From: tornaria <tornaria@users.noreply.github.com>
To: ml@inbox.vuxu.org
Subject: Re: [PR PATCH] [Updated] [BETA] sagemath: update to 10.5.beta2
Date: Sat, 24 Aug 2024 06:03:35 +0200 [thread overview]
Message-ID: <20240824040335.4BF672D0B1@inbox.vuxu.org> (raw)
In-Reply-To: <gh-mailinglist-notifications-41a7ca26-5023-4802-975b-f1789d68868e-void-packages-51902@inbox.vuxu.org>
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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.
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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
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[-- Attachment #2: github-pr-sagemath-51902.patch --]
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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
next prev parent reply other threads:[~2024-08-24 4:03 UTC|newest]
Thread overview: 13+ messages / expand[flat|nested] mbox.gz Atom feed top
2024-08-18 17:54 [PR PATCH] " 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 [this message]
2024-09-08 16:10 ` tornaria
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
2024-09-22 12:01 ` [PR PATCH] [Updated] " tornaria
2024-10-15 19:18 ` [PR PATCH] [Updated] [BETA] sagemath: update to 10.5.beta5 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
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