New package: sagemath-9.5

srcpkgs/sagemath/patches/01-dont_link_ratpoints.patch

@@ -0,0 +1,10 @@
+ - do not link ratpoints where it's not used
+
+--- a/src/sage/schemes/elliptic_curves/descent_two_isogeny.pyx
++++ b/src/sage/schemes/elliptic_curves/descent_two_isogeny.pyx
+@@ -1,5 +1,3 @@
+-# distutils: libraries = ratpoints
+-
+ r"""
+ Descent on elliptic curves over `\QQ` with a 2-isogeny
+ """

srcpkgs/sagemath/patches/02-fix_get_shared_lib_path--see_29644.patch

@@ -0,0 +1,13 @@
+ - fix _get_shared_lib_path() so we don't need to configure GAP_SO
+
+--- a/src/sage/env.py
++++ b/src/sage/env.py
+@@ -293,7 +293,7 @@ def _get_shared_lib_path(*libnames: str) -> Optional[str]:
+             if sys.platform == 'darwin':
+                 ext = 'dylib'
+             else:
+-                ext = 'so'
++                ext = 'so*'
+
+             if SAGE_LOCAL:
+                 search_directories.append(Path(SAGE_LOCAL) / 'lib')

srcpkgs/sagemath/patches/03-doctest_have_program.patch

@@ -0,0 +1,20 @@
+ - we don't know `SAGE_VENV/bin` contains `sage`, but `sys.argv[0]` should
+   be the full path to `sage-ipython` and the same directory should have `sage`
+
+--- a/src/sage/misc/sage_ostools.pyx
++++ b/src/sage/misc/sage_ostools.pyx
+@@ -32,12 +32,11 @@ def have_program(program, path=None):
+         True
+         sage: have_program('there_is_not_a_program_with_this_name')
+         False
+-        sage: from sage.env import SAGE_VENV
+-        sage: have_program('sage', os.path.join(SAGE_VENV, 'bin'))
++        sage: have_program('sage', os.path.dirname(sys.argv[0]))
+         True
+         sage: have_program('sage', '/there_is_not_a_path_with_this_name')
+         False
+-        sage: have_program('there_is_not_a_program_with_this_name', os.path.join(SAGE_VENV, 'bin'))
++        sage: have_program('there_is_not_a_program_with_this_name', "/bin")
+         False
+     """
+     if path is None:

srcpkgs/sagemath/patches/04-doctest_sage_getfile.patch

@@ -0,0 +1,22 @@
+ - add one doctest for coverage
+
+--- a/src/sage/misc/sageinspect.py
++++ b/src/sage/misc/sageinspect.py
+@@ -1341,10 +1342,12 @@ def sage_getfile(obj):
+     EXAMPLES::
+
+         sage: from sage.misc.sageinspect import sage_getfile
+-        sage: sage_getfile(sage.rings.rational)[-23:]
+-        'sage/rings/rational.pyx'
+-        sage: sage_getfile(Sq)[-42:]
+-        'sage/algebras/steenrod/steenrod_algebra.py'
++        sage: sage_getfile(sage.rings.rational)
++        '...sage/rings/rational.pyx'
++        sage: sage_getfile(Sq)
++        '...sage/algebras/steenrod/steenrod_algebra.py'
++        sage: sage_getfile(x)
++        '...sage/symbolic/expression.pyx'
+
+     The following tests against some bugs fixed in :trac:`9976`::
+
+

srcpkgs/sagemath/patches/05-fix_sage_getfile.patch

@@ -0,0 +1,16 @@
+ - fix sage_getfile() by checking all possible EXTENSION_SUFFIXES
+
+--- a/src/sage/misc/sageinspect.py
++++ b/src/sage/misc/sageinspect.py
+@@ -1400,8 +1403,9 @@ def sage_getfile(obj):
+         sourcefile = inspect.getabsfile(obj)
+     except TypeError: # this happens for Python builtins
+         return ''
+-    if sourcefile.endswith(loadable_module_extension()):
+-        return sourcefile[:-len(loadable_module_extension())]+os.path.extsep+'pyx'
++    for suffix in import_machinery.EXTENSION_SUFFIXES:
++        if sourcefile.endswith(suffix):
++            return sourcefile[:-len(suffix)]+os.path.extsep+'pyx'
+     return sourcefile
+
+

