diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix index 0bbf2cec0dc..014a1302147 100644 --- a/pkgs/applications/science/math/sage/default.nix +++ b/pkgs/applications/science/math/sage/default.nix @@ -131,7 +131,6 @@ let }); # *not* to confuse with the python package "pynac" - # https://trac.sagemath.org/ticket/24838 (depends on arb update) pynac = nixpkgs.pynac.override { inherit singular flint; }; eclib = nixpkgs.eclib.override { inherit pari ntl; }; @@ -167,6 +166,7 @@ let ecl = nixpkgs.ecl_16_1_2; # sage currently uses an unreleased version of pari + # https://trac.sagemath.org/ticket/25567 pari = (nixpkgs.pari.override { withThread = false; }).overrideAttrs (attrs: rec { version = "2.10-1280-g88fb5b3"; # on update remove pari-stackwarn patch from `sage-src.nix` src = fetchurl { diff --git a/pkgs/applications/science/math/sage/patches/arb-2.13.0.patch b/pkgs/applications/science/math/sage/patches/arb-2.13.0.patch deleted file mode 100644 index a20f1670a25..00000000000 --- a/pkgs/applications/science/math/sage/patches/arb-2.13.0.patch +++ /dev/null @@ -1,427 +0,0 @@ -commit c885927e25b29bd23869e02379c2918da430323e -Author: Timo Kaufmann -Date: Sat Jun 30 02:26:15 2018 +0200 - -diff --git a/build/pkgs/arb/checksums.ini b/build/pkgs/arb/checksums.ini -index 1924ee03c3..9323b97391 100644 ---- a/build/pkgs/arb/checksums.ini -+++ b/build/pkgs/arb/checksums.ini -@@ -1,4 +1,4 @@ - tarball=arb-VERSION.tar.gz --sha1=27476d0529e48a07d92da90bd0fb80dd18f443e3 --md5=733285d9705d10b8024e551ffa81952f --cksum=2391183744 -+sha1=44eda7bf8eaa666c45b1fc2c1b5bd08756d94b58 -+md5=fa24de9fffe4394fb6a7a6792e2ecc5f -+cksum=3689220688 -diff --git a/build/pkgs/arb/package-version.txt b/build/pkgs/arb/package-version.txt -index c8810e9bdb..fb2c0766b7 100644 ---- a/build/pkgs/arb/package-version.txt -+++ b/build/pkgs/arb/package-version.txt -@@ -1 +1 @@ --2.12.0.p0 -+2.13.0 -diff --git a/build/pkgs/arb/patches/arb-pie-hardening-conflict.patch b/build/pkgs/arb/patches/arb-pie-hardening-conflict.patch -deleted file mode 100644 -index 3e5c0e708b..0000000000 ---- a/build/pkgs/arb/patches/arb-pie-hardening-conflict.patch -+++ /dev/null -@@ -1,17 +0,0 @@ --In newer binutils, ld options -r and -pie conflict. --Patch due to Jörg-Volker Peetz --(source : https://groups.google.com/d/msg/sage-devel/TduebNoZuBE/sEULolL0BQAJ), --packaged by Emmanuel Charpentier -- --diff -ru arb-2.8.1-orig/Makefile.subdirs arb-2.8.1-new/Makefile.subdirs ----- arb-2.8.1-orig/Makefile.subdirs 2015-12-31 17:30:01.000000000 +0100 --+++ arb-2.8.1-new/Makefile.subdirs 2016-11-07 18:50:34.540051779 +0100 --@@ -52,7 +52,7 @@ -- $(QUIET_CC) $(CC) $(CFLAGS) $(INCS) -c $< -o $@ -MMD -MP -MF "$(BUILD_DIR)/$(MOD_DIR)_$*.d" -MT "$(BUILD_DIR)/$(MOD_DIR)_$*.d" -MT "$@" -- -- $(MOD_LOBJ): $(LOBJS) --- $(QUIET_CC) $(CC) $(ABI_FLAG) -Wl,-r $^ -o $@ -nostdlib --+ $(QUIET_CC) $(CC) $(ABI_FLAG) -r $^ -o $@ -nostdlib -- -- -include $(LOBJS:.lo=.d) -- -diff --git a/src/sage/rings/complex_arb.pyx b/src/sage/rings/complex_arb.pyx -index 70d51e655a..00e7caea2c 100644 ---- a/src/sage/rings/complex_arb.pyx -+++ b/src/sage/rings/complex_arb.pyx -@@ -857,14 +857,14 @@ class ComplexBallField(UniqueRepresentation, Field): - [0.500000000000000 +/- 2.09e-16] - - sage: CBF.integral(lambda x, _: x.gamma(), 1 - CBF(i), 1 + CBF(i)) -- [+/- 3.95e-15] + [1.5723926694981 +/- 4.53e-14]*I -+ [+/- 4...e-15] + [1.5723926694981 +/- 4...e-14]*I - - sage: C = ComplexBallField(100) - sage: C.integral(lambda x, _: x.cos() * x.sin(), 0, 1) - [0.35403670913678559674939205737 +/- 8.89e-30] - - sage: CBF.integral(lambda x, _: (x + x.exp()).sin(), 0, 8) -- [0.34740017266 +/- 6.36e-12] -+ [0.34740017266 +/- 6...e-12] - - sage: C = ComplexBallField(2000) - sage: C.integral(lambda x, _: (x + x.exp()).sin(), 0, 8) # long time -@@ -879,14 +879,14 @@ class ComplexBallField(UniqueRepresentation, Field): - ....: else: - ....: return z.sqrt() - sage: CBF.integral(my_sqrt, -1 + CBF(i), -1 - CBF(i)) -- [+/- 1.14e-14] + [-0.4752076627926 +/- 5.18e-14]*I -+ [+/- 1.14e-14] + [-0.4752076627926 +/- 5...e-14]*I - - Note, though, that proper handling of the ``analytic`` flag is required - even when the path does not touch the branch cut:: - - sage: correct = CBF.integral(my_sqrt, 1, 2); correct - [1.21895141649746 +/- 3.73e-15] -- sage: RBF(integral(sqrt(x), x, 1, 2)) -+ sage: RBF(integral(sqrt(x), x, 1, 2)) # long time - [1.21895141649746 +/- 1.79e-15] - sage: wrong = CBF.integral(lambda z, _: z.sqrt(), 1, 2) # WRONG! - sage: correct - wrong -@@ -915,9 +915,9 @@ class ComplexBallField(UniqueRepresentation, Field): - the integrand is unbounded:: - - sage: CBF.integral(lambda x, _: 1/x, -1, 1) -- [+/- inf] + [+/- inf]*I -+ nan + nan*I - sage: CBF.integral(lambda x, _: 1/x, 10^-1000, 1) -- [+/- inf] + [+/- inf]*I -+ nan + nan*I - sage: CBF.integral(lambda x, _: 1/x, 10^-1000, 1, abs_tol=1e-10) - [2302.5850930 +/- 1.26e-8] - -@@ -928,14 +928,15 @@ class ComplexBallField(UniqueRepresentation, Field): - sage: CBF.integral(lambda x, _: x.exp(), -1020, -1010, abs_tol=1e-450) - [2.304377150950e-439 +/- 9.74e-452] - sage: CBF.integral(lambda x, _: x.exp(), -1020, -1010, abs_tol=0) -- [2.304377150949e-439 +/- 7.53e-452] -- sage: CBF.integral(lambda x, _: x.exp(), -1020, -1010, rel_tol=1e-4, abs_tol=0) -- [2.30438e-439 +/- 3.90e-445] -+ [2.304377150950e-439 +/- 7...e-452] -+ sage: CBF.integral(lambda x, _: x.exp(), -1020, -1010, rel_tol=1e-2, abs_tol=0) -+ [2.30438e-439 +/- 5.94e-445] - -- sage: CBF.integral(lambda x, _: x*(1/x).sin(), 0, 1) -- [+/- 0.644] -- sage: CBF.integral(lambda x, _: x*(1/x).sin(), 0, 1, use_heap=True) -- [0.3785300 +/- 4.32e-8] -+ sage: epsi = CBF(1e-10) -+ sage: CBF.integral(lambda x, _: x*(1/x).sin(), epsi, 1) -+ [0.38 +/- 8.54e-3] -+ sage: CBF.integral(lambda x, _: x*(1/x).sin(), epsi, 1, use_heap=True) -+ [0.37853002 +/- 8.73e-9] - - ALGORITHM: - -@@ -951,12 +952,12 @@ class ComplexBallField(UniqueRepresentation, Field): - - sage: i = QuadraticField(-1).gen() - sage: CBF.integral(lambda x, _: (1 + i*x).gamma(), -1, 1) -- [1.5723926694981 +/- 4.53e-14] + [+/- 3.95e-15]*I -+ [1.5723926694981 +/- 4...e-14] + [+/- 4...e-15]*I - -- sage: ComplexBallField(10000).integral(lambda x, _: x.sin(), 0, 1, rel_tol=1e-400) -- [0.459... +/- ...e-4...] -+ sage: ComplexBallField(10000).integral(lambda x, _: x.sin(), 0, 1, rel_tol=1e-300) -+ [0.459... +/- ...e-3...] - sage: CBF.integral(lambda x, _: x.sin(), 0, 100, rel_tol=10) -- [+/- 7.61] -+ [0.138 +/- 5.53e-4] - - sage: ComplexBallField(10000).integral(lambda x, _: x.sin(), 0, 1, abs_tol=1e-400) - [0.459697... +/- ...e-4...] -@@ -2389,9 +2390,9 @@ cdef class ComplexBall(RingElement): - sage: ~CBF(i/3) - [-3.00000000000000 +/- 9.44e-16]*I - sage: ~CBF(0) -- [+/- inf] -+ nan - sage: ~CBF(RIF(10,11)) -- [0.1 +/- 9.53e-3] -+ [0.1 +/- 9.10e-3] - """ - cdef ComplexBall res = self._new() - if _do_sig(prec(self)): sig_on() -@@ -2512,9 +2513,9 @@ cdef class ComplexBall(RingElement): - sage: CBF(-2, 1)/CBF(1, 1/3) - [-1.500000000000000 +/- 8.83e-16] + [1.500000000000000 +/- 5.64e-16]*I - sage: CBF(2+I)/CBF(0) -- [+/- inf] + [+/- inf]*I -+ nan + nan*I - sage: CBF(1)/CBF(0) -- [+/- inf] -+ nan - sage: CBF(1)/CBF(RBF(0, 1.)) - nan - """ -@@ -2543,9 +2544,9 @@ cdef class ComplexBall(RingElement): - sage: CBF(0)^(1/3) - 0 - sage: CBF(0)^(-1) -- [+/- inf] -+ nan - sage: CBF(0)^(-2) -- [+/- inf] + [+/- inf]*I -+ nan + nan*I - - TESTS:: - -@@ -2656,12 +2657,12 @@ cdef class ComplexBall(RingElement): - sage: CBF(1).rising_factorial(5) - 120.0000000000000 - sage: CBF(1/3, 1/2).rising_factorial(300) -- [-3.87949484514e+612 +/- 5.23e+600] + [-3.52042209763e+612 +/- 5.55e+600]*I -+ [-3.87949484514e+612 +/- 5...e+600] + [-3.52042209763e+612 +/- 5...e+600]*I - - sage: CBF(1).rising_factorial(-1) - nan - sage: CBF(1).rising_factorial(2**64) -- [+/- 2.30e+347382171305201370464] -+ [+/- 2.30e+347382171326740403407] - sage: ComplexBallField(128)(1).rising_factorial(2**64) - [2.343691126796861348e+347382171305201285713 +/- 4.71e+347382171305201285694] - sage: CBF(1/2).rising_factorial(CBF(2,3)) -@@ -2700,7 +2701,7 @@ cdef class ComplexBall(RingElement): - [1.000000000000000 +/- 2.83e-16] + [-0.441271200305303 +/- 2.82e-16]*I - - sage: CBF('inf').log() -- nan + nan*I -+ [+/- inf] - sage: CBF(2).log(0) - nan + nan*I - """ -@@ -2808,7 +2809,7 @@ cdef class ComplexBall(RingElement): - sage: CBF(pi/2, 1/10).tan() - [+/- 2.87e-14] + [10.0333111322540 +/- 2.36e-14]*I - sage: CBF(pi/2).tan() -- [+/- inf] -+ nan - """ - cdef ComplexBall res = self._new() - if _do_sig(prec(self)): sig_on() -@@ -2825,7 +2826,7 @@ cdef class ComplexBall(RingElement): - sage: CBF(pi, 1/10).cot() - [+/- 5.74e-14] + [-10.0333111322540 +/- 2.81e-14]*I - sage: CBF(pi).cot() -- [+/- inf] -+ nan - """ - cdef ComplexBall res = self._new() - if _do_sig(prec(self)): sig_on() -@@ -3211,9 +3212,9 @@ cdef class ComplexBall(RingElement): - 1.000000000000000*I - - sage: CBF(2+3*I).hypergeometric([1/4,1/3],[1/2]) -- [0.7871684267473 +/- 7.34e-14] + [0.2749254173721 +/- 9.23e-14]*I -+ [0.7871684267473 +/- 7...e-14] + [0.2749254173721 +/- 9...e-14]*I - sage: CBF(2+3*I).hypergeometric([1/4,1/3],[1/2],regularized=True) -- [0.4441122268685 +/- 3.96e-14] + [0.1551100567338 +/- 5.75e-14]*I -+ [0.4441122268685 +/- 3...e-14] + [0.1551100567338 +/- 5...e-14]*I - - sage: CBF(5).hypergeometric([2,3], [-5]) - nan + nan*I -@@ -4041,9 +4042,9 @@ cdef class ComplexBall(RingElement): - - sage: phi = CBF(1,1) - sage: (CBF.pi()/2).elliptic_e_inc(phi) -- [1.283840957898 +/- 3.23e-13] + [-0.5317843366915 +/- 7.79e-14]*I -+ [1.283840957898 +/- 3...e-13] + [-0.5317843366915 +/- 7...e-14]*I - sage: phi.elliptic_e() -- [1.2838409578982 +/- 5.90e-14] + [-0.5317843366915 +/- 3.35e-14]*I -+ [1.2838409578982 +/- 5...e-14] + [-0.5317843366915 +/- 3...e-14]*I - - sage: phi = CBF(2, 3/7) - sage: (CBF.pi()/2).elliptic_e_inc(phi) -@@ -4312,8 +4313,7 @@ cdef class ComplexBall(RingElement): - sage: CBF(10).laguerre_L(3, 2) - [-6.666666666667 +/- 4.15e-13] - sage: CBF(5,7).laguerre_L(CBF(2,3), CBF(1,-2)) -- [5515.315030271 +/- 4.37e-10] + [-12386.942845271 +/- 5.47e-10]*I -- -+ [5515.315030271 +/- 4...e-10] + [-12386.942845271 +/- 5...e-10]*I - """ - cdef ComplexBall my_n = self._parent.coerce(n) - cdef ComplexBall my_m = self._parent.coerce(m) -@@ -4357,9 +4357,9 @@ cdef class ComplexBall(RingElement): - EXAMPLES:: - - sage: CBF(1/2).legendre_P(5) -- [0.08984375000000000 +/- 4.5...e-18] -+ [0.0898437500000000 +/- 7...e-17] - sage: CBF(1,2).legendre_P(CBF(2,3), CBF(0,1)) -- [0.10996180744364 +/- 7.45e-15] + [0.14312767804055 +/- 8.38e-15]*I -+ [0.10996180744364 +/- 7.12e-15] + [0.14312767804055 +/- 8.07e-15]*I - sage: CBF(-10).legendre_P(5, 325/100) - [-22104403.487377 +/- 6.81e-7] + [53364750.687392 +/- 7.25e-7]*I - sage: CBF(-10).legendre_P(5, 325/100, type=3) -@@ -4393,9 +4393,9 @@ cdef class ComplexBall(RingElement): - sage: CBF(1/2).legendre_Q(5) - [0.55508089057168 +/- 2.79e-15] - sage: CBF(1,2).legendre_Q(CBF(2,3), CBF(0,1)) -- [0.167678710 +/- 4.60e-10] + [-0.161558598 +/- 7.47e-10]*I -+ [0.167678710 +/- 3.91e-10] + [-0.161558598 +/- 6.77e-10]*I - sage: CBF(-10).legendre_Q(5, 325/100) -- [-83825154.36008 +/- 4.94e-6] + [-34721515.80396 +/- 5.40e-6]*I -+ [-83825154.36008 +/- 5.02e-6] + [-34721515.80396 +/- 5.42e-6]*I - sage: CBF(-10).legendre_Q(5, 325/100, type=3) - [-4.797306921692e-6 +/- 6.82e-19] + [-4.797306921692e-6 +/- 6.57e-19]*I - -diff --git a/src/sage/rings/polynomial/polynomial_complex_arb.pyx b/src/sage/rings/polynomial/polynomial_complex_arb.pyx -index c436d4705b..ef611a566b 100644 ---- a/src/sage/rings/polynomial/polynomial_complex_arb.pyx -+++ b/src/sage/rings/polynomial/polynomial_complex_arb.pyx -@@ -543,7 +543,7 @@ cdef class Polynomial_complex_arb(Polynomial): - sage: (1 - x/3).inverse_series_trunc(3) - ([0.1111111111111111 +/- 5.99e-17])*x^2 + ([0.3333333333333333 +/- 7.04e-17])*x + 1.000000000000000 - sage: x.inverse_series_trunc(1) -- [+/- inf] -+ nan - sage: Pol(0).inverse_series_trunc(2) - (nan + nan*I)*x + nan + nan*I - -@@ -671,7 +671,7 @@ cdef class Polynomial_complex_arb(Polynomial): - sage: pol._sqrt_series(2) - ([+/- 7.51e-3] + [+/- 0.501]*I)*x + [+/- 5.01e-3] + [+/- 1.01]*I - sage: x._sqrt_series(2) -- ([+/- inf] + [+/- inf]*I)*x -+ (nan + nan*I)*x - """ - cdef Polynomial_complex_arb res = self._new() - if n < 0: -diff --git a/src/sage/rings/real_arb.pyx b/src/sage/rings/real_arb.pyx -index c9f68e38d7..76e3037a9a 100644 ---- a/src/sage/rings/real_arb.pyx -+++ b/src/sage/rings/real_arb.pyx -@@ -161,7 +161,7 @@ values and should be preferred:: - - sage: RBF(NaN) < RBF(infinity) - False -- sage: 1/RBF(0) <= RBF(infinity) -+ sage: RBF(0).add_error(infinity) <= RBF(infinity) - True - - TESTS:: -@@ -252,6 +252,8 @@ cdef void mpfi_to_arb(arb_t target, const mpfi_t source, const long precision): - (+infinity, +infinity) - sage: RBF(RIF(-infinity)).endpoints() - (-infinity, -infinity) -+ sage: RBF(RIF(-infinity, infinity)).endpoints() -+ (-infinity, +infinity) - sage: RIF(RBF(infinity)).endpoints() - (+infinity, +infinity) - sage: RIF(RBF(-infinity)).endpoints() -@@ -266,10 +268,11 @@ cdef void mpfi_to_arb(arb_t target, const mpfi_t source, const long precision): - if _do_sig(precision): sig_on() - mpfi_get_left(left, source) - mpfi_get_right(right, source) -- arb_set_interval_mpfr(target, left, right, precision) -- # Work around weakness of arb_set_interval_mpfr(tgt, inf, inf) -- if mpfr_equal_p(left, right): -- mag_zero(arb_radref(target)) -+ if mpfr_inf_p(left) and mpfr_inf_p(right) and mpfr_sgn(left) < 0 < mpfr_sgn(right): -+ # Work around a weakness of arb_set_interval_mpfr(tgt, -inf, inf) -+ arb_zero_pm_inf(target) -+ else: -+ arb_set_interval_mpfr(target, left, right, precision) - if _do_sig(precision): sig_off() - - mpfr_clear(left) -@@ -649,17 +652,15 @@ class RealBallField(UniqueRepresentation, Field): - EXAMPLES:: - - sage: RBF.some_elements() -- [1.000000000000000, -- [0.3333333333333333 +/- 7.04e-17], -+ [0, 1.000000000000000, [0.3333333333333333 +/- 7.04e-17], - [-4.733045976388941e+363922934236666733021124 +/- 3.46e+363922934236666733021108], -- [+/- inf], -- [+/- inf], -- nan] -+ [+/- inf], [+/- inf], [+/- inf], nan] - """ - import sage.symbolic.constants -- return [self(1), self(1)/3, -+ inf = self(sage.rings.infinity.Infinity) -+ return [self(0), self(1), self(1)/3, - -self(2)**(Integer(2)**80), -- self(sage.rings.infinity.Infinity), ~self(0), -+ inf, -inf, self.zero().add_error(inf), - self.element_class(self, sage.symbolic.constants.NotANumber())] - - def _sum_of_products(self, terms): -@@ -881,7 +882,7 @@ class RealBallField(UniqueRepresentation, Field): - sage: RBF.gamma(5) - 24.00000000000000 - sage: RBF.gamma(10**20) -- [+/- 5.92e+1956570551809674821757] -+ [+/- 5.50e+1956570552410610660600] - sage: RBF.gamma(1/3) - [2.678938534707747 +/- 8.99e-16] - sage: RBF.gamma(-5) -@@ -2247,7 +2248,7 @@ cdef class RealBall(RingElement): - sage: inf = RBF(+infinity) - sage: other_inf = RBF(+infinity, 42.r) - sage: neg_inf = RBF(-infinity) -- sage: extended_line = 1/RBF(0) -+ sage: extended_line = RBF(0).add_error(infinity) - sage: exact_nan = inf - inf - sage: exact_nan.mid(), exact_nan.rad() - (NaN, 0.00000000) -@@ -2659,7 +2660,7 @@ cdef class RealBall(RingElement): - sage: ~RBF(5) - [0.2000000000000000 +/- 4.45e-17] - sage: ~RBF(0) -- [+/- inf] -+ nan - sage: RBF(RIF(-0.1,0.1)) - [+/- 0.101] - -@@ -2739,7 +2740,7 @@ cdef class RealBall(RingElement): - sage: RBF(pi)/RBF(e) - [1.155727349790922 +/- 8.43e-16] - sage: RBF(2)/RBF(0) -- [+/- inf] -+ nan - """ - cdef RealBall res = self._new() - if _do_sig(prec(self)): sig_on() -@@ -2765,7 +2766,7 @@ cdef class RealBall(RingElement): - sage: RBF(-1)^(1/3) - nan - sage: RBF(0)^(-1) -- [+/- inf] -+ nan - sage: RBF(-e)**RBF(pi) - nan - -@@ -3129,7 +3130,7 @@ cdef class RealBall(RingElement): - sage: RBF(1).tan() - [1.557407724654902 +/- 3.26e-16] - sage: RBF(pi/2).tan() -- [+/- inf] -+ nan - """ - cdef RealBall res = self._new() - if _do_sig(prec(self)): sig_on() -@@ -3146,7 +3147,7 @@ cdef class RealBall(RingElement): - sage: RBF(1).cot() - [0.642092615934331 +/- 4.79e-16] - sage: RBF(pi).cot() -- [+/- inf] -+ nan - """ - cdef RealBall res = self._new() - if _do_sig(prec(self)): sig_on() -@@ -3257,7 +3258,7 @@ cdef class RealBall(RingElement): - sage: RBF(1).coth() - [1.313035285499331 +/- 4.97e-16] - sage: RBF(0).coth() -- [+/- inf] -+ nan - """ - cdef RealBall res = self._new() - if _do_sig(prec(self)): sig_on() diff --git a/pkgs/applications/science/math/sage/patches/known-padics-bug.patch b/pkgs/applications/science/math/sage/patches/known-padics-bug.patch new file mode 100644 index 00000000000..bdccd73e0ce --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/known-padics-bug.patch @@ -0,0 +1,15 @@ +diff --git a/build/pkgs/openblas/package-version.txt b/build/pkgs/openblas/package-version.txt +index 3bc45c25d4..7c7c224887 100644 +--- a/src/sage/schemes/elliptic_curves/padics.py ++++ b/src/sage/schemes/elliptic_curves/padics.py +@@ -292,8 +292,8 @@ def padic_regulator(self, p, prec=20, height=None, check_hypotheses=True): + + sage: max_prec = 30 # make sure we get past p^2 # long time + sage: full = E.padic_regulator(5, max_prec) # long time +- sage: for prec in range(1, max_prec): # long time +- ....: assert E.padic_regulator(5, prec) == full # long time ++ sage: for prec in range(1, max_prec): # known bug (#25969) # long time ++ ....: assert E.padic_regulator(5, prec) == full # known bug (#25969) # long time + + A case where the generator belongs to the formal group already + (:trac:`3632`):: diff --git a/pkgs/applications/science/math/sage/patches/maxima-5.41.0-doctests.patch b/pkgs/applications/science/math/sage/patches/maxima-5.41.0-doctests.patch deleted file mode 100644 index fad434e52ad..00000000000 --- a/pkgs/applications/science/math/sage/patches/maxima-5.41.0-doctests.patch +++ /dev/null @@ -1,48 +0,0 @@ -diff --git a/src/sage/interfaces/maxima_abstract.py b/src/sage/interfaces/maxima_abstract.py -index 961c20aaac..3d601d8939 100644 ---- a/src/sage/interfaces/maxima_abstract.py -+++ b/src/sage/interfaces/maxima_abstract.py -@@ -1743,7 +1743,7 @@ class MaximaAbstractElement(ExtraTabCompletion, InterfaceElement): - sage: y,d = var('y,d') - sage: f = function('f') - sage: latex(maxima(derivative(f(x*y), x))) -- \left(\left.{{{\it \partial}}\over{{\it \partial}\, {\it t_0}}}\,f\left({\it t_0}\right) \right|_{{\it t_0}={\it x}\, {\it y}}\right)\,{\it y} -+ \left(\left.{{{\it \partial}}\over{{\it \partial}\, {\it t}_{0}}}\,f\left({\it t}_{0}\right) \right|_{{\it t}_{0}={\it x}\, {\it y}}\right)\,{\it y} - sage: latex(maxima(derivative(f(x,y,d), d,x,x,y))) - {{{\it \partial}^4}\over{{\it \partial}\,{\it d}\, {\it \partial}\,{\it x}^2\,{\it \partial}\, {\it y}}}\,f\left({\it x} , {\it y} , {\it d}\right) - sage: latex(maxima(d/(d-2))) -diff --git a/src/sage/manifolds/differentiable/metric.py b/src/sage/manifolds/differentiable/metric.py -index 3cd6ad3235..1e18af1a6b 100644 ---- a/src/sage/manifolds/differentiable/metric.py -+++ b/src/sage/manifolds/differentiable/metric.py -@@ -993,7 +993,7 @@ class PseudoRiemannianMetric(TensorField): - 2-dimensional differentiable manifold S^2 - sage: g.riemann()[:] - [[[[0, 0], [0, 0]], [[0, sin(th)^2], [-sin(th)^2, 0]]], -- [[[0, (cos(th)^2 - 1)/sin(th)^2], [1, 0]], [[0, 0], [0, 0]]]] -+ [[[0, -1], [1, 0]], [[0, 0], [0, 0]]]] - - In dimension 2, the Riemann tensor can be expressed entirely in terms of - the Ricci scalar `r`: -diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx -index dfb8751467..27402e54ab 100644 ---- a/src/sage/symbolic/expression.pyx -+++ b/src/sage/symbolic/expression.pyx -@@ -7154,7 +7154,7 @@ cdef class Expression(CommutativeRingElement): - sage: ex = lcm(sin(x)^2 - 1, sin(x)^2 + sin(x)); ex - (sin(x)^2 + sin(x))*(sin(x)^2 - 1)/(sin(x) + 1) - sage: ex.simplify_full() -- -cos(x)^2*sin(x) -+ sin(x)^3 - sin(x) - - TESTS: - -@@ -10004,7 +10004,7 @@ cdef class Expression(CommutativeRingElement): - - sage: f=tan(3*x) - sage: f.simplify_trig() -- (4*cos(x)^2 - 1)*sin(x)/(4*cos(x)^3 - 3*cos(x)) -+ -(4*cos(x)^2 - 1)*sin(x)/(4*cos(x)*sin(x)^2 - cos(x)) - sage: f.simplify_trig(False) - sin(3*x)/cos(3*x) - diff --git a/pkgs/applications/science/math/sage/patches/pynac-0.7.22.patch b/pkgs/applications/science/math/sage/patches/pynac-0.7.22.patch deleted file mode 100644 index 22f274d608d..00000000000 --- a/pkgs/applications/science/math/sage/patches/pynac-0.7.22.patch +++ /dev/null @@ -1,479 +0,0 @@ -diff --git