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New package: sagemath-9.5

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Gonzalo Tornaría 2022-01-31 12:50:38 -03:00 committed by Leah Neukirchen
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"sage.schemes.hyperelliptic_curves.hyperelliptic_padic_field": {"walltime": 32},
"sage.schemes.hyperelliptic_curves.monsky_washnitzer": {"walltime": 8},
"sage.schemes.projective.projective_rational_point": {"walltime": 8},
"sage.schemes.riemann_surfaces.riemann_surface": {"walltime": 64},
"sage.schemes.toric.chow_group": {"walltime": 8},
"sage.schemes.toric.sheaf.klyachko": {"walltime": 8},
"sage.stats.distributions.discrete_gaussian_integer": {"walltime": 8},
"sage.stats.time_series": {"walltime": 8},
"sage.structure.coerce_dict": {"walltime": 32},
"sage.structure.element": {"walltime": 16},
"sage.structure.sage_object": {"walltime": 8},
"sage.symbolic.expression": {"walltime": 32},
"sage.symbolic.integration.integral": {"walltime": 32},
"sage.symbolic.random_tests": {"walltime": 32},
"sage.symbolic.relation": {"walltime": 8},
"sage.tests.book_schilling_zabrocki_kschur_primer": {"walltime": 32},
"sage.tests.book_stein_ent": {"walltime": 16},
"sage.tests.books.computational-mathematics-with-sagemath.combinat_doctest": {"walltime": 32},
"sage.tests.books.computational-mathematics-with-sagemath.float_doctest": {"walltime": 16},
"sage.tests.books.computational-mathematics-with-sagemath.graphique_doctest": {"walltime": 32},
"sage.tests.books.computational-mathematics-with-sagemath.graphtheory_doctest": {"walltime": 8},
"sage.tests.books.computational-mathematics-with-sagemath.integration_doctest": {"walltime": 32},
"sage.tests.books.computational-mathematics-with-sagemath.mpoly_doctest": {"walltime": 8},
"sage.tests.books.computational-mathematics-with-sagemath.nonlinear_doctest": {"walltime": 8},
"sage.tests.books.computational-mathematics-with-sagemath.recequadiff_doctest": {"walltime": 8},
"sage.tests.books.computational-mathematics-with-sagemath.sol.graphique_doctest": {"walltime": 16},
"sage.tests.books.computational-mathematics-with-sagemath.sol.numbertheory_doctest": {"walltime": 16},
"sage.tests.books.computational-mathematics-with-sagemath.sol.polynomes_doctest": {"walltime": 16},
"sage.tests.cmdline": {"walltime": 64},
"sage.tests.gosper-sum": {"walltime": 16},
"sage.tests.parigp": {"walltime": 8},
"sage.topology.simplicial_complex": {"walltime": 8},
"sage.topology.simplicial_complex_examples": {"walltime": 16}
}

10
srcpkgs/sagemath/patches/01-dont_link_ratpoints.patch Normal file
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@ -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
"""

13
srcpkgs/sagemath/patches/02-fix_get_shared_lib_path--see_29644.patch Normal file
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@ -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')

20
srcpkgs/sagemath/patches/03-doctest_have_program.patch Normal file
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@ -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:

22
srcpkgs/sagemath/patches/04-doctest_sage_getfile.patch Normal file
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@ -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`::

16
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@ -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

15
srcpkgs/sagemath/patches/07-ignore_warning.patch Normal file
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@ -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 ###############################

27
srcpkgs/sagemath/patches/08-dont_run_pytest--see_31924.patch Normal file
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@ -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)

14
srcpkgs/sagemath/patches/09-doctest_numerical_fix.patch Normal file
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@ -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::

14
srcpkgs/sagemath/patches/10-fix_very_slow_doctest-polynomial_zmod_flint.patch Normal file
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@ -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)

106
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@ -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]

97
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@ -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

