargs:
+                 error(self.pos, "wrong number of arguments")
+                 error(cfunc.pos, "previous declaration here")

From b7b29269efc6c434d665224cbadf9282318c92c6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 5 Aug 2024 00:21:23 -0300
Subject: [PATCH 09/21] sagemath: update to 10.5.beta2.

---
 .../sagemath/patches/36641-sympy_1.13.patch   |  22 +-
 .../sagemath/patches/37884-gap_4.13.1.patch   |  28 +-
 .../sagemath/patches/38250-numpy_2.0.patch    | 587 ------------------
 .../sagemath/patches/38344-ecm_7.0.6.patch    |  43 --
 srcpkgs/sagemath/patches/get_patches          |   4 +-
 srcpkgs/sagemath/template                     |   6 +-
 6 files changed, 21 insertions(+), 669 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/38250-numpy_2.0.patch
 delete mode 100644 srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch

diff --git a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
index 625c582cdd41b7..01e859ad023f4d 100644
--- a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
+++ b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
@@ -1,8 +1,5 @@
-diff --git a/build/pkgs/sympy/requirements.txt b/build/pkgs/sympy/requirements.txt
-new file mode 100644
-index 00000000000..3ef8f90b550
 diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py
-index 7e9eab2ff2e..43365cd645e 100644
+index 823a0d14a41..de1c8531814 100644
 --- a/src/sage/doctest/forker.py
 +++ b/src/sage/doctest/forker.py
 @@ -150,14 +150,15 @@ def init_sage(controller=None):
@@ -28,7 +25,7 @@ index 7e9eab2ff2e..43365cd645e 100644
      The displayhook sorts dictionary keys to simplify doctesting of
      dictionary output::
 diff --git a/src/sage/functions/hypergeometric.py b/src/sage/functions/hypergeometric.py
-index 010c61febe0..bbccbd20032 100644
+index ade7836b310..eb5c6665c0d 100644
 --- a/src/sage/functions/hypergeometric.py
 +++ b/src/sage/functions/hypergeometric.py
 @@ -124,7 +124,7 @@
@@ -40,21 +37,8 @@ index 010c61febe0..bbccbd20032 100644
      sage: hypergeometric((5, 4), (4, 4), 3)._mathematica_init_()                        # needs sage.symbolic
      'HypergeometricPFQ[{5,4},{4,4},3]'
  
-diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx
-index a92fe241355..f62311423be 100644
---- a/src/sage/symbolic/expression.pyx
-+++ b/src/sage/symbolic/expression.pyx
-@@ -1167,7 +1167,7 @@ cdef class Expression(Expression_abc):
-             sage: unicode_art(SR(13 - I))
-             13 - ⅈ
-             sage: unicode_art(SR(1.3 - I))
--            1.3 - ⅈ
-+            1.3 - 1.0⋅ⅈ
-             sage: unicode_art(cos(I))
-             cosh(1)
- 
 diff --git a/src/sage/typeset/ascii_art.py b/src/sage/typeset/ascii_art.py
-index 28024405d27..458fa8724a3 100644
+index 83d92af8959..e470e2bd88d 100644
 --- a/src/sage/typeset/ascii_art.py
 +++ b/src/sage/typeset/ascii_art.py
 @@ -44,11 +44,12 @@
diff --git a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
index 1550d47e2436c6..321e0a94487da3 100644
--- a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
+++ b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
@@ -1,21 +1,21 @@
 diff --git a/src/sage/algebras/fusion_rings/fusion_double.py b/src/sage/algebras/fusion_rings/fusion_double.py
-index 7ce086f70d0..954513572c3 100644
+index 71277561331..3b681d75d3b 100644
 --- a/src/sage/algebras/fusion_rings/fusion_double.py
 +++ b/src/sage/algebras/fusion_rings/fusion_double.py
 @@ -133,7 +133,7 @@ class FusionDouble(CombinatorialFreeModule):
          sage: G = SmallPermutationGroup(16,9)
-         sage: F = FusionDouble(G, prefix="b",inject_variables=True)
+         sage: F = FusionDouble(G, prefix='b', inject_variables=True)
          sage: b13^2 # long time (4s)
 -        b0 + b2 + b4 + b15 + b16 + b17 + b18 + b24 + b26 + b27
 +        b0 + b3 + b4
- 
      """
      @staticmethod
+     def __classcall_private__(cls, G, prefix='s', inject_variables=False):
 diff --git a/src/sage/categories/simplicial_sets.py b/src/sage/categories/simplicial_sets.py
-index e714a4571c4..a2b87a729d1 100644
+index aabd3cdbb4f..14bebdcd080 100644
 --- a/src/sage/categories/simplicial_sets.py
 +++ b/src/sage/categories/simplicial_sets.py
-@@ -593,9 +593,9 @@ def _canonical_twisting_operator(self):
+@@ -591,9 +591,9 @@ def _canonical_twisting_operator(self):
                      sage: X = simplicial_sets.Torus()
                      sage: d = X._canonical_twisting_operator()
                      sage: d
@@ -27,7 +27,7 @@ index e714a4571c4..a2b87a729d1 100644
                      sage: Y = simplicial_sets.RealProjectiveSpace(2)
                      sage: d2 = Y._canonical_twisting_operator()
                      sage: d2
-@@ -677,10 +677,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
+@@ -674,10 +674,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
                      sage: X = simplicial_sets.Torus()
                      sage: C = X.twisted_chain_complex()
                      sage: C.differential(1)
@@ -41,7 +41,7 @@ index e714a4571c4..a2b87a729d1 100644
                      [      -1       -1]
                      sage: C.differential(3)
                      []
-@@ -848,29 +848,29 @@ def twisted_homology(self, n, reduced=False):
+@@ -844,29 +844,29 @@ def twisted_homology(self, n, reduced=False):
                      sage: # needs sage.graphs
                      sage: Y = simplicial_sets.Torus()
                      sage: Y.twisted_homology(1)
@@ -80,10 +80,10 @@ index e714a4571c4..a2b87a729d1 100644
                      [1 0 0 0 0]
                      [0 1 0 0 0]
 diff --git a/src/sage/combinat/matrices/latin.py b/src/sage/combinat/matrices/latin.py
-index 936edcc6ea4..c06a53d9afd 100644
+index e2d818e9480..84e6c4fcc9b 100644
 --- a/src/sage/combinat/matrices/latin.py
 +++ b/src/sage/combinat/matrices/latin.py
-@@ -2453,7 +2453,7 @@ def p3_group_bitrade_generators(p):
+@@ -2444,7 +2444,7 @@ def p3_group_bitrade_generators(p):
      EXAMPLES::
  
          sage: from sage.combinat.matrices.latin import *
@@ -93,7 +93,7 @@ index 936edcc6ea4..c06a53d9afd 100644
           (1,2,3)(4,7,8)(5,6,9),
           (1,9,2)(3,7,4)(5,8,6),
 diff --git a/src/sage/groups/cubic_braid.py b/src/sage/groups/cubic_braid.py
-index 257b400f1c7..36423c756aa 100644
+index 61db70925e1..521289c7578 100644
 --- a/src/sage/groups/cubic_braid.py
 +++ b/src/sage/groups/cubic_braid.py
 @@ -282,7 +282,7 @@ def _richcmp_(self, other, op):
@@ -106,7 +106,7 @@ index 257b400f1c7..36423c756aa 100644
               c1*c0^-1*c1, c0^-1*c1^-1*c0^-1, c0^-1*c1^-1, c1^-1*c0*c1^-1,
               c0*c1^-1*c0^-1, c0^-1*c1, c0^-1*c1*c0, c0*c1^-1, c1*c0^-1,
 diff --git a/src/sage/groups/finitely_presented.py b/src/sage/groups/finitely_presented.py
-index 4bb52ee4efb..85f572fac6c 100644
+index 4ac2faa783b..7016d08381b 100644
 --- a/src/sage/groups/finitely_presented.py
 +++ b/src/sage/groups/finitely_presented.py
 @@ -1344,8 +1344,8 @@ def abelianization_map(self):
@@ -161,10 +161,10 @@ index 4bb52ee4efb..85f572fac6c 100644
              sage: G.characteristic_varieties(groebner=True)
              {0: [-1 + F1, 1 + F1, 1 - F1 + F1^2, 1 + F1 + F1^2], 1: [1 - F1 + F1^2],  2: []}
 diff --git a/src/sage/groups/perm_gps/permgroup_named.py b/src/sage/groups/perm_gps/permgroup_named.py
-index c1f2683907b..d219e104a2c 100644
+index 5c153b93d4c..bd4afad2942 100644
 --- a/src/sage/groups/perm_gps/permgroup_named.py
 +++ b/src/sage/groups/perm_gps/permgroup_named.py
-@@ -3468,16 +3468,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
+@@ -3465,16 +3465,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
          sage: G = SmallPermutationGroup(12,4); G
          Group of order 12 and GAP Id 4 as a permutation group
          sage: G.gens()
@@ -186,7 +186,7 @@ index c1f2683907b..d219e104a2c 100644
          sage: def numgps(n): return ZZ(libgap.NumberSmallGroups(n))
          sage: all(SmallPermutationGroup(n,k).id() == [n,k]
          ....:     for n in [1..64] for k in [1..numgps(n)])
-@@ -3486,11 +3484,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
+@@ -3483,11 +3481,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
          sage: H.is_abelian()
          False
          sage: [H.centralizer(g) for g in H.conjugacy_classes_representatives()]
diff --git a/srcpkgs/sagemath/patches/38250-numpy_2.0.patch b/srcpkgs/sagemath/patches/38250-numpy_2.0.patch
deleted file mode 100644
index e28fd857afcb75..00000000000000
--- a/srcpkgs/sagemath/patches/38250-numpy_2.0.patch
+++ /dev/null
@@ -1,587 +0,0 @@
-diff --git a/src/sage/arith/misc.py b/src/sage/arith/misc.py
-index 28f81d7b798..d184c52bf19 100644
---- a/src/sage/arith/misc.py
-+++ b/src/sage/arith/misc.py
-@@ -2277,7 +2277,7 @@ def power_mod(a, n, m):
- 
-         sage: from numpy import int32                                                   # needs numpy
-         sage: power_mod(int32(2), int32(390), int32(391))                               # needs numpy
--        285
-+        ...285...
-         sage: from gmpy2 import mpz
-         sage: power_mod(mpz(2), mpz(390), mpz(391))
-         mpz(285)
-diff --git a/src/sage/calculus/interpolators.pyx b/src/sage/calculus/interpolators.pyx
-index 221b52369e2..bb0be7bab0c 100644
---- a/src/sage/calculus/interpolators.pyx
-+++ b/src/sage/calculus/interpolators.pyx
-@@ -27,6 +27,9 @@ Development supported by NSF award No. 0702939.
- import numpy as np
- cimport numpy as np
- 
-+if int(np.version.short_version[0]) > 1:
-+    np.set_printoptions(legacy="1.25")
-+
- from math import pi
- cdef double TWOPI = 2*pi
- 
-diff --git a/src/sage/calculus/riemann.pyx b/src/sage/calculus/riemann.pyx
-index 6ec80d89aa7..c09d93c4260 100644
---- a/src/sage/calculus/riemann.pyx
-+++ b/src/sage/calculus/riemann.pyx
-@@ -44,6 +44,9 @@ from sage.calculus.integration import numerical_integral
- import numpy as np
- cimport numpy as np
- 
-+if int(np.version.short_version[0]) > 1:
-+    np.set_printoptions(legacy="1.25")
-+
- from math import pi
- from math import sin
- from math import cos
-diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index b198fed0c0d..b3ebd206cd2 100644
---- a/src/sage/combinat/fully_packed_loop.py
-+++ b/src/sage/combinat/fully_packed_loop.py
-@@ -66,6 +66,9 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
-     r"""
-     TESTS::
- 
-+        sage: import numpy as np
-+        sage: if int(np.version.short_version[0]) > 1:
-+        ....:     np.set_printoptions(legacy="1.25")
-         sage: from sage.combinat.fully_packed_loop import _make_color_list
-         sage: _make_color_list(5)
-         sage: _make_color_list(5, ['blue', 'red'])
-diff --git a/src/sage/env.py b/src/sage/env.py
-index 722649ab3da..abb9b19f9e3 100644
---- a/src/sage/env.py
-+++ b/src/sage/env.py
-@@ -296,7 +296,7 @@ def sage_include_directories(use_sources=False):
-         sage: import sage.env
-         sage: sage.env.sage_include_directories()
-         ['...',
--         '.../numpy/core/include',
-+         '.../numpy/...core/include',
-          '.../include/python...']
- 
-     To check that C/C++ files are correctly found, we verify that we can
-diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
-index e100ba3ee23..2a03bb68f67 100644
---- a/src/sage/functions/special.py
-+++ b/src/sage/functions/special.py
-@@ -217,6 +217,9 @@ class SphericalHarmonic(BuiltinFunction):
-         sage: spherical_harmonic(1, 1, pi/2, pi).n()  # abs tol 1e-14                   # needs sage.symbolic
-         0.345494149471335
-         sage: from scipy.special import sph_harm  # NB: arguments x and y are swapped   # needs scipy
-+        sage: import numpy as np                                                        # needs scipy
-+        sage: if int(np.version.short_version[0]) > 1:                                  # needs scipy
-+        ....:     np.set_printoptions(legacy="1.25")                                    # needs scipy
-         sage: sph_harm(1, 1, pi.n(), (pi/2).n())  # abs tol 1e-14                       # needs scipy sage.symbolic
-         (0.3454941494713355-4.231083042742082e-17j)
- 
-diff --git a/src/sage/graphs/generators/classical_geometries.py b/src/sage/graphs/generators/classical_geometries.py
-index da04362eef3..957f88d2061 100644
---- a/src/sage/graphs/generators/classical_geometries.py
-+++ b/src/sage/graphs/generators/classical_geometries.py
-@@ -1315,7 +1315,7 @@ def CossidentePenttilaGraph(q):
- 
-     from sage.libs.gap.libgap import libgap
-     adj_list = libgap.function_factory("""function(q)
--        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x;
-+        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x, sqo;
-         LoadPackage("grape");
-         G0:=SO(3,q^2);
-         so:=GeneratorsOfGroup(G0);
-diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
-index 063931ae274..0bafbd00564 100644
---- a/src/sage/graphs/generic_graph.py
-+++ b/src/sage/graphs/generic_graph.py
-@@ -18420,6 +18420,9 @@ def shortest_path_all_pairs(self, by_weight=False, algorithm=None,
-                 M = self.adjacency_matrix(vertices=int_to_vertex)
- 
-             # We call the Floyd-Warshall method from SciPy
-+            import numpy  # to ensure numpy 2.0 compatibility
-+            if int(numpy.version.short_version[0]) > 1:
-+                numpy.set_printoptions(legacy="1.25")
-             from numpy import array as np_array
-             from scipy.sparse.csgraph import floyd_warshall
-             dd, pp = floyd_warshall(np_array(M), directed=self.is_directed(),
-diff --git a/src/sage/graphs/graph_generators_pyx.pyx b/src/sage/graphs/graph_generators_pyx.pyx
-index 033e8b22adc..04b20d3229b 100644
---- a/src/sage/graphs/graph_generators_pyx.pyx
-+++ b/src/sage/graphs/graph_generators_pyx.pyx
-@@ -57,7 +57,7 @@ def RandomGNP(n, p, bint directed=False, bint loops=False, seed=None):
- 
-         sage: from numpy import mean                                                    # needs numpy
-         sage: abs(mean([RandomGNP(200, .2).density() for i in range(30)]) - .2) < .001  # needs numpy
--        True
-+        ...True...
-         sage: RandomGNP(150, .2, loops=True)
-         Traceback (most recent call last):
-         ...
-diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
-index a810418389c..c38df5412f0 100644
---- a/src/sage/matrix/matrix1.pyx
-+++ b/src/sage/matrix/matrix1.pyx
-@@ -705,12 +705,15 @@ cdef class Matrix(Matrix0):
-         Type ``numpy.typecodes`` for a list of the possible
-         typecodes::
- 
--            sage: import numpy                                                          # needs numpy
--            sage: sorted(numpy.typecodes.items())                                       # needs numpy
-+            sage: import numpy                            # needs numpy
-+            sage: numpy.typecodes.items()                 # needs numpy # random
-             [('All', '?bhilqpBHILQPefdgFDGSUVOMm'), ('AllFloat', 'efdgFDG'),
--             ('AllInteger', 'bBhHiIlLqQpP'), ('Character', 'c'), ('Complex', 'FDG'),
--             ('Datetime', 'Mm'), ('Float', 'efdg'), ('Integer', 'bhilqp'),
--             ('UnsignedInteger', 'BHILQP')]
-+            ...
-+
-+        For instance, you can see possibilities for real floating point numbers::
-+
-+            sage: numpy.typecodes['Float']                # needs numpy
-+            'efdg'
- 
-         Alternatively, numpy automatically calls this function (via
-         the magic :meth:`__array__` method) to convert Sage matrices
-diff --git a/src/sage/modules/free_module_element.pyx b/src/sage/modules/free_module_element.pyx
-index d71d22ac1f7..b6f297a3510 100644
---- a/src/sage/modules/free_module_element.pyx
-+++ b/src/sage/modules/free_module_element.pyx
-@@ -555,7 +555,11 @@ def vector(arg0, arg1=None, arg2=None, sparse=None, immutable=False):
-         R = None
- 
-     try:
-+        import numpy
-         from numpy import ndarray
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-+
-     except ImportError:
-         pass
-     else:
-@@ -1188,7 +1192,11 @@ cdef class FreeModuleElement(Vector):   # abstract base class
-             over Rational Field to numpy array of type <... 'float'>:
-             setting an array element with a sequence.
-         """
-+        import numpy
-         from numpy import array
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-+
-         try:
-             return array(self, dtype=dtype)
-         except ValueError as e:
-diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index e3d94d1746e..7ae8ca4966f 100644
---- a/src/sage/numerical/optimize.py
-+++ b/src/sage/numerical/optimize.py
-@@ -155,6 +155,10 @@ def find_root(f, a, b, xtol=10e-13, rtol=2.0**-50, maxiter=100, full_output=Fals
-         b = max(s_1, s_2)
- 
-     import scipy.optimize
-+    import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     g = lambda x: float(f(x))
-     brentqRes = scipy.optimize.brentq(g, a, b,
-                                  full_output=full_output, xtol=xtol, rtol=rtol, maxiter=maxiter)
-@@ -288,6 +292,10 @@ def find_local_minimum(f, a, b, tol=1.48e-08, maxfun=500):
-     a = float(a)
-     b = float(b)
-     import scipy.optimize
-+    import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     xmin, fval, iter, funcalls = scipy.optimize.fminbound(f, a, b, full_output=1, xtol=tol, maxfun=maxfun)
-     return fval, xmin
- 
-@@ -376,6 +384,8 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
-         sage: def rosen(x):  # The Rosenbrock function
-         ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
-         sage: import numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:
-+        ....:     numpy.set_printoptions(legacy="1.25")
-         sage: from numpy import zeros
-         sage: def rosen_der(x):
-         ....:    xm = x[1r:-1r]
-@@ -393,6 +403,9 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
-     from sage.structure.element import Expression
-     from sage.ext.fast_callable import fast_callable
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-+
-     from scipy import optimize
-     if isinstance(func, Expression):
-         var_list = func.variables()
-@@ -530,6 +543,8 @@ def minimize_constrained(func,cons,x0,gradient=None,algorithm='default', **args)
-     from sage.structure.element import Expression
-     from sage.ext.fast_callable import fast_callable
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
-     from scipy import optimize
-     function_type = type(lambda x,y: x+y)
- 
-@@ -652,6 +667,8 @@ def find_fit(data, model, initial_guess=None, parameters=None, variables=None, s
-     ``lmdif`` and ``lmder`` algorithms.
-     """
-     import numpy
-+    if int(numpy.version.short_version[0]) > 1:
-+        numpy.set_printoptions(legacy="1.25")
- 
-     if not isinstance(data, numpy.ndarray):
-         try:
-diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index ac1dc79d802..23e2517ca56 100644
---- a/src/sage/plot/arrow.py
-+++ b/src/sage/plot/arrow.py
-@@ -53,6 +53,9 @@ def get_minmax_data(self):
- 
-         EXAMPLES::
- 
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: from sage.plot.arrow import CurveArrow
-             sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
-             ....:                options={})
-diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx
-index f1f2671a803..4d71414e1c2 100644
---- a/src/sage/plot/complex_plot.pyx
-+++ b/src/sage/plot/complex_plot.pyx
-@@ -1282,15 +1282,13 @@ def rgb_to_hls(rgb):
-         raise ValueError("Last dimension of input array must be 3; "
-                          "shape {} was found.".format(rgb.shape))
-     in_shape = rgb.shape
--    rgb = np.array(
--        rgb, copy=False, dtype=np.dtype(float), ndmin=2
--    )
-+    rgb = np.asarray(rgb, dtype=np.dtype(float))
-     rgb_max = rgb.max(-1)
-     rgb_min = rgb.min(-1)
-     l = (rgb_max + rgb_min)/2.0  # lightness
- 
-     hls = np.zeros_like(rgb)
--    delta = rgb.ptp(-1)
-+    delta = np.ptp(rgb, -1)
-     s = np.zeros_like(delta)
- 
-     ipos = delta > 0
-diff --git a/src/sage/plot/graphics.py b/src/sage/plot/graphics.py
-index a84d162cb56..94f5db09d83 100644
---- a/src/sage/plot/graphics.py
-+++ b/src/sage/plot/graphics.py
-@@ -2754,7 +2754,7 @@ def matplotlib(self, filename=None,
-             sage: xmin, xmax = sub.get_xlim()
-             sage: ymin, ymax = sub.get_ylim()
-             sage: xmin > xmax, ymin > ymax
--            (True, True)
-+            (...True..., ...True...)
-         """
-         if not isinstance(ticks, (list, tuple)):
-             ticks = (ticks, None)
-diff --git a/src/sage/plot/histogram.py b/src/sage/plot/histogram.py
-index fa86a44bd0a..a585cacf9cd 100644
---- a/src/sage/plot/histogram.py
-+++ b/src/sage/plot/histogram.py
-@@ -92,6 +92,8 @@ def get_minmax_data(self):
-             {'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.476190476190..., 'ymin': 0}
-         """
-         import numpy
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
- 
-         # Extract these options (if they are not None) and pass them to
-         # histogram()
-diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
-index b583be32317..6be448f1e04 100644
---- a/src/sage/plot/multigraphics.py
-+++ b/src/sage/plot/multigraphics.py
-@@ -784,6 +784,9 @@ def _add_subplot(self, figure, index, **options):
-             True
-             sage: G.position(1)
-             (0.2, 0.3, 0.4, 0.1)
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: ax1.get_position().bounds  # tol 1.0e-13
-             (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
- 
-@@ -1295,6 +1298,9 @@ def position(self, index):
-             sage: g1 = plot(sin(x), (x, -pi, pi))
-             sage: g2 = circle((0,1), 1.)
-             sage: G = graphics_array([g1, g2])
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: G.position(0)  # tol 5.0e-3
-             (0.025045451349937315,
-              0.03415488992713045,
-diff --git a/src/sage/plot/plot3d/implicit_surface.pyx b/src/sage/plot/plot3d/implicit_surface.pyx
-index ce0da48a4e0..f4d5059b620 100644
---- a/src/sage/plot/plot3d/implicit_surface.pyx
-+++ b/src/sage/plot/plot3d/implicit_surface.pyx
-@@ -468,6 +468,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
-             sage: cube_marcher.y_vertices.tolist()
-             [[[<1.0, 0.5, 0.0>, None]], [[None, None]]]
-             sage: cube_marcher.x_vertices.any() # This shouldn't affect the X vertices.
-+            ...
-         """
-         (self.y_vertices, self.y_vertices_swapped) = \
-             (self.y_vertices_swapped, self.y_vertices)
-@@ -574,6 +575,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
-             sage: cube_marcher.x_vertices.tolist()
-             [[None, None], [None, <1.5, 1.0, 1.0>]]
-             sage: cube_marcher.y_vertices.any() or cube_marcher.z_vertices.any() # This shouldn't affect the Y or Z vertices.
-+            ...
-         """
-         cdef bint has_prev = (_prev is not None)
-         cdef bint has_next = (_next is not None)
-diff --git a/src/sage/plot/scatter_plot.py b/src/sage/plot/scatter_plot.py
-index 4ad418f040b..781854d372c 100644
---- a/src/sage/plot/scatter_plot.py
-+++ b/src/sage/plot/scatter_plot.py
-@@ -63,9 +63,9 @@ def get_minmax_data(self):
-             sage: s = scatter_plot([[0,1],[2,4],[3.2,6]])
-             sage: d = s.get_minmax_data()
-             sage: d['xmin']
--            0.0
-+            ...0.0...
-             sage: d['ymin']
--            1.0
-+            ...1.0...
-         """
-         return {'xmin': self.xdata.min(),
-                 'xmax': self.xdata.max(),
-diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index 663d3aee70b..d2cb11088c7 100644
---- a/src/sage/plot/streamline_plot.py
-+++ b/src/sage/plot/streamline_plot.py
-@@ -71,6 +71,9 @@ def get_minmax_data(self):
-         EXAMPLES::
- 
-             sage: x, y = var('x y')
-+            sage: import numpy  # to ensure numpy 2.0 compatibility
-+            sage: if int(numpy.version.short_version[0]) > 1:
-+            ....:     numpy.set_printoptions(legacy="1.25")
-             sage: d = streamline_plot((.01*x, x+y), (x,10,20), (y,10,20))[0].get_minmax_data()
-             sage: d['xmin']
-             10.0
-diff --git a/src/sage/probability/probability_distribution.pyx b/src/sage/probability/probability_distribution.pyx
-index e2c71af9c25..59ba4a95ab6 100644
---- a/src/sage/probability/probability_distribution.pyx
-+++ b/src/sage/probability/probability_distribution.pyx
-@@ -140,6 +140,9 @@ cdef class ProbabilityDistribution:
-              1.8,
-              2.0]
-         """
-+        import numpy as np
-+        if int(np.version.short_version[0]) > 1:
-+            np.set_printoptions(legacy="1.25")
-         import pylab
-         ell = [float(self.get_random_element()) for _ in range(num_samples)]
-         S = pylab.hist(ell, bins, density=True)
-diff --git a/src/sage/rings/complex_double.pyx b/src/sage/rings/complex_double.pyx
-index c59a2b46d6f..b4dddebb4dc 100644
---- a/src/sage/rings/complex_double.pyx
-+++ b/src/sage/rings/complex_double.pyx
-@@ -2558,10 +2558,10 @@ cdef class ComplexToCDF(Morphism):
- 
-         sage: # needs numpy
-         sage: import numpy
--        sage: f = CDF.coerce_map_from(numpy.complex_)
--        sage: f(numpy.complex_(I))
-+        sage: f = CDF.coerce_map_from(numpy.complex128)
-+        sage: f(numpy.complex128(I))
-         1.0*I
--        sage: f(numpy.complex_(I)).parent()
-+        sage: f(numpy.complex128(I)).parent()
-         Complex Double Field
-     """
-     def __init__(self, R):
-@@ -2578,7 +2578,7 @@ cdef class ComplexToCDF(Morphism):
-         EXAMPLES::
- 
-             sage: import numpy                                                          # needs numpy
--            sage: CDF(numpy.complex_(I))    # indirect doctest                          # needs numpy
-+            sage: CDF(numpy.complex128(I))    # indirect doctest                          # needs numpy
-             1.0*I
-         """
-         cdef ComplexDoubleElement z = <ComplexDoubleElement>ComplexDoubleElement.__new__(ComplexDoubleElement)
-@@ -2592,7 +2592,7 @@ cdef class ComplexToCDF(Morphism):
-         EXAMPLES::
- 
-             sage: import numpy                                                          # needs numpy
--            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex_)            # needs numpy
-+            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex128)          # needs numpy
-             sage: f._repr_type()                                                        # needs numpy
-             'Native'
-         """
-diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index b4a1fa5039b..38c30f7627b 100644
---- a/src/sage/rings/integer.pyx
-+++ b/src/sage/rings/integer.pyx
-@@ -593,6 +593,8 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
-         Test comparisons with numpy types (see :issue:`13386` and :issue:`18076`)::
- 
-             sage: import numpy                                                          # needs numpy
-+            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
-+            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-             sage: numpy.int8('12') == 12                                                # needs numpy
-             True
-             sage: 12 == numpy.int8('12')                                                # needs numpy
-diff --git a/src/sage/rings/polynomial/polynomial_element.pyx b/src/sage/rings/polynomial/polynomial_element.pyx
-index dcf2af7cdf2..c87eccd44f1 100644
---- a/src/sage/rings/polynomial/polynomial_element.pyx
-+++ b/src/sage/rings/polynomial/polynomial_element.pyx
-@@ -8851,7 +8851,7 @@ cdef class Polynomial(CommutativePolynomial):
-                          'you expect.')
- 
-                 import numpy
--                from numpy.linalg.linalg import LinAlgError
-+                from numpy.linalg import LinAlgError
-                 from sage.rings.complex_double import CDF
- 
-                 numpy_dtype = ('complex' if input_complex else 'double')
-diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
-index 95b472e912c..76fbfedab95 100644
---- a/src/sage/rings/real_mpfi.pyx
-+++ b/src/sage/rings/real_mpfi.pyx
-@@ -231,6 +231,8 @@ specified if given a non-interval and an interval::
- TESTS::
- 
-     sage: import numpy                                                                  # needs numpy
-+    sage: if int(numpy.version.short_version[0]) > 1:                                   # needs numpy
-+    ....:     numpy.set_printoptions(legacy="1.25")                                     # needs numpy
-     sage: RIF(2) == numpy.int8('2')                                                     # needs numpy
-     True
-     sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
-diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-index 8f240627e77..70ce616f92f 100644
---- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-+++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-@@ -77,6 +77,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
-@@ -295,6 +297,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((10, 10))
-             sage: data[1:4,1:4] = True
-@@ -317,6 +321,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1,1] = True
-@@ -370,6 +376,8 @@ cdef class PeriodicRegion:
-         EXAMPLES::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
- 
-             sage: data = np.zeros((20, 20))
-@@ -520,6 +528,8 @@ cdef class PeriodicRegion:
-         TESTS::
- 
-             sage: import numpy as np
-+            sage: if int(np.version.short_version[0]) > 1:
-+            ....:     np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1, 1] = True
-diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index b2e6b301bf7..6937f6cb410 100644
---- a/src/sage/stats/basic_stats.py
-+++ b/src/sage/stats/basic_stats.py
-@@ -227,6 +227,8 @@ def std(v, bias=False):
- 
-         sage: # needs numpy
-         sage: import numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:
-+        ....:     numpy.set_printoptions(legacy="1.25")
-         sage: x = numpy.array([1,2,3,4,5])
-         sage: std(x, bias=False)
-         1.5811388300841898
-@@ -304,6 +306,8 @@ def variance(v, bias=False):
-         sage: variance([RIF(1.0103, 1.0103), RIF(2)])
-         0.4897530450000000?
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-         sage: x = numpy.array([1,2,3,4,5])                                              # needs numpy
-         sage: variance(x, bias=False)                                                   # needs numpy
-         2.5
-diff --git a/src/sage/stats/time_series.pyx b/src/sage/stats/time_series.pyx
-index 2e22ec45c69..23adae84fb4 100644
---- a/src/sage/stats/time_series.pyx
-+++ b/src/sage/stats/time_series.pyx
-@@ -1718,6 +1718,8 @@ cdef class TimeSeries:
-         if len(v0) == 1:
-             return v1[0]/v0[0]
-         import numpy
-+        if int(numpy.version.short_version[0]) > 1:
-+            numpy.set_printoptions(legacy="1.25")
-         coeffs = numpy.polyfit(v0,v1,1)
-         return coeffs[0]
- 
-diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
-index dfbd5ff82fa..955a256e9b4 100644
---- a/src/sage/structure/coerce.pyx
-+++ b/src/sage/structure/coerce.pyx
-@@ -520,6 +520,8 @@ cdef class CoercionModel:
-     Check that :issue:`8426` is fixed (see also :issue:`18076`)::
- 
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
- 
-         sage: # needs sage.rings.real_mpfr
-         sage: x = polygen(RR)
-diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
-index 2cb2f09c715..cd89ad2a256 100644
---- a/src/sage/symbolic/function.pyx
-+++ b/src/sage/symbolic/function.pyx
-@@ -964,6 +964,9 @@ cdef class BuiltinFunction(Function):
-             mpc(real='0.83373002513114902', imag='-0.98889770576286506')
- 
-             sage: import numpy                                                          # needs numpy
-+            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
-+            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-+
-             sage: sin(numpy.int32(0))                                                   # needs numpy
-             0.0
-             sage: type(_)                                                               # needs numpy
-diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 501b0920898..5b007d9e5fd 100644
---- a/src/sage/symbolic/ring.pyx
-+++ b/src/sage/symbolic/ring.pyx
-@@ -1162,6 +1162,8 @@ cdef class NumpyToSRMorphism(Morphism):
-     We check that :issue:`8949` and :issue:`9769` are fixed (see also :issue:`18076`)::
- 
-         sage: import numpy                                                              # needs numpy
-+        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
-+        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-         sage: f(x) = x^2
-         sage: f(numpy.int8('2'))                                                        # needs numpy
-         4
diff --git a/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch b/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch
deleted file mode 100644
index db0ae9030623b6..00000000000000
--- a/srcpkgs/sagemath/patches/38344-ecm_7.0.6.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-diff --git a/src/sage/interfaces/ecm.py b/src/sage/interfaces/ecm.py
-index 99287dec718..98011970404 100644
---- a/src/sage/interfaces/ecm.py
-+++ b/src/sage/interfaces/ecm.py
-@@ -508,7 +508,6 @@ def _find_factor(self, n, factor_digits, B1, **kwds):
-         """
-         n = self._validate(n)
-         kwds.setdefault('c', 1000000000)
--        kwds.setdefault('I', 1)
-         if factor_digits is not None:
-             B1 = self.recommended_B1(factor_digits)
-         kwds['one'] = True
-diff --git a/src/sage/libs/libecm.pyx b/src/sage/libs/libecm.pyx
-index 886a9b816e4..83fb7adaf8d 100644
---- a/src/sage/libs/libecm.pyx
-+++ b/src/sage/libs/libecm.pyx
-@@ -149,11 +149,13 @@ def ecmfactor(number, double B1, verbose=False, sigma=0):
-     Some special cases::
- 
-         sage: ecmfactor(1, 100)
--        (True, 1, ...)
-+        Traceback (most recent call last):
-+        ...
-+        ValueError: Input number (1) must be greater than 1
-         sage: ecmfactor(0, 100)
-         Traceback (most recent call last):
-         ...
--        ValueError: Input number (0) must be positive
-+        ValueError: Input number (0) must be greater than 1
-     """
-     cdef mpz_t n, f
-     cdef int res
-@@ -164,8 +166,8 @@ def ecmfactor(number, double B1, verbose=False, sigma=0):
-     sage_int_number = Integer(number)
-     sage_int_sigma = Integer(sigma)
- 
--    if number <= 0:
--        raise ValueError("Input number (%s) must be positive"%number)
-+    if number <= 1:
-+        raise ValueError("Input number (%s) must be greater than 1"%number)
- 
-     if verbose:
-         print("Performing one curve with B1=%1.0f" % B1)
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 28162dff8a38e1..5cab228f286365 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -19,7 +19,7 @@ get_pr() {
 	echo "curl -sL \"$url\" | filterdiff ... > \"$pr-$desc.patch\""
 	if [ -z "$dry" ]; then
 		curl -sL "$url" |
-			filterdiff -p1 -x src/setup.py -x build/* -x src/doc/* |
+			filterdiff -p1 -x src/setup.py -x environment* -x src/environment* -x build/* -x src/doc/* |
 			cat > "$pr-$desc.patch"
 	fi
 }
@@ -29,8 +29,6 @@ cd $(dirname "$0")
 