srcpkgs/sagemath/patches/07-ignore_warning.patch

@@ -0,0 +1,15 @@
+ - this ignores a warning caused by old notebook
+
+--- a/src/sage/all.py
++++ b/src/sage/all.py
+@@ -100,6 +100,9 @@ warnings.filterwarnings('ignore', category=DeprecationWarning,
+                         message='The distutils(.sysconfig module| package) is deprecated',
+                         module='Cython|distutils|numpy|sage.env|sage.features')
+
++warnings.filterwarnings('ignore', category=DeprecationWarning,
++                        message=r"invalid escape sequence '\\s'")
++
+ ################ end setup warnings ###############################
+
+
+

srcpkgs/sagemath/patches/08-dont_run_pytest--see_31924.patch

@@ -0,0 +1,27 @@
+ - using pytest is broken, see #31924
+
+--- a/src/bin/sage-runtests
++++ b/src/bin/sage-runtests
+@@ -154,21 +154,4 @@ if __name__ == "__main__":
+     DC = DocTestController(args, args.filenames)
+     err = DC.run()
+
+-    try:
+-        exit_code_pytest = 0
+-        import pytest
+-        pytest_options = ["--import-mode", "importlib"]
+-        if args.verbose:
+-            pytest_options.append("-v")
+-        exit_code_pytest = pytest.main(pytest_options + args.filenames)
+-        if exit_code_pytest == 5:
+-            # Exit code 5 means there were no test files, pass in this case
+-            exit_code_pytest = 0
+-
+-    except ModuleNotFoundError:
+-        print("Pytest is not installed, skip checking tests that rely on it.")
+-
+-    if err == 0:
+-        sys.exit(exit_code_pytest)
+-    else:
+-        sys.exit(err)
++    sys.exit(err)

srcpkgs/sagemath/patches/09-doctest_numerical_fix.patch

@@ -0,0 +1,14 @@
+ - This fixes a doctest failure due to a small numerical issue when running
+   maxima-sbcl on 32 bit
+
+--- a/src/sage/interfaces/maxima_abstract.py
++++ b/src/sage/interfaces/maxima_abstract.py
+@@ -1525,7 +1525,7 @@ class MaximaAbstractElement(ExtraTabCompletion, InterfaceElement):
+         EXAMPLES::
+
+             sage: maxima('exp(-sqrt(x))').nintegral('x',0,1)
+-            (0.5284822353142306, 4.1633141378838...e-11, 231, 0)
++            (0.5284822353142306, 4.163...e-11, 231, 0)
+
+         Note that GP also does numerical integration, and can do so to very
+         high precision very quickly::

srcpkgs/sagemath/patches/10-fix_very_slow_doctest-polynomial_zmod_flint.patch

@@ -0,0 +1,14 @@
+--- a/src/sage/rings/polynomial/polynomial_zmod_flint.pyx
++++ b/src/sage/rings/polynomial/polynomial_zmod_flint.pyx
+@@ -237,8 +237,9 @@ cdef class Polynomial_zmod_flint(Polynomial_template):
+
+             sage: a = ZZ['x'](range(100000))
+             sage: R = Integers(3)['x']
+-            sage: R(a)  # long time (7s on sage.math, 2013)
+-            2*x^99998 + ... + x
++            sage: p = R(a)
++            sage: p.truncate(10)  # testing the whole poly is VERY SLOW
++            2*x^8 + x^7 + 2*x^5 + x^4 + 2*x^2 + x
+         """
+         sig_on()
+         fmpz_poly_get_nmod_poly(&self.x, x)