a/src/sage/calculus/calculus.py b/src/sage/calculus/calculus.py -index 3a417d9d5c..fadaadbaf6 100644 ---- a/src/sage/calculus/calculus.py -+++ b/src/sage/calculus/calculus.py -@@ -231,7 +231,7 @@ Another example:: - sage: f(x=3) - arcsinh(1) - sage: f.derivative(x) -- 1/3/sqrt(1/9*x^2 + 1) -+ 1/sqrt(x^2 + 9) - - We compute the length of the parabola from 0 to 2:: - -@@ -1509,8 +1509,8 @@ def laplace(ex, t, s, algorithm='maxima'): - Testing SymPy:: - - sage: laplace(t^n, t, s, algorithm='sympy') -- (s^(-n)*gamma(n + 1)/s, 0, -re(n) < 1) -- -+ (gamma(n + 1)/(s*s^n), 0, -re(n) < 1) -+ - Testing Maxima:: - - sage: laplace(t^n, t, s, algorithm='maxima') -diff --git a/src/sage/functions/hypergeometric.py b/src/sage/functions/hypergeometric.py -index 1fc2db5c94..f3e49b9cdb 100644 ---- a/src/sage/functions/hypergeometric.py -+++ b/src/sage/functions/hypergeometric.py -@@ -34,7 +34,7 @@ Simplification (note that ``simplify_full`` does not yet call - sage: a.simplify_hypergeometric() - 1/((-e^x + 1)^e^x) - sage: a.simplify_hypergeometric(algorithm='sage') -- (-e^x + 1)^(-e^x) -+ 1/((-e^x + 1)^e^x) - - Equality testing:: - -@@ -145,7 +145,7 @@ Series expansions of confluent hypergeometric functions:: - - sage: hypergeometric_M(2, 2, x).series(x, 3) - 1 + 1*x + 1/2*x^2 + Order(x^3) -- sage: hypergeometric_U(2, 2, x).series(x == 3, 100).subs(x=1).n() -+ sage: hypergeometric_U(2, 2, x).series(x == 3, 100).subs(x=1).n() # known bug (see :trac:`25688`) - 0.403652637676806 - sage: hypergeometric_U(2, 2, 1).n() - 0.403652637676806 -@@ -773,7 +773,7 @@ def closed_form(hyp): - sage: closed_form(hypergeometric([], [], z)) - e^z - sage: closed_form(hypergeometric([a], [], z)) -- (-z + 1)^(-a) -+ 1/((-z + 1)^a) - sage: closed_form(hypergeometric([1, 1, 2], [1, 1], z)) - (z - 1)^(-2) - sage: closed_form(hypergeometric([2, 3], [1], x)) -@@ -1121,7 +1121,7 @@ class Hypergeometric_U(BuiltinFunction): - sage: var('a b z') - (a, b, z) - sage: hypergeometric_U(a, b, z).generalized() -- z^(-a)*hypergeometric((a, a - b + 1), (), -1/z) -+ hypergeometric((a, a - b + 1), (), -1/z)/z^a - sage: hypergeometric_U(1, 3, 1/2).generalized() - 2*hypergeometric((1, -1), (), -2) - sage: hypergeometric_U(3, I, 2).generalized() -diff --git a/src/sage/functions/log.py b/src/sage/functions/log.py -index 75d1bf8060..61968582af 100644 ---- a/src/sage/functions/log.py -+++ b/src/sage/functions/log.py -@@ -518,17 +518,17 @@ class Function_polylog(GinacFunction): - - sage: BF = RealBallField(100) - sage: polylog(2, BF(1/3)) -- [0.36621322997706348761674629766 +/- 4.51e-30] -+ [0.36621322997706348761674629766... +/- ...] - sage: polylog(2, BF(4/3)) -- nan -+ [2.27001825336107090380391448586 +/- 5.64e-30] + [-0.90377988538400159956755721265 +/- 8.39e-30]*I - sage: parent(_) -- Real ball field with 100 bits of precision -+ Complex ball field with 100 bits of precision - sage: polylog(2, CBF(1/3)) -- [0.366213229977063 +/- 5.85e-16] -+ [0.366213229977063 +/- ...] - sage: parent(_) - Complex ball field with 53 bits of precision - sage: polylog(2, CBF(1)) -- [1.644934066848226 +/- 6.59e-16] -+ [1.644934066848226 +/- ...] - sage: parent(_) - Complex ball field with 53 bits of precision - """ -diff --git a/src/sage/functions/trig.py b/src/sage/functions/trig.py -index e7e7a311cd..1f2926d6c9 100644 ---- a/src/sage/functions/trig.py -+++ b/src/sage/functions/trig.py -@@ -529,13 +529,8 @@ class Function_arcsin(GinacFunction): - arcsin - sage: asin(complex(1,1)) - (0.6662394324925152+1.0612750619050357j) -- -- Check that :trac:`22823` is fixed:: -- -- sage: bool(asin(SR(2.1)) == NaN) -- True -- sage: asin(SR(2.1)).is_real() -- False -+ sage: asin(SR(2.1)) -+ 1.57079632679490 - 1.37285914424258*I - """ - GinacFunction.__init__(self, 'arcsin', latex_name=r"\arcsin", - conversions=dict(maxima='asin', sympy='asin', fricas="asin", giac="asin")) -@@ -595,13 +590,8 @@ class Function_arccos(GinacFunction): - arccos - sage: acos(complex(1,1)) - (0.9045568943023814-1.0612750619050357j) -- -- Check that :trac:`22823` is fixed:: -- -- sage: bool(acos(SR(2.1)) == NaN) -- True -- sage: acos(SR(2.1)).is_real() -- False -+ sage: acos(SR(2.1)) -+ 1.37285914424258*I - """ - GinacFunction.__init__(self, 'arccos', latex_name=r"\arccos", - conversions=dict(maxima='acos', sympy='acos', fricas='acos', giac='acos')) -@@ -807,7 +797,7 @@ class Function_arcsec(GinacFunction): - sage: arcsec(2).n(100) - 1.0471975511965977461542144611 - sage: arcsec(1/2).n(100) -- NaN -+ 1.3169578969248167086250463473*I - sage: RDF(arcsec(2)) # abs tol 1e-15 - 1.0471975511965976 - sage: arcsec(1 + I) -@@ -958,7 +948,9 @@ class Function_arctan2(GinacFunction): - sage: atan2(0,0,hold=True) - arctan2(0, 0) - sage: atan2(0,0,hold=True).n() -- NaN -+ Traceback (most recent call last): -+ ... -+ RuntimeError: atan2(): division by zero - - Check if :trac:`10062` is fixed, this was caused by - ``(I*I).is_positive()`` returning ``True``:: -diff --git a/src/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py b/src/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py -index 3b5c8d1729..1c6b73a16c 100644 ---- a/src/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py -+++ b/src/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py -@@ -1422,8 +1422,10 @@ class HyperbolicGeodesicUHP(HyperbolicGeodesic): - expressions do not generate runtime errors. :: - - sage: g=HyperbolicPlane().UHP().get_geodesic(-1+I,1+I) -- sage: g.midpoint() -- Point in UHP 1/2*(sqrt(2)*e^(1/2*arccosh(3)) - sqrt(2) + (I - 1)*e^(1/2*arccosh(3)) + I - 1)/((1/4*I - 1/4)*sqrt(2)*e^(1/2*arccosh(3)) - (1/4*I - 1/4)*sqrt(2) + 1/2*e^(1/2*arccosh(3)) + 1/2) -+ sage: point = g.midpoint(); point -+ Point in UHP -1/2*(sqrt(2)*... -+ sage: QQbar(point.coordinates()).radical_expression() -+ I*sqrt(2) - - Check that floating points remain floating points - in :meth:`midpoint` :: -diff --git a/src/sage/interfaces/fricas.py b/src/sage/interfaces/fricas.py -index 82aae78e37..8501ea2a18 100644 ---- a/src/sage/interfaces/fricas.py -+++ b/src/sage/interfaces/fricas.py -@@ -1084,14 +1084,14 @@ class FriCASElement(ExpectElement): - 0.451026811796262, - 0.732815101786507, - 0.837981225008390, -- NaN, -- NaN, -+ 1.57079632679490 - 0.467145308103262*I, -+ 0.467145308103262*I, - 1.11976951499863, - 0.451026811796262, - 0.732815101786507, - 0.837981225008390, -- NaN, -- NaN] -+ 1.57079632679490 - 0.467145308103262*I, -+ 0.467145308103262*I] - sage: l = [tanh, sinh, cosh, coth, sech, csch, asinh, acosh, atanh, acoth, asech, acsch, arcsinh, arccosh, arctanh, arccoth, arcsech, arccsch] - sage: [f(x)._fricas_().sage().subs(x=0.9) for f in l] # optional - fricas - [0.716297870199024, -diff --git a/src/sage/libs/pynac/pynac.pyx b/src/sage/libs/pynac/pynac.pyx -index 9e9d8f664b..e3406f007e 100644 ---- a/src/sage/libs/pynac/pynac.pyx -+++ b/src/sage/libs/pynac/pynac.pyx -@@ -1824,7 +1824,7 @@ cdef py_atan2(x, y): - sage: atan2(CC(I), CC(I+1)) - 0.553574358897045 + 0.402359478108525*I - sage: atan2(CBF(I), CBF(I+1)) -- [0.55357435889705 +/- 5.58e-15] + [0.402359478108525 +/- 7.11e-16]*I -+ [0.55357435889705 +/- ...] + [0.402359478108525 +/- ...]