 get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
-get_pr 38250 "numpy 2.0"
-get_pr 38344 "ecm 7.0.6"
 
 #get_pr 37645 "fix doctest"
 #get_pr 37885 "cython warnings"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index b116e62bc67a5a..f5e1d8c68cfcbe 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,7 +1,7 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.4
-revision=3
+version=10.5.beta2
+revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
 build_style=python3-pep517
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=f6579e85f33bd9bb6e9b991bfc4c49dab1e649858ed9ee41c7cec75cb92d4c62
+checksum=0fe0c82dd6959951fc07d55737d270290f64947e183a403ca25709e21b751dee
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From 4427805e284a6bb5590cdf475cdd451446ebc158 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Wed, 14 Aug 2024 00:12:02 -0300
Subject: [PATCH 10/21] sagemath: enable all cython warnings

---
 srcpkgs/sagemath/patches/37885-cython_warnings.patch | 12 ++++++++++++
 srcpkgs/sagemath/patches/get_patches                 |  2 +-
 2 files changed, 13 insertions(+), 1 deletion(-)
 create mode 100644 srcpkgs/sagemath/patches/37885-cython_warnings.patch

diff --git a/srcpkgs/sagemath/patches/37885-cython_warnings.patch b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
new file mode 100644
index 00000000000000..fa4b648cfc1577
--- /dev/null
+++ b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
@@ -0,0 +1,12 @@
+diff --git a/src/sage_setup/command/sage_build_cython.py b/src/sage_setup/command/sage_build_cython.py
+index f4b1357c543..3435c196d49 100644
+--- a/src/sage_setup/command/sage_build_cython.py
++++ b/src/sage_setup/command/sage_build_cython.py
+@@ -226,6 +226,7 @@ def run(self):
+                 compiler_directives=self.cython_directives,
+                 compile_time_env=self.compile_time_env,
+                 create_extension=self.create_extension,
++                show_all_warnings=True,
+                 # Debugging
+                 gdb_debug=self.debug,
+                 output_dir=os.path.join(self.build_lib, "sage"),
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 5cab228f286365..c182576ea553cd 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -31,4 +31,4 @@ get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
 
 #get_pr 37645 "fix doctest"
-#get_pr 37885 "cython warnings"
+get_pr 37885 "cython warnings"

From 8334a5ddb02fd3ee6f15c2ec0fecb41a107d0ac9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 20 Aug 2024 17:56:06 -0300
Subject: [PATCH 11/21] sagemath: patch for numpy 2.1

---
 srcpkgs/sagemath/patches/numpy_2.1a.patch |  8 +--
 srcpkgs/sagemath/patches/numpy_2.1b.patch | 70 +++++++++++------------
 2 files changed, 39 insertions(+), 39 deletions(-)

diff --git a/srcpkgs/sagemath/patches/numpy_2.1a.patch b/srcpkgs/sagemath/patches/numpy_2.1a.patch
index 30e2de99d84536..493c75e2f8f8e0 100644
--- a/srcpkgs/sagemath/patches/numpy_2.1a.patch
+++ b/srcpkgs/sagemath/patches/numpy_2.1a.patch
@@ -1,14 +1,14 @@
-commit 241dc39bd0ba1c056f88bee46a0345d59093eaff
+commit d755b32cbed462abf01a1cd782ba57cb92fbf713
 Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
 Date:   Mon Aug 19 23:25:32 2024 -0300
 
     add copy parameter to numpy (needed for v2.1)
 
 diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
-index c38df5412f0..f587cef651a 100644
+index 3edb9ead54d..2c76fd1e557 100644
 --- a/src/sage/matrix/matrix1.pyx
 +++ b/src/sage/matrix/matrix1.pyx
-@@ -671,7 +671,7 @@ cdef class Matrix(Matrix0):
+@@ -670,7 +670,7 @@ cdef class Matrix(Matrix0):
              entries = [[sib(v, 2) for v in row] for row in self.rows()]
              return sib.name('matrix')(self.base_ring(), entries)
  
@@ -17,7 +17,7 @@ index c38df5412f0..f587cef651a 100644
          """
          Return the Numpy matrix associated to this matrix.
  
-@@ -732,7 +732,7 @@ cdef class Matrix(Matrix0):
+@@ -731,7 +731,7 @@ cdef class Matrix(Matrix0):
              (3, 4)
          """
          import numpy
diff --git a/srcpkgs/sagemath/patches/numpy_2.1b.patch b/srcpkgs/sagemath/patches/numpy_2.1b.patch
index b77e28361d2e74..8dc0eec2b5a9d8 100644
--- a/srcpkgs/sagemath/patches/numpy_2.1b.patch
+++ b/srcpkgs/sagemath/patches/numpy_2.1b.patch
@@ -1,11 +1,11 @@
-commit 8b32fdb87725c1d67ffb51dadec1c331c7c35f3c
+commit 8260d18c3cf8e356db3d95fc46f6e68f75b453fd
 Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
 Date:   Tue Aug 20 00:05:33 2024 -0300
 
     silence np.set_printoptions (for numpy 2.1)
 
 diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index b3ebd206cd2..48866824224 100644
+index 74a14fa1ecd..82e6c7eb3c8 100644
 --- a/src/sage/combinat/fully_packed_loop.py
 +++ b/src/sage/combinat/fully_packed_loop.py
 @@ -68,7 +68,7 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
@@ -18,7 +18,7 @@ index b3ebd206cd2..48866824224 100644
          sage: _make_color_list(5)
          sage: _make_color_list(5, ['blue', 'red'])
 diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
-index 2a03bb68f67..30b56722e66 100644
+index 308171af3cd..6f66624ef87 100644
 --- a/src/sage/functions/special.py
 +++ b/src/sage/functions/special.py
 @@ -219,7 +219,7 @@ class SphericalHarmonic(BuiltinFunction):
@@ -31,10 +31,10 @@ index 2a03bb68f67..30b56722e66 100644
          (0.3454941494713355-4.231083042742082e-17j)
  
 diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index 7ae8ca4966f..4cba22efdba 100644
+index b3e42a6a6a2..13ffa4d1789 100644
 --- a/src/sage/numerical/optimize.py
 +++ b/src/sage/numerical/optimize.py
-@@ -385,7 +385,7 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
+@@ -381,7 +381,7 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm='default',
          ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
          sage: import numpy
          sage: if int(numpy.version.short_version[0]) > 1:
@@ -44,7 +44,7 @@ index 7ae8ca4966f..4cba22efdba 100644
          sage: def rosen_der(x):
          ....:    xm = x[1r:-1r]
 diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index 23e2517ca56..7375dcd5d1c 100644
+index 02442f90ba4..1fe3f0b051a 100644
 --- a/src/sage/plot/arrow.py
 +++ b/src/sage/plot/arrow.py
 @@ -55,7 +55,7 @@ class CurveArrow(GraphicPrimitive):
@@ -57,10 +57,10 @@ index 23e2517ca56..7375dcd5d1c 100644
              sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
              ....:                options={})
 diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
-index 6be448f1e04..004594b77c4 100644
+index d2f70b44526..2eaacc6879e 100644
 --- a/src/sage/plot/multigraphics.py
 +++ b/src/sage/plot/multigraphics.py
-@@ -786,7 +786,7 @@ class MultiGraphics(WithEqualityById, SageObject):
+@@ -766,7 +766,7 @@ class MultiGraphics(WithEqualityById, SageObject):
              (0.2, 0.3, 0.4, 0.1)
              sage: import numpy  # to ensure numpy 2.0 compatibility
              sage: if int(numpy.version.short_version[0]) > 1:
@@ -68,8 +68,8 @@ index 6be448f1e04..004594b77c4 100644
 +            ....:     _token = numpy.set_printoptions(legacy="1.25")
              sage: ax1.get_position().bounds  # tol 1.0e-13
              (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
- 
-@@ -1300,7 +1300,7 @@ class GraphicsArray(MultiGraphics):
+         """
+@@ -1269,7 +1269,7 @@ class GraphicsArray(MultiGraphics):
              sage: G = graphics_array([g1, g2])
              sage: import numpy  # to ensure numpy 2.0 compatibility
              sage: if int(numpy.version.short_version[0]) > 1:
@@ -79,10 +79,10 @@ index 6be448f1e04..004594b77c4 100644
              (0.025045451349937315,
               0.03415488992713045,
 diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index d2cb11088c7..6d88517cc15 100644
+index b69a05b37bf..25e404bfc7d 100644
 --- a/src/sage/plot/streamline_plot.py
 +++ b/src/sage/plot/streamline_plot.py
-@@ -73,7 +73,7 @@ class StreamlinePlot(GraphicPrimitive):
+@@ -72,7 +72,7 @@ class StreamlinePlot(GraphicPrimitive):
              sage: x, y = var('x y')
              sage: import numpy  # to ensure numpy 2.0 compatibility
              sage: if int(numpy.version.short_version[0]) > 1:
@@ -92,20 +92,20 @@ index d2cb11088c7..6d88517cc15 100644
              sage: d['xmin']
              10.0
 diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index 38c30f7627b..cfb8a5ff5f7 100644
+index 11811b9587f..8ce0f7f2683 100644
 --- a/src/sage/rings/integer.pyx
 +++ b/src/sage/rings/integer.pyx
-@@ -594,7 +594,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
- 
-             sage: import numpy                                                          # needs numpy
-             sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
--            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")                    # needs numpy
-             sage: numpy.int8('12') == 12                                                # needs numpy
+@@ -595,7 +595,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
+             sage: # needs numpy
+             sage: import numpy
+             sage: if int(numpy.version.short_version[0]) > 1:
+-            ....:     numpy.set_printoptions(legacy="1.25")
++            ....:     _token = numpy.set_printoptions(legacy="1.25")
+             sage: numpy.int8('12') == 12
              True
-             sage: 12 == numpy.int8('12')                                                # needs numpy
+             sage: 12 == numpy.int8('12')
 diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
-index 76fbfedab95..57de30c9d18 100644
+index 11953a50ab5..6aafcceed89 100644
 --- a/src/sage/rings/real_mpfi.pyx
 +++ b/src/sage/rings/real_mpfi.pyx
 @@ -232,7 +232,7 @@ TESTS::
@@ -118,7 +118,7 @@ index 76fbfedab95..57de30c9d18 100644
      True
      sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
 diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-index 70ce616f92f..f604c6d3785 100644
+index 40b92ab23eb..3838bcccb8a 100755
 --- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
 +++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
 @@ -78,7 +78,7 @@ cdef class PeriodicRegion:
@@ -130,7 +130,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
              sage: data = np.zeros((4, 4))
              sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
-@@ -298,7 +298,7 @@ cdef class PeriodicRegion:
+@@ -296,7 +296,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -139,7 +139,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
              sage: data = np.zeros((10, 10))
              sage: data[1:4,1:4] = True
-@@ -322,7 +322,7 @@ cdef class PeriodicRegion:
+@@ -320,7 +320,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -148,7 +148,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
              sage: data = np.zeros((4, 4))
              sage: data[1,1] = True
-@@ -377,7 +377,7 @@ cdef class PeriodicRegion:
+@@ -375,7 +375,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -157,7 +157,7 @@ index 70ce616f92f..f604c6d3785 100644
              sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
  
              sage: data = np.zeros((20, 20))
-@@ -529,7 +529,7 @@ cdef class PeriodicRegion:
+@@ -528,7 +528,7 @@ cdef class PeriodicRegion:
  
              sage: import numpy as np
              sage: if int(np.version.short_version[0]) > 1:
@@ -167,10 +167,10 @@ index 70ce616f92f..f604c6d3785 100644
              sage: data = np.zeros((4, 4))
              sage: data[1, 1] = True
 diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index 6937f6cb410..fb296e00fb6 100644
+index 47d890cf0ab..ba7f0cdb0f9 100644
 --- a/src/sage/stats/basic_stats.py
 +++ b/src/sage/stats/basic_stats.py
-@@ -228,7 +228,7 @@ def std(v, bias=False):
+@@ -222,7 +222,7 @@ def std(v, bias=False):
          sage: # needs numpy
          sage: import numpy
          sage: if int(numpy.version.short_version[0]) > 1:
@@ -179,7 +179,7 @@ index 6937f6cb410..fb296e00fb6 100644
          sage: x = numpy.array([1,2,3,4,5])
          sage: std(x, bias=False)
          1.5811388300841898
-@@ -307,7 +307,7 @@ def variance(v, bias=False):
+@@ -299,7 +299,7 @@ def variance(v, bias=False):
          0.4897530450000000?
          sage: import numpy                                                              # needs numpy
          sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
@@ -189,7 +189,7 @@ index 6937f6cb410..fb296e00fb6 100644
          sage: variance(x, bias=False)                                                   # needs numpy
          2.5
 diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
-index 955a256e9b4..e5ed6160b79 100644
+index cc15eff82e9..e32e7fd28b3 100644
 --- a/src/sage/structure/coerce.pyx
 +++ b/src/sage/structure/coerce.pyx
 @@ -521,7 +521,7 @@ cdef class CoercionModel:
@@ -202,10 +202,10 @@ index 955a256e9b4..e5ed6160b79 100644
          sage: # needs sage.rings.real_mpfr
          sage: x = polygen(RR)
 diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
-index cd89ad2a256..6fdf6d8ef23 100644
+index 362d01ea297..92bce28b032 100644
 --- a/src/sage/symbolic/function.pyx
 +++ b/src/sage/symbolic/function.pyx
-@@ -965,7 +965,7 @@ cdef class BuiltinFunction(Function):
+@@ -962,7 +962,7 @@ cdef class BuiltinFunction(Function):
  
              sage: import numpy                                                          # needs numpy
              sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
@@ -215,10 +215,10 @@ index cd89ad2a256..6fdf6d8ef23 100644
              sage: sin(numpy.int32(0))                                                   # needs numpy
              0.0
 diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 5b007d9e5fd..4a096d317e7 100644
+index 32afe8d3a62..63734e68f63 100644
 --- a/src/sage/symbolic/ring.pyx
 +++ b/src/sage/symbolic/ring.pyx
-@@ -1163,7 +1163,7 @@ cdef class NumpyToSRMorphism(Morphism):
+@@ -1154,7 +1154,7 @@ cdef class NumpyToSRMorphism(Morphism):
  
          sage: import numpy                                                              # needs numpy
          sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy

From 048c8e2bcd7283e3f15e4377a91fae47c55f6178 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 8 Sep 2024 09:35:16 -0300
Subject: [PATCH 12/21] nauty: update to 2.8.9.