srcpkgs/sagemath/patches/11-fix_very_slow_doctest-isogeny_small_degree.patch

@@ -0,0 +1,106 @@
+diff --git a/src/sage/schemes/elliptic_curves/isogeny_small_degree.py b/src/sage/schemes/elliptic_curves/isogeny_small_degree.py
+index 43727346269..9d3ccd475cd 100644
+--- a/src/sage/schemes/elliptic_curves/isogeny_small_degree.py
++++ b/src/sage/schemes/elliptic_curves/isogeny_small_degree.py
+@@ -186,7 +186,7 @@ def Psi(l, use_stored=True):
+         sage: assert Psi(3, use_stored=True) == Psi(3, use_stored=False)
+         sage: assert Psi(5, use_stored=True) == Psi(5, use_stored=False)
+         sage: assert Psi(7, use_stored=True) == Psi(7, use_stored=False)
+-        sage: assert Psi(13, use_stored=True) == Psi(13, use_stored=False) # not tested (very long time)
++        sage: assert Psi(13, use_stored=True) == Psi(13, use_stored=False)  # long time (2s)
+     """
+     if l not in [2, 3, 5, 7, 13]:
+         raise ValueError("Genus zero primes are 2, 3, 5, 7 or 13.")
+@@ -1207,7 +1207,7 @@ def isogenies_13_0(E, minimal_models=True):
+         sage: K.<a> = NumberField(f)
+         sage: E = EllipticCurve(j=K(0)); E.ainvs()
+         (0, 0, 0, 0, 1)
+-        sage: [phi.codomain().ainvs() for phi in isogenies_13_0(E)]
++        sage: [phi.codomain().ainvs() for phi in isogenies_13_0(E)]  # long time (4s)
+         [(0,
+           0,
+           20360599/165164973653422080*a^11 - 3643073/41291243413355520*a^10 - 101/8789110986240*a^9 + 5557619461/573489491852160*a^8 - 82824971/11947697746920*a^7 - 19487/21127670640*a^6 - 475752603733/29409717530880*a^5 + 87205112531/7352429382720*a^4 + 8349/521670880*a^3 + 5858744881/12764634345*a^2 - 1858703809/2836585410*a + 58759402/48906645,
+@@ -1325,7 +1325,7 @@ def isogenies_13_1728(E, minimal_models=True):
+         sage: f = x^12 + 1092*x^10 - 432432*x^8 + 6641024*x^6 - 282896640*x^4 - 149879808*x^2 - 349360128
+         sage: K.<a> = NumberField(f)
+         sage: E = EllipticCurve(K, [1,0])
+-        sage: [phi.codomain().ainvs() for phi in isogenies_13_1728(E)]
++        sage: [phi.codomain().ainvs() for phi in isogenies_13_1728(E)]  # long time (3s)
+         [(0,
+         0,
+         0,
+@@ -1550,8 +1550,11 @@ def Psi2(l):
+         sage: from sage.schemes.elliptic_curves.isogeny_small_degree import Psi2
+         sage: Psi2(11)
+         x^5 - 55*x^4*u + 994*x^3*u^2 - 8774*x^2*u^3 + 41453*x*u^4 - 928945/11*u^5 + 33*x^4 + 276*x^3*u - 7794*x^2*u^2 + 4452*x*u^3 + 1319331/11*u^4 + 216*x^3*v - 4536*x^2*u*v + 31752*x*u^2*v - 842616/11*u^3*v + 162*x^3 + 38718*x^2*u - 610578*x*u^2 + 33434694/11*u^3 - 4536*x^2*v + 73872*x*u*v - 2745576/11*u^2*v - 16470*x^2 + 580068*x*u - 67821354/11*u^2 - 185976*x*v + 14143896/11*u*v + 7533*x - 20437029/11*u - 12389112/11*v + 19964151/11
+-        sage: Psi2(71)  # long time (1 second)
+-        -2209380711722505179506258739515288584116147237393815266468076436521/71*u^210 + ... - 14790739586438315394567393301990769678157425619440464678252277649/71
++        sage: f = Psi2(71)