*I - - Check that :trac:`23776` is fixed and RDF input gives real output:: - -diff --git a/src/sage/matrix/matrix_symbolic_dense.pyx b/src/sage/matrix/matrix_symbolic_dense.pyx -index 46a15e53eb..7a0beb437b 100644 ---- a/src/sage/matrix/matrix_symbolic_dense.pyx -+++ b/src/sage/matrix/matrix_symbolic_dense.pyx -@@ -200,7 +200,7 @@ cdef class Matrix_symbolic_dense(Matrix_generic_dense): - sage: eval, [evec], mult = es[0] - sage: delta = eval*evec - evec*A - sage: abs(abs(delta)) < 1e-10 -- sqrt(9/25*((2*sqrt(6) - 3)*(sqrt(6) - 2) + 7*sqrt(6) - 18)^2 + 9/25*((sqrt(6) - 2)*(sqrt(6) - 4) + 6*sqrt(6) - 14)^2) < (1.00000000000000e-10) -+ 3/5*sqrt(((2*sqrt(6) - 3)*(sqrt(6) - 2) + 7*sqrt(6) - 18)^2 + ((sqrt(6) - 2)*(sqrt(6) - 4) + 6*sqrt(6) - 14)^2) < (1.00000000000000e-10) - sage: abs(abs(delta)).n() < 1e-10 - True - -diff --git a/src/sage/modules/matrix_morphism.py b/src/sage/modules/matrix_morphism.py -index 17a1d6e290..03892ceec0 100644 ---- a/src/sage/modules/matrix_morphism.py -+++ b/src/sage/modules/matrix_morphism.py -@@ -214,9 +214,9 @@ class MatrixMorphism_abstract(sage.categories.morphism.Morphism): - sage: f((1, 0)) - Traceback (most recent call last): - ... -- TypeError: Unable to coerce entries (=[1.00000000000000*I, 0.000000000000000]) to coefficients in Real Field with 53 bits of precision -+ TypeError: Unable to coerce entries (=[1.00000000000000*I, 0]) to coefficients in Real Field with 53 bits of precision - sage: f((1, 0), coerce=False) -- (1.00000000000000*I, 0.000000000000000) -+ (1.00000000000000*I, 0) - - """ - if self.domain().is_ambient(): -diff --git a/src/sage/plot/plot.py b/src/sage/plot/plot.py -index 77cdeb8c46..e501e74036 100644 ---- a/src/sage/plot/plot.py -+++ b/src/sage/plot/plot.py -@@ -2061,7 +2061,7 @@ def _plot(funcs, xrange, parametric=False, - plot properly (:trac:`13246`):: - - sage: parametric_plot((x, arcsec(x)), (x, -2, 2)) -- Graphics object consisting of 1 graphics primitive -+ Graphics object consisting of 2 graphics primitives - - """ - from sage.plot.colors import Color -diff --git a/src/sage/repl/display/formatter.py b/src/sage/repl/display/formatter.py -index 8ce2e839d7..948207c95e 100644 ---- a/src/sage/repl/display/formatter.py -+++ b/src/sage/repl/display/formatter.py -@@ -25,11 +25,11 @@ generally, all sage expression as an ASCII art object:: - sage: shell = get_test_shell() - sage: shell.run_cell('%display ascii_art') - sage: shell.run_cell('integral(x^2/pi^x, x)') -- / 2 2 \ -x*log(pi) -- -\x *log (pi) + 2*x*log(pi) + 2/*e -- --------------------------------------------- -- 3 -- log (pi) -+ -x / 2 2 \ -+ -pi *\x *log (pi) + 2*x*log(pi) + 2/ -+ -------------------------------------- -+ 3 -+ log (pi) - sage: shell.run_cell("i = var('i')") - sage: shell.run_cell('sum(i*x^i, i, 0, 10)') - 10 9 8 7 6 5 4 3 2 -diff --git a/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py b/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py -index d8ebbf4f76..8c60f65e99 100644 ---- a/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py -+++ b/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py -@@ -151,8 +151,8 @@ A multiple point example (Example 6.5 of [RaWi2012]_):: - [(x + 2*y - 1, 1), (2*x + y - 1, 1)]) - sage: F1 = decomp[1] - sage: F1.asymptotics(p, alpha, 2) -- (-3*((2*a^2 - 5*a*b + 2*b^2)*r^2 + (a + b)*r + 3)*((1/3)^(-a)*(1/3)^(-b))^r, -- (1/3)^(-a)*(1/3)^(-b), -3*(2*a^2 - 5*a*b + 2*b^2)*r^2 - 3*(a + b)*r - 9) -+ (-3*((2*a^2 - 5*a*b + 2*b^2)*r^2 + (a + b)*r + 3)*(1/((1/3)^a*(1/3)^b))^r, -+ 1/((1/3)^a*(1/3)^b), -3*(2*a^2 - 5*a*b + 2*b^2)*r^2 - 3*(a + b)*r - 9) - sage: alpha = [4, 3] - sage: decomp = F.asymptotic_decomposition(alpha) - sage: F1 = decomp[1] -@@ -2159,7 +2159,7 @@ class FractionWithFactoredDenominator(RingElement): - sage: p = {x: 1/3, y: 1/3} - sage: alpha = (var('a'), var('b')) - sage: F.asymptotics_multiple(p, alpha, 2, var('r')) # long time -- (3*((1/3)^(-a)*(1/3)^(-b))^r*e^(2/3), (1/3)^(-a)*(1/3)^(-b), 3*e^(2/3)) -+ (3*(1/((1/3)^a*(1/3)^b))^r*e^(2/3), 1/((1/3)^a*(1/3)^b), 3*e^(2/3)) - """ - from itertools import product - from sage.calculus.functions import jacobian -diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py -index 16a268a02c..5fd244e93b 100644 ---- a/src/sage/stats/basic_stats.py -+++ b/src/sage/stats/basic_stats.py -@@ -183,7 +183,7 @@ def std(v, bias=False): - sage: std([]) - NaN - sage: std([I, sqrt(2), 3/5]) -- sqrt(1/450*(10*sqrt(2) - 5*I - 3)^2 + 1/450*(5*sqrt(2) - 10*I + 3)^2 + 1/450*(5*sqrt(2) + 5*I - 6)^2) -+ 1/15*sqrt(1/2)*sqrt((10*sqrt(2) - 5*I - 3)^2 + (5*sqrt(2) - 10*I + 3)^2 + (5*sqrt(2) + 5*I - 6)^2) - sage: std([RIF(1.0103, 1.0103), RIF(2)]) - 0.6998235813403261? - sage: import numpy -diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx -index ab4c05de3a..60f0dc549a 100644 ---- a/src/sage/symbolic/expression.pyx -+++ b/src/sage/symbolic/expression.pyx -@@ -622,7 +622,7 @@ cdef class Expression(CommutativeRingElement): - sage: x^(-5) - x^(-5) - sage: x^(-y) -- x^(-y) -+ 1/(x^y) - sage: 2*x^(-1) - 2/x - sage: i*x -@@ -3621,14 +3621,14 @@ cdef class Expression(CommutativeRingElement): - sage: repl_dict = {b_0: b_0, b_3: b_1, b_2: b_3, b_1: b_2} - sage: P = precomp.substitute(repl_dict) - sage: P.expand() -- -2^(-b_0)*2^(-b_2)*2^b_3 - 2^b_0*2^(-b_2)*2^b_3 - -- 2^(-b_0)*2^b_2*2^b_3 + 2^b_0*2^b_2*2^b_3 - 2*2^(-b_0)*2^(-b_2) -- - 2*2^b_0*2^(-b_2) - 2*2^(-b_0)*2^b_2 + 2*2^b_0*2^b_2 + -- 2^(-b_0)*2^b_3 + 2^b_0*2^b_3 + 2^(-b_2)*2^b_3 + 2^b_2*2^b_3 + -- 2*2^(-b_0) + 2*2^b_0 + 2*2^(-b_2) + 2*2^b_2 - 9*2^b_3 - -- 2^(-b_0)*2^(-b_2)/2^b_3 - 2^b_0*2^(-b_2)/2^b_3 - -- 2^(-b_0)*2^b_2/2^b_3 + 2^b_0*2^b_2/2^b_3 + 2^(-b_0)/2^b_3 + -- 2^b_0/2^b_3 + 2^(-b_2)/2^b_3 + 2^b_2/2^b_3 - 9/2^b_3 - 18 -+ 2^b_0*2^b_2*2^b_3 + 2*2^b_0*2^b_2 + 2^b_0*2^b_3 + 2^b_2*2^b_3 + -+ 2*2^b_0 + 2*2^b_2 - 9*2^b_3 + 2^b_0*2^b_2/2^b_3 - -+ 2^b_0*2^b_3/2^b_2 - 2^b_2*2^b_3/2^b_0 - 2*2^b_0/2^b_2 - -+ 2*2^b_2/2^b_0 + 2^b_0/2^b_3 + 2^b_2/2^b_3 + 2^b_3/2^b_0 + -+ 2^b_3/2^b_2 + 2/2^b_0 + 2/2^b_2 - 2^b_0/(2^b_2*2^b_3) - -+ 2^b_2/(2^b_0*2^b_3) - 9/2^b_3 - 2^b_3/(2^b_0*2^b_2) - -+ 2/(2^b_0*2^b_2) + 1/(2^b_0*2^b_3) + 1/(2^b_2*2^b_3) - -+ 1/(2^b_0*2^b_2*2^b_3) - 18 - - sage: _0,b_1,b_2=var('b_0,b_1,b_2') - sage: f = 1/27*b_2^2/(2^b_2)^2 + 1/27*b_1^2/(2^b_1)^2 + \ -@@ -3809,7 +3809,7 @@ cdef class Expression(CommutativeRingElement): - - sage: x = SR.symbol('x', domain='real') - sage: (x^3)^(1/3) -- (x^3)^(1/3) -+ x - sage: (x^4)^(1/4) - abs(x) - sage: (x^8)^(1/4) -@@ -3872,7 +3872,7 @@ cdef class Expression(CommutativeRingElement): - sage: 2^(x/log(2)) - e^x - sage: 2^(-x^2/2/log(2)) -- e^(-1/2*x^2) -+ 