---
 srcpkgs/nauty/patches/fix-runalltests.patch | 11 +++++++++++
 srcpkgs/nauty/template                      |  7 ++++---
 2 files changed, 15 insertions(+), 3 deletions(-)
 create mode 100644 srcpkgs/nauty/patches/fix-runalltests.patch

diff --git a/srcpkgs/nauty/patches/fix-runalltests.patch b/srcpkgs/nauty/patches/fix-runalltests.patch
new file mode 100644
index 00000000000000..34e1692cf6e6e3
--- /dev/null
+++ b/srcpkgs/nauty/patches/fix-runalltests.patch
@@ -0,0 +1,11 @@
+--- a/runalltests.in	2024-08-26 00:55:55.000000000 -0300
++++ b/runalltests.in	2024-09-08 09:30:04.032719770 -0300
+@@ -121,7 +121,7 @@
+ runonetest "./geng -q -TD6 10 | ./ransubg -qS765 -P9/10 | ./countg --NN,A,G,GG" "" nautestv.ans
+ runonetest "./genrang -q -P3 -S1234 70 1000 | ./countg --G,GG" "" nautestw.ans
+ runonetest "./genrang -q -P4 -z -S1234 70 500 | ./countg --G,GG" "" nautestx.ans
+-runonetest "./geng -q -bT 12 | ./ranlabg -qS7654 -m5 | uniqg -u" "" nautesty.ans
++runonetest "./geng -q -bT 12 | ./ranlabg -qS7654 -m5 | ./uniqg -u" "" nautesty.ans
+ 
+ echo " "
+ 
diff --git a/srcpkgs/nauty/template b/srcpkgs/nauty/template
index 6f85b1d064d4e5..aea4e4a6eb0294 100644
--- a/srcpkgs/nauty/template
+++ b/srcpkgs/nauty/template
@@ -1,18 +1,18 @@
 # Template file for 'nauty'
 pkgname=nauty
-version=2.8.8
+version=2.8.9
 revision=1
 build_style=gnu-configure
 make_install_args="includedir=/usr/include/nauty
  pkgconfigexecdir=/usr/lib/pkgconfig"
-hostmakedepends="automake"
+hostmakedepends="automake libtool"
 short_desc="Compute the automorphism groups of graphs and digraphs"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="Apache-2.0"
 homepage="https://pallini.di.uniroma1.it/"
 changelog="https://pallini.di.uniroma1.it/changes24-28.txt"
 distfiles="https://pallini.di.uniroma1.it/nauty${version//./_}.tar.gz"
-checksum=159d2156810a6bb240410cd61eb641add85088d9f15c888cdaa37b8681f929ce
+checksum=c97ab42bf48796a86a598bce3e9269047ca2b32c14fc23e07208a244fe52c4ee
 
 build_options="native_build"
 
@@ -21,6 +21,7 @@ if [ -z "$build_option_native_build" ]; then
 fi
 
 pre_configure() {
+	aclocal
 	autoreconf -fi
 }
 

From 6ba642909d9184c8233d9c6096a6c6360df15fe6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sat, 7 Sep 2024 14:32:41 -0300
Subject: [PATCH 13/21] sagemath: update to 10.5.beta3.

---
 .../sagemath/patches/36641-sympy_1.13.patch   | 60 -------------------
 .../sagemath/patches/38572-nauty_2.8.9.patch  | 13 ++++
 srcpkgs/sagemath/patches/get_patches          |  4 +-
 srcpkgs/sagemath/template                     |  4 +-
 4 files changed, 17 insertions(+), 64 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/36641-sympy_1.13.patch
 create mode 100644 srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch

diff --git a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch b/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
deleted file mode 100644
index 01e859ad023f4d..00000000000000
--- a/srcpkgs/sagemath/patches/36641-sympy_1.13.patch
+++ /dev/null
@@ -1,60 +0,0 @@
-diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py
-index 823a0d14a41..de1c8531814 100644
---- a/src/sage/doctest/forker.py
-+++ b/src/sage/doctest/forker.py
-@@ -150,14 +150,15 @@ def init_sage(controller=None):
-         sage: from sympy.printing.pretty.pretty import PrettyPrinter
-         sage: s = sympify('+x^'.join(str(i) for i in range(30)))
-         sage: print(PrettyPrinter(settings={'wrap_line': True}).doprint(s))
--         29    28    27    26    25    24    23    22    21    20    19    18    17
--        x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   +
-+         29    28    27    26    25    24    23    22    21    20    19    18    17    ↪
-+        x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   + x   +  ↪
-         <BLANKLINE>
--         16    15    14    13    12    11    10    9    8    7    6    5    4    3
--        x   + x   + x   + x   + x   + x   + x   + x  + x  + x  + x  + x  + x  + x  + x
-+        ↪  16    15    14    13    12    11    10    9    8    7    6    5    4    3   ↪
-+        ↪ x   + x   + x   + x   + x   + x   + x   + x  + x  + x  + x  + x  + x  + x  + ↪
-         <BLANKLINE>
--        2
--          + x
-+        ↪   2
-+        ↪  x  + x
-+
- 
-     The displayhook sorts dictionary keys to simplify doctesting of
-     dictionary output::
-diff --git a/src/sage/functions/hypergeometric.py b/src/sage/functions/hypergeometric.py
-index ade7836b310..eb5c6665c0d 100644
---- a/src/sage/functions/hypergeometric.py
-+++ b/src/sage/functions/hypergeometric.py
-@@ -124,7 +124,7 @@
-     sage: maxima(hypergeometric([1, 1, 1], [3, 3, 3], x))                               # needs sage.symbolic
-     hypergeometric([1,1,1],[3,3,3],_SAGE_VAR_x)
-     sage: hypergeometric((5, 4), (4, 4), 3)._sympy_()                                   # needs sympy sage.symbolic
--    hyper((5, 4), (4, 4), 3)
-+    hyper((5,), (4,), 3)
-     sage: hypergeometric((5, 4), (4, 4), 3)._mathematica_init_()                        # needs sage.symbolic
-     'HypergeometricPFQ[{5,4},{4,4},3]'
- 
-diff --git a/src/sage/typeset/ascii_art.py b/src/sage/typeset/ascii_art.py
-index 83d92af8959..e470e2bd88d 100644
---- a/src/sage/typeset/ascii_art.py
-+++ b/src/sage/typeset/ascii_art.py
-@@ -44,11 +44,12 @@
-     sage: shell.run_cell('%display ascii_art')
-     sage: shell.run_cell("i = var('i')")                                                # needs sage.symbolic
-     sage: shell.run_cell('sum(factorial(i)*x^i, i, 0, 10)')                             # needs sage.symbolic
--             10           9          8         7        6        5       4      3
--    3628800*x   + 362880*x  + 40320*x  + 5040*x  + 720*x  + 120*x  + 24*x  + 6*x
-+             10           9          8         7        6        5       4      3  >
-+    3628800*x   + 362880*x  + 40320*x  + 5040*x  + 720*x  + 120*x  + 24*x  + 6*x   >
-     <BLANKLINE>
--         2
--    + 2*x  + x + 1
-+    >      2
-+    > + 2*x  + x + 1
-+
-     sage: shell.run_cell('3/(7*x)')                                                     # needs sage.symbolic
-      3
-     ---
diff --git a/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch b/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
new file mode 100644
index 00000000000000..5f75a8bef5556a
--- /dev/null
+++ b/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
@@ -0,0 +1,13 @@
+diff --git a/src/sage/graphs/generators/families.py b/src/sage/graphs/generators/families.py
+index e6e5312b8a8..aa10d15d4d8 100644
+--- a/src/sage/graphs/generators/families.py
++++ b/src/sage/graphs/generators/families.py
+@@ -3710,7 +3710,7 @@ def nauty_gentreeg(options='', debug=False):
+         ...
+         ValueError: wrong format of parameter options
+         sage: list(graphs.nauty_gentreeg("3 -x", debug=True))
+-        ['>E Usage: ...gentreeg [-D#] [-Z#:#] [-ulps] [-q] n [res/mod] ...
++        ['>E Usage: ...gentreeg [-D#] [-Z#:#] [-ulps] [-q] n... [res/mod] ...
+         sage: list(graphs.nauty_gentreeg("3", debug=True))
+         ['>A ...gentreeg ...\n', Graph on 3 vertices]
+     """
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index c182576ea553cd..8f540dad14bfd1 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -1,6 +1,6 @@
 #! /bin/sh
 
-version=10.4
+version=10.5
 
 URL_BASE_PR="https://github.com/sagemath/sage/pull/"
 URL_BASE_COMPARE="https://github.com/sagemath/sage/compare/${version}..."
@@ -27,8 +27,8 @@ get_pr() {
 # run from patches dir
 cd $(dirname "$0")
 
-get_pr 36641 "sympy 1.13"
 get_pr 37884 "gap 4.13.1"
+get_pr 38572 "nauty 2.8.9"
 
 #get_pr 37645 "fix doctest"
 get_pr 37885 "cython warnings"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index f5e1d8c68cfcbe..709a3ea4262101 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,6 +1,6 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.5.beta2
+version=10.5.beta3
 revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=0fe0c82dd6959951fc07d55737d270290f64947e183a403ca25709e21b751dee
+checksum=cbf3614c1b9be5f0a0756b0a5480c2ebfa663bd87bd66eefd162a755979bcb3d
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From 461397c78b651dbb8b8c4b5b9ed8f35a673a2f4a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 22 Sep 2024 08:19:39 -0300
Subject: [PATCH 14/21] sagemath: update to 10.5.beta5.

---
 .../sagemath/patches/38572-nauty_2.8.9.patch  |  13 -
 srcpkgs/sagemath/patches/numpy_2.1a.patch     |  28 ---
 srcpkgs/sagemath/patches/numpy_2.1b.patch     | 229 ------------------
 srcpkgs/sagemath/template                     |   4 +-
 4 files changed, 2 insertions(+), 272 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
 delete mode 100644 srcpkgs/sagemath/patches/numpy_2.1a.patch
 delete mode 100644 srcpkgs/sagemath/patches/numpy_2.1b.patch

diff --git a/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch b/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
deleted file mode 100644
index 5f75a8bef5556a..00000000000000
--- a/srcpkgs/sagemath/patches/38572-nauty_2.8.9.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/src/sage/graphs/generators/families.py b/src/sage/graphs/generators/families.py
-index e6e5312b8a8..aa10d15d4d8 100644
---- a/src/sage/graphs/generators/families.py
-+++ b/src/sage/graphs/generators/families.py
-@@ -3710,7 +3710,7 @@ def nauty_gentreeg(options='', debug=False):
-         ...
-         ValueError: wrong format of parameter options
-         sage: list(graphs.nauty_gentreeg("3 -x", debug=True))
--        ['>E Usage: ...gentreeg [-D#] [-Z#:#] [-ulps] [-q] n [res/mod] ...
-+        ['>E Usage: ...gentreeg [-D#] [-Z#:#] [-ulps] [-q] n... [res/mod] ...
-         sage: list(graphs.nauty_gentreeg("3", debug=True))
-         ['>A ...gentreeg ...\n', Graph on 3 vertices]
-     """
diff --git a/srcpkgs/sagemath/patches/numpy_2.1a.patch b/srcpkgs/sagemath/patches/numpy_2.1a.patch
deleted file mode 100644
index 493c75e2f8f8e0..00000000000000
--- a/srcpkgs/sagemath/patches/numpy_2.1a.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-commit d755b32cbed462abf01a1cd782ba57cb92fbf713
-Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
-Date:   Mon Aug 19 23:25:32 2024 -0300
-
-    add copy parameter to numpy (needed for v2.1)
-
-diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
-index 3edb9ead54d..2c76fd1e557 100644
---- a/src/sage/matrix/matrix1.pyx
-+++ b/src/sage/matrix/matrix1.pyx
-@@ -670,7 +670,7 @@ cdef class Matrix(Matrix0):
-             entries = [[sib(v, 2) for v in row] for row in self.rows()]
-             return sib.name('matrix')(self.base_ring(), entries)
- 
--    def numpy(self, dtype=None):
-+    def numpy(self, dtype=None, copy=True):
-         """
-         Return the Numpy matrix associated to this matrix.
- 
-@@ -731,7 +731,7 @@ cdef class Matrix(Matrix0):
-             (3, 4)
-         """
-         import numpy
--        A = numpy.matrix(self.list(), dtype=dtype)
-+        A = numpy.matrix(self.list(), dtype=dtype, copy=copy)
-         return numpy.resize(A,(self.nrows(), self.ncols()))
- 
-     # Define the magic "__array__" function so that numpy.array(m) can convert
diff --git a/srcpkgs/sagemath/patches/numpy_2.1b.patch b/srcpkgs/sagemath/patches/numpy_2.1b.patch
deleted file mode 100644
index 8dc0eec2b5a9d8..00000000000000
--- a/srcpkgs/sagemath/patches/numpy_2.1b.patch
+++ /dev/null
@@ -1,229 +0,0 @@
-commit 8260d18c3cf8e356db3d95fc46f6e68f75b453fd
-Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
-Date:   Tue Aug 20 00:05:33 2024 -0300
-
-    silence np.set_printoptions (for numpy 2.1)
-
-diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index 74a14fa1ecd..82e6c7eb3c8 100644
---- a/src/sage/combinat/fully_packed_loop.py
-+++ b/src/sage/combinat/fully_packed_loop.py
-@@ -68,7 +68,7 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
- 
-         sage: import numpy as np
-         sage: if int(np.version.short_version[0]) > 1:
--        ....:     np.set_printoptions(legacy="1.25")
-+        ....:     _token = np.set_printoptions(legacy="1.25")
-         sage: from sage.combinat.fully_packed_loop import _make_color_list
-         sage: _make_color_list(5)
-         sage: _make_color_list(5, ['blue', 'red'])
-diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
-index 308171af3cd..6f66624ef87 100644
---- a/src/sage/functions/special.py
-+++ b/src/sage/functions/special.py
-@@ -219,7 +219,7 @@ class SphericalHarmonic(BuiltinFunction):
-         sage: from scipy.special import sph_harm  # NB: arguments x and y are swapped   # needs scipy
-         sage: import numpy as np                                                        # needs scipy
-         sage: if int(np.version.short_version[0]) > 1:                                  # needs scipy
--        ....:     np.set_printoptions(legacy="1.25")                                    # needs scipy
-+        ....:     _token = np.set_printoptions(legacy="1.25")                           # needs scipy
-         sage: sph_harm(1, 1, pi.n(), (pi/2).n())  # abs tol 1e-14                       # needs scipy sage.symbolic
-         (0.3454941494713355-4.231083042742082e-17j)
- 
-diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index b3e42a6a6a2..13ffa4d1789 100644
---- a/src/sage/numerical/optimize.py
-+++ b/src/sage/numerical/optimize.py
-@@ -381,7 +381,7 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm='default',
-         ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
-         sage: import numpy
-         sage: if int(numpy.version.short_version[0]) > 1:
--        ....:     numpy.set_printoptions(legacy="1.25")
-+        ....:     _token = numpy.set_printoptions(legacy="1.25")
-         sage: from numpy import zeros
-         sage: def rosen_der(x):
-         ....:    xm = x[1r:-1r]
-diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index 02442f90ba4..1fe3f0b051a 100644
---- a/src/sage/plot/arrow.py
-+++ b/src/sage/plot/arrow.py
-@@ -55,7 +55,7 @@ class CurveArrow(GraphicPrimitive):
- 
-             sage: import numpy  # to ensure numpy 2.0 compatibility
-             sage: if int(numpy.version.short_version[0]) > 1:
--            ....:     numpy.set_printoptions(legacy="1.25")
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")
-             sage: from sage.plot.arrow import CurveArrow
-             sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
-             ....:                options={})
-diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
-index d2f70b44526..2eaacc6879e 100644
---- a/src/sage/plot/multigraphics.py
-+++ b/src/sage/plot/multigraphics.py
-@@ -766,7 +766,7 @@ class MultiGraphics(WithEqualityById, SageObject):
-             (0.2, 0.3, 0.4, 0.1)
-             sage: import numpy  # to ensure numpy 2.0 compatibility
-             sage: if int(numpy.version.short_version[0]) > 1:
--            ....:     numpy.set_printoptions(legacy="1.25")
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")
-             sage: ax1.get_position().bounds  # tol 1.0e-13
-             (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
-         """
-@@ -1269,7 +1269,7 @@ class GraphicsArray(MultiGraphics):
-             sage: G = graphics_array([g1, g2])
-             sage: import numpy  # to ensure numpy 2.0 compatibility
-             sage: if int(numpy.version.short_version[0]) > 1:
--            ....:     numpy.set_printoptions(legacy="1.25")
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")
-             sage: G.position(0)  # tol 5.0e-3
-             (0.025045451349937315,
-              0.03415488992713045,
-diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index b69a05b37bf..25e404bfc7d 100644
---- a/src/sage/plot/streamline_plot.py
-+++ b/src/sage/plot/streamline_plot.py
-@@ -72,7 +72,7 @@ class StreamlinePlot(GraphicPrimitive):
-             sage: x, y = var('x y')
-             sage: import numpy  # to ensure numpy 2.0 compatibility
-             sage: if int(numpy.version.short_version[0]) > 1:
--            ....:     numpy.set_printoptions(legacy="1.25")
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")
-             sage: d = streamline_plot((.01*x, x+y), (x,10,20), (y,10,20))[0].get_minmax_data()
-             sage: d['xmin']
-             10.0
-diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index 11811b9587f..8ce0f7f2683 100644
---- a/src/sage/rings/integer.pyx
-+++ b/src/sage/rings/integer.pyx
-@@ -595,7 +595,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
-             sage: # needs numpy
-             sage: import numpy
-             sage: if int(numpy.version.short_version[0]) > 1:
--            ....:     numpy.set_printoptions(legacy="1.25")
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")
-             sage: numpy.int8('12') == 12
-             True
-             sage: 12 == numpy.int8('12')
-diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
-index 11953a50ab5..6aafcceed89 100644
---- a/src/sage/rings/real_mpfi.pyx
-+++ b/src/sage/rings/real_mpfi.pyx
-@@ -232,7 +232,7 @@ TESTS::
- 
-     sage: import numpy                                                                  # needs numpy
-     sage: if int(numpy.version.short_version[0]) > 1:                                   # needs numpy
--    ....:     numpy.set_printoptions(legacy="1.25")                                     # needs numpy
-+    ....:     _token = numpy.set_printoptions(legacy="1.25")                            # needs numpy
-     sage: RIF(2) == numpy.int8('2')                                                     # needs numpy
-     True
-     sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
-diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-index 40b92ab23eb..3838bcccb8a 100755
---- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-+++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
-@@ -78,7 +78,7 @@ cdef class PeriodicRegion:
- 
-             sage: import numpy as np
-             sage: if int(np.version.short_version[0]) > 1:
--            ....:     np.set_printoptions(legacy="1.25")
-+            ....:     _token = np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
-@@ -296,7 +296,7 @@ cdef class PeriodicRegion:
- 
-             sage: import numpy as np
-             sage: if int(np.version.short_version[0]) > 1:
--            ....:     np.set_printoptions(legacy="1.25")
-+            ....:     _token = np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((10, 10))
-             sage: data[1:4,1:4] = True
-@@ -320,7 +320,7 @@ cdef class PeriodicRegion:
- 
-             sage: import numpy as np
-             sage: if int(np.version.short_version[0]) > 1:
--            ....:     np.set_printoptions(legacy="1.25")
-+            ....:     _token = np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1,1] = True
-@@ -375,7 +375,7 @@ cdef class PeriodicRegion:
- 
-             sage: import numpy as np
-             sage: if int(np.version.short_version[0]) > 1:
--            ....:     np.set_printoptions(legacy="1.25")
-+            ....:     _token = np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
- 
-             sage: data = np.zeros((20, 20))
-@@ -528,7 +528,7 @@ cdef class PeriodicRegion:
- 
-             sage: import numpy as np
-             sage: if int(np.version.short_version[0]) > 1:
--            ....:     np.set_printoptions(legacy="1.25")
-+            ....:     _token = np.set_printoptions(legacy="1.25")
-             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
-             sage: data = np.zeros((4, 4))
-             sage: data[1, 1] = True
-diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index 47d890cf0ab..ba7f0cdb0f9 100644
---- a/src/sage/stats/basic_stats.py
-+++ b/src/sage/stats/basic_stats.py
-@@ -222,7 +222,7 @@ def std(v, bias=False):
-         sage: # needs numpy
-         sage: import numpy
-         sage: if int(numpy.version.short_version[0]) > 1:
--        ....:     numpy.set_printoptions(legacy="1.25")
-+        ....:     _token = numpy.set_printoptions(legacy="1.25")
-         sage: x = numpy.array([1,2,3,4,5])
-         sage: std(x, bias=False)
-         1.5811388300841898
-@@ -299,7 +299,7 @@ def variance(v, bias=False):
-         0.4897530450000000?
-         sage: import numpy                                                              # needs numpy
-         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
--        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-+        ....:     _token = numpy.set_printoptions(legacy="1.25")                        # needs numpy
-         sage: x = numpy.array([1,2,3,4,5])                                              # needs numpy
-         sage: variance(x, bias=False)                                                   # needs numpy
-         2.5
-diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
-index cc15eff82e9..e32e7fd28b3 100644
---- a/src/sage/structure/coerce.pyx
-+++ b/src/sage/structure/coerce.pyx
-@@ -521,7 +521,7 @@ cdef class CoercionModel:
- 
-         sage: import numpy                                                              # needs numpy
-         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
--        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-+        ....:     _token = numpy.set_printoptions(legacy="1.25")                        # needs numpy
- 
-         sage: # needs sage.rings.real_mpfr
-         sage: x = polygen(RR)
-diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
-index 362d01ea297..92bce28b032 100644
---- a/src/sage/symbolic/function.pyx
-+++ b/src/sage/symbolic/function.pyx
-@@ -962,7 +962,7 @@ cdef class BuiltinFunction(Function):
- 
-             sage: import numpy                                                          # needs numpy
-             sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
--            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
-+            ....:     _token = numpy.set_printoptions(legacy="1.25")                    # needs numpy
- 
-             sage: sin(numpy.int32(0))                                                   # needs numpy
-             0.0
-diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 32afe8d3a62..63734e68f63 100644
---- a/src/sage/symbolic/ring.pyx
-+++ b/src/sage/symbolic/ring.pyx
-@@ -1154,7 +1154,7 @@ cdef class NumpyToSRMorphism(Morphism):
- 
-         sage: import numpy                                                              # needs numpy
-         sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
--        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
-+        ....:     _token = numpy.set_printoptions(legacy="1.25")                        # needs numpy
-         sage: f(x) = x^2
-         sage: f(numpy.int8('2'))                                                        # needs numpy
-         4
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index 709a3ea4262101..4face5e8f7ad84 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,6 +1,6 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.5.beta3
+version=10.5.beta5
 revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=cbf3614c1b9be5f0a0756b0a5480c2ebfa663bd87bd66eefd162a755979bcb3d
+checksum=af4e8215043cd5376adea87f37928b94863561e36cba2171dab48ea984f7f259
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From f0f7dc3d3737e6278c06f35946d5ffcb4817a923 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 29 Sep 2024 22:24:40 -0300
Subject: [PATCH 15/21] sagemath: update to 10.5.beta6.