++        sage: f.coefficient([0, 210, 0])
++        -2209380711722505179506258739515288584116147237393815266468076436521/71
++        sage: f.coefficient([0, 0, 0])
++        -14790739586438315394567393301990769678157425619440464678252277649/71
+
+     TESTS::
+
+@@ -1665,17 +1668,17 @@ def isogenies_prime_degree_genus_plus_0(E, l=None, minimal_models=True):
+         sage: K = QuadraticField(5,'a')
+         sage: a = K.gen()
+         sage: E = EllipticCurve_from_j(184068066743177379840*a - 411588709724712960000)
+-        sage: isogenies_prime_degree_genus_plus_0(E, 47) # long time (4.3s)
++        sage: isogenies_prime_degree_genus_plus_0(E, 47)  # long time (2s)
+         [Isogeny of degree 47 from Elliptic Curve defined by y^2 = x^3 + (454562028554080355857852049849975895490560*a-1016431595837124114668689286176511361024000)*x + (-249456798429896080881440540950393713303830363999480904280965120*a+557802358738710443451273320227578156598454035482869042774016000) over Number Field in a with defining polynomial x^2 - 5 with a = 2.236067977499790? to Elliptic Curve defined by y^2 = x^3 + (39533118442361013730577638493616965245992960*a-88398740199669828340617478832005245173760000)*x + (214030321479466610282320528611562368963830105830555363061803253760*a-478586348074220699687616322532666163722004497458452316582576128000) over Number Field in a with defining polynomial x^2 - 5 with a = 2.236067977499790?]
+
+         sage: K = QuadraticField(-66827,'a')
+         sage: a = K.gen()
+         sage: E = EllipticCurve_from_j(-98669236224000*a + 4401720074240000)
+-        sage: isogenies_prime_degree_genus_plus_0(E, 59)   # long time (25s, 2012)
++        sage: isogenies_prime_degree_genus_plus_0(E, 59)   # long time (5s)
+         [Isogeny of degree 59 from Elliptic Curve defined by y^2 = x^3 + (2605886146782144762297974784000*a+1893681048912773634944634716160000)*x + (-116918454256410782232296183198067568744071168000*a+17012043538294664027185882358514011304812871680000) over Number Field in a with defining polynomial x^2 + 66827 with a = 258.5091874576221?*I to Elliptic Curve defined by y^2 = x^3 + (-19387084027159786821400775098368000*a-4882059104868154225052787156713472000)*x + (-25659862010101415428713331477227179429538847260672000*a-2596038148441293485938798119003462972840818381946880000) over Number Field in a with defining polynomial x^2 + 66827 with a = 258.5091874576221?*I]
+
+         sage: E = EllipticCurve_from_j(GF(13)(5))
+-        sage: isogenies_prime_degree_genus_plus_0(E, 71) # long time
++        sage: isogenies_prime_degree_genus_plus_0(E, 71)
+         [Isogeny of degree 71 from Elliptic Curve defined by y^2 = x^3 + x + 4 over Finite Field of size 13 to Elliptic Curve defined by y^2 = x^3 + 10*x + 7 over Finite Field of size 13, Isogeny of degree 71 from Elliptic Curve defined by y^2 = x^3 + x + 4 over Finite Field of size 13 to Elliptic Curve defined by y^2 = x^3 + 10*x + 7 over Finite Field of size 13]
+
+         sage: E = EllipticCurve(GF(13),[0,1,1,1,0])