126
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@ -0,0 +1,126 @@
From 24cc94b1988a90f3bd22a2368ec30c086283af13 Mon Sep 17 00:00:00 2001
From: Antonio Rojas <arojas@archlinux.org>
Date: Sun, 16 Jan 2022 11:55:04 +0100
Subject: Add abs tol to some arb tests
---
src/sage/functions/error.py | 2 +-
src/sage/rings/complex_arb.pyx | 6 +++---
src/sage/rings/real_arb.pyx | 10 +++++-----
3 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/src/sage/functions/error.py b/src/sage/functions/error.py
index f48d04f..06f0b24 100644
--- a/src/sage/functions/error.py
+++ b/src/sage/functions/error.py
@@ -267,7 +267,7 @@ class Function_erf(BuiltinFunction):
Check that real ball evaluation is fixed :trac:`28061`::
- sage: RealBallField(128)(erf(5))
+ sage: RealBallField(128)(erf(5)) # abs tol 1e-38
[0.99999999999846254020557196514981165651 +/- 7.33e-39]
"""
R = parent or s_parent(x)
diff --git a/src/sage/rings/complex_arb.pyx b/src/sage/rings/complex_arb.pyx
index f986970..93ff565 100644
--- a/src/sage/rings/complex_arb.pyx
+++ b/src/sage/rings/complex_arb.pyx
@@ -3974,8 +3974,8 @@ cdef class ComplexBall(RingElement):
EXAMPLES::
- sage: CBF(20).erfc()
- [5.39586561160790e-176 +/- ...e-191]
+ sage: CBF(20).erfc() # abs tol 1e-190
+ [5.39586561160790e-176 +/- 6.73e-191]
sage: CBF(100, 100).erfc()
[0.00065234366376858 +/- ...e-18] + [-0.00393572636292141 +/- ...e-18]*I
"""
@@ -4280,7 +4280,7 @@ cdef class ComplexBall(RingElement):
TESTS:
- sage: CBF(Shi(I))
+ sage: CBF(Shi(I)) # abs tol 1e-15
[0.946083070367183 +/- 9.22e-16]*I
"""
cdef ComplexBall result = self._new()
diff --git a/src/sage/rings/real_arb.pyx b/src/sage/rings/real_arb.pyx
index 4a81784..292bfea 100644
--- a/src/sage/rings/real_arb.pyx
+++ b/src/sage/rings/real_arb.pyx
@@ -3506,7 +3506,7 @@ cdef class RealBall(RingElement):
EXAMPLES::
- sage: RBF(1/2).erf()
+ sage: RBF(1/2).erf() # abs tol 1e-16
[0.520499877813047 +/- 6.10e-16]
"""
cdef RealBall res = self._new()
@@ -3556,12 +3556,12 @@ cdef class RealBall(RingElement):
EXAMPLES::
- sage: RBF(1).Si()
+ sage: RBF(1).Si() # abs tol 1e-15
[0.946083070367183 +/- 9.22e-16]
TESTS::
- sage: RBF(Si(1))
+ sage: RBF(Si(1)) # abs tol 1e-15
[0.946083070367183 +/- 9.22e-16]
"""
cdef RealBall res = self._new()
@@ -3578,12 +3578,12 @@ cdef class RealBall(RingElement):
EXAMPLES::
- sage: RBF(1).Ci() # abs tol 1e-16
+ sage: RBF(1).Ci() # abs tol 1e-15
[0.337403922900968 +/- 3.25e-16]
TESTS::
- sage: RBF(Ci(1)) # abs tol 1e-16
+ sage: RBF(Ci(1)) # abs tol 1e-15
[0.337403922900968 +/- 3.25e-16]
"""
cdef RealBall res = self._new()
--
cgit v1.0-1-gd88e
From 53532ddd4e2dc92469c1590ebf0c40f8f69bf579 Mon Sep 17 00:00:00 2001
From: Antonio Rojas <arojas@archlinux.org>
Date: Sun, 16 Jan 2022 14:16:53 +0100
Subject: Decrease abs tol
---
src/sage/rings/real_arb.pyx | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/sage/rings/real_arb.pyx b/src/sage/rings/real_arb.pyx
index 292bfea..eb30f7f 100644
--- a/src/sage/rings/real_arb.pyx
+++ b/src/sage/rings/real_arb.pyx
@@ -3578,12 +3578,12 @@ cdef class RealBall(RingElement):
EXAMPLES::
- sage: RBF(1).Ci() # abs tol 1e-15
+ sage: RBF(1).Ci() # abs tol 5e-16
[0.337403922900968 +/- 3.25e-16]
TESTS::
- sage: RBF(Ci(1)) # abs tol 1e-15
+ sage: RBF(Ci(1)) # abs tol 5e-16
[0.337403922900968 +/- 3.25e-16]
"""
cdef RealBall res = self._new()
--
cgit v1.0-1-gd88e