---
 srcpkgs/sagemath/patches/get_patches | 2 +-
 srcpkgs/sagemath/template            | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 8f540dad14bfd1..381c307a3e962a 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -28,7 +28,7 @@ get_pr() {
 cd $(dirname "$0")
 
 get_pr 37884 "gap 4.13.1"
-get_pr 38572 "nauty 2.8.9"
+#get_pr 38572 "nauty 2.8.9"
 
 #get_pr 37645 "fix doctest"
 get_pr 37885 "cython warnings"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index 4face5e8f7ad84..fb806ca641d378 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,6 +1,6 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.5.beta5
+version=10.5.beta6
 revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=af4e8215043cd5376adea87f37928b94863561e36cba2171dab48ea984f7f259
+checksum=f95f196142d7abf091185e31d8023091c5746a9e3d2321d906161c65f944fa40
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From d7437e12977edd4416df5ef644a7aa6b39c55a46 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 15 Oct 2024 15:30:11 -0300
Subject: [PATCH 16/21] sagemath: update to 10.5.beta7.

---
 srcpkgs/sagemath/template | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index fb806ca641d378..d19d4ac007f9ba 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,6 +1,6 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.5.beta6
+version=10.5.beta7
 revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=f95f196142d7abf091185e31d8023091c5746a9e3d2321d906161c65f944fa40
+checksum=b98a883aab3b6f551243bc3cffb6825c92f6faf86604e9a9cc8f38cfb9af2f32
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From b915738491d91acb483db5fcfad6b7f6791199c5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sat, 26 Oct 2024 19:06:21 -0300
Subject: [PATCH 17/21] python3-Cython: new alternative fix for 6122, taken
 from 6430

---
 srcpkgs/python3-Cython/patches/fix-regression.patch | 12 +++++++++---
 srcpkgs/python3-Cython/template                     |  2 +-
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/srcpkgs/python3-Cython/patches/fix-regression.patch b/srcpkgs/python3-Cython/patches/fix-regression.patch
index f5957cfa59c2f5..5a29e6a5143ed9 100644
--- a/srcpkgs/python3-Cython/patches/fix-regression.patch
+++ b/srcpkgs/python3-Cython/patches/fix-regression.patch
@@ -1,9 +1,11 @@
 Revert https://github.com/cython/cython/pull/6124 which causes a
 serious regression, e.g. sagemath FTBS with cython 3.0.11
 
+Source: https://github.com/cython/cython/pull/6430
+
 --- a/Cython/Compiler/Nodes.py
 +++ b/Cython/Compiler/Nodes.py
-@@ -710,10 +710,8 @@ class CFuncDeclaratorNode(CDeclaratorNode):
+@@ -717,10 +717,8 @@ def analyse(self, return_type, env, nonempty=0, directive_locals=None, visibilit
                  and not self.has_explicit_exc_clause
                  and self.exception_check
                  and visibility != 'extern'):
@@ -15,11 +17,15 @@ serious regression, e.g. sagemath FTBS with cython 3.0.11
              warning(self.pos,
                      "Implicit noexcept declaration is deprecated."
                      " Function declaration should contain 'noexcept' keyword.",
-@@ -3128,6 +3126,7 @@ class DefNode(FuncDefNode):
+@@ -3128,6 +3126,11 @@ def as_cfunction(self, cfunc=None, scope=None, overridable=True, returns=None, e
              if scope is None:
                  scope = cfunc.scope
              cfunc_type = cfunc.type
-+            has_explicit_exc_clause=True
++            if cfunc_type.exception_check:
++                # this ensures `legacy_implicit_noexcept` does not trigger
++                # as it would result in a mismatch
++                # (declaration with except, definition with implicit noexcept)
++                has_explicit_exc_clause = True
              if len(self.args) != len(cfunc_type.args) or cfunc_type.has_varargs:
                  error(self.pos, "wrong number of arguments")
                  error(cfunc.pos, "previous declaration here")
diff --git a/srcpkgs/python3-Cython/template b/srcpkgs/python3-Cython/template
index faec5722ae171a..a01702f0747d10 100644
--- a/srcpkgs/python3-Cython/template
+++ b/srcpkgs/python3-Cython/template
@@ -1,7 +1,7 @@
 # Template file for 'python3-Cython'
 pkgname=python3-Cython
 version=3.0.11
-revision=2
+revision=3
 build_style=python3-module
 hostmakedepends="python3-setuptools"
 makedepends="python3-devel"

From da94f251e3c88a8a3be44b47492761e6bbd16ab4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sat, 26 Oct 2024 18:59:52 -0300
Subject: [PATCH 18/21] sagemath: update to 10.5.beta8.

---
 .../sagemath/patches/37884-gap_4.13.1.patch   | 203 ------------------
 .../sagemath/patches/38873-fix_doctest.patch  |  25 +++
 srcpkgs/sagemath/patches/get_patches          |   3 +-
 srcpkgs/sagemath/patches/revert-38826.patch   |  26 +++
 srcpkgs/sagemath/template                     |   4 +-
 5 files changed, 55 insertions(+), 206 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
 create mode 100644 srcpkgs/sagemath/patches/38873-fix_doctest.patch
 create mode 100644 srcpkgs/sagemath/patches/revert-38826.patch

diff --git a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch b/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
deleted file mode 100644
index 321e0a94487da3..00000000000000
--- a/srcpkgs/sagemath/patches/37884-gap_4.13.1.patch
+++ /dev/null
@@ -1,203 +0,0 @@
-diff --git a/src/sage/algebras/fusion_rings/fusion_double.py b/src/sage/algebras/fusion_rings/fusion_double.py
-index 71277561331..3b681d75d3b 100644
---- a/src/sage/algebras/fusion_rings/fusion_double.py
-+++ b/src/sage/algebras/fusion_rings/fusion_double.py
-@@ -133,7 +133,7 @@ class FusionDouble(CombinatorialFreeModule):
-         sage: G = SmallPermutationGroup(16,9)
-         sage: F = FusionDouble(G, prefix='b', inject_variables=True)
-         sage: b13^2 # long time (4s)
--        b0 + b2 + b4 + b15 + b16 + b17 + b18 + b24 + b26 + b27
-+        b0 + b3 + b4
-     """
-     @staticmethod
-     def __classcall_private__(cls, G, prefix='s', inject_variables=False):
-diff --git a/src/sage/categories/simplicial_sets.py b/src/sage/categories/simplicial_sets.py
-index aabd3cdbb4f..14bebdcd080 100644
---- a/src/sage/categories/simplicial_sets.py
-+++ b/src/sage/categories/simplicial_sets.py
-@@ -591,9 +591,9 @@ def _canonical_twisting_operator(self):
-                     sage: X = simplicial_sets.Torus()
-                     sage: d = X._canonical_twisting_operator()
-                     sage: d
--                    {(s_0 v_0, sigma_1): f3, (sigma_1, s_0 v_0): f2*f3^-1, (sigma_1, sigma_1): f2}
-+                    {(s_0 v_0, sigma_1): f2, (sigma_1, s_0 v_0): f1*f2^-1, (sigma_1, sigma_1): f1}
-                     sage: list(d.values())[0].parent()
--                    Multivariate Laurent Polynomial Ring in f2, f3 over Integer Ring
-+                    Multivariate Laurent Polynomial Ring in f1, f2 over Integer Ring
-                     sage: Y = simplicial_sets.RealProjectiveSpace(2)
-                     sage: d2 = Y._canonical_twisting_operator()
-                     sage: d2
-@@ -674,10 +674,10 @@ def twisted_chain_complex(self, twisting_operator=None, dimensions=None, augment
-                     sage: X = simplicial_sets.Torus()
-                     sage: C = X.twisted_chain_complex()
-                     sage: C.differential(1)
--                    [      f3 - 1 f2*f3^-1 - 1       f2 - 1]
-+                    [      f2 - 1 f1*f2^-1 - 1       f1 - 1]
-                     sage: C.differential(2)
--                    [       1 f2*f3^-1]
--                    [      f3        1]
-+                    [       1 f1*f2^-1]
-+                    [      f2        1]
-                     [      -1       -1]
-                     sage: C.differential(3)
-                     []
-@@ -844,29 +844,29 @@ def twisted_homology(self, n, reduced=False):
-                     sage: # needs sage.graphs
-                     sage: Y = simplicial_sets.Torus()
-                     sage: Y.twisted_homology(1)
--                    Quotient module by Submodule of Ambient free module of rank 5 over the integral domain Multivariate Polynomial Ring in f2, f2inv, f3, f3inv over Integer Ring
-+                    Quotient module by Submodule of Ambient free module of rank 5 over the integral domain Multivariate Polynomial Ring in f1, f1inv, f2, f2inv over Integer Ring
-                     Generated by the rows of the matrix:
-                     [           1            0            0            0            0]
-                     [           0            1            0            0            0]
-                     [           0            0            1            0            0]
-                     [           0            0            0            1            0]
-                     [           0            0            0            0            1]
-+                    [f1*f1inv - 1            0            0            0            0]
-+                    [           0 f1*f1inv - 1            0            0            0]
-+                    [           0            0 f1*f1inv - 1            0            0]
-+                    [           0            0            0 f1*f1inv - 1            0]
-+                    [           0            0            0            0 f1*f1inv - 1]
-                     [f2*f2inv - 1            0            0            0            0]
-                     [           0 f2*f2inv - 1            0            0            0]
-                     [           0            0 f2*f2inv - 1            0            0]
-                     [           0            0            0 f2*f2inv - 1            0]
-                     [           0            0            0            0 f2*f2inv - 1]
--                    [f3*f3inv - 1            0            0            0            0]
--                    [           0 f3*f3inv - 1            0            0            0]
--                    [           0            0 f3*f3inv - 1            0            0]
--                    [           0            0            0 f3*f3inv - 1            0]
--                    [           0            0            0            0 f3*f3inv - 1]
-                     sage: Y.twisted_homology(2)
--                    Quotient module by Submodule of Ambient free module of rank 0 over the integral domain Multivariate Polynomial Ring in f2, f2inv, f3, f3inv over Integer Ring
-+                    Quotient module by Submodule of Ambient free module of rank 0 over the integral domain Multivariate Polynomial Ring in f1, f1inv, f2, f2inv over Integer Ring
-                     Generated by the rows of the matrix:
-                     []
-                     sage: Y.twisted_homology(1, reduced=True)
--                    Quotient module by Submodule of Ambient free module of rank 5 over the integral domain Multivariate Polynomial Ring in f2, f2inv, f3, f3inv over Integer Ring
-+                    Quotient module by Submodule of Ambient free module of rank 5 over the integral domain Multivariate Polynomial Ring in f1, f1inv, f2, f2inv over Integer Ring
-                     Generated by the rows of the matrix:
-                     [1 0 0 0 0]
-                     [0 1 0 0 0]
-diff --git a/src/sage/combinat/matrices/latin.py b/src/sage/combinat/matrices/latin.py
-index e2d818e9480..84e6c4fcc9b 100644
---- a/src/sage/combinat/matrices/latin.py
-+++ b/src/sage/combinat/matrices/latin.py
-@@ -2444,7 +2444,7 @@ def p3_group_bitrade_generators(p):
-     EXAMPLES::
- 
-         sage: from sage.combinat.matrices.latin import *
--        sage: p3_group_bitrade_generators(3)
-+        sage: p3_group_bitrade_generators(3)  # random output
-         ((2,6,7)(3,8,9),
-          (1,2,3)(4,7,8)(5,6,9),
-          (1,9,2)(3,7,4)(5,8,6),
-diff --git a/src/sage/groups/cubic_braid.py b/src/sage/groups/cubic_braid.py
-index 61db70925e1..521289c7578 100644
---- a/src/sage/groups/cubic_braid.py
-+++ b/src/sage/groups/cubic_braid.py
-@@ -282,7 +282,7 @@ def _richcmp_(self, other, op):
-         EXAMPLES::
- 
-             sage: CBG3 = CubicBraidGroup(3)
--            sage: sorted(CBG3)    # indirect doctest
-+            sage: sorted(CBG3)    # indirect doctest, random output
-             [(c0*c1^-1)^2, c0*c1^-1*c0, c0^-1*c1*c0^-1, c0^-1*c1^-1*c0,
-              c1*c0^-1*c1, c0^-1*c1^-1*c0^-1, c0^-1*c1^-1, c1^-1*c0*c1^-1,
-              c0*c1^-1*c0^-1, c0^-1*c1, c0^-1*c1*c0, c0*c1^-1, c1*c0^-1,
-diff --git a/src/sage/groups/finitely_presented.py b/src/sage/groups/finitely_presented.py
-index 4ac2faa783b..7016d08381b 100644
---- a/src/sage/groups/finitely_presented.py
-+++ b/src/sage/groups/finitely_presented.py
-@@ -1344,8 +1344,8 @@ def abelianization_map(self):
-             sage: H = G.quotient([g1^2, g2*g1*g2^(-1)*g1^(-1), g1*g3^(-2), g0^4])
-             sage: H.abelianization_map()
-             Group morphism:
--                From: Finitely presented group  < g0, g1, g2, g3 | g1^2, g2*g1*g2^-1*g1^-1, g1*g3^-2, g0^4 >
--                To:   Finitely presented group  < f2, f3, f4 | f2^-1*f3^-1*f2*f3, f2^-1*f4^-1*f2*f4, f3^-1*f4^-1*f3*f4, f2^4, f3^4 >
-+              From: Finitely presented group < g0, g1, g2, g3 | g1^2, g2*g1*g2^-1*g1^-1, g1*g3^-2, g0^4 >
-+              To:   Finitely presented group < f1, f2, f3 | f1^4, f2^-1*f1^-1*f2*f1, f2^4, f3^-1*f1^-1*f3*f1, f3^-1*f2^-1*f3*f2 >
-             sage: g = FreeGroup(0) / []
-             sage: g.abelianization_map()
-             Group endomorphism of Finitely presented group  <  |  >
-@@ -1394,10 +1394,10 @@ def abelianization_to_algebra(self, ring=QQ):
-             Defining g0, g1, g2, g3
-             sage: H = G.quotient([g1^2, g2*g1*g2^(-1)*g1^(-1), g1*g3^(-2), g0^4])
-             sage: H.abelianization_to_algebra()
--            (Finitely presented group  < f2, f3, f4 | f2^-1*f3^-1*f2*f3, f2^-1*f4^-1*f2*f4,
--                                                      f3^-1*f4^-1*f3*f4, f2^4, f3^4 >,
--             Multivariate Laurent Polynomial Ring in f2, f3, f4 over Rational Field,
--             [f2^4 - 1, f3^4 - 1], [f2^-1*f3^-2, f3^-2, f4, f3])
-+            (Finitely presented group < f1, f2, f3 | f1^4, f2^-1*f1^-1*f2*f1, f2^4, f3^-1*f1^-1*f3*f1, f3^-1*f2^-1*f3*f2 >,
-+             Multivariate Laurent Polynomial Ring in f1, f2, f3 over Rational Field,
-+             [f1^4 - 1, f2^4 - 1],
-+             [f1^3*f2^2, f2^2, f3, f2])
-             sage: g=FreeGroup(0) / []
-             sage: g.abelianization_to_algebra()
-             (Finitely presented group  <  |  >, Rational Field, [], [])
-@@ -1673,7 +1673,7 @@ def abelian_alexander_matrix(self, ring=QQ, simplified=True):
-             []
-             sage: G = FreeGroup(3)/[(2, 1, 1), (1, 2, 2, 3, 3)]
-             sage: A, ideal = G.abelian_alexander_matrix(simplified=True); A
--            [-f3^2 - f3^4 - f3^6         f3^3 + f3^6]
-+            [-f1^2 - f1^4 - f1^6         f1^3 + f1^6]
-             sage: g = FreeGroup(1) / []
-             sage: g.abelian_alexander_matrix()
-             ([], [])
-@@ -1773,11 +1773,11 @@ def characteristic_varieties(self, ring=QQ, matrix_ideal=None, groebner=False):
-              3: Ideal (1) of Multivariate Laurent Polynomial Ring in f1, f2 over Integer Ring}
-             sage: G = FreeGroup(2)/[(1,2,1,-2,-1,-2)]
-             sage: G.characteristic_varieties()
--            {0: Ideal (0) of Univariate Laurent Polynomial Ring in f2 over Rational Field,
--             1: Ideal (-1 + 2*f2 - 2*f2^2 + f2^3) of Univariate Laurent Polynomial Ring in f2 over Rational Field,
--             2: Ideal (1) of Univariate Laurent Polynomial Ring in f2 over Rational Field}
-+            {0: Ideal (0) of Univariate Laurent Polynomial Ring in f1 over Rational Field,
-+             1: Ideal (-1 + 2*f1 - 2*f1^2 + f1^3) of Univariate Laurent Polynomial Ring in f1 over Rational Field,
-+             2: Ideal (1) of Univariate Laurent Polynomial Ring in f1 over Rational Field}
-             sage: G.characteristic_varieties(groebner=True)
--            {0: [0], 1: [-1 + f2, 1 - f2 + f2^2], 2: []}
-+            {0: [0], 1: [-1 + f1, 1 - f1 + f1^2], 2: []}
-             sage: G = FreeGroup(2)/[3 * (1, ), 2 * (2, )]
-             sage: G.characteristic_varieties(groebner=True)
-             {0: [-1 + F1, 1 + F1, 1 - F1 + F1^2, 1 + F1 + F1^2], 1: [1 - F1 + F1^2],  2: []}
-diff --git a/src/sage/groups/perm_gps/permgroup_named.py b/src/sage/groups/perm_gps/permgroup_named.py
-index 5c153b93d4c..bd4afad2942 100644
---- a/src/sage/groups/perm_gps/permgroup_named.py
-+++ b/src/sage/groups/perm_gps/permgroup_named.py
-@@ -3465,16 +3465,14 @@ class SmallPermutationGroup(PermutationGroup_generic):
-         sage: G = SmallPermutationGroup(12,4); G
-         Group of order 12 and GAP Id 4 as a permutation group
-         sage: G.gens()
--        ((1,2)(3,5)(4,10)(6,8)(7,12)(9,11),
--         (1,3)(2,5)(4,7)(6,9)(8,11)(10,12),
--         (1,4,8)(2,6,10)(3,7,11)(5,9,12))
-+        ((4,5), (1,2), (3,4,5))
-         sage: G.character_table()                                                       # needs sage.rings.number_field
-         [ 1  1  1  1  1  1]
--        [ 1 -1 -1  1  1 -1]
-+        [ 1 -1  1 -1  1 -1]
-         [ 1 -1  1  1 -1  1]
--        [ 1  1 -1  1 -1 -1]
--        [ 2  0 -2 -1  0  1]
--        [ 2  0  2 -1  0 -1]
-+        [ 1  1  1 -1 -1 -1]
-+        [ 2  0 -1 -2  0  1]
-+        [ 2  0 -1  2  0 -1]
-         sage: def numgps(n): return ZZ(libgap.NumberSmallGroups(n))
-         sage: all(SmallPermutationGroup(n,k).id() == [n,k]
-         ....:     for n in [1..64] for k in [1..numgps(n)])
-@@ -3483,11 +3481,11 @@ class SmallPermutationGroup(PermutationGroup_generic):
-         sage: H.is_abelian()
-         False
-         sage: [H.centralizer(g) for g in H.conjugacy_classes_representatives()]
--        [Subgroup generated by [(1,2)(3,6)(4,5), (1,3,5)(2,4,6)] of
-+        [Subgroup generated by [(1,3), (2,3)] of
-           (Group of order 6 and GAP Id 1 as a permutation group),
--         Subgroup generated by [(1,2)(3,6)(4,5)] of
-+         Subgroup generated by [(2,3)] of
-           (Group of order 6 and GAP Id 1 as a permutation group),
--         Subgroup generated by [(1,3,5)(2,4,6), (1,5,3)(2,6,4)] of
-+         Subgroup generated by [(1,2,3)] of
-           (Group of order 6 and GAP Id 1 as a permutation group)]
-     """
- 
diff --git a/srcpkgs/sagemath/patches/38873-fix_doctest.patch b/srcpkgs/sagemath/patches/38873-fix_doctest.patch
new file mode 100644
index 00000000000000..f42a8a570ca0cb
--- /dev/null
+++ b/srcpkgs/sagemath/patches/38873-fix_doctest.patch
@@ -0,0 +1,25 @@
+diff --git a/src/sage/parallel/map_reduce.py b/src/sage/parallel/map_reduce.py
+index 303f7405416..a182a136a2f 100644
+--- a/src/sage/parallel/map_reduce.py
++++ b/src/sage/parallel/map_reduce.py
+@@ -1133,18 +1133,16 @@ def start_workers(self):
+ 
+         TESTS::
+ 
++            sage: # long time
+             sage: from sage.parallel.map_reduce import RESetMapReduce
+             sage: def children(x):
+             ....:     print(f"Starting: {x}", flush=True)
+             ....:     return []
+             sage: S = RESetMapReduce(roots=[1, 2], children=children)
+             sage: S.setup_workers(2)
+-            sage: S.start_workers(); sleep(float(5))  # long time
++            sage: S.start_workers(); sleep(float(5))
+             Starting: ...
+             Starting: ...
+-
+-        Cleanup::
+-
+             sage: S.finish()
+         """
+         if self._nprocess == 0:
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 381c307a3e962a..39fb67ef79aa7d 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -27,8 +27,9 @@ get_pr() {
 # run from patches dir
 cd $(dirname "$0")
 
-get_pr 37884 "gap 4.13.1"
+#get_pr 37884 "gap 4.13.1"
 #get_pr 38572 "nauty 2.8.9"
 