+@@ -2117,11 +2120,11 @@ def isogenies_prime_degree_general(E, l, minimal_models=True):
+         sage: isogenies_prime_degree_general(E, 19)
+         [Isogeny of degree 19 from Elliptic Curve defined by y^2 + y = x^3 - 1862*x - 30956 over Rational Field to Elliptic Curve defined by y^2 + y = x^3 - 672182*x + 212325489 over Rational Field]
+         sage: E = EllipticCurve([0, -1, 0, -6288, 211072])
+-        sage: isogenies_prime_degree_general(E, 37)  # long time (10s)
++        sage: isogenies_prime_degree_general(E, 37)  # long time (2s)
+         [Isogeny of degree 37 from Elliptic Curve defined by y^2 = x^3 - x^2 - 6288*x + 211072 over Rational Field to Elliptic Curve defined by y^2 = x^3 - x^2 - 163137088*x - 801950801728 over Rational Field]
+
+         sage: E = EllipticCurve([-3440, 77658])
+-        sage: isogenies_prime_degree_general(E, 43)  # long time (16s)
++        sage: isogenies_prime_degree_general(E, 43)  # long time (2s)
+         [Isogeny of degree 43 from Elliptic Curve defined by y^2 = x^3 - 3440*x + 77658 over Rational Field to Elliptic Curve defined by y^2 = x^3 - 6360560*x - 6174354606 over Rational Field]
+
+     Isogenies of degree equal to the characteristic are computed (but
+@@ -2175,7 +2178,7 @@ def isogenies_prime_degree_general(E, l, minimal_models=True):
+
+         sage: K.<i> = QuadraticField(-1)
+         sage: E = EllipticCurve(K,[0,0,0,1,0])
+-        sage: [phi.codomain().ainvs() for phi in E.isogenies_prime_degree(37)] # long time
++        sage: [phi.codomain().ainvs() for phi in E.isogenies_prime_degree(37)]  # long time (6s)
+         [(0, 0, 0, -840*i + 1081, 0), (0, 0, 0, 840*i + 1081, 0)]
+     """
+     if not l.is_prime():
+@@ -2329,14 +2332,14 @@ def isogenies_prime_degree(E, l, minimal_models=True):
+         sage: E = EllipticCurve(GF(101), [-3440, 77658])
+         sage: E.isogenies_prime_degree(71) # fast
+         []
+-        sage: E.isogenies_prime_degree(73) # slower (2s)
++        sage: E.isogenies_prime_degree(73)  # long time (2s)
+         []
+
+     Test that :trac:`32269` is fixed::
+
+         sage: K = QuadraticField(-11)
+         sage: E = EllipticCurve(K, [0,1,0,-117,-541])
+-        sage: E.isogenies_prime_degree(37)
++        sage: E.isogenies_prime_degree(37)  # long time (9s)
+         [Isogeny of degree 37 from Elliptic Curve defined by y^2 = x^3 + x^2 + (-117)*x + (-541) over Number Field in a with defining polynomial x^2 + 11 with a = 3.316624790355400?*I to Elliptic Curve defined by y^2 = x^3 + x^2 + (30800*a+123963)*x + (3931312*a-21805005) over Number Field in a with defining polynomial x^2 + 11 with a = 3.316624790355400?*I,
+          Isogeny of degree 37 from Elliptic Curve defined by y^2 = x^3 + x^2 + (-117)*x + (-541) over Number Field in a with defining polynomial x^2 + 11 with a = 3.316624790355400?*I to Elliptic Curve defined by y^2 = x^3 + x^2 + (-30800*a+123963)*x + (-3931312*a-21805005) over Number Field in a with defining polynomial x^2 + 11 with a = 3.316624790355400?*I]
+