1/e^(1/2*x^2) - sage: x^(x/log(x)) - x^(x/log(x)) - sage: assume(x > 0) -@@ -4816,18 +4816,24 @@ cdef class Expression(CommutativeRingElement): - sage: ((x+y)^(x+y)).match(w0^w0) - {$0: x + y} - sage: t = ((a+b)*(a+c)).match((a+w0)*(a+w1)) -- sage: t[w0], t[w1] -- (c, b) -+ sage: set([t[w0], t[w1]]) == set([b, c]) -+ True - sage: ((a+b)*(a+c)).match((w0+b)*(w0+c)) - {$0: a} - sage: t = ((a+b)*(a+c)).match((w0+w1)*(w0+w2)) -- sage: t[w0], t[w1], t[w2] -- (a, c, b) -- sage: print(((a+b)*(a+c)).match((w0+w1)*(w1+w2))) -- None -+ sage: t[w0] -+ a -+ sage: set([t[w1], t[w2]]) == set([b, c]) -+ True -+ sage: t = ((a+b)*(a+c)).match((w0+w1)*(w1+w2)) -+ sage: t[w1] -+ a -+ sage: set([t[w0], t[w2]]) == set([b, c]) -+ True - sage: t = (a*(x+y)+a*z+b).match(a*w0+w1) -- sage: t[w0], t[w1] -- (x + y, a*z + b) -+ sage: s = set([t[w0], t[w1]]) -+ sage: s == set([x+y, a*z+b]) or s == set([z, a*(x+y)+b]) -+ True - sage: print((a+b+c+d+f+g).match(c)) - None - sage: (a+b+c+d+f+g).has(c) -@@ -4836,7 +4842,7 @@ cdef class Expression(CommutativeRingElement): - {$0: a + b + d + f + g} - sage: (a+b+c+d+f+g).match(c+g+w0) - {$0: a + b + d + f} -- sage: (a+b).match(a+b+w0) -+ sage: (a+b).match(a+b+w0) # known bug - {$0: 0} - sage: print((a*b^2).match(a^w0*b^w1)) - None -@@ -5009,7 +5015,7 @@ cdef class Expression(CommutativeRingElement): - a^3 + b^3 + (x + y)^3 - - sage: t.subs(w0 == w0^2) -- (x^2 + y^2)^18 + a^16 + b^16 -+ a^8 + b^8 + (x^2 + y^2)^6 - - sage: t.subs(a == b, b == c) - (x + y)^3 + b^2 + c^2 -@@ -8392,9 +8398,13 @@ cdef class Expression(CommutativeRingElement): - sage: SR(I).arctan2(1) - arctan2(I, 1) - sage: SR(CDF(0,1)).arctan2(1) -- NaN + +infinity*I -- sage: SR(1).arctan2(CDF(0,1)) # known bug -- 0.7853981633974484 - 19.012501686914433*I -+ Traceback (most recent call last): -+ ... -+ ValueError: power::eval(): division by zero -+ sage: SR(1).arctan2(CDF(0,1)) -+ Traceback (most recent call last): -+ ... -+ ValueError: power::eval(): division by zero - - sage: arctan2(0,oo) - 0 -@@ -8656,7 +8666,7 @@ cdef class Expression(CommutativeRingElement): - 1/2*I*pi - sage: SR(1/2).arccosh() - arccosh(1/2) -- sage: SR(CDF(1/2)).arccosh() # rel tol 1e-15 -+ sage: SR(CDF(1/2)).arccosh() # rel tol 1e-15 - 1.0471975511965976*I - sage: maxima('acosh(0.5)') - 1.04719755119659...*%i -@@ -11687,7 +11697,7 @@ cdef class Expression(CommutativeRingElement): - sage: a.solve(t) - [] - sage: b = a.canonicalize_radical(); b -- -23040.0*(-2.0*e^(1800*t) + 25.0*e^(900*t) - 32.0)*e^(-2400*t) -+ (46080.0*e^(1800*t) - 576000.0*e^(900*t) + 737280.0)*e^(-2400*t) - sage: b.solve(t) - [] - sage: b.solve(t, to_poly_solve=True) -@@ -12163,14 +12173,14 @@ cdef class Expression(CommutativeRingElement): - - sage: (n,k,j)=var('n,k,j') - sage: sum(binomial(n,k)*binomial(k-1,j)*(-1)**(k-1-j),k,j+1,n) -- -(-1)^(-j)*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n) -+ -(-1)^j*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n) - sage: assume(j>-1) - sage: sum(binomial(n,k)*binomial(k-1,j)*(-1)**(k-1-j),k,j+1,n) - 1 - sage: forget() - sage: assume(n>=j) - sage: sum(binomial(n,k)*binomial(k-1,j)*(-1)**(k-1-j),k,j+1,n) -- -(-1)^(-j)*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n) -+ -(-1)^j*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n) - sage: forget() - sage: assume(j==-1) - sage: sum(binomial(n,k)*binomial(k-1,j)*(-1)**(k-1-j),k,j+1,n) -@@ -12178,7 +12188,7 @@ cdef class Expression(CommutativeRingElement): - sage: forget() - sage: assume(j<-1) - sage: sum(binomial(n,k)*binomial(k-1,j)*(-1)**(k-1-j),k,j+1,n) -- -(-1)^(-j)*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n) -+ -(-1)^j*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n) - sage: forget() - - Check that :trac:`16176` is fixed:: -diff --git a/src/sage/symbolic/relation.py b/src/sage/symbolic/relation.py -index da6f0eef42..4bd65ef572 100644 ---- a/src/sage/symbolic/relation.py -+++ b/src/sage/symbolic/relation.py -@@ -895,7 +895,7 @@ def solve(f, *args, **kwds): - sage: (r[0][x], r[0][y]) - (2*lambert_w(1/2), 1) - sage: solve(-2*x**3 + 4*x**2 - 2*x + 6 > 0, x, algorithm='sympy') -- [x < (1/6*sqrt(77) + 79/54)^(1/3) + 1/9/(1/6*sqrt(77) + 79/54)^(1/3) + 2/3] -+ [x < 1/3*(1/2)^(1/3)*(9*sqrt(77) + 79)^(1/3) + 2/3*(1/2)^(2/3)/(9*sqrt(77) + 79)^(1/3) + 2/3] - sage: solve(sqrt(2*x^2 - 7) - (3 - x),x,algorithm='sympy') - [x == -8, x == 2] - sage: solve(sqrt(2*x + 9) - sqrt(x + 1) - sqrt(x + 4),x,algorithm='sympy') diff --git a/pkgs/applications/science/math/sage/patches/python3-syntax-without-write.patch b/pkgs/applications/science/math/sage/patches/python3-syntax-without-write.patch deleted file mode 100644 index ff1dcd22acf..00000000000 --- a/pkgs/applications/science/math/sage/patches/python3-syntax-without-write.patch +++ /dev/null @@ -1,40 +0,0 @@ -diff --git a/src/sage/tests/py3_syntax.py b/src/sage/tests/py3_syntax.py -index e564860b48..86ab3725f9 100644 ---- a/src/sage/tests/py3_syntax.py -+++ b/src/sage/tests/py3_syntax.py -@@ -179,15 +179,30 @@ class Python3SyntaxTest(SortedDirectoryWalkerABC): - sage: py3_syntax = Python3SyntaxTest() - sage: py3_syntax.test(src.name) - Invalid Python 3 syntax found: -- File "...py", line 1 -- print "invalid print statement" -- ^ -- SyntaxError: Missing parentheses in call to 'print' -+ Missing parentheses in call to 'print'... - sage: os.unlink(src.name) - """ -+ -+ # compile all given files in memory, printing all errors -+ # inspired by the py_compile module (but without writing to file) -+ script = """ -+import sys -+import importlib.machinery -+rv = 0 -+for file in sys.argv[1:]: -+ loader = importlib.machinery.SourceFileLoader('', file) -+ source_bytes = loader.get_data(file) -+ try: -+ code = loader.source_to_code(source_bytes, file) -+ except Exception as err: -+ print(err) -+ rv = 1 -+sys.exit(rv) -+""" - cmd = [ - 'python3', -- '-m', 'py_compile' -+ '-c', -+ script, - ] + list(filenames) - process = subprocess.Popen( - cmd, diff --git a/pkgs/applications/science/math/sage/patches/sagenb-sphinx-1.7.patch b/pkgs/applications/science/math/sage/patches/sagenb-sphinx-1.7.patch deleted file mode 100644 index 42deef4eab0..00000000000 --- a/pkgs/applications/science/math/sage/patches/sagenb-sphinx-1.7.patch +++ /dev/null @@ -1,31 +0,0 @@ -From 7419e0246230594ebfd5e7a2fe6b80d67abfc98a Mon Sep 17 00:00:00 2001 -From: Jeroen Demeyer -Date: Tue, 20 Mar 2018 10:40:41 +0100 -Subject: Fix sphinxify doctests - ---- - sagenb/misc/sphinxify.py | 6 +++--- - 1 file changed, 3 insertions(+), 3 deletions(-) - -diff --git a/sagenb/misc/sphinxify.py b/sagenb/misc/sphinxify.py -index 4f76d41..15623d9 100644 ---- a/sagenb/misc/sphinxify.py -+++ b/sagenb/misc/sphinxify.py -@@ -47,11 +47,11 @@ def sphinxify(docstring, format='html'): - - sage: from sage.misc.sphinxify import sphinxify - sage: sphinxify('A test') -- '...
\n \n