40
srcpkgs/sagemath/patches/trac-33226-fix_doctests_giac-1.7.0-33ea2adf01e9e2ce9f1e33779f0b1ac0d9d1989c.patch Normal file
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@ -0,0 +1,40 @@
From 33ea2adf01e9e2ce9f1e33779f0b1ac0d9d1989c Mon Sep 17 00:00:00 2001
From: Michael Orlitzky <michael@orlitzky.com>
Date: Mon, 24 Jan 2022 09:03:29 -0500
Subject: Trac #33226: update doctests for giac-1.7.0.45.
We have two failing doctests with giac-1.7.0.45: one is a trivial
tolerance issue, but the other is a symbolic integration result for
which giac is no longer willing to return a symbolic answer. We add
"abs tol" to the numeric test, and drop the symbolic one entirely.
---
src/sage/functions/min_max.py | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/sage/functions/min_max.py b/src/sage/functions/min_max.py
index fc18373..9b7d6d9 100644
--- a/src/sage/functions/min_max.py
+++ b/src/sage/functions/min_max.py
@@ -228,15 +228,15 @@ class MaxSymbolic(MinMax_base):
...
TypeError: cannot evaluate symbolic expression numerically
- ::
+ We can usually integrate these expressions, but can't
+ guarantee a symbolic answer in closed form::
sage: f = max_symbolic(sin(x), cos(x))
sage: r = integral(f, x, 0, 1)
...
- sage: r
- sqrt(2) - cos(1)
- sage: r.n()
+ sage: r.n() # abs tol 1e-8
0.873911256504955
+
"""
return max_symbolic(args)
--
cgit v1.0-1-gd88e

14
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@ -0,0 +1,14 @@
- this is not a proper fix... should fix sage_getfile() instead
--- a/src/sage/misc/sageinspect.py
+++ b/src/sage/misc/sageinspect.py
@@ -187,7 +187,8 @@ def loadable_module_extension():
True
"""
# Return the full platform-specific extension module suffix
- return import_machinery.EXTENSION_SUFFIXES[0]
+ # PATCHED for void linux, we use the shortest extension (.so)
+ return import_machinery.EXTENSION_SUFFIXES[-1]
def isclassinstance(obj):

13
srcpkgs/sagemath/patches/zzz-skip_doctest_no_threejs.patch Normal file
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@ -0,0 +1,13 @@
- we don't have threejs in void
--- a/src/sage/repl/ipython_kernel/install.py
+++ b/src/sage/repl/ipython_kernel/install.py
@@ -124,7 +124,7 @@ class SageKernelSpec(object):
sage: spec = SageKernelSpec(prefix=tmp_dir())
sage: spec.use_local_threejs()
sage: threejs = os.path.join(spec.nbextensions_dir, 'threejs-sage')
- sage: os.path.isdir(threejs)
+ sage: os.path.isdir(threejs) # optional - threejs
True
"""
src = THREEJS_DIR