srcpkgs/sagemath/patches/12-fix_very_slow_doctest-function_field.patch

@@ -0,0 +1,97 @@
+--- a/src/sage/rings/function_field/function_field.py
++++ b/src/sage/rings/function_field/function_field.py
+@@ -111,22 +111,21 @@ Function fields over the algebraic field are supported::
+     sage: m = L.completion(pl, prec=5)
+     sage: m(x)
+     I + s + O(s^5)
+-    sage: m(y)
++    sage: m(y)                             # long time (4s)
+     -2*s + (-4 - I)*s^2 + (-15 - 4*I)*s^3 + (-75 - 23*I)*s^4 + (-413 - 154*I)*s^5 + O(s^6)
+-    sage: m(y)^2 + m(y) + m(x) + 1/m(x)
++    sage: m(y)^2 + m(y) + m(x) + 1/m(x)    # long time (8s)
+     O(s^5)
+
+ TESTS::
+
+     sage: TestSuite(J).run()
+-    sage: TestSuite(K).run(max_runs=1024) # long time (5s)
+-    sage: TestSuite(L).run(max_runs=64)   # long time (10s)
+-    sage: TestSuite(M).run(max_runs=32)   # long time (30s)
+-    sage: TestSuite(N).run(max_runs=64, skip = '_test_derivation')  # long time (8s)
+-    sage: TestSuite(O).run(max_runs=128, skip = '_test_derivation') # long time (8s)
+-
++    sage: TestSuite(K).run(max_runs=256)   # long time (10s)
++    sage: TestSuite(L).run(max_runs=8)     # long time (25s)
++    sage: TestSuite(M).run(max_runs=8)     # long time (35s)
++    sage: TestSuite(N).run(max_runs=8, skip = '_test_derivation')    # long time (15s)
++    sage: TestSuite(O).run()
+     sage: TestSuite(R).run()
+-    sage: TestSuite(S).run() # long time (3s)
++    sage: TestSuite(S).run()               # long time (4s)
+
+ Global function fields
+ ----------------------
+@@ -287,7 +286,7 @@ class FunctionField(Field):
+         TESTS::
+
+             sage: K.<x> = FunctionField(QQ)
+-            sage: TestSuite(K).run()
++            sage: TestSuite(K).run()               # long time (3s)
+         """
+         Field.__init__(self, base_field, names=names, category=category)
+
+@@ -729,7 +728,7 @@ class FunctionField(Field):
+         EXAMPLES::
+
+             sage: K.<x> = FunctionField(QQ)
+-            sage: TestSuite(K).run() # indirect doctest
++            sage: TestSuite(K).run()    # indirect doctest, long time (3s)
+         """
+         tester = self._tester(**options)
+         S = tester.some_elements()
+@@ -1209,7 +1208,7 @@ class FunctionField_polymod(FunctionField):
+             sage: K.<x> = FunctionField(QQ); R.<y> = K[]
+             sage: L = K.extension(y^5 - x^3 - 3*x + x*y); L
+             Function field in y defined by y^5 + x*y - x^3 - 3*x
+-            sage: TestSuite(L).run()  # long time
++            sage: TestSuite(L).run(max_runs=512)   # long time (15s)
+
+         We can set the variable name, which doesn't have to be y::
+
+@@ -2888,7 +2887,8 @@ class FunctionField_simple(FunctionField_polymod):
+             sage: F.<y> = K.extension(Y^3 - x^2*(x^2 + x + 1)^2)
+             sage: O = K.maximal_order()
+             sage: pls = [O.ideal(x-QQbar(sqrt(c))).place() for c in [-2, -1, 0, 1, 2]]
+-            sage: all(q.place_below() == p for p in pls for q in F.places_above(p))
++            sage: all(q.place_below() == p         # long time (4s)
++            ....:     for p in pls for q in F.places_above(p))
+             True
+         """
+         R = self.base_field()
+@@ -3091,7 +3091,7 @@ class FunctionField_global(FunctionField_simple):
+
+         sage: K.<x> = FunctionField(GF(4)); _.<Y> = K[]
+         sage: L.<y> = K.extension((1 - x)*Y^7 - x^3)
+-        sage: L.gaps()
++        sage: L.gaps()                         # long time (6s)
+         [1, 2, 3]
+
+     or may define a trivial extension::
+@@ -3111,7 +3111,7 @@ class FunctionField_global(FunctionField_simple):
+
+             sage: K.<x> = FunctionField(GF(5)); _.<Y> = K[]
+             sage: L.<y> = K.extension(Y^3 - (x^3 - 1)/(x^3 - 2))
+-            sage: TestSuite(L).run()
++            sage: TestSuite(L).run()               # long time (7s)
+         """
+         FunctionField_polymod.__init__(self, polynomial, names)
+
+@@ -3807,7 +3807,7 @@ class RationalFunctionField(FunctionField):
+
+             sage: K.<t> = FunctionField(CC); K
+             Rational function field in t over Complex Field with 53 bits of precision
+-            sage: TestSuite(K).run()
++            sage: TestSuite(K).run()               # long time (5s)
+
+             sage: FunctionField(QQ[I], 'alpha')
+             Rational function field in alpha over Number Field in I with defining polynomial x^2 + 1 with I = 1*I