A test

\n\n\n
' -+ '
\n \n

A test

\n\n\n
' - sage: sphinxify('**Testing**\n`monospace`') -- '...
Testing\n\n\n\n
' -+ '
Testing\n\n\n\n
' - sage: sphinxify('`x=y`') -- '...
\n \n

x=y

\n\n\n
' -+ '
\n \n

x=y

\n\n\n
' - sage: sphinxify('`x=y`', format='text') - 'x=y\n' - sage: sphinxify(':math:`x=y`', format='text') --- -cgit v1.0-1-gd88e - diff --git a/pkgs/applications/science/math/sage/patches/sphinx-1.7.patch b/pkgs/applications/science/math/sage/patches/sphinx-1.7.patch deleted file mode 100644 index c67b8942e28..00000000000 --- a/pkgs/applications/science/math/sage/patches/sphinx-1.7.patch +++ /dev/null @@ -1,62 +0,0 @@ -diff --git a/src/bin/sage b/src/bin/sage -index 397f30cbed..3fc473c343 100755 ---- a/src/bin/sage -+++ b/src/bin/sage -@@ -980,8 +980,11 @@ if [ "$1" = '-rsyncdist' -o "$1" = "--rsyncdist" ]; then - fi - - if [ "$1" = "-docbuild" -o "$1" = "--docbuild" ]; then -+ # Redirect stdin from /dev/null. This helps with running TeX which -+ # tends to ask interactive questions if something goes wrong. These -+ # cause the build to hang. If stdin is /dev/null, TeX just aborts. - shift -- exec sage-python23 -m "sage_setup.docbuild" "$@" -+ exec sage-python23 -m sage_setup.docbuild "$@" Introduction to the -adics -+
  • Introduction to the -adics
    • - """ - debug_inf(app, "???? Trying intersphinx for %s"%node['reftarget']) - builder = app.builder -diff --git a/src/sage/misc/sphinxify.py b/src/sage/misc/sphinxify.py -index 4f76d4113a..8f426b5989 100644 ---- a/src/sage/misc/sphinxify.py -+++ b/src/sage/misc/sphinxify.py -@@ -47,11 +47,11 @@ def sphinxify(docstring, format='html'): - - sage: from sage.misc.sphinxify import sphinxify - sage: sphinxify('A test') -- '...
    \n \n

    A test

    \n\n\n
    ' -+ '
    \n \n

    A test

    \n\n\n
    ' - sage: sphinxify('**Testing**\n`monospace`') -- '...
    Testing\n\n\n\n
    ' -+ '
    Testing\n\n \n