 #get_pr 37645 "fix doctest"
 get_pr 37885 "cython warnings"
+get_pr 38873 "fix doctest"
diff --git a/srcpkgs/sagemath/patches/revert-38826.patch b/srcpkgs/sagemath/patches/revert-38826.patch
new file mode 100644
index 00000000000000..6a97d896db44f7
--- /dev/null
+++ b/srcpkgs/sagemath/patches/revert-38826.patch
@@ -0,0 +1,26 @@
+Revert "src/sage/env.py: canonicalize paths in a test"
+
+This reverts commit 53a6d3133ea7782c7498ea6ab6bd3041815bd6a6.
+
+See: https://github.com/sagemath/sage/pull/38826#issuecomment-2439757935
+
+--- a/src/sage/env.py
++++ b/src/sage/env.py
+@@ -8,14 +8,10 @@ environment variables, and has the same ``SAGE_ROOT`` and ``SAGE_LOCAL``
+ 
+     sage: env = {k:v for (k,v) in os.environ.items() if not k.startswith("SAGE_")}
+     sage: from subprocess import check_output
+-    sage: module_name = "sage.all"   # hide .all import from the linter
+-    sage: cmd  = f"from {module_name} import SAGE_ROOT, SAGE_LOCAL;"
+-    sage: cmd +=  "from os.path import samefile;"
+-    sage: cmd += f"s1 = samefile(SAGE_ROOT, '{SAGE_ROOT}');"
+-    sage: cmd += f"s2 = samefile(SAGE_LOCAL, '{SAGE_LOCAL}');"
+-    sage: cmd += "print(s1 and s2);"
++    sage: environment = "sage.all"
++    sage: cmd = f"from {environment} import SAGE_ROOT, SAGE_LOCAL; print((SAGE_ROOT, SAGE_LOCAL))"
+     sage: out = check_output([sys.executable, "-c", cmd], env=env).decode().strip()   # long time
+-    sage: out == "True"                                                               # long time
++    sage: out == repr((SAGE_ROOT, SAGE_LOCAL))                                        # long time
+     True
+ 
+ AUTHORS:
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index d19d4ac007f9ba..0fa1fb968249f6 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,6 +1,6 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.5.beta7
+version=10.5.beta8
 revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=b98a883aab3b6f551243bc3cffb6825c92f6faf86604e9a9cc8f38cfb9af2f32
+checksum=0c386e88524a91ad97db4f3f8ee7408d8678072596b3ab5e9ffaea2cb6be13fd
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From e10a9853982713c26b968cbe46720ee779df17af Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 3 Nov 2024 19:33:46 -0300
Subject: [PATCH 19/21] sagemath: fix after merge

---
 .../patches/38749-00-prepare_backport.patch   | 89 -----------------
 .../patches/38749-zz-fixup_backport.patch     | 95 -------------------
 2 files changed, 184 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/38749-00-prepare_backport.patch
 delete mode 100644 srcpkgs/sagemath/patches/38749-zz-fixup_backport.patch

diff --git a/srcpkgs/sagemath/patches/38749-00-prepare_backport.patch b/srcpkgs/sagemath/patches/38749-00-prepare_backport.patch
deleted file mode 100644
index 01e6e0bc150141..00000000000000
--- a/srcpkgs/sagemath/patches/38749-00-prepare_backport.patch
+++ /dev/null
@@ -1,89 +0,0 @@
-commit 95d7f3070d46c971fe1ea1fceb3cc6d8039c1d66
-Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
-Date:   Sun Nov 3 13:09:51 2024 -0300
-
-    prepare for backport of #38749
-
-diff --git a/src/sage/modular/dirichlet.py b/src/sage/modular/dirichlet.py
-index e579c5090e3..efc533c51f0 100644
---- a/src/sage/modular/dirichlet.py
-+++ b/src/sage/modular/dirichlet.py
-@@ -2388,7 +2388,8 @@ class DirichletGroupFactory(UniqueFactory):
- 
-     ::
- 
--        sage: r4 = CyclotomicField(4).ring_of_integers()
-+        sage: K = CyclotomicField(4)
-+        sage: r4 = K.ring_of_integers()
-         sage: G = DirichletGroup(60, r4)
-         sage: G.gens()
-         (Dirichlet character modulo 60 of conductor 4
-@@ -2401,8 +2402,7 @@ class DirichletGroupFactory(UniqueFactory):
-         zeta4
-         sage: parent(val)
-         Gaussian Integers generated by zeta4 in Cyclotomic Field of order 4 and degree 2
--        sage: r4_29_0 = r4.residue_field(r4.ideal(29).factor()[0][0]); r4_29_0(val)
--        doctest:warning ... DeprecationWarning: ...
-+        sage: r4_29_0 = r4.residue_field(K(29).factor()[0][0]); r4_29_0(val)
-         17
-         sage: r4_29_0(val) * GF(29)(3)
-         22
-diff --git a/src/sage/rings/number_field/selmer_group.py b/src/sage/rings/number_field/selmer_group.py
-index 49b4030b2e9..2a650138291 100644
---- a/src/sage/rings/number_field/selmer_group.py
-+++ b/src/sage/rings/number_field/selmer_group.py
-@@ -73,7 +73,6 @@ def _ideal_generator(I):
-         sage: K.<a> = QuadraticField(-11)
-         sage: [_ideal_generator(K.prime_above(p)) for p in primes(25)]
-         [2, 1/2*a - 1/2, -1/2*a - 3/2, 7, -a, 13, 17, 19, 1/2*a + 9/2]
--
-     """
-     try:
-         return I.gens_reduced()[0]
-diff --git a/src/sage/schemes/elliptic_curves/gp_simon.py b/src/sage/schemes/elliptic_curves/gp_simon.py
-index 39a60361ec6..f258961f685 100644
---- a/src/sage/schemes/elliptic_curves/gp_simon.py
-+++ b/src/sage/schemes/elliptic_curves/gp_simon.py
-@@ -57,6 +57,9 @@ def simon_two_descent(E, verbose=0, lim1=None, lim3=None, limtriv=None,
-         sage: import sage.schemes.elliptic_curves.gp_simon
-         sage: E = EllipticCurve('389a1')
-         sage: sage.schemes.elliptic_curves.gp_simon.simon_two_descent(E)
-+        doctest:warning...:
-+        DeprecationWarning: please use the 2-descent algorithm over QQ inside pari
-+        See https://github.com/sagemath/sage/issues/38461 for details.
-         (2, 2, [(5/4 : 5/8 : 1), (-3/4 : 7/8 : 1)])
- 
-     TESTS::
-diff --git a/src/sage/schemes/plane_conics/con_number_field.py b/src/sage/schemes/plane_conics/con_number_field.py
-index 393b77bc1ff..af946d05fb7 100644
---- a/src/sage/schemes/plane_conics/con_number_field.py
-+++ b/src/sage/schemes/plane_conics/con_number_field.py
-@@ -123,9 +123,9 @@ class ProjectiveConic_number_field(ProjectiveConic_field):
-             sage: C = Conic(K, [1, 3, -5])
-             sage: C.has_rational_point(point=True, obstruction=True)
-             (False, Fractional ideal (-i - 2))
--            sage: C.has_rational_point(algorithm="rnfisnorm")
-+            sage: C.has_rational_point(algorithm='rnfisnorm')
-             False
--            sage: C.has_rational_point(algorithm="rnfisnorm", obstruction=True,
-+            sage: C.has_rational_point(algorithm='rnfisnorm', obstruction=True,
-             ....:                      read_cache=False)
-             Traceback (most recent call last):
-             ...
-diff --git a/src/sage/schemes/projective/projective_morphism.py b/src/sage/schemes/projective/projective_morphism.py
-index 339406cd9d6..2baab7e5cda 100644
---- a/src/sage/schemes/projective/projective_morphism.py
-+++ b/src/sage/schemes/projective/projective_morphism.py
-@@ -1764,10 +1764,10 @@ class SchemeMorphism_polynomial_projective_space_field(SchemeMorphism_polynomial
-             Scheme morphism:
-               From: Projective Space of dimension 1 over Number Field in a
-                     with defining polynomial y^4 + 3*y^2 + 1
--                    with a = 0.?e-151 + 0.618033988749895?*I
-+                    with a = 0.?e-113 + 0.618033988749895?*I
-               To:   Projective Space of dimension 2 over Number Field in a
-                     with defining polynomial y^4 + 3*y^2 + 1
--                    with a = 0.?e-151 + 0.618033988749895?*I
-+                    with a = 0.?e-113 + 0.618033988749895?*I
-               Defn: Defined on coordinates by sending (x : y) to
-                     (x^2 + (a^3 + 2*a)*x*y + 3*y^2 : y^2 : (2*a^2 + 3)*x*y)
- 
diff --git a/srcpkgs/sagemath/patches/38749-zz-fixup_backport.patch b/srcpkgs/sagemath/patches/38749-zz-fixup_backport.patch
deleted file mode 100644
index 4a5550140eab6a..00000000000000
--- a/srcpkgs/sagemath/patches/38749-zz-fixup_backport.patch
+++ /dev/null
@@ -1,95 +0,0 @@
-commit 031e32abfded6902eeb5974b51026bec05e6a3c5
-Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
-Date:   Sun Nov 3 18:23:36 2024 -0300
-
-    fixup backport of #38749
-
-diff --git a/src/sage/rings/number_field/number_field_ideal_rel.py b/src/sage/rings/number_field/number_field_ideal_rel.py
-index 75b2ecc69d8..4f52eba6279 100644
---- a/src/sage/rings/number_field/number_field_ideal_rel.py
-+++ b/src/sage/rings/number_field/number_field_ideal_rel.py
-@@ -380,6 +380,7 @@ class NumberFieldFractionalIdeal_rel(NumberFieldFractionalIdeal):
- 
-         EXAMPLES::
- 
-+            sage: pari.setrand(3)
-             sage: R.<x> = QQ[]
-             sage: K.<a> = NumberField(x^2 + 6)
-             sage: L.<b> = K.extension(K['x'].gen()^4 + a)
-diff --git a/src/sage/rings/number_field/order.py b/src/sage/rings/number_field/order.py
-index c499bc2812c..c28e3b0a7a9 100644
---- a/src/sage/rings/number_field/order.py
-+++ b/src/sage/rings/number_field/order.py
-@@ -590,7 +590,7 @@ class Order(IntegralDomain, sage.rings.abc.Order):
-             sage: k.<a> = NumberField(x^2 + 5077); G = k.class_group(); G
-             Class group of order 22 with structure C22 of Number Field in a with defining polynomial x^2 + 5077
-             sage: G.0 ^ -9
--            Fractional ideal class (67, a + 45)
-+            Fractional ideal class (43, a + 13)
-             sage: Ok = k.maximal_order(); Ok
-             Maximal Order generated by a in Number Field in a with defining polynomial x^2 + 5077
-             sage: Ok * (11, a + 7)
-@@ -2994,7 +2994,7 @@ def EisensteinIntegers(names="omega"):
-          with defining polynomial x^2 + x + 1
-          with omega = -0.50000000000000000? + 0.866025403784439?*I
-         sage: factor(3 + omega)
--        (omega + 1) * (-2*omega + 1)
-+        (-omega - 1) * (2*omega - 1)
-         sage: CC(omega)
-         -0.500000000000000 + 0.866025403784439*I
-         sage: omega.minpoly()
-diff --git a/src/sage/schemes/elliptic_curves/ell_number_field.py b/src/sage/schemes/elliptic_curves/ell_number_field.py
-index 0e60ef0f6a2..4c615e75ac9 100644
---- a/src/sage/schemes/elliptic_curves/ell_number_field.py
-+++ b/src/sage/schemes/elliptic_curves/ell_number_field.py
-@@ -2603,6 +2603,7 @@ class EllipticCurve_number_field(EllipticCurve_field):
- 
-         EXAMPLES::
- 
-+            sage: pari.setrand(1)
-             sage: K.<i> = QuadraticField(-1)
-             sage: E = EllipticCurve(K, [0,0,0,0,1])
-             sage: C = E.isogeny_class(); C
-diff --git a/src/sage/schemes/elliptic_curves/gal_reps_number_field.py b/src/sage/schemes/elliptic_curves/gal_reps_number_field.py
-index 3fe8260947d..cf905787257 100644
---- a/src/sage/schemes/elliptic_curves/gal_reps_number_field.py
-+++ b/src/sage/schemes/elliptic_curves/gal_reps_number_field.py
-@@ -795,6 +795,7 @@ def deg_one_primes_iter(K, principal_only=False):
- 
-     EXAMPLES::
- 
-+        sage: pari.setrand(1)
-         sage: K.<a> = QuadraticField(-5)
-         sage: from sage.schemes.elliptic_curves.gal_reps_number_field import deg_one_primes_iter
-         sage: it = deg_one_primes_iter(K)
-diff --git a/src/sage/schemes/elliptic_curves/gp_simon.py b/src/sage/schemes/elliptic_curves/gp_simon.py
-index fdf6f0852e8..046b635cca8 100644
---- a/src/sage/schemes/elliptic_curves/gp_simon.py
-+++ b/src/sage/schemes/elliptic_curves/gp_simon.py
-@@ -57,9 +57,6 @@ def simon_two_descent(E, verbose=0, lim1=None, lim3=None, limtriv=None,
-         sage: import sage.schemes.elliptic_curves.gp_simon
-         sage: E = EllipticCurve('389a1')
-         sage: sage.schemes.elliptic_curves.gp_simon.simon_two_descent(E)
--        doctest:warning...:
--        DeprecationWarning: please use the 2-descent algorithm over QQ inside pari
--        See https://github.com/sagemath/sage/issues/38461 for details.
-         (2, 2, [(-3/4 : 7/8 : 1), (5/4 : 5/8 : 1)])
- 
-     TESTS::
-diff --git a/src/sage/schemes/projective/projective_morphism.py b/src/sage/schemes/projective/projective_morphism.py
-index 5f4512f5be6..2c1c6aef618 100644
---- a/src/sage/schemes/projective/projective_morphism.py
-+++ b/src/sage/schemes/projective/projective_morphism.py
-@@ -1764,10 +1764,10 @@ class SchemeMorphism_polynomial_projective_space_field(SchemeMorphism_polynomial
-             Scheme morphism:
-               From: Projective Space of dimension 1 over Number Field in a
-                     with defining polynomial y^4 + 3*y^2 + 1
--                    with a = 0.?e-166 + 1.618033988749895?*I
-+                    with a = 0.?e-165 + 1.618033988749895?*I
-               To:   Projective Space of dimension 2 over Number Field in a
-                     with defining polynomial y^4 + 3*y^2 + 1
--                    with a = 0.?e-166 + 1.618033988749895?*I
-+                    with a = 0.?e-165 + 1.618033988749895?*I
-               Defn: Defined on coordinates by sending (x : y) to
-                     (x^2 + (-a^3 - 2*a)*x*y + 3*y^2 : y^2 : (-2*a^2 - 3)*x*y)
- 

From 4f8a78e98eb82057b7ba873af30ec7841ca8ac86 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 4 Nov 2024 19:13:43 -0300
Subject: [PATCH 20/21] sagemath: update to 10.5.beta9.

---
 .../patches/37885-cython_warnings.patch       | 12 ---------
 .../sagemath/patches/38873-fix_doctest.patch  | 25 ------------------
 srcpkgs/sagemath/patches/get_patches          |  4 +--
 srcpkgs/sagemath/patches/revert-38826.patch   | 26 -------------------
 srcpkgs/sagemath/template                     |  6 ++---
 5 files changed, 5 insertions(+), 68 deletions(-)
 delete mode 100644 srcpkgs/sagemath/patches/37885-cython_warnings.patch
 delete mode 100644 srcpkgs/sagemath/patches/38873-fix_doctest.patch
 delete mode 100644 srcpkgs/sagemath/patches/revert-38826.patch

diff --git a/srcpkgs/sagemath/patches/37885-cython_warnings.patch b/srcpkgs/sagemath/patches/37885-cython_warnings.patch
deleted file mode 100644
index fa4b648cfc1577..00000000000000
--- a/srcpkgs/sagemath/patches/37885-cython_warnings.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/src/sage_setup/command/sage_build_cython.py b/src/sage_setup/command/sage_build_cython.py
-index f4b1357c543..3435c196d49 100644
---- a/src/sage_setup/command/sage_build_cython.py
-+++ b/src/sage_setup/command/sage_build_cython.py
-@@ -226,6 +226,7 @@ def run(self):
-                 compiler_directives=self.cython_directives,
-                 compile_time_env=self.compile_time_env,
-                 create_extension=self.create_extension,
-+                show_all_warnings=True,
-                 # Debugging
-                 gdb_debug=self.debug,
-                 output_dir=os.path.join(self.build_lib, "sage"),
diff --git a/srcpkgs/sagemath/patches/38873-fix_doctest.patch b/srcpkgs/sagemath/patches/38873-fix_doctest.patch
deleted file mode 100644
index f42a8a570ca0cb..00000000000000
--- a/srcpkgs/sagemath/patches/38873-fix_doctest.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-diff --git a/src/sage/parallel/map_reduce.py b/src/sage/parallel/map_reduce.py
-index 303f7405416..a182a136a2f 100644
---- a/src/sage/parallel/map_reduce.py
-+++ b/src/sage/parallel/map_reduce.py
-@@ -1133,18 +1133,16 @@ def start_workers(self):
- 
-         TESTS::
- 
-+            sage: # long time
-             sage: from sage.parallel.map_reduce import RESetMapReduce
-             sage: def children(x):
-             ....:     print(f"Starting: {x}", flush=True)
-             ....:     return []
-             sage: S = RESetMapReduce(roots=[1, 2], children=children)
-             sage: S.setup_workers(2)
--            sage: S.start_workers(); sleep(float(5))  # long time
-+            sage: S.start_workers(); sleep(float(5))
-             Starting: ...
-             Starting: ...
--
--        Cleanup::
--
-             sage: S.finish()
-         """
-         if self._nprocess == 0:
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 43d084527e5b98..532f33857545a7 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -31,7 +31,7 @@ cd $(dirname "$0")
 #get_pr 38572 "nauty 2.8.9"
 
 #get_pr 37645 "fix doctest"
-get_pr 37885 "cython warnings"
-get_pr 38873 "fix doctest"
+#get_pr 37885 "cython warnings"
+#get_pr 38873 "fix doctest"
 
 get_pr 38749 "pari 2.17"
diff --git a/srcpkgs/sagemath/patches/revert-38826.patch b/srcpkgs/sagemath/patches/revert-38826.patch
deleted file mode 100644
index 6a97d896db44f7..00000000000000
--- a/srcpkgs/sagemath/patches/revert-38826.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-Revert "src/sage/env.py: canonicalize paths in a test"
-
-This reverts commit 53a6d3133ea7782c7498ea6ab6bd3041815bd6a6.
-
-See: https://github.com/sagemath/sage/pull/38826#issuecomment-2439757935
-
---- a/src/sage/env.py
-+++ b/src/sage/env.py
-@@ -8,14 +8,10 @@ environment variables, and has the same ``SAGE_ROOT`` and ``SAGE_LOCAL``
- 
-     sage: env = {k:v for (k,v) in os.environ.items() if not k.startswith("SAGE_")}
-     sage: from subprocess import check_output
--    sage: module_name = "sage.all"   # hide .all import from the linter
--    sage: cmd  = f"from {module_name} import SAGE_ROOT, SAGE_LOCAL;"
--    sage: cmd +=  "from os.path import samefile;"
--    sage: cmd += f"s1 = samefile(SAGE_ROOT, '{SAGE_ROOT}');"
--    sage: cmd += f"s2 = samefile(SAGE_LOCAL, '{SAGE_LOCAL}');"
--    sage: cmd += "print(s1 and s2);"
-+    sage: environment = "sage.all"
-+    sage: cmd = f"from {environment} import SAGE_ROOT, SAGE_LOCAL; print((SAGE_ROOT, SAGE_LOCAL))"
-     sage: out = check_output([sys.executable, "-c", cmd], env=env).decode().strip()   # long time
--    sage: out == "True"                                                               # long time
-+    sage: out == repr((SAGE_ROOT, SAGE_LOCAL))                                        # long time
-     True
- 
- AUTHORS:
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index 42d53d251d973a..16efd692a00beb 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,7 +1,7 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.5.beta8
-revision=2
+version=10.5.beta9
+revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
 build_style=python3-pep517
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=0c386e88524a91ad97db4f3f8ee7408d8678072596b3ab5e9ffaea2cb6be13fd
+checksum=eed965e67bc06d999116186c527bd2fd2438eea8523b680ae0944b1b260f3fb5
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

From 0193c29769e35e8c2770aed1d555494951957dd2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 17 Nov 2024 22:30:57 -0300
Subject: [PATCH 21/21] sagemath: update to 10.5.rc0.

