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"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} +} diff --git a/srcpkgs/sagemath/patches/01-dont_link_ratpoints.patch b/srcpkgs/sagemath/patches/01-dont_link_ratpoints.patch new file mode 100644 index 00000000000000..e5c3f5776aa263 --- /dev/null +++ b/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 + """ diff --git a/srcpkgs/sagemath/patches/02-fix_get_shared_lib_path--see_29644.patch b/srcpkgs/sagemath/patches/02-fix_get_shared_lib_path--see_29644.patch new file mode 100644 index 00000000000000..d3672b094c1c72 --- /dev/null +++ b/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') diff --git a/srcpkgs/sagemath/patches/03-doctest_have_program.patch b/srcpkgs/sagemath/patches/03-doctest_have_program.patch new file mode 100644 index 00000000000000..27ba3776470c9f --- /dev/null +++ b/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: diff --git a/srcpkgs/sagemath/patches/04-doctest_sage_getfile.patch b/srcpkgs/sagemath/patches/04-doctest_sage_getfile.patch new file mode 100644 index 00000000000000..95bce107f854b8 --- /dev/null +++ b/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`:: + + diff --git a/srcpkgs/sagemath/patches/05-fix_sage_getfile.patch b/srcpkgs/sagemath/patches/05-fix_sage_getfile.patch new file mode 100644 index 00000000000000..56c58078f3198d --- /dev/null +++ b/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 + + diff --git a/srcpkgs/sagemath/patches/07-ignore_warning.patch b/srcpkgs/sagemath/patches/07-ignore_warning.patch new file mode 100644 index 00000000000000..69668678a40b0c --- /dev/null +++ b/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 ############################### + + + diff --git a/srcpkgs/sagemath/patches/08-dont_run_pytest--see_31924.patch b/srcpkgs/sagemath/patches/08-dont_run_pytest--see_31924.patch new file mode 100644 index 00000000000000..06bd2ccae6fb5f --- /dev/null +++ b/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) diff --git a/srcpkgs/sagemath/patches/09-doctest_numerical_fix.patch b/srcpkgs/sagemath/patches/09-doctest_numerical_fix.patch new file mode 100644 index 00000000000000..8780c8a97efaf0 --- /dev/null +++ b/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:: diff --git a/srcpkgs/sagemath/patches/10-fix_very_slow_doctest-polynomial_zmod_flint.patch b/srcpkgs/sagemath/patches/10-fix_very_slow_doctest-polynomial_zmod_flint.patch new file mode 100644 index 00000000000000..bae8387cf94a49 --- /dev/null +++ b/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) diff --git a/srcpkgs/sagemath/patches/11-fix_very_slow_doctest-isogeny_small_degree.patch b/srcpkgs/sagemath/patches/11-fix_very_slow_doctest-isogeny_small_degree.patch new file mode 100644 index 00000000000000..f3da5bbb555e91 --- /dev/null +++ b/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. = 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. = 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. = 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] + diff --git a/srcpkgs/sagemath/patches/12-fix_very_slow_doctest-function_field.patch b/srcpkgs/sagemath/patches/12-fix_very_slow_doctest-function_field.patch new file mode 100644 index 00000000000000..3b7b1ea843df97 --- /dev/null +++ b/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. = 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. = 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. = FunctionField(QQ); R. = 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. = 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. = FunctionField(GF(4)); _. = K[] + sage: L. = 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. = FunctionField(GF(5)); _. = K[] + sage: L. = 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. = 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 diff --git a/srcpkgs/sagemath/patches/trac-33189-fix_doctests_for_arb_2.22-53532ddd4e2dc92469c1590ebf0c40f8f69bf579.patch b/srcpkgs/sagemath/patches/trac-33189-fix_doctests_for_arb_2.22-53532ddd4e2dc92469c1590ebf0c40f8f69bf579.patch new file mode 100644 index 00000000000000..b861af7ec982a2 --- /dev/null +++ b/srcpkgs/sagemath/patches/trac-33189-fix_doctests_for_arb_2.22-53532ddd4e2dc92469c1590ebf0c40f8f69bf579.patch @@ -0,0 +1,126 @@ +From 24cc94b1988a90f3bd22a2368ec30c086283af13 Mon Sep 17 00:00:00 2001 +From: Antonio Rojas +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 +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 + diff --git a/srcpkgs/sagemath/patches/trac-33226-fix_doctests_giac-1.7.0-33ea2adf01e9e2ce9f1e33779f0b1ac0d9d1989c.patch b/srcpkgs/sagemath/patches/trac-33226-fix_doctests_giac-1.7.0-33ea2adf01e9e2ce9f1e33779f0b1ac0d9d1989c.patch new file mode 100644 index 00000000000000..d4e8f8be60e3e8 --- /dev/null +++ b/srcpkgs/sagemath/patches/trac-33226-fix_doctests_giac-1.7.0-33ea2adf01e9e2ce9f1e33779f0b1ac0d9d1989c.patch @@ -0,0 +1,40 @@ +From 33ea2adf01e9e2ce9f1e33779f0b1ac0d9d1989c Mon Sep 17 00:00:00 2001 +From: Michael Orlitzky +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 + diff --git a/srcpkgs/sagemath/patches/zzz-loadable_module_extension.patch b/srcpkgs/sagemath/patches/zzz-loadable_module_extension.patch new file mode 100644 index 00000000000000..f3eb0aad2cca26 --- /dev/null +++ b/srcpkgs/sagemath/patches/zzz-loadable_module_extension.patch @@ -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): diff --git a/srcpkgs/sagemath/patches/zzz-skip_doctest_no_threejs.patch b/srcpkgs/sagemath/patches/zzz-skip_doctest_no_threejs.patch new file mode 100644 index 00000000000000..5cb62f56e90214 --- /dev/null +++ b/srcpkgs/sagemath/patches/zzz-skip_doctest_no_threejs.patch @@ -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 diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template new file mode 100644 index 00000000000000..710a9e80c0521c --- /dev/null +++ b/srcpkgs/sagemath/template @@ -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="$depends" +short_desc="Open source mathematics software" +maintainer="Gonzalo Tornaría " +license="GPL-2.0-or-later" +homepage="http://sagemath.org/" +distfiles="https://github.com/sagemath/sage/archive/refs/tags/$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} +}