129
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@ -0,0 +1,129 @@
# Template file for 'sagemath'
pkgname=sagemath
version=9.5
revision=1
wrksrc=sage-$version
build_wrksrc=pkgs/sagemath-standard
build_style=python3-module
_bindir=/usr/lib/sagemath/bin
make_install_args="--install-scripts=$_bindir"
hostmakedepends="m4 pkg-config python3-Cython python3-Jinja2 python3-pkgconfig
python3-setuptools"
makedepends="arb-devel boost-devel brial-devel cliquer-devel ecl eclib-devel
ecm-devel fflas-ffpack flintlib-devel gap-devel gd-devel giac-devel glpk-devel
gsl-devel iml-devel lcalc-devel libbraiding-devel libhomfly-devel libmpc-devel
libpng-devel linbox-devel lrcalc-devel m4ri-devel m4rie-devel mpfi-devel
mpfr-devel ntl-devel openblas-devel pari-devel planarity-devel python3-cypari2
python3-cysignals python3-devel python3-gmpy2 python3-memory_allocator
python3-numpy rankwidth-devel singular symmetrica-devel zn_poly"
depends="FlintQS eclib-devel fflas-ffpack flintlib-devel gcc-fortran gd-devel
gfan giac gsl-devel gzip libpng-devel linbox-devel m4ri-devel maxima-ecl
mpfr-devel nauty ntl-devel palp pari-devel pari-elldata-small pari-galdata
pari-galpol-small pari-seadata-small pkg-config python3-Cython python3-cypari2
python3-cysignals python3-devel python3-fpylll python3-ipython
python3-ipython_ipykernel python3-jupyter_ipywidgets python3-matplotlib
python3-memory_allocator python3-networkx python3-pip python3-pkgconfig
python3-pplpy python3-primecountpy python3-requests python3-scipy
python3-sympy python3-traitlets sage-data-combinatorial_designs
sage-data-conway_polynomials sage-data-elliptic_curves sage-data-graphs
sage-data-polytopes_db sympow tachyon"
checkdepends="$depends"
short_desc="Open source mathematics software"
maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
license="GPL-2.0-or-later"
homepage="http://sagemath.org/"
distfiles="https://github.com/sagemath/sage/archive/refs/tags/$version.tar.gz"
checksum=8d70a3b26080802c5b2e33dda4c23795d494d8216a0c2ecfcd608ebab0e64ff6
post_patch() {
# these are unused and nothing else uses ratpoints
rm sage/libs/ratpoints.{pyx,pxd}
# git tree needs bootstrapping
pushd $wrksrc/build/pkgs/sagelib
PATH=../../bin:$PATH BOOTSTRAP_QUIET=no ./bootstrap
popd
}
do_configure() {
# set variables in sage.env since we do not install sage_conf
cat >> sage/env.py <<-EOF
CONWAY_POLYNOMIALS_DATA_DIR = "/usr/share/sagemath/conway_polynomials"
GRAPHS_DATA_DIR = "/usr/share/sagemath/graphs"
ELLCURVE_DATA_DIR = "/usr/share/sagemath/ellcurves"
POLYTOPE_DATA_DIR = "/usr/share/sagemath/reflexive_polytopes"
COMBINATORIAL_DESIGN_DATA_DIR = "/usr/share/sagemath/combinatorial_designs"
CREMONA_MINI_DATA_DIR = "/usr/share/sagemath/cremona"
CREMONA_LARGE_DATA_DIR = "/usr/share/sagemath/cremona"
EOF
# don't install sage-venv-config: it is used to set SAGE_VENV=/usr and
# then sage-env prepends "$SAGE_VENV/bin" to PATH which is undesired
vsed -e '/sage-venv-config/d' -i $wrksrc/src/setup.cfg
}
pre_build() {
export PYTHONPATH=../sage-setup
export SAGE_NUM_THREADS="$XBPS_MAKEJOBS"
}
post_build() {
_scripts=$(cd build/scripts* && pwd)
cat >> $_scripts/sage-env-config <<-'EOF'
PATH=$(dirname $SELF):$PATH
EOF
}
pre_install() {
export PYTHONPATH=../sage-setup
export SAGE_NUM_THREADS="$XBPS_MAKEJOBS"
}
post_install() {
# fix jupyter kernel spec
vsed -i -e 's|"/usr/bin/sage", "--python"|"/usr/bin/python"|' \
${DESTDIR}/usr/share/jupyter/kernels/sagemath/kernel.json
# replace broken symlinks by good copies (sagemath logo images)
for file in $(ls sage/ext_data/notebook-ipython); do
rm ${DESTDIR}/usr/share/jupyter/kernels/sagemath/$file
cp -a sage/ext_data/notebook-ipython/$file \
${DESTDIR}/usr/share/jupyter/kernels/sagemath
done
# we don't have docs here
rm ${DESTDIR}/usr/share/jupyter/kernels/sagemath/doc
# we don't have threejs in void
rm ${DESTDIR}/usr/share/jupyter/nbextensions/threejs-sage
# symlink main binary
vmkdir usr/bin
ln -s $_bindir/sage ${DESTDIR}/usr/bin/sage-${version}
ln -s sage-${version} ${DESTDIR}/usr/bin/sage
}
do_check() {
_scripts=$(cd build/scripts* && pwd)
export PYTHONPATH=$(cd build/lib* && pwd)
# get out of $build_wrksrc, otherwise python picks the wrong sage module
cd $(mktemp -dp build)
if [ -f ${XBPS_DISTDIR}/sagemath-check ] ; then
_sed='s|#.*||;/^\s*$/d;s|[^ ]*/sage/|'$PYTHONPATH'/sage/|g' \
_test_files=$(sed -e "$_sed" ${XBPS_DISTDIR}/sagemath-check)
fi
if [ -z "$_test_files" ]; then
_test_files=--all
fi
cp ${FILESDIR}/timings2.json .
_test_args="--stats_path=timings2.json"
if [ "$XBPS_CHECK_PKGS" = full ]; then
_test_args+=" --long --warn-long 60.0"
else
_test_args+=" --warn-long 30.0"
fi
if [ "$XBPS_BUILD_ENVIRONMENT" = "void-packages-ci" ]; then
# for CI use a predictable random seed
_test_args+=" --random-seed=0"
fi
$_scripts/sage -tp ${XBPS_MAKEJOBS} ${_test_args} ${_test_files}
}