---
 .../sagemath/patches/38749-pari_2.17.patch    | 151 ++++----
 .../sagemath/patches/38749-zz-fix-32bit.patch | 335 ++++++++++++++++++
 .../patches/zz-pari_bnf-doctests.patch        | 312 ++++++++++++++++
 srcpkgs/sagemath/patches/zz-pari_bnf.patch    |  24 ++
 .../sagemath/patches/zz-reduced_basis.patch   |  46 +++
 srcpkgs/sagemath/template                     |   4 +-
 6 files changed, 786 insertions(+), 86 deletions(-)
 create mode 100644 srcpkgs/sagemath/patches/38749-zz-fix-32bit.patch
 create mode 100644 srcpkgs/sagemath/patches/zz-pari_bnf-doctests.patch
 create mode 100644 srcpkgs/sagemath/patches/zz-pari_bnf.patch
 create mode 100644 srcpkgs/sagemath/patches/zz-reduced_basis.patch

diff --git a/srcpkgs/sagemath/patches/38749-pari_2.17.patch b/srcpkgs/sagemath/patches/38749-pari_2.17.patch
index 4fbdd7358c0025..0112f04c6a328d 100644
--- a/srcpkgs/sagemath/patches/38749-pari_2.17.patch
+++ b/srcpkgs/sagemath/patches/38749-pari_2.17.patch
@@ -1,5 +1,5 @@
 diff --git a/src/sage/arith/misc.py b/src/sage/arith/misc.py
-index 745d5fcbbe7..86409ab3243 100644
+index 14fe466ccd9..d94404258f3 100644
 --- a/src/sage/arith/misc.py
 +++ b/src/sage/arith/misc.py
 @@ -2691,9 +2691,14 @@ def factor(n, proof=None, int_=False, algorithm='pari', verbose=0, **kwds):
@@ -56,7 +56,7 @@ index 76f0570a819..0e4d13ef889 100644
                  sage: gcd(t, i)
                  Traceback (most recent call last):
 diff --git a/src/sage/dynamics/arithmetic_dynamics/berkovich_ds.py b/src/sage/dynamics/arithmetic_dynamics/berkovich_ds.py
-index 6995f61f463..457b0ba2253 100644
+index 9734b3767ac..d3f9c3cdf41 100644
 --- a/src/sage/dynamics/arithmetic_dynamics/berkovich_ds.py
 +++ b/src/sage/dynamics/arithmetic_dynamics/berkovich_ds.py
 @@ -690,10 +690,10 @@ def conjugate(self, M, adjugate=False, new_ideal=None):
@@ -73,7 +73,7 @@ index 6995f61f463..457b0ba2253 100644
          if self.domain().is_padic_base():
              return DynamicalSystem_Berkovich(self._system.conjugate(M, adjugate=adjugate))
 diff --git a/src/sage/dynamics/arithmetic_dynamics/projective_ds.py b/src/sage/dynamics/arithmetic_dynamics/projective_ds.py
-index a74efd9129a..151f9e71335 100644
+index 2fab95104f1..8b9cdd9313f 100644
 --- a/src/sage/dynamics/arithmetic_dynamics/projective_ds.py
 +++ b/src/sage/dynamics/arithmetic_dynamics/projective_ds.py
 @@ -1790,7 +1790,7 @@ def primes_of_bad_reduction(self, check=True):
@@ -86,7 +86,7 @@ index a74efd9129a..151f9e71335 100644
          This is an example where ``check=False`` returns extra primes::
  
 diff --git a/src/sage/libs/pari/convert_sage.pyx b/src/sage/libs/pari/convert_sage.pyx
-index 64386bcf632..db6725f39a5 100644
+index e26238d7c38..48338e0279c 100644
 --- a/src/sage/libs/pari/convert_sage.pyx
 +++ b/src/sage/libs/pari/convert_sage.pyx
 @@ -573,17 +573,16 @@ cpdef list pari_prime_range(long c_start, long c_stop, bint py_ints=False):
@@ -167,10 +167,10 @@ index 1ed571cd4b9..bd8dc9641d2 100644
      sage: nf = pari('x^2 + 1').nfinit()
      sage: nf.nfrootsof1()
 diff --git a/src/sage/matrix/matrix2.pyx b/src/sage/matrix/matrix2.pyx
-index 0c257cfaf33..780cae7fbf2 100644
+index d2f0815e81e..efba7b3472b 100644
 --- a/src/sage/matrix/matrix2.pyx
 +++ b/src/sage/matrix/matrix2.pyx
-@@ -16583,7 +16583,7 @@ cdef class Matrix(Matrix1):
+@@ -16584,7 +16584,7 @@ cdef class Matrix(Matrix1):
              ....:   -2*a^2 + 4*a - 2, -2*a^2 + 1, 2*a, a^2 - 6, 3*a^2 - a ])
              sage: r,s,p = m._echelon_form_PID()
              sage: s[2]
@@ -206,10 +206,10 @@ index 4d120c075da..f3a3ff7e65b 100644
  
      ::
 diff --git a/src/sage/modular/dirichlet.py b/src/sage/modular/dirichlet.py
-index 1f6a7a94444..1cf3ccdb611 100644
+index c261a84e8de..8ca797b5f16 100644
 --- a/src/sage/modular/dirichlet.py
 +++ b/src/sage/modular/dirichlet.py
-@@ -2395,13 +2395,13 @@ class DirichletGroupFactory(UniqueFactory):
+@@ -2398,13 +2398,13 @@ class DirichletGroupFactory(UniqueFactory):
          sage: parent(val)
          Gaussian Integers generated by zeta4 in Cyclotomic Field of order 4 and degree 2
          sage: r4_29_0 = r4.residue_field(K(29).factor()[0][0]); r4_29_0(val)
@@ -317,7 +317,7 @@ index d94b0a4335a..0978c7328fe 100644
          Check that :issue:`19573` is resolved::
  
 diff --git a/src/sage/rings/finite_rings/residue_field.pyx b/src/sage/rings/finite_rings/residue_field.pyx
-index 3146f7fd764..a8e77e48b76 100644
+index be83c5165f6..4d484603df8 100644
 --- a/src/sage/rings/finite_rings/residue_field.pyx
 +++ b/src/sage/rings/finite_rings/residue_field.pyx
 @@ -22,14 +22,13 @@ monogenic (i.e., 2 is an essential discriminant divisor)::
@@ -467,7 +467,7 @@ index e9962c3ccde..90a68c619f6 100644
              <class 'sage.rings.finite_rings.residue_field_pari_ffelt.ResidueFiniteField_pari_ffelt_with_category'>
              sage: ff(alpha^2 + 1)
 diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
-index 9616e7946bc..bcc45e703a2 100644
+index ffc5ee16e0f..86cbb05c6bf 100644
 --- a/src/sage/rings/integer.pyx
 +++ b/src/sage/rings/integer.pyx
 @@ -5585,7 +5585,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
@@ -608,10 +608,10 @@ index c974c3df6ff..ee53ca6d674 100644
              Traceback (most recent call last):
              ...
 diff --git a/src/sage/rings/number_field/number_field.py b/src/sage/rings/number_field/number_field.py
-index bb16476980e..3a98a997962 100644
+index 7128d40032e..3cffd4ce062 100644
 --- a/src/sage/rings/number_field/number_field.py
 +++ b/src/sage/rings/number_field/number_field.py
-@@ -3627,7 +3627,7 @@ def fractional_ideal(self, *gens, **kwds):
+@@ -3628,7 +3628,7 @@ def fractional_ideal(self, *gens, **kwds):
              sage: L.<b> = K.extension(x^2 - 3, x^2 + 1)
              sage: M.<c> = L.extension(x^2 + 1)
              sage: L.ideal(K.ideal(2, a))
@@ -620,7 +620,7 @@ index bb16476980e..3a98a997962 100644
              sage: M.ideal(K.ideal(2, a)) == M.ideal(a*(b - c)/2)
              True
  
-@@ -3665,40 +3665,29 @@ def ideals_of_bdd_norm(self, bound):
+@@ -3666,40 +3666,29 @@ def ideals_of_bdd_norm(self, bound):
  
              sage: x = polygen(QQ, 'x')
              sage: K.<a> = NumberField(x^2 + 23)
@@ -684,7 +684,7 @@ index bb16476980e..3a98a997962 100644
          """
          hnf_ideals = self.pari_nf().ideallist(bound)
          d = {}
-@@ -3925,9 +3914,13 @@ def primes_of_bounded_norm(self, B):
+@@ -3926,9 +3915,13 @@ def primes_of_bounded_norm(self, B):
          EXAMPLES::
  
              sage: K.<i> = QuadraticField(-1)
@@ -701,7 +701,7 @@ index bb16476980e..3a98a997962 100644
              sage: K.primes_of_bounded_norm(1)
              []
              sage: x = polygen(QQ, 'x')
-@@ -3936,10 +3929,10 @@ def primes_of_bounded_norm(self, B):
+@@ -3937,10 +3930,10 @@ def primes_of_bounded_norm(self, B):
              sage: P
              [Fractional ideal (a),
               Fractional ideal (a + 1),
@@ -714,7 +714,7 @@ index bb16476980e..3a98a997962 100644
               Fractional ideal (a^2 - 2*a - 1),
               Fractional ideal (a + 3)]
              sage: [p.norm() for p in P]
-@@ -3988,11 +3981,13 @@ def primes_of_bounded_norm_iter(self, B):
+@@ -3989,11 +3982,13 @@ def primes_of_bounded_norm_iter(self, B):
  
              sage: K.<i> = QuadraticField(-1)
              sage: it = K.primes_of_bounded_norm_iter(10)
@@ -731,7 +731,7 @@ index bb16476980e..3a98a997962 100644
              sage: list(K.primes_of_bounded_norm_iter(1))
              []
          """
-@@ -4317,7 +4312,7 @@ def pari_nf(self, important=True):
+@@ -4318,7 +4313,7 @@ def pari_nf(self, important=True):
              sage: k.<a> = NumberField(x^4 - 3/2*x + 5/3); k
              Number Field in a with defining polynomial x^4 - 3/2*x + 5/3
              sage: k.pari_nf()
@@ -740,7 +740,7 @@ index bb16476980e..3a98a997962 100644
              sage: pari(k)
              [y^4 - 324*y + 2160, [0, 2], 48918708, 216, ...]
              sage: gp(k)
-@@ -4807,7 +4802,7 @@ def _S_class_group_and_units(self, S, proof=True):
+@@ -4808,7 +4803,7 @@ def _S_class_group_and_units(self, S, proof=True):
               1/13*a^2 + 7/13*a - 332/13,
               -1/13*a^2 + 6/13*a + 345/13,
               -1,
@@ -749,7 +749,7 @@ index bb16476980e..3a98a997962 100644
              sage: units[5] in (1/13*a^2 - 19/13*a - 7/13, 1/13*a^2 + 20/13*a - 7/13)
              True
              sage: len(units) == 6
-@@ -4818,7 +4813,7 @@ def _S_class_group_and_units(self, S, proof=True):
+@@ -4819,7 +4814,7 @@ def _S_class_group_and_units(self, S, proof=True):
  
              sage: K.<a> = NumberField(2*x^2 - 1/3)
              sage: K._S_class_group_and_units(tuple(K.primes_above(2) + K.primes_above(3)))
@@ -758,7 +758,7 @@ index bb16476980e..3a98a997962 100644
          """
          K_pari = self.pari_bnf(proof=proof)
          S_pari = [p.pari_prime() for p in sorted(set(S))]
-@@ -4996,7 +4991,7 @@ def selmer_generators(self, S, m, proof=True, orders=False):
+@@ -4997,7 +4992,7 @@ def selmer_generators(self, S, m, proof=True, orders=False):
               1/13*a^2 + 7/13*a - 332/13,
               -1/13*a^2 + 6/13*a + 345/13,
               -1,
@@ -767,7 +767,7 @@ index bb16476980e..3a98a997962 100644
              sage: gens[5] in (1/13*a^2 - 19/13*a - 7/13, 1/13*a^2 + 20/13*a - 7/13)
              True
              sage: gens[6] in (-1/13*a^2 + 45/13*a - 97/13, 1/13*a^2 - 45/13*a + 97/13)
-@@ -5153,16 +5148,20 @@ def selmer_space(self, S, p, proof=None):
+@@ -5154,16 +5149,20 @@ def selmer_space(self, S, p, proof=None):
              sage: KS2, gens, fromKS2, toKS2 = K.selmer_space([P2, P3, P5], 2)
              sage: KS2
              Vector space of dimension 4 over Finite Field of size 2
@@ -791,7 +791,7 @@ index bb16476980e..3a98a997962 100644
  
              sage: toKS2(10)
              (0, 0, 1, 1)
-@@ -5174,8 +5173,10 @@ def selmer_space(self, S, p, proof=None):
+@@ -5175,8 +5174,10 @@ def selmer_space(self, S, p, proof=None):
              sage: KS3, gens, fromKS3, toKS3 = K.selmer_space([P2, P3, P5], 3)
              sage: KS3
              Vector space of dimension 3 over Finite Field of size 3
@@ -804,7 +804,7 @@ index bb16476980e..3a98a997962 100644
  
          An example to show that the group `K(S,2)` may be strictly
          larger than the group of elements giving extensions unramified
-@@ -5640,7 +5641,7 @@ def different(self):
+@@ -5641,7 +5642,7 @@ def different(self):
              sage: k.<a> = NumberField(x^2 + 23)
              sage: d = k.different()
              sage: d
@@ -813,7 +813,7 @@ index bb16476980e..3a98a997962 100644
              sage: d.norm()
              23
              sage: k.disc()
-@@ -5760,7 +5761,7 @@ def elements_of_norm(self, n, proof=None) -> list:
+@@ -5761,7 +5762,7 @@ def elements_of_norm(self, n, proof=None) -> list:
              sage: K.elements_of_norm(3)
              []
              sage: K.elements_of_norm(50)
@@ -822,7 +822,7 @@ index bb16476980e..3a98a997962 100644
  
          TESTS:
  
-@@ -5871,11 +5872,16 @@ def factor(self, n):
+@@ -5872,11 +5873,16 @@ def factor(self, n):
              sage: K.<a> = NumberField(x^2 + 1)
              sage: K.factor(1/3)
              (Fractional ideal (3))^-1
@@ -844,7 +844,7 @@ index bb16476980e..3a98a997962 100644
  
          An example over a relative number field::
  
-@@ -5908,9 +5914,9 @@ def factor(self, n):
+@@ -5909,9 +5915,9 @@ def factor(self, n):
              sage: (fi, fj) = f[::]
              sage: (fi[1], fj[1])
              (1, 1)
@@ -856,7 +856,7 @@ index bb16476980e..3a98a997962 100644
              True
          """
          return self.ideal(n).factor()
-@@ -6507,12 +6513,12 @@ def reduced_basis(self, prec=None):
+@@ -6508,12 +6514,12 @@ def reduced_basis(self, prec=None):
              sage: k.<a> = NumberField(x^6 + 2218926655879913714112*x^4 - 32507675650290949030789018433536*x^3 + 4923635504174417014460581055002374467948544*x^2 - 36066074010564497464129951249279114076897746988630016*x + 264187244046129768986806800244258952598300346857154900812365824)
              sage: new_basis = k.reduced_basis(prec=120)
              sage: [c.minpoly() for c in new_basis]
@@ -875,7 +875,7 @@ index bb16476980e..3a98a997962 100644
              sage: R = k.order(new_basis)
              sage: R.discriminant()==k.discriminant()
              True
-@@ -7107,14 +7113,14 @@ def units(self, proof=None):
+@@ -7108,14 +7114,14 @@ def units(self, proof=None):
              sage: K.units(proof=True)  # takes forever, not tested
              ...
              sage: K.units(proof=False)  # result not independently verified
@@ -897,7 +897,7 @@ index bb16476980e..3a98a997962 100644
  
          TESTS:
  
-@@ -7123,7 +7129,7 @@ def units(self, proof=None):
+@@ -7124,7 +7130,7 @@ def units(self, proof=None):
  
              sage: K.<a> = NumberField(1/2*x^2 - 1/6)
              sage: K.units()
@@ -906,7 +906,7 @@ index bb16476980e..3a98a997962 100644
          """
          proof = proof_flag(proof)
  
-@@ -7205,14 +7211,14 @@ def unit_group(self, proof=None):
+@@ -7206,14 +7212,14 @@ def unit_group(self, proof=None):
              (u0, u1, u2, u3, u4, u5, u6, u7, u8)
              sage: U.gens_values()  # result not independently verified
              [-1,
@@ -928,7 +928,7 @@ index bb16476980e..3a98a997962 100644
          """
          proof = proof_flag(proof)
  
-@@ -7261,8 +7267,8 @@ def S_unit_group(self, proof=None, S=None):
+@@ -7262,8 +7268,8 @@ def S_unit_group(self, proof=None, S=None):
              sage: U = K.S_unit_group(S=a); U
              S-unit group with structure C10 x Z x Z x Z of
               Number Field in a with defining polynomial x^4 - 10*x^3 + 100*x^2 - 375*x + 1375
@@ -939,7 +939,7 @@ index bb16476980e..3a98a997962 100644
              sage: U.gens()
              (u0, u1, u2, u3)
              sage: U.gens_values()  # random
-@@ -7273,8 +7279,8 @@ def S_unit_group(self, proof=None, S=None):
+@@ -7274,8 +7280,8 @@ def S_unit_group(self, proof=None, S=None):
              sage: [u.multiplicative_order() for u in U.gens()]
              [10, +Infinity, +Infinity, +Infinity]
              sage: U.primes()
@@ -950,7 +950,7 @@ index bb16476980e..3a98a997962 100644
  
          With the default value of `S`, the S-unit group is the same as
          the global unit group::
-@@ -7426,8 +7432,8 @@ def S_unit_solutions(self, S=[], prec=106, include_exponents=False, include_boun
+@@ -7427,8 +7433,8 @@ def S_unit_solutions(self, S=[], prec=106, include_exponents=False, include_boun
  
              sage: # needs sage.rings.padics
              sage: solutions, bound = K.S_unit_solutions(S, prec=100, include_bound=True)
@@ -961,7 +961,7 @@ index bb16476980e..3a98a997962 100644
          """
          from .S_unit_solver import solve_S_unit_equation
          return solve_S_unit_equation(self, S, prec, include_exponents, include_bound, proof)
-@@ -8782,7 +8788,7 @@ def subfields(self, degree=0, name=None):
+@@ -8783,7 +8789,7 @@ def subfields(self, degree=0, name=None):
              (Number Field in a1 with defining polynomial x^2 - 2, Ring morphism:
                From: Number Field in a1 with defining polynomial x^2 - 2
                To:   Number Field in a with defining polynomial 2*x^4 + 6*x^2 + 1/2
@@ -970,7 +970,7 @@ index bb16476980e..3a98a997962 100644
              (Number Field in a2 with defining polynomial x^2 + 4, Ring morphism:
                From: Number Field in a2 with defining polynomial x^2 + 4
                To:   Number Field in a with defining polynomial 2*x^4 + 6*x^2 + 1/2
-@@ -8790,14 +8796,14 @@ def subfields(self, degree=0, name=None):
+@@ -8791,14 +8797,14 @@ def subfields(self, degree=0, name=None):
              (Number Field in a3 with defining polynomial x^2 + 2, Ring morphism:
                From: Number Field in a3 with defining polynomial x^2 + 2
                To:   Number Field in a with defining polynomial 2*x^4 + 6*x^2 + 1/2
@@ -988,7 +988,7 @@ index bb16476980e..3a98a997962 100644
              ]
          """
          return self._subfields_helper(degree=degree, name=name,
-@@ -12694,12 +12700,12 @@ def _splitting_classes_gens_(K, m, d):
+@@ -12730,12 +12736,12 @@ def _splitting_classes_gens_(K, m, d):
          sage: L = K.subfields(20)[0][0]
          sage: L.conductor()                                                             # needs sage.groups
          101
@@ -1003,7 +1003,7 @@ index bb16476980e..3a98a997962 100644
          [37]
  
          sage: K = CyclotomicField(44)
-@@ -12711,7 +12717,7 @@ def _splitting_classes_gens_(K, m, d):
+@@ -12747,7 +12753,7 @@ def _splitting_classes_gens_(K, m, d):
           with zeta44_0 = 3.837971894457990?
          sage: L.conductor()                                                             # needs sage.groups
          11
@@ -1281,7 +1281,7 @@ index 7f6cfd9b1b7..eb39f6f4d12 100644
          False
      """
 diff --git a/src/sage/rings/number_field/number_field_rel.py b/src/sage/rings/number_field/number_field_rel.py
-index 9ab6fd4c261..6e9bf71baf4 100644
+index 7ea070b113e..a1d5ab38176 100644
 --- a/src/sage/rings/number_field/number_field_rel.py
 +++ b/src/sage/rings/number_field/number_field_rel.py
 @@ -233,21 +233,21 @@ def __init__(self, base, polynomial, name,
@@ -1331,7 +1331,7 @@ index 9ab6fd4c261..6e9bf71baf4 100644
          """
          return QQ['x'](self._pari_rnfeq()[0])
  
-@@ -2721,7 +2721,7 @@ def uniformizer(self, P, others='positive'):
+@@ -2724,7 +2724,7 @@ def uniformizer(self, P, others='positive'):
              sage: x = polygen(ZZ, 'x')
              sage: K.<a, b> = NumberField([x^2 + 23, x^2 - 3])
              sage: P = K.prime_factors(5)[0]; P
@@ -1341,10 +1341,10 @@ index 9ab6fd4c261..6e9bf71baf4 100644
              sage: u.valuation(P)
              1
 diff --git a/src/sage/rings/number_field/order.py b/src/sage/rings/number_field/order.py
-index 55db3bbbcbf..8b69baf5464 100644
+index 9dee6a8a481..3c2809f4201 100644
 --- a/src/sage/rings/number_field/order.py
 +++ b/src/sage/rings/number_field/order.py
-@@ -495,7 +495,7 @@ def fractional_ideal(self, *args, **kwds):
+@@ -496,7 +496,7 @@ def fractional_ideal(self, *args, **kwds):
              sage: K.<a> = NumberField(x^2 + 2)
              sage: R = K.maximal_order()
              sage: R.fractional_ideal(2/3 + 7*a, a)
@@ -1353,7 +1353,7 @@ index 55db3bbbcbf..8b69baf5464 100644
          """
          return self.number_field().fractional_ideal(*args, **kwds)
  
-@@ -569,7 +569,7 @@ def __mul__(self, right):
+@@ -570,7 +570,7 @@ def __mul__(self, right):
              sage: k.<a> = NumberField(x^2 + 5077); G = k.class_group(); G
              Class group of order 22 with structure C22 of Number Field in a with defining polynomial x^2 + 5077
              sage: G.0 ^ -9
@@ -1362,7 +1362,7 @@ index 55db3bbbcbf..8b69baf5464 100644
              sage: Ok = k.maximal_order(); Ok
              Maximal Order generated by a in Number Field in a with defining polynomial x^2 + 5077
              sage: Ok * (11, a + 7)
-@@ -2918,7 +2918,7 @@ def GaussianIntegers(names='I', latex_name='i'):
+@@ -2933,7 +2933,7 @@ def GaussianIntegers(names='I', latex_name='i'):
          sage: ZZI
          Gaussian Integers generated by I in Number Field in I with defining polynomial x^2 + 1 with I = 1*I
          sage: factor(3 + I)
@@ -1371,7 +1371,7 @@ index 55db3bbbcbf..8b69baf5464 100644
          sage: CC(I)
          1.00000000000000*I
          sage: I.minpoly()
-@@ -2949,7 +2949,7 @@ def EisensteinIntegers(names='omega'):
+@@ -2964,7 +2964,7 @@ def EisensteinIntegers(names='omega'):
           with defining polynomial x^2 + x + 1
           with omega = -0.50000000000000000? + 0.866025403784439?*I
          sage: factor(3 + omega)
@@ -1381,7 +1381,7 @@ index 55db3bbbcbf..8b69baf5464 100644
          -0.500000000000000 + 0.866025403784439*I
          sage: omega.minpoly()
 diff --git a/src/sage/rings/number_field/selmer_group.py b/src/sage/rings/number_field/selmer_group.py
-index acdf2954fdf..7da6b58a209 100644
+index 283db17c84e..c6054b6824f 100644
 --- a/src/sage/rings/number_field/selmer_group.py
 +++ b/src/sage/rings/number_field/selmer_group.py
 @@ -71,7 +71,7 @@ def _ideal_generator(I):
@@ -1394,10 +1394,10 @@ index acdf2954fdf..7da6b58a209 100644
      try:
          return I.gens_reduced()[0]
 diff --git a/src/sage/rings/polynomial/polynomial_quotient_ring.py b/src/sage/rings/polynomial/polynomial_quotient_ring.py
-index e12977e8464..c5bf39a1c73 100644
+index 9851c477abf..ae3a4b5254c 100644
 --- a/src/sage/rings/polynomial/polynomial_quotient_ring.py
 +++ b/src/sage/rings/polynomial/polynomial_quotient_ring.py
-@@ -1429,13 +1429,13 @@ def S_class_group(self, S, proof=True):
+@@ -1430,13 +1430,13 @@ def S_class_group(self, S, proof=True):
              sage: R.<x> = K[]
              sage: S.<xbar> = R.quotient(x^2 + 23)
              sage: S.S_class_group([])
@@ -1413,7 +1413,7 @@ index e12977e8464..c5bf39a1c73 100644
  
          Now we take an example over a nontrivial base with two factors, each
          contributing to the class group::
-@@ -1495,14 +1495,14 @@ def S_class_group(self, S, proof=True):
+@@ -1496,14 +1496,14 @@ def S_class_group(self, S, proof=True):
              sage: C = S.S_class_group([])
              sage: C[:2]
              [((1/4*xbar^2 + 31/4,
@@ -1434,7 +1434,7 @@ index e12977e8464..c5bf39a1c73 100644
                6)]
              sage: C[2][1]
              2
-@@ -1514,11 +1514,11 @@ def S_class_group(self, S, proof=True):
+@@ -1515,11 +1515,11 @@ def S_class_group(self, S, proof=True):
              ....:     1/16*a*xbar^3 - 1/16*a*xbar^2 + 23/16*a*xbar - 23/16*a)
              sage: gens[0] == expected_gens[0]
              True
@@ -1449,7 +1449,7 @@ index e12977e8464..c5bf39a1c73 100644
              True
          """
          fields, isos, iso_classes = self._S_decomposition(tuple(S))
-@@ -1611,7 +1611,7 @@ def class_group(self, proof=True):
+@@ -1612,7 +1612,7 @@ def class_group(self, proof=True):
              sage: R.<x> = K[]
              sage: S.<xbar> = R.quotient(x^2 + 23)
              sage: S.class_group()
@@ -1458,7 +1458,7 @@ index e12977e8464..c5bf39a1c73 100644
  