    x=y

    \n\n\n
    ' -+ '
    \n \n

    x=y

    \n\n\n
    ' - sage: sphinxify('`x=y`', format='text') - 'x=y\n' - sage: sphinxify(':math:`x=y`', format='text') -diff --git a/src/sage_setup/docbuild/sphinxbuild.py b/src/sage_setup/docbuild/sphinxbuild.py -index fda76a4174..d3413239dd 100644 ---- a/src/sage_setup/docbuild/sphinxbuild.py -+++ b/src/sage_setup/docbuild/sphinxbuild.py -@@ -207,7 +207,7 @@ def runsphinx(): - try: - sys.stdout = SageSphinxLogger(sys.stdout, os.path.basename(output_dir)) - sys.stderr = SageSphinxLogger(sys.stderr, os.path.basename(output_dir)) -- sphinx.cmdline.main(sys.argv) -+ sphinx.cmdline.main(sys.argv[1:]) - finally: - sys.stdout = saved_stdout - sys.stderr = saved_stderr diff --git a/pkgs/applications/science/math/sage/patches/spkg-scripts.patch b/pkgs/applications/science/math/sage/patches/spkg-scripts.patch new file mode 100644 index 00000000000..4d37998b288 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/spkg-scripts.patch @@ -0,0 +1,46 @@ +commit f02714d4aea80e17cb8df62bab75d7c1a1b61a8e +Author: Timo Kaufmann +Date: Mon Jul 9 18:26:18 2018 +0200 + + Don't attempt to create dirs when showing pkg info + + The script dir cannot be assumed to be writeable after installation. + +diff --git a/build/bin/sage-spkg b/build/bin/sage-spkg +index f3e02aeae5..190d558ad1 100755 +--- a/build/bin/sage-spkg ++++ b/build/bin/sage-spkg +@@ -167,14 +167,6 @@ if [ -z "$SAGE_BUILD_DIR" ]; then + export SAGE_BUILD_DIR="$SAGE_LOCAL/var/tmp/sage/build" + fi + +-for dir in "$SAGE_SPKG_INST" "$SAGE_SPKG_SCRIPTS"; do +- mkdir -p "$dir" +- if [ $? -ne 0 ]; then +- error_msg "Error creating directory $dir" +- exit 1 +- fi +-done +- + + # Remove '.' from PYTHONPATH, which may also come from SAGE_PATH, to avoid + # trouble with setuptools / easy_install (cf. #10192, #10176): +@@ -563,11 +555,13 @@ fi + # Setup directories + ################################################################## + +-mkdir -p "$SAGE_BUILD_DIR" +-if [ $? -ne 0 ]; then +- error_msg "Error creating directory $SAGE_BUILD_DIR" +- exit 1 +-fi ++for dir in "$SAGE_SPKG_INST" "$SAGE_SPKG_SCRIPTS" "$SAGE_BUILD_DIR"; do ++ mkdir -p "$dir" ++ if [ $? -ne 0 ]; then ++ error_msg "Error creating directory $dir" ++ exit 1 ++ fi ++done + + # Trac #5852: check write permissions + if [ ! -w "$SAGE_BUILD_DIR" ]; then diff --git a/pkgs/applications/science/math/sage/patches/zn_poly_version.patch b/pkgs/applications/science/math/sage/patches/zn_poly_version.patch deleted file mode 100644 index 92ea4303e47..00000000000 --- a/pkgs/applications/science/math/sage/patches/zn_poly_version.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/src/sage/misc/package.py b/src/sage/misc/package.py -index 7ff4f21675..1d72168833 100644 ---- a/src/sage/misc/package.py -+++ b/src/sage/misc/package.py -@@ -350,7 +350,7 @@ def package_versions(package_type, local=False): - sage: 'gap' in std - True - sage: std['zn_poly'] -- ('0.9.p11', '0.9.p11') -+ ('0.9', '0.9.p11') - """ - return {pkg['name']: (pkg['installed_version'], pkg['remote_version']) for pkg in list_packages(package_type, local=local).values()} - diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix index c97785c574c..735f8495f9e 100644 --- a/pkgs/applications/science/math/sage/sage-src.nix +++ b/pkgs/applications/science/math/sage/sage-src.nix @@ -3,17 +3,20 @@ , fetchpatch }: stdenv.mkDerivation rec { - version = "8.2"; + version = "8.3"; name = "sage-src-${version}"; src = fetchFromGitHub { owner = "sagemath"; repo = "sage"; rev = version; - sha256 = "0d7vc16s7dj23an2cb8v5bhbnc6nsw20qhnnxr0xh8qg629027b8"; + sha256 = "0mbm99m5xry21xpi4q3q96gx392liwbifywf5awvl0j85a7rkfyx"; }; nixPatches = [ + # https://trac.sagemath.org/ticket/25809 + ./patches/spkg-scripts.patch + # https://trac.sagemath.org/ticket/25309 (fetchpatch { name = "spkg-paths.patch"; @@ -26,14 +29,7 @@ stdenv.mkDerivation rec { sha256 = "14s50yg3hpw9cp3v581dx7zfmpm2j972im7x30iwki8k45mjvk3i"; }) - # https://trac.sagemath.org/ticket/25328 - # https://trac.sagemath.org/ticket/25546 # https://trac.sagemath.org/ticket/25722 - (fetchpatch { - name = "install-jupyter-kernel-in-correct-prefix.patch"; - url = "https://git.sagemath.org/sage.git/patch?id=72167b98e3f64326df6b2c78785df25539472fcc"; - sha256 = "0pscnjhm7r2yr2rxnv4kkkq626vwaja720lixa3m3w9rwlxll5a7"; - }) ./patches/test-in-tmpdir.patch # https://trac.sagemath.org/ticket/25358 @@ -43,27 +39,13 @@ stdenv.mkDerivation rec { sha256 = "1hhannz7xzprijakn2w2d0rhd5zv2zikik9p51i87bas3nc658f7"; }) - # https://trac.sagemath.org/ticket/25357 rebased on 8.2 - ./patches/python3-syntax-without-write.patch - - # https://trac.sagemath.org/ticket/25314 - (fetchpatch { - name = "make-qepcad-test-optional.patch"; - url = "https://git.sagemath.org/sage.git/patch/?h=fe294c58bd035ef427e268901d54a6faa0058138"; - sha256 = "003d5baf5c0n5rfg010ijwkwz8kg0s414cxwczs2vhdayxdixbix"; - }) - + # Unfortunately inclusion in upstream sage was rejected. Instead the bug was + # fixed in python, but of course not backported to 2.7. So we'll probably + # have to keep this around until 2.7 is deprecated. # https://trac.sagemath.org/ticket/25316 + # https://github.com/python/cpython/pull/7476 ./patches/python-5755-hotpatch.patch - # https://trac.sagemath.org/ticket/25354 - # https://trac.sagemath.org/ticket/25531 - (fetchpatch { - name = "cysignals-include.patch"; - url = "https://git.sagemath.org/sage.git/patch/?h=28778bd25a37c80884d2b24e0683fb2989300cef"; - sha256 = "0fiiiw91pgs8avm9ggj8hb64bhqzl6jcw094d94nhirmh8w2jmc5"; - }) - # https://trac.sagemath.org/ticket/25315 (fetchpatch { name = "find-libraries-in-dyld-library-path.patch"; @@ -75,9 +57,6 @@ stdenv.mkDerivation rec { # https://trac.sagemath.org/ticket/25312 ./patches/pari-stackwarn.patch - # https://trac.sagemath.org/ticket/25311 - ./patches/zn_poly_version.patch - # https://trac.sagemath.org/ticket/25345 # (upstream patch doesn't apply on 8.2 source) ./patches/dochtml-optional.patch @@ -106,27 +85,6 @@ stdenv.mkDerivation rec { # the last version. ./patches/eclib-regulator-precision.patch - # sphinx 1.6 -> 1.7 upgrade - # https://trac.sagemath.org/ticket/24935 - ./patches/sphinx-1.7.patch - - # Adapt hashes to new boost version - # https://trac.sagemath.org/ticket/22243 - # (this ticket doesn't only upgrade boost but also avoids this problem in the future) - (fetchpatch { - name = "boost-upgrade.patch"; - url = "https://git.sagemath.org/sage.git/patch?id=a24a9c6b30b93957333a3116196214a931325b69"; - sha256 = "0z3870g2ms2a81vnw08dc2i4k7jr62w8fggvcdwaavgd1wvdxwfl"; - }) - - # gfan 0.6.2 - # https://trac.sagemath.org/ticket/23353 - (fetchpatch { - name = "gfan-update.patch"; - url = "https://git.sagemath.org/sage.git/patch/?h=420215fc469cde733ec7a339e59b78ad6eec804c&id=112498a293ea2bf563e41aed35f1aa608f01b349"; - sha256 = "0ga3hkx8cr23dpc919lgvpi5lmy0d728jkq9z6kf0fl9s8g31mxb"; - }) - # New glpk version has new warnings, filter those out until upstream sage has found a solution # https://trac.sagemath.org/ticket/24824 (fetchpatch { @@ -135,58 +93,14 @@ stdenv.mkDerivation rec { stripLen = 1; }) - # https://trac.sagemath.org/ticket/25329 - (fetchpatch { - name = "dont-check-exact-glpk-version.patch"; - url = "https://git.sagemath.org/sage.git/patch?id2=8bdc326ba57d1bb9664f63cf165a9e9920cc1afc&id=89d068d8d77316bfffa6bf8e9ebf70b3b3b88e5c"; - sha256 = "00knwxs6fmymfgfl0q5kcavmxm9sf90a4r76y35n5s55gj8pl918"; - }) - - # https://trac.sagemath.org/ticket/25355 - (fetchpatch { - name = "maxima-5.41.0.patch"; - url = "https://git.sagemath.org/sage.git/patch/?id=87328023c4739abdf24108038201e3fa9bdfc739"; - sha256 = "0hxi7qr5mfx1bc32r8j7iba4gzd7c6v63asylyf5cbyp86azpb7i"; - }) - - # Update cddlib from 0.94g to 0.94h. - # https://trac.sagemath.org/ticket/25341 (doesn't apply to 8.2 sources) - (fetchpatch { - url = "https://salsa.debian.org/science-team/sagemath/raw/58bbba93a807ca2933ca317501d093a1bb4b84db/debian/patches/u2-version-cddlib-094h.patch"; - sha256 = "0fmw7pzbaxs2dshky6iw9pr8i23p9ih2y2lw661qypdrxh5xw03k"; - stripLen = 1; - }) - (fetchpatch { - name = "revert-cddlib-doctest-changes.patch"; - url = "https://git.sagemath.org/sage.git/patch/?id=269c1e1551285566b8ba7a2b890989e5590e9f11"; - sha256 = "12bcjhq7hm2pmmj2bgjvcffjyls2x7q61ivlnaj5v5bsvhc183iy"; - revert = true; - }) - - # Only formatting changes. # https://trac.sagemath.org/ticket/25260 ./patches/numpy-1.14.3.patch - - # https://trac.sagemath.org/ticket/24374 - (fetchpatch { - name = "networkx-2.1.patch"; - url = "https://salsa.debian.org/science-team/sagemath/raw/487df9ae48ca1d93d9b1cb3af8745d31e30fb741/debian/patches/u0-version-networkx-2.1.patch"; - sha256 = "1xxxawygbgxgvlv7b4w8hhzgdnva4rhmgdxaiaa3pwdwln0yc750"; - stripLen = 1; - }) - - # https://trac.sagemath.org/ticket/24927 rebased - ./patches/arb-2.13.0.patch - - # https://trac.sagemath.org/ticket/24838 rebased - ./patches/pynac-0.7.22.patch - - # https://trac.sagemath.org/ticket/25862 - ./patches/eclib-20180710.patch ]; - patches = nixPatches ++ packageUpgradePatches; + patches = nixPatches ++ packageUpgradePatches ++ [ + ./patches/known-padics-bug.patch + ]; postPatch = '' # make sure shebangs etc are fixed, but sage-python23 still works