From: tornaria <tornaria@users.noreply.github.com>
To: ml@inbox.vuxu.org
Subject: Re: [PR PATCH] [Updated] [BETA] sagemath: update to 10.5.beta7
Date: Tue, 29 Oct 2024 01:41:01 +0100 [thread overview]
Message-ID: <20241029004101.5943F307A2@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.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
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#### 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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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
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A patch file from https://github.com/void-linux/void-packages/pull/51902.patch is attached
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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
next prev parent reply other threads:[~2024-10-29 0:41 UTC|newest]
Thread overview: 13+ messages / expand[flat|nested] mbox.gz Atom feed top
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
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 ` tornaria [this message]
2024-11-18 2:52 ` [PR PATCH] [Updated] [BETA] sagemath: update to 10.5.beta8 tornaria
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