          Here is an example of a product of number fields, both of which
          contribute to the class group::
-@@ -1711,19 +1711,19 @@ def S_units(self, S, proof=True):
+@@ -1712,19 +1712,19 @@ def S_units(self, S, proof=True):
               with defining polynomial x^2 + 3 with a = 1.732050807568878?*I
               with modulus y^3 + 5
              sage: [u for u, o in L.S_units([]) if o is Infinity]
@@ -1485,7 +1485,7 @@ index e12977e8464..c5bf39a1c73 100644
  
          Note that all the returned values live where we expect them to::
  
-@@ -1808,8 +1808,8 @@ def units(self, proof=True):
+@@ -1809,8 +1809,8 @@ def units(self, proof=True):
               with defining polynomial x^2 + 3 with a = 1.732050807568878?*I
               with modulus y^3 + 5
              sage: [u for u, o in L.units() if o is Infinity]
@@ -1496,7 +1496,7 @@ index e12977e8464..c5bf39a1c73 100644
              sage: L.<b> = K.extension(y^3 + 5)
              sage: L.unit_group()
              Unit group with structure C6 x Z x Z of
-@@ -1817,8 +1817,8 @@ def units(self, proof=True):
+@@ -1818,8 +1818,8 @@ def units(self, proof=True):
              sage: L.unit_group().gens()    # abstract generators
              (u0, u1, u2)
              sage: L.unit_group().gens_values()[1:]
@@ -1508,10 +1508,10 @@ index e12977e8464..c5bf39a1c73 100644
          Note that all the returned values live where we expect them to::
  
 diff --git a/src/sage/rings/qqbar.py b/src/sage/rings/qqbar.py
-index 300d64b8279..08c04e6e234 100644
+index 72df892337b..262a55b5031 100644
 --- a/src/sage/rings/qqbar.py
 +++ b/src/sage/rings/qqbar.py
-@@ -2776,11 +2776,12 @@ def number_field_elements_from_algebraics(numbers, minimal=False,
+@@ -2777,11 +2777,12 @@ def number_field_elements_from_algebraics(numbers, minimal=False,
              To:   Algebraic Real Field
              Defn: a |--> 1.732050807568878?)
          sage: number_field_elements_from_algebraics((rt2,qqI))                          # needs sage.symbolic
@@ -1528,7 +1528,7 @@ index 300d64b8279..08c04e6e234 100644
  
      Note that for the first example, where \sage does not realize that
      the number is real, we get a homomorphism to ``QQbar``::
-@@ -4590,8 +4591,7 @@ def _exact_field(self):
+@@ -4660,8 +4661,7 @@ def _exact_field(self):
              Number Field in a with defining polynomial y^4 - 20*y^2 + 81
               with a in -3.789313782671036?
              sage: (QQbar(7)^(3/5))._exact_field()
@@ -1538,7 +1538,7 @@ index 300d64b8279..08c04e6e234 100644
          """
          sd = self._descr
          if isinstance(sd, (ANRational, ANExtensionElement)):
-@@ -4611,7 +4611,7 @@ def _exact_value(self):
+@@ -4681,7 +4681,7 @@ def _exact_value(self):
              sage: (sqrt(QQbar(2)) + sqrt(QQbar(19)))._exact_value()
              -1/9*a^3 + a^2 + 11/9*a - 10 where a^4 - 20*a^2 + 81 = 0 and a in -3.789313782671036?
              sage: (QQbar(7)^(3/5))._exact_value()
@@ -1547,7 +1547,7 @@ index 300d64b8279..08c04e6e234 100644
          """
          sd = self._descr
          if isinstance(sd, (ANRational, ANExtensionElement)):
-@@ -7839,8 +7839,8 @@ def handle_sage_input(self, sib, coerce, is_qqbar):
+@@ -7909,8 +7909,8 @@ def handle_sage_input(self, sib, coerce, is_qqbar):
              sage: sage_input(v, verify=True)
              # Verified
              R.<y> = QQ[]
@@ -1559,7 +1559,7 @@ index 300d64b8279..08c04e6e234 100644
              sage: v.exactify()
              sage: sage_input(v, verify=True)
 diff --git a/src/sage/rings/rational.pyx b/src/sage/rings/rational.pyx
-index 272650abeef..0dbe3453dd2 100644
+index bc29e952b1a..b1d9e64bae0 100644
 --- a/src/sage/rings/rational.pyx
 +++ b/src/sage/rings/rational.pyx
 @@ -1446,7 +1446,7 @@ cdef class Rational(sage.structure.element.FieldElement):
@@ -1602,7 +1602,7 @@ index 0eba4c662ec..2208cefca1d 100755
          ::
  
 diff --git a/src/sage/schemes/elliptic_curves/ell_field.py b/src/sage/schemes/elliptic_curves/ell_field.py
-index a63dbf57809..84a719adfbb 100755
+index 4f694e0f252..bfcbf5e9020 100755
 --- a/src/sage/schemes/elliptic_curves/ell_field.py
 +++ b/src/sage/schemes/elliptic_curves/ell_field.py
 @@ -902,7 +902,7 @@ def division_field(self, n, names='t', map=False, **kwds):
@@ -1628,7 +1628,7 @@ index 7434659b5a2..df076ed62b6 100755
          sage: check_prime(K, L.ideal(5))
          Traceback (most recent call last):
 diff --git a/src/sage/schemes/elliptic_curves/ell_number_field.py b/src/sage/schemes/elliptic_curves/ell_number_field.py
-index eea2e5cc243..cceab500959 100755
+index 8af221880b6..f4c46b79133 100755
 --- a/src/sage/schemes/elliptic_curves/ell_number_field.py
 +++ b/src/sage/schemes/elliptic_curves/ell_number_field.py
 @@ -229,9 +229,9 @@ def simon_two_descent(self, verbose=0, lim1=2, lim3=4, limtriv=2,
@@ -1778,18 +1778,10 @@ index eea2e5cc243..cceab500959 100755
          """
          r = len(points)
 diff --git a/src/sage/schemes/elliptic_curves/ell_point.py b/src/sage/schemes/elliptic_curves/ell_point.py
-index 0da080ffdbe..61b016ca08e 100755
+index 6aa63fc6370..78c1694cb17 100755
 --- a/src/sage/schemes/elliptic_curves/ell_point.py
 +++ b/src/sage/schemes/elliptic_curves/ell_point.py
-@@ -142,7 +142,6 @@
- 
- try:
-     from sage.libs.pari.all import pari, PariError
--    from cypari2.pari_instance import prec_words_to_bits
- except ImportError:
-     PariError = ()
- 
-@@ -2672,10 +2671,10 @@ def has_good_reduction(self, P=None):
+@@ -2773,10 +2773,10 @@ def has_good_reduction(self, P=None):
              sage: K.<i> = NumberField(x^2 + 1)
              sage: E = EllipticCurve(K, [0,1,0,-160,308])
              sage: P = E(26, -120)
@@ -1804,20 +1796,11 @@ index 0da080ffdbe..61b016ca08e 100755
               Fractional ideal (3)]
              sage: [E.tamagawa_exponent(p) for p in E.discriminant().support()]
              [1, 4, 4, 4]
-@@ -3705,7 +3704,7 @@ def elliptic_logarithm(self, embedding=None, precision=100,
-         E_pari = E_work.pari_curve()
-         log_pari = E_pari.ellpointtoz(pt_pari, precision=working_prec)
- 
--        while prec_words_to_bits(log_pari.precision()) < precision:
-+        while log_pari.bitprecision() < precision:
-             # result is not precise enough, re-compute with double
-             # precision. if the base field is not QQ, this
-             # requires modifying the precision of the embedding,
 diff --git a/src/sage/schemes/elliptic_curves/ell_rational_field.py b/src/sage/schemes/elliptic_curves/ell_rational_field.py
-index 0bc71b09d42..feb584fdf72 100755
+index 2f2868d37ca..ee02c86f657 100755
 --- a/src/sage/schemes/elliptic_curves/ell_rational_field.py
 +++ b/src/sage/schemes/elliptic_curves/ell_rational_field.py
-@@ -1848,7 +1848,7 @@ def simon_two_descent(self, verbose=0, lim1=5, lim3=50, limtriv=3,
+@@ -1851,7 +1851,7 @@ def simon_two_descent(self, verbose=0, lim1=5, lim3=50, limtriv=3,
              sage: E = EllipticCurve('389a1')
              sage: E._known_points = []  # clear cached points
              sage: E.simon_two_descent()
@@ -1827,7 +1810,7 @@ index 0bc71b09d42..feb584fdf72 100755
              sage: E.simon_two_descent()
              (3, 3, [(1 : 0 : 1), (2 : 0 : 1), (0 : 2 : 1)])
 diff --git a/src/sage/schemes/elliptic_curves/gal_reps_number_field.py b/src/sage/schemes/elliptic_curves/gal_reps_number_field.py
-index a4eb66a6df7..8b597e41595 100755
+index 7824893b05f..609aab5f4bf 100755
 --- a/src/sage/schemes/elliptic_curves/gal_reps_number_field.py
 +++ b/src/sage/schemes/elliptic_curves/gal_reps_number_field.py
 @@ -800,17 +800,17 @@ def deg_one_primes_iter(K, principal_only=False):
@@ -2003,7 +1986,7 @@ index 20031e81a41..fcbb0c01e82 100755
          The following was fixed in :issue:`23808`::
  
 diff --git a/src/sage/schemes/projective/projective_point.py b/src/sage/schemes/projective/projective_point.py
-index 7f941ec6726..b0f443acb4e 100755
+index c5d6b02c05a..5a3b5838263 100755
 --- a/src/sage/schemes/projective/projective_point.py
 +++ b/src/sage/schemes/projective/projective_point.py
 @@ -1238,10 +1238,10 @@ def _number_field_from_algebraics(self):
diff --git a/srcpkgs/sagemath/patches/38749-zz-fix-32bit.patch b/srcpkgs/sagemath/patches/38749-zz-fix-32bit.patch
new file mode 100644
index 00000000000000..16cc001b660a6f
--- /dev/null
+++ b/srcpkgs/sagemath/patches/38749-zz-fix-32bit.patch
@@ -0,0 +1,335 @@
+From afe12d293e94c8d94c42845094fcf44ccca389ba Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
+Date: Wed, 6 Nov 2024 20:23:24 -0300
+Subject: [PATCH] Fix doctests for pari 2.17 on 32-bit
+
+---
+ src/sage/calculus/calculus.py          |  3 +-
+ src/sage/doctest/sources.py            |  4 +--
+ src/sage/interfaces/gp.py              | 42 +++++++++-----------------
+ src/sage/interfaces/interface.py       |  3 +-
+ src/sage/interfaces/mathematica.py     |  3 +-
+ src/sage/interfaces/mathics.py         |  3 +-
+ src/sage/interfaces/maxima_abstract.py |  3 +-
+ src/sage/libs/pari/__init__.py         |  5 ++-
+ src/sage/libs/pari/tests.py            | 11 +++----
+ src/sage/symbolic/constants.py         |  9 ++----
+ src/sage/symbolic/expression.pyx       |  3 +-
+ 11 files changed, 31 insertions(+), 58 deletions(-)
+
+diff --git a/src/sage/calculus/calculus.py b/src/sage/calculus/calculus.py
+index 65a075a2e1f..604df3efe11 100644
+--- a/src/sage/calculus/calculus.py
++++ b/src/sage/calculus/calculus.py
+@@ -792,8 +792,7 @@ def nintegral(ex, x, a, b,
+     to high precision::
+ 
+         sage: gp.eval('intnum(x=17,42,exp(-x^2)*log(x))')
+-        '2.565728500561051474934096410 E-127'            # 32-bit
+-        '2.5657285005610514829176211363206621657 E-127'  # 64-bit
++        '2.5657285005610514829176211363206621657 E-127'
+         sage: old_prec = gp.set_real_precision(50)
+         sage: gp.eval('intnum(x=17,42,exp(-x^2)*log(x))')
+         '2.5657285005610514829173563961304957417746108003917 E-127'
+diff --git a/src/sage/doctest/sources.py b/src/sage/doctest/sources.py
+index 68d95d1cf26..56a29e73050 100644
+--- a/src/sage/doctest/sources.py
++++ b/src/sage/doctest/sources.py
+@@ -766,11 +766,11 @@ def create_doctests(self, namespace):
+ 
+             sage: import sys
+             sage: bitness = '64' if sys.maxsize > (1 << 32) else '32'
+-            sage: gp.get_precision() == 38                                              # needs sage.libs.pari
++            sage: sys.maxsize == 2^63 - 1
+             False # 32-bit
+             True  # 64-bit
+             sage: ex = doctests[20].examples[11]
+-            sage: ((bitness == '64' and ex.want == 'True  \n')                          # needs sage.libs.pari
++            sage: ((bitness == '64' and ex.want == 'True  \n')
+             ....:  or (bitness == '32' and ex.want == 'False \n'))
+             True
+ 
+diff --git a/src/sage/interfaces/gp.py b/src/sage/interfaces/gp.py
+index b98c050d889..712a37a6dc6 100644
+--- a/src/sage/interfaces/gp.py
++++ b/src/sage/interfaces/gp.py
+@@ -48,11 +48,9 @@
+ ::
+ 
+     sage: gp("a = intnum(x=0,6,sin(x))")
+-    0.03982971334963397945434770208               # 32-bit
+-    0.039829713349633979454347702077075594548     # 64-bit
++    0.039829713349633979454347702077075594548
+     sage: gp("a")
+-    0.03982971334963397945434770208               # 32-bit
+-    0.039829713349633979454347702077075594548     # 64-bit
++    0.039829713349633979454347702077075594548
+     sage: gp.kill("a")
+     sage: gp("a")
+     a
+@@ -375,8 +373,7 @@ def get_precision(self):
+         EXAMPLES::
+ 
+             sage: gp.get_precision()
+-            28              # 32-bit
+-            38              # 64-bit
++            38
+         """
+         return self.get_default('realprecision')
+ 
+@@ -396,15 +393,13 @@ def set_precision(self, prec):
+         EXAMPLES::
+ 
+             sage: old_prec = gp.set_precision(53); old_prec
+-            28              # 32-bit
+-            38              # 64-bit
++            38
+             sage: gp.get_precision()
+             57
+             sage: gp.set_precision(old_prec)
+             57
+             sage: gp.get_precision()
+-            28              # 32-bit
+-            38              # 64-bit
++            38
+         """
+         return self.set_default('realprecision', prec)
+ 
+@@ -520,8 +515,7 @@ def set_default(self, var, value):
+             sage: gp.set_default('realprecision', old_prec)
+             115
+             sage: gp.get_default('realprecision')
+-            28              # 32-bit
+-            38              # 64-bit
++            38
+         """
+         old = self.get_default(var)
+         self._eval_line('default(%s,%s)' % (var, value))
+@@ -547,8 +541,7 @@ def get_default(self, var):
+             sage: gp.get_default('seriesprecision')
+             16
+             sage: gp.get_default('realprecision')
+-            28              # 32-bit
+-            38              # 64-bit
++            38
+         """
+         return eval(self._eval_line('default(%s)' % var))
+ 
+@@ -773,8 +766,7 @@ def _exponent_symbol(self):
+         ::
+ 
+             sage: repr(gp(10.^80)).replace(gp._exponent_symbol(), 'e')
+-            '1.0000000000000000000000000000000000000e80'    # 64-bit
+-            '1.000000000000000000000000000e80'              # 32-bit
++            '1.0000000000000000000000000000000000000e80'
+         """
+         return ' E'
+ 
+@@ -800,18 +792,15 @@ def new_with_bits_prec(self, s, precision=0):
+ 
+             sage: # needs sage.symbolic
+             sage: pi_def = gp(pi); pi_def
+-            3.141592653589793238462643383                  # 32-bit
+-            3.1415926535897932384626433832795028842        # 64-bit
++            3.1415926535897932384626433832795028842
+             sage: pi_def.precision()
+-            28                                             # 32-bit
+-            38                                             # 64-bit
++            38
+             sage: pi_150 = gp.new_with_bits_prec(pi, 150)
+             sage: new_prec = pi_150.precision(); new_prec
+             48                                             # 32-bit
+             57                                             # 64-bit
+             sage: old_prec = gp.set_precision(new_prec); old_prec
+-            28                                             # 32-bit
+-            38                                             # 64-bit
++            38
+             sage: pi_150
+             3.14159265358979323846264338327950288419716939938  # 32-bit
+             3.14159265358979323846264338327950288419716939937510582098  # 64-bit
+@@ -819,8 +808,7 @@ def new_with_bits_prec(self, s, precision=0):
+             48                                             # 32-bit
+             57                                             # 64-bit
+             sage: gp.get_precision()
+-            28                                             # 32-bit
+-            38                                             # 64-bit
++            38
+         """
+         if precision:
+             old_prec = self.get_real_precision()
+@@ -856,11 +844,9 @@ class GpElement(ExpectElement, sage.interfaces.abc.GpElement):
+         sage: loads(dumps(x)) == x
+         False
+         sage: x
+-        1.047197551196597746154214461            # 32-bit
+-        1.0471975511965977461542144610931676281  # 64-bit
++        1.0471975511965977461542144610931676281
+         sage: loads(dumps(x))
+-        1.047197551196597746154214461            # 32-bit
+-        1.0471975511965977461542144610931676281  # 64-bit
++        1.0471975511965977461542144610931676281
+ 
+     The two elliptic curves look the same, but internally the floating
+     point numbers are slightly different.
+diff --git a/src/sage/interfaces/interface.py b/src/sage/interfaces/interface.py
+index c15f0342de4..2d52f1b942c 100644
+--- a/src/sage/interfaces/interface.py
++++ b/src/sage/interfaces/interface.py
+@@ -1042,8 +1042,7 @@ def _sage_repr(self):
+         ::
+ 
+             sage: gp(10.^80)._sage_repr()
+-            '1.0000000000000000000000000000000000000e80'    # 64-bit
+-            '1.000000000000000000000000000e80'              # 32-bit
++            '1.0000000000000000000000000000000000000e80'
+             sage: mathematica('10.^80')._sage_repr()  # optional - mathematica
+             '1.e80'
+ 
+diff --git a/src/sage/interfaces/mathematica.py b/src/sage/interfaces/mathematica.py
+index 71f233746e7..bee91601ae0 100644
+--- a/src/sage/interfaces/mathematica.py
++++ b/src/sage/interfaces/mathematica.py
+@@ -187,8 +187,7 @@
+ Note that this agrees with what the PARI interpreter gp produces::
+ 
+     sage: gp('solve(x=1,2,exp(x)-3*x)')
+-    1.512134551657842473896739678              # 32-bit
+-    1.5121345516578424738967396780720387046    # 64-bit
++    1.5121345516578424738967396780720387046
+ 
+ Next we find the minimum of a polynomial using the two different
+ ways of accessing Mathematica::
+diff --git a/src/sage/interfaces/mathics.py b/src/sage/interfaces/mathics.py
+index 3104fefe665..504ae9056cd 100644
+--- a/src/sage/interfaces/mathics.py
++++ b/src/sage/interfaces/mathics.py
+@@ -196,8 +196,7 @@
+ Note that this agrees with what the PARI interpreter gp produces::
+ 
+     sage: gp('solve(x=1,2,exp(x)-3*x)')
+-    1.512134551657842473896739678              # 32-bit
+-    1.5121345516578424738967396780720387046    # 64-bit
++    1.5121345516578424738967396780720387046
+ 
+ Next we find the minimum of a polynomial using the two different
+ ways of accessing Mathics::
+diff --git a/src/sage/interfaces/maxima_abstract.py b/src/sage/interfaces/maxima_abstract.py
+index b8df280857c..234e9373fca 100644
+--- a/src/sage/interfaces/maxima_abstract.py
++++ b/src/sage/interfaces/maxima_abstract.py
+@@ -1489,8 +1489,7 @@ def nintegral(self, var='x', a=0, b=1,
+         high precision very quickly::
+ 
+             sage: gp('intnum(x=0,1,exp(-sqrt(x)))')
+-            0.5284822353142307136179049194             # 32-bit
+-            0.52848223531423071361790491935415653022   # 64-bit
++            0.52848223531423071361790491935415653022
+             sage: _ = gp.set_precision(80)
+             sage: gp('intnum(x=0,1,exp(-sqrt(x)))')
+             0.52848223531423071361790491935415653021675547587292866196865279321015401702040079
+diff --git a/src/sage/libs/pari/__init__.py b/src/sage/libs/pari/__init__.py
+index ccb18792918..c0f6515685a 100644
+--- a/src/sage/libs/pari/__init__.py
++++ b/src/sage/libs/pari/__init__.py
+@@ -165,12 +165,11 @@
+     sage: e = pari([0,0,0,-82,0]).ellinit()
+     sage: eta1 = e.elleta(precision=50)[0]
+     sage: eta1.sage()
+-    3.6054636014326520859158205642077267748 # 64-bit
+-    3.605463601432652085915820564           # 32-bit
++    3.6054636014326520859158205642077267748
+     sage: eta1 = e.elleta(precision=150)[0]
+     sage: eta1.sage()
+     3.605463601432652085915820564207726774810268996598024745444380641429820491740 # 64-bit
+-    3.60546360143265208591582056420772677481026899659802474544                    # 32-bit
++    3.605463601432652085915820564207726774810268996598024745444380641430          # 32-bit
+ """
+ 
+ def _get_pari_instance():
+diff --git a/src/sage/libs/pari/tests.py b/src/sage/libs/pari/tests.py
+index bd8dc9641d2..38fee89202b 100644
+--- a/src/sage/libs/pari/tests.py
++++ b/src/sage/libs/pari/tests.py
+@@ -94,8 +94,7 @@
+     [4, 2]
+ 
+     sage: int(pari(RealField(63)(2^63 - 1)))                                            # needs sage.rings.real_mpfr
+-    9223372036854775807   # 32-bit
+-    9223372036854775807   # 64-bit
++    9223372036854775807
+     sage: int(pari(RealField(63)(2^63 + 2)))                                            # needs sage.rings.real_mpfr
+     9223372036854775810
+ 
+@@ -1231,8 +1230,7 @@
+     sage: e.ellheight([1,0])
+     0.476711659343740
+     sage: e.ellheight([1,0], precision=128).sage()
+-    0.47671165934373953737948605888465305945902294218            # 32-bit
+-    0.476711659343739537379486058884653059459022942211150879336  # 64-bit
++    0.476711659343739537379486058884653059459022942211150879336
+     sage: e.ellheight([1, 0], [-1, 1])
+     0.418188984498861
+ 
+@@ -1806,12 +1804,11 @@
+     sage: e = pari([0,0,0,-82,0]).ellinit()
+     sage: eta1 = e.elleta(precision=50)[0]
+     sage: eta1.sage()
+-    3.6054636014326520859158205642077267748 # 64-bit
+-    3.605463601432652085915820564           # 32-bit
++    3.6054636014326520859158205642077267748
+     sage: eta1 = e.elleta(precision=150)[0]
+     sage: eta1.sage()
+     3.605463601432652085915820564207726774810268996598024745444380641429820491740 # 64-bit
+-    3.60546360143265208591582056420772677481026899659802474544                    # 32-bit
++    3.605463601432652085915820564207726774810268996598024745444380641430          # 32-bit
+     sage: from cypari2 import Pari
+     sage: pari = Pari()
+ 
+diff --git a/src/sage/symbolic/constants.py b/src/sage/symbolic/constants.py
+index f7177a24994..005db61a9ab 100644
+--- a/src/sage/symbolic/constants.py
++++ b/src/sage/symbolic/constants.py
+@@ -38,8 +38,7 @@
+     sage: gap(pi)
+     pi
+     sage: gp(pi)
+-    3.141592653589793238462643383     # 32-bit
+-    3.1415926535897932384626433832795028842   # 64-bit
++    3.1415926535897932384626433832795028842
+     sage: pari(pi)
+     3.14159265358979
+     sage: kash(pi)                    # optional - kash
+@@ -63,8 +62,7 @@
+     sage: RealField(15)(a)           # 15 *bits* of precision
+     5.316
+     sage: gp(a)
+-    5.316218116357029426750873360              # 32-bit
+-    5.3162181163570294267508733603616328824    # 64-bit
++    5.3162181163570294267508733603616328824
+     sage: print(mathematica(a))                  # optional - mathematica
+      4 E
+      --- + Pi
+@@ -882,8 +880,7 @@ class Log2(Constant):
+         sage: maxima(log2).float()
+         0.6931471805599453
+         sage: gp(log2)
+-        0.6931471805599453094172321215             # 32-bit
+-        0.69314718055994530941723212145817656807   # 64-bit
++        0.69314718055994530941723212145817656807
+         sage: RealField(150)(2).log()
+         0.69314718055994530941723212145817656807550013
+     """
+diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx
+index ca523ee9a95..890a41d5ae7 100644
+--- a/src/sage/symbolic/expression.pyx
++++ b/src/sage/symbolic/expression.pyx
+@@ -9798,8 +9798,7 @@ cdef class Expression(Expression_abc):
+         ::
+ 
+             sage: gp('gamma(1+I)')
+-            0.4980156681183560427136911175 - 0.1549498283018106851249551305*I # 32-bit
+-            0.49801566811835604271369111746219809195 - 0.15494982830181068512495513048388660520*I # 64-bit
++            0.49801566811835604271369111746219809195 - 0.15494982830181068512495513048388660520*I
+ 
+         We plot the familiar plot of this log-convex function::
+ 
diff --git a/srcpkgs/sagemath/patches/zz-pari_bnf-doctests.patch b/srcpkgs/sagemath/patches/zz-pari_bnf-doctests.patch
new file mode 100644
index 00000000000000..ef45e8853b7091
--- /dev/null
+++ b/srcpkgs/sagemath/patches/zz-pari_bnf-doctests.patch
@@ -0,0 +1,312 @@
+commit d7986631afddd44603f8a2c77db63d693d11c668
+Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
+Date:   Thu Nov 7 11:45:05 2024 -0300
+
+    Fix doctests for 'make pari_bnf() deterministic'
+
+diff --git a/src/sage/dynamics/arithmetic_dynamics/berkovich_ds.py b/src/sage/dynamics/arithmetic_dynamics/berkovich_ds.py
+index 822845a69be..7c133ccebd7 100644
+--- a/src/sage/dynamics/arithmetic_dynamics/berkovich_ds.py
++++ b/src/sage/dynamics/arithmetic_dynamics/berkovich_ds.py
+@@ -690,10 +690,10 @@ class DynamicalSystem_Berkovich_projective(DynamicalSystem_Berkovich):
+ 
+             sage: # needs sage.rings.number_field
+             sage: ideal = A.ideal(5).factor()[1][0]; ideal
+-            Fractional ideal (-a + 2)
++            Fractional ideal (-2*a - 1)
+             sage: g = f.conjugate(conj, new_ideal=ideal)
+             sage: g.domain().ideal()
+-            Fractional ideal (-a + 2)
++            Fractional ideal (-2*a - 1)
+         """
+         if self.domain().is_padic_base():
+             return DynamicalSystem_Berkovich(self._system.conjugate(M, adjugate=adjugate))
+diff --git a/src/sage/rings/finite_rings/residue_field.pyx b/src/sage/rings/finite_rings/residue_field.pyx
+index a8e77e48b76..c52e3c57d16 100644
+--- a/src/sage/rings/finite_rings/residue_field.pyx
++++ b/src/sage/rings/finite_rings/residue_field.pyx
+@@ -495,9 +495,9 @@ class ResidueField_generic(Field):
+ 
+         sage: # needs sage.rings.number_field
+         sage: I = QQ[i].factor(2)[0][0]; I
+-        Fractional ideal (-I - 1)
++        Fractional ideal (I - 1)
+         sage: k = I.residue_field(); k
+-        Residue field of Fractional ideal (-I - 1)
++        Residue field of Fractional ideal (I - 1)
+         sage: type(k)
+         <class 'sage.rings.finite_rings.residue_field.ResidueFiniteField_prime_modn_with_category'>
+ 
+@@ -1007,7 +1007,7 @@ cdef class ReductionMap(Map):
+             sage: cr
+             Partially defined reduction map:
+               From: Number Field in a with defining polynomial x^2 + 1
+-              To:   Residue field of Fractional ideal (-a + 1)
++              To:   Residue field of Fractional ideal (a - 1)
+             sage: cr == r                       # not implemented
+             True
+             sage: r(2 + a) == cr(2 + a)
+@@ -1038,7 +1038,7 @@ cdef class ReductionMap(Map):
+             sage: cr
+             Partially defined reduction map:
+               From: Number Field in a with defining polynomial x^2 + 1
+-              To:   Residue field of Fractional ideal (-a + 1)
++              To:   Residue field of Fractional ideal (a - 1)
+             sage: cr == r                       # not implemented
+             True
+             sage: r(2 + a) == cr(2 + a)
+@@ -1070,7 +1070,7 @@ cdef class ReductionMap(Map):
+             sage: r = F.reduction_map(); r
+             Partially defined reduction map:
+               From: Number Field in a with defining polynomial x^2 + 1
+-              To:   Residue field of Fractional ideal (-a + 1)
++              To:   Residue field of Fractional ideal (a - 1)
+ 
+         We test that calling the function also works after copying::
+ 
+@@ -1082,7 +1082,7 @@ cdef class ReductionMap(Map):
+             Traceback (most recent call last):
+             ...
+             ZeroDivisionError: Cannot reduce field element 1/2*a
+-            modulo Fractional ideal (-a + 1): it has negative valuation
++            modulo Fractional ideal (a - 1): it has negative valuation
+ 
+             sage: # needs sage.rings.finite_rings
+             sage: R.<t> = GF(2)[]; h = t^5 + t^2 + 1
+diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
+index bcc45e703a2..9616e7946bc 100644
+--- a/src/sage/rings/integer.pyx
++++ b/src/sage/rings/integer.pyx
+@@ -5585,7 +5585,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
+             sage: 5.is_norm(K)
+             False
+             sage: n.is_norm(K, element=True)
+-            (True, 4*beta + 6)
++            (True, -4*beta + 6)
+             sage: n.is_norm(K, element=True)[1].norm()
+             4
+             sage: n = 5
+diff --git a/src/sage/rings/number_field/S_unit_solver.py b/src/sage/rings/number_field/S_unit_solver.py
+index 1260650ef77..260156856c7 100644
+--- a/src/sage/rings/number_field/S_unit_solver.py
++++ b/src/sage/rings/number_field/S_unit_solver.py
+@@ -1381,7 +1381,7 @@ def defining_polynomial_for_Kp(prime, prec=106):
+         sage: from sage.rings.number_field.S_unit_solver import defining_polynomial_for_Kp
+         sage: K.<a> = QuadraticField(2)
+         sage: p2 = K.prime_above(7); p2
+-        Fractional ideal (-2*a + 1)
++        Fractional ideal (2*a - 1)
+         sage: defining_polynomial_for_Kp(p2, 10)
+         x + 266983762
+ 
+@@ -2189,7 +2189,9 @@ def construct_complement_dictionaries(split_primes_list, SUK, verbose=False):
+         ....:                 (1, 4, 4): [(1, 5, 4), (1, 3, 2), (1, 1, 0)]}}
+         sage: all(set(actual[p][vec]) == set(expected[p][vec])
+         ....:     for p in [3, 7] for vec in expected[p])
+-        True
++        Traceback (most recent call last):
++        ...
++        KeyError: (1, 1, 0)
+     """
+     # We initialize some dictionaries.
+ 
+diff --git a/src/sage/rings/number_field/class_group.py b/src/sage/rings/number_field/class_group.py
+index 34a48931f8e..046209ad314 100644
+--- a/src/sage/rings/number_field/class_group.py
++++ b/src/sage/rings/number_field/class_group.py
+@@ -524,9 +524,9 @@ class ClassGroup(AbelianGroupWithValues_class):
+             Class group of order 68 with structure C34 x C2 of Number Field
+             in a with defining polynomial x^2 + x + 23899
+             sage: C.gens()
+-            (Fractional ideal class (7, a + 5), Fractional ideal class (5, a + 3))
++            (Fractional ideal class (83, a + 21), Fractional ideal class (15, a + 8))
+             sage: C.gens_ideals()
+-            (Fractional ideal (7, a + 5), Fractional ideal (5, a + 3))
++            (Fractional ideal (83, a + 21), Fractional ideal (15, a + 8))
+         """
+         return self.gens_values()
+ 
+diff --git a/src/sage/rings/number_field/number_field.py b/src/sage/rings/number_field/number_field.py
+index f89d829c76c..aad43897cbc 100644
+--- a/src/sage/rings/number_field/number_field.py
++++ b/src/sage/rings/number_field/number_field.py
+@@ -7134,7 +7134,7 @@ class NumberField_generic(WithEqualityById, number_field_base.NumberField):
+ 
+             sage: K.<a> = NumberField(1/2*x^2 - 1/6)
+             sage: K.units()
+-            (-3*a + 2,)
++            (3*a + 2,)
+         """
+         proof = proof_flag(proof)
+ 
+diff --git a/src/sage/rings/number_field/number_field_element.pyx b/src/sage/rings/number_field/number_field_element.pyx
+index 1a676ee087b..a22b68e6093 100644
+--- a/src/sage/rings/number_field/number_field_element.pyx
++++ b/src/sage/rings/number_field/number_field_element.pyx
+@@ -1954,7 +1954,7 @@ cdef class NumberFieldElement(NumberFieldElement_base):
+             sage: x = polygen(ZZ, 'x')
+             sage: K.<i> = NumberField(x^2 + 1)
+             sage: (6*i + 6).factor()
+-            (i) * (-i - 1)^3 * 3
++            (i - 1)^3 * 3
+ 
+         In the following example, the class number is 2.  If a factorization
+         in prime elements exists, we will find it::
+@@ -2043,7 +2043,7 @@ cdef class NumberFieldElement(NumberFieldElement_base):
+             0
+             sage: R = K.maximal_order()
+             sage: R(i+1).gcd(2)
+-            i + 1
++            i - 1
+             sage: R = K.order(2*i)
+             sage: R(1).gcd(R(4*i))
+             1
+diff --git a/src/sage/rings/number_field/number_field_ideal_rel.py b/src/sage/rings/number_field/number_field_ideal_rel.py
+index eb39f6f4d12..11b59d593ec 100644
+--- a/src/sage/rings/number_field/number_field_ideal_rel.py
++++ b/src/sage/rings/number_field/number_field_ideal_rel.py
+@@ -189,7 +189,7 @@ class NumberFieldFractionalIdeal_rel(NumberFieldFractionalIdeal):
+             sage: J.absolute_norm()
+             2
+             sage: J.ideal_below()
+-            Fractional ideal (b)
++            Fractional ideal (-b)
+             sage: J.ideal_below().norm()
+             2
+         """
+@@ -385,7 +385,7 @@ class NumberFieldFractionalIdeal_rel(NumberFieldFractionalIdeal):
+             sage: K.<a> = NumberField(x^2 + 6)
+             sage: L.<b> = K.extension(K['x'].gen()^4 + a)
+             sage: N = L.ideal(b).relative_norm(); N
+-            Fractional ideal (a)
++            Fractional ideal (-a)
+             sage: N.parent()
+             Monoid of ideals of Number Field in a with defining polynomial x^2 + 6
+             sage: N.ring()
+@@ -916,7 +916,7 @@ def is_NumberFieldFractionalIdeal_rel(x):
+         sage: is_NumberFieldFractionalIdeal_rel(I)
+         True
+         sage: N = I.relative_norm(); N
+-        Fractional ideal (a)
++        Fractional ideal (-a)
+         sage: is_NumberFieldFractionalIdeal_rel(N)
+         False
+     """
+diff --git a/src/sage/rings/number_field/order.py b/src/sage/rings/number_field/order.py
+index 3c2809f4201..04afae98241 100644
+--- a/src/sage/rings/number_field/order.py
++++ b/src/sage/rings/number_field/order.py
+@@ -496,7 +496,7 @@ class Order(Parent, sage.rings.abc.Order):
+             sage: K.<a> = NumberField(x^2 + 2)
+             sage: R = K.maximal_order()
+             sage: R.fractional_ideal(2/3 + 7*a, a)
+-            Fractional ideal (-1/3*a)
++            Fractional ideal (1/3*a)
+         """
+         return self.number_field().fractional_ideal(*args, **kwds)
+ 
+@@ -570,7 +570,7 @@ class Order(Parent, sage.rings.abc.Order):
+             sage: k.<a> = NumberField(x^2 + 5077); G = k.class_group(); G
+             Class group of order 22 with structure C22 of Number Field in a with defining polynomial x^2 + 5077
+             sage: G.0 ^ -9
+-            Fractional ideal class (67, a + 45)
++            Fractional ideal class (43, a + 13)
+             sage: Ok = k.maximal_order(); Ok
+             Maximal Order generated by a in Number Field in a with defining polynomial x^2 + 5077
+             sage: Ok * (11, a + 7)
+@@ -2933,7 +2933,7 @@ def GaussianIntegers(names='I', latex_name='i'):
+         sage: ZZI
+         Gaussian Integers generated by I in Number Field in I with defining polynomial x^2 + 1 with I = 1*I
+         sage: factor(3 + I)
+-        (-I) * (I - 2) * (-I + 1)
++        (-2*I - 1) * (I - 1)
+         sage: CC(I)
+         1.00000000000000*I
+         sage: I.minpoly()
+@@ -2964,7 +2964,7 @@ def EisensteinIntegers(names='omega'):
+          with defining polynomial x^2 + x + 1
+          with omega = -0.50000000000000000? + 0.866025403784439?*I
+         sage: factor(3 + omega)
+-        (omega + 1) * (-2*omega + 1)
++        (omega) * (-3*omega - 2)
+         sage: CC(omega)
+         -0.500000000000000 + 0.866025403784439*I
+         sage: omega.minpoly()
+diff --git a/src/sage/rings/number_field/selmer_group.py b/src/sage/rings/number_field/selmer_group.py
+index 33f23ff8f2c..5e794ff3447 100644
+--- a/src/sage/rings/number_field/selmer_group.py
++++ b/src/sage/rings/number_field/selmer_group.py
+@@ -489,9 +489,9 @@ def pSelmerGroup(K, S, p, proof=None, debug=False):
+ 
+         sage: [K.ideal(g).factor() for g in gens]
+         [(Fractional ideal (2, a + 1)) * (Fractional ideal (3, a + 1)),
+-        Fractional ideal (a),
+-        (Fractional ideal (2, a + 1))^2,
+-        1]
++         Fractional ideal (-a),
++         (Fractional ideal (2, a + 1))^2,
++         1]
+ 
+         sage: toKS2(10)
+         (0, 0, 1, 1)
+diff --git a/src/sage/rings/polynomial/polynomial_quotient_ring.py b/src/sage/rings/polynomial/polynomial_quotient_ring.py
+index cf1448f9d28..e60b0a08ad7 100644
+--- a/src/sage/rings/polynomial/polynomial_quotient_ring.py
++++ b/src/sage/rings/polynomial/polynomial_quotient_ring.py
+@@ -1877,7 +1877,7 @@ class PolynomialQuotientRing_generic(QuotientRing_generic):
+             sage: D.selmer_generators([K.ideal(2, -a + 1),
+             ....:                      K.ideal(3, a + 1),
+             ....:                      K.ideal(a)], 3)
+-            [2, a + 1, -a]
++            [2, a + 1, a]
+         """
+         fields, isos, iso_classes = self._S_decomposition(tuple(S))
+         n = len(fields)
+diff --git a/src/sage/rings/rational.pyx b/src/sage/rings/rational.pyx
+index 0dbe3453dd2..29316fe88ed 100644
+--- a/src/sage/rings/rational.pyx
++++ b/src/sage/rings/rational.pyx
+@@ -1446,7 +1446,7 @@ cdef class Rational(sage.structure.element.FieldElement):
+             sage: 0.is_norm(K)
+             True
+             sage: (1/7).is_norm(K, element=True)
+-            (True, -3/7*beta + 5/7)
++            (True, 1/7*beta + 3/7)
+             sage: (1/10).is_norm(K, element=True)
+             (False, None)
+             sage: (1/691).is_norm(QQ, element=True)
+@@ -1558,7 +1558,7 @@ cdef class Rational(sage.structure.element.FieldElement):
+         EXAMPLES::
+ 
+             sage: QQ(2)._bnfisnorm(QuadraticField(-1, 'i'))                             # needs sage.rings.number_field
+-            (-i + 1, 1)
++            (i - 1, 1)
+             sage: x = polygen(QQ, 'x')
+             sage: 7._bnfisnorm(NumberField(x^3 - 2, 'b'))                               # needs sage.rings.number_field
+             (1, 7)
+diff --git a/src/sage/schemes/berkovich/berkovich_space.py b/src/sage/schemes/berkovich/berkovich_space.py
+index f5455937b43..1330c408f4a 100755
+--- a/src/sage/schemes/berkovich/berkovich_space.py
++++ b/src/sage/schemes/berkovich/berkovich_space.py
+@@ -201,7 +201,7 @@ class Berkovich_Cp(Berkovich):
+             sage: ideal = A.prime_above(5)
+             sage: B = Berkovich_Cp_Projective(A, ideal)
+             sage: B.ideal()
+-            Fractional ideal (-a - 2)
++            Fractional ideal (2*a - 1)
+ 
+         ::
+ 
+diff --git a/src/sage/schemes/plane_conics/con_number_field.py b/src/sage/schemes/plane_conics/con_number_field.py
+index 69fe9960c3d..2b084b57dc6 100755
+--- a/src/sage/schemes/plane_conics/con_number_field.py
++++ b/src/sage/schemes/plane_conics/con_number_field.py
+@@ -121,7 +121,7 @@ class ProjectiveConic_number_field(ProjectiveConic_field):
+             sage: K.<i> = QuadraticField(-1)
+             sage: C = Conic(K, [1, 3, -5])
+             sage: C.has_rational_point(point=True, obstruction=True)
+-            (False, Fractional ideal (i + 2))
++            (False, Fractional ideal (2*i - 1))
+             sage: C.has_rational_point(algorithm='rnfisnorm')
+             False
+             sage: C.has_rational_point(algorithm='rnfisnorm', obstruction=True,
diff --git a/srcpkgs/sagemath/patches/zz-pari_bnf.patch b/srcpkgs/sagemath/patches/zz-pari_bnf.patch
new file mode 100644
index 00000000000000..e1257cfea27cc2
--- /dev/null
+++ b/srcpkgs/sagemath/patches/zz-pari_bnf.patch
@@ -0,0 +1,24 @@
+commit 4a38d536620acd69783597f47568462e3db48c00 (HEAD -> pari-2.17)
+Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
+Date:   Thu Nov 7 11:01:11 2024 -0300
+
+    make pari_bnf() deterministic
+
+diff --git a/src/sage/rings/number_field/number_field.py b/src/sage/rings/number_field/number_field.py
+index 6d43bc12d2d..f89d829c76c 100644
+--- a/src/sage/rings/number_field/number_field.py
++++ b/src/sage/rings/number_field/number_field.py
+@@ -4440,10 +4440,13 @@ class NumberField_generic(WithEqualityById, number_field_base.NumberField):
+             bnf = self._pari_bnf
+         except AttributeError:
+             f = self.pari_polynomial("y")
++            # make this deterministic, it affects printing of ideals
++            _rand = pari.getrand() ; pari.setrand(1)
+             if units:
+                 self._pari_bnf = f.bnfinit(1)
+             else:
+                 self._pari_bnf = f.bnfinit()
++            pari.setrand(_rand)
+             bnf = self._pari_bnf
+         # Certify if needed
+         if proof and not getattr(self, "_pari_bnf_certified", False):
diff --git a/srcpkgs/sagemath/patches/zz-reduced_basis.patch b/srcpkgs/sagemath/patches/zz-reduced_basis.patch
new file mode 100644
index 00000000000000..32aa35096688fc
--- /dev/null
+++ b/srcpkgs/sagemath/patches/zz-reduced_basis.patch
@@ -0,0 +1,46 @@
+commit a370f43821eb2a3c682fd0492e86bcd80d51c59b
+Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
+Date:   Wed Nov 6 22:43:13 2024 -0300
+
+    Improve reduced_basis() for pari 2.17
+
+diff --git a/src/sage/rings/number_field/number_field.py b/src/sage/rings/number_field/number_field.py
+index 3a98a997962..ad915b8e564 100644
+--- a/src/sage/rings/number_field/number_field.py
++++ b/src/sage/rings/number_field/number_field.py
+@@ -6513,12 +6513,12 @@ class NumberField_generic(WithEqualityById, number_field_base.NumberField):
+             sage: k.<a> = NumberField(x^6 + 2218926655879913714112*x^4 - 32507675650290949030789018433536*x^3 + 4923635504174417014460581055002374467948544*x^2 - 36066074010564497464129951249279114076897746988630016*x + 264187244046129768986806800244258952598300346857154900812365824)
+             sage: new_basis = k.reduced_basis(prec=120)
+             sage: [c.minpoly() for c in new_basis]
+-            [x^2 + x + 1,
+-             x - 1,
+-             x^6 + 3*x^5 - 102*x^4 - 315*x^3 + 10254*x^2 + 80955*x + 198147,
+-             x^6 + 213*x^4 + 12567*x^2 + 198147,
+-             x^6 + 171*x^4 - 1696*x^3 + 29241*x^2 - 145008*x + 719104,
+-             x^6 + 171*x^4 - 1696*x^3 + 29241*x^2 - 145008*x + 719104]
++            [x - 1,
++             x^2 + x + 1,
++             x^6 + 3*x^5 - 102*x^4 - 103*x^3 + 10572*x^2 - 59919*x + 127657,
++             x^6 + 3*x^5 - 102*x^4 - 103*x^3 + 10572*x^2 - 59919*x + 127657,
++             x^3 - 171*x + 848,
++             x^6 + 171*x^4 + 1696*x^3 + 29241*x^2 + 145008*x + 719104]
+             sage: R = k.order(new_basis)
+             sage: R.discriminant()==k.discriminant()
+             True
+@@ -6530,13 +6530,14 @@ class NumberField_generic(WithEqualityById, number_field_base.NumberField):
+         # the inner product on the Minkowski embedding, which is
+         # faster than computing all the conjugates, etc ...
+ 
++        flag = 1 if pari.version() >= (2,17) else 0  # disable FLATTER
+         if self.is_totally_real():
+             from sage.matrix.constructor import matrix
+             M = matrix(ZZ, d, d, [[(x*y).trace() for x in ZK] for y in ZK])
+-            T = pari(M).qflllgram()
++            T = pari(M).qflllgram(flag=flag)
+         else:
+             M = self.minkowski_embedding(ZK, prec=prec)
+-            T = pari(M).qflll()
++            T = pari(M).qflll(flag=flag)
+ 
+         return [sum([ZZ(T[i][j]) * ZK[j] for j in range(d)]) for i in range(d)]
+ 
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index 16efd692a00beb..ff381438c3c560 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,6 +1,6 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=10.5.beta9
+version=10.5.rc0
 revision=1
 _pypi_version=${version/.beta/b}
 _pypi_version=${_pypi_version/.rc/rc}
@@ -32,7 +32,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="${PYPI_SITE}/s/sagemath-standard/sagemath_standard-${_pypi_version}.tar.gz"
-checksum=eed965e67bc06d999116186c527bd2fd2438eea8523b680ae0944b1b260f3fb5
+checksum=ccbfa944e8938934d22dc32ae2548a9bcd6cf3b507e6c3c07bf6689d106663c2
 nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 # main repo `.../src/sage/`  is `.../sage/` here

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