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Update to sagemath 7.6

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pcpa 2017-04-18 16:03:03 -04:00
parent 7e3068b9f2
commit f642d2e41d
16 changed files with 177 additions and 148 deletions
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1
.gitignore vendored
View file

@ -12,3 +12,4 @@
/sage-7.3.tar.gz
/sage-7.4.tar.gz
/sage-7.5.1.tar.gz
/sage-7.6.tar.gz

8
sagemath-4ti2.patch
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@ -1,7 +1,7 @@
diff -up src/sage/sandpiles/sandpile.py.orig src/sage/sandpiles/sandpile.py
--- src/sage/sandpiles/sandpile.py.orig 2017-03-04 13:25:45.385473644 -0500
+++ src/sage/sandpiles/sandpile.py 2017-03-04 13:25:53.872473969 -0500
@@ -346,9 +346,6 @@ from sage.arith.all import falling_facto
--- src/sage/sandpiles/sandpile.py.orig 2017-04-11 09:56:54.907264014 -0400
+++ src/sage/sandpiles/sandpile.py 2017-04-11 09:57:04.274264373 -0400
@@ -347,9 +347,6 @@ from sage.arith.all import falling_facto
from sage.rings.all import Integer, PolynomialRing, QQ, ZZ
from sage.symbolic.all import I, pi
@ -11,7 +11,7 @@ diff -up src/sage/sandpiles/sandpile.py.orig src/sage/sandpiles/sandpile.py
class Sandpile(DiGraph):
"""
Class for Dhar's abelian sandpile model.
@@ -5197,7 +5194,7 @@ class SandpileDivisor(dict):
@@ -5202,7 +5199,7 @@ class SandpileDivisor(dict):
sign_file.close()
# compute
try:

13
sagemath-atlas.patch
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@ -1,6 +1,6 @@
diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig 2017-03-29 19:33:34.149118879 -0400
+++ src/module_list.py 2017-03-29 19:34:09.520120233 -0400
--- src/module_list.py.orig 2017-04-11 10:03:27.798279059 -0400
+++ src/module_list.py 2017-04-11 10:05:34.272283903 -0400
@@ -12,20 +12,14 @@ SAGE_INC = '/usr/include'
import pkgconfig
@ -26,19 +26,20 @@ diff -up src/module_list.py.orig src/module_list.py
# FFLAS-FFPACK
fflas_ffpack_pc = pkgconfig.parse('fflas-ffpack')
@@ -45,7 +39,8 @@ givaro_cflags = pkgconfig.cflags('givaro
@@ -44,7 +38,9 @@ givaro_cflags = pkgconfig.cflags('givaro
# The above cblas should already be in the list thanks to #20646
gsl_pc = pkgconfig.parse('gsl')
gsl_libs = gsl_pc['libraries']
gsl_libs.remove('gslcblas')
-gsl_library_dirs = gsl_pc['library_dirs']
+gsl_libs.remove('gslcblas')
+gsl_libs.extend(cblas_libs)
+gsl_library_dirs = list(cblas_pc['library_dirs'])
gsl_include_dirs = gsl_pc['include_dirs']
# GD image library
diff -up src/sage/misc/cython.py.orig src/sage/misc/cython.py
--- src/sage/misc/cython.py.orig 2017-03-29 19:33:27.181118612 -0400
+++ src/sage/misc/cython.py 2017-03-29 19:33:36.568118971 -0400
--- src/sage/misc/cython.py.orig 2017-04-11 10:05:44.166284281 -0400
+++ src/sage/misc/cython.py 2017-04-11 10:06:00.016284888 -0400
@@ -30,15 +30,11 @@ import pkgconfig

22
sagemath-extensions.patch
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@ -1,7 +1,7 @@
diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig 2017-03-04 13:10:19.482438188 -0500
+++ src/module_list.py 2017-03-04 13:13:17.345444999 -0500
@@ -166,7 +166,6 @@ library_order["stdc++"] = 1000
--- src/module_list.py.orig 2017-04-11 09:54:40.320258860 -0400
+++ src/module_list.py 2017-04-11 09:54:50.432259248 -0400
@@ -165,7 +165,6 @@ library_order["stdc++"] = 1000
###
#############################################################
@ -9,7 +9,7 @@ diff -up src/module_list.py.orig src/module_list.py
UNAME = os.uname()
def uname_specific(name, value, alternative):
@@ -382,21 +381,21 @@ ext_modules = [
@@ -381,21 +380,21 @@ ext_modules = [
sources = ['sage/graphs/matchpoly.pyx'],
extra_compile_args = ['-std=c99']),
@ -46,7 +46,7 @@ diff -up src/module_list.py.orig src/module_list.py
Extension('sage.graphs.planarity',
sources = ['sage/graphs/planarity.pyx'],
@@ -415,10 +414,10 @@ ext_modules = [
@@ -414,10 +413,10 @@ ext_modules = [
Extension('sage.graphs.graph_decompositions.cutwidth',
sources = ['sage/graphs/graph_decompositions/cutwidth.pyx']),
@ -61,7 +61,7 @@ diff -up src/module_list.py.orig src/module_list.py
Extension('sage.graphs.spanning_tree',
sources = ['sage/graphs/spanning_tree.pyx']),
@@ -545,18 +544,18 @@ ext_modules = [
@@ -512,18 +511,18 @@ ext_modules = [
##
################################
@ -87,7 +87,7 @@ diff -up src/module_list.py.orig src/module_list.py
["sage/libs/fes.pyx"],
language = "c",
libraries = ['fes'],
@@ -580,17 +579,17 @@ ext_modules = [
@@ -547,17 +546,17 @@ ext_modules = [
Extension('sage.libs.gmp.pylong',
sources = ['sage/libs/gmp/pylong.pyx']),
@ -114,7 +114,7 @@ diff -up src/module_list.py.orig src/module_list.py
Extension('*', ['sage/libs/linbox/*.pyx']),
@@ -917,10 +916,10 @@ ext_modules = [
@@ -895,10 +894,10 @@ ext_modules = [
Extension('sage.matrix.matrix_window',
sources = ['sage/matrix/matrix_window.pyx']),
@ -129,7 +129,7 @@ diff -up src/module_list.py.orig src/module_list.py
Extension('sage.matrix.misc',
sources = ['sage/matrix/misc.pyx'],
@@ -1099,19 +1098,19 @@ ext_modules = [
@@ -1077,19 +1076,19 @@ ext_modules = [
Extension("sage.numerical.backends.interactivelp_backend",
["sage/numerical/backends/interactivelp_backend.pyx"]),
@ -161,7 +161,7 @@ diff -up src/module_list.py.orig src/module_list.py
["sage/numerical/backends/coin_backend.pyx"],
language = 'c++',
libraries = ["Cbc", "CbcSolver", "Cgl", "Clp", "CoinUtils",
@@ -1583,7 +1582,7 @@ ext_modules = [
@@ -1572,7 +1571,7 @@ ext_modules = [
##
################################
@ -170,7 +170,7 @@ diff -up src/module_list.py.orig src/module_list.py
sources = ["sage/sat/solvers/cryptominisat/cryptominisat.pyx"],
include_dirs = [os.path.join(SAGE_INC, "cmsat")] + zlib_include_dirs,
language = "c++",
@@ -1591,7 +1590,7 @@ ext_modules = [
@@ -1580,7 +1579,7 @@ ext_modules = [
library_dirs = zlib_library_dirs,
package = 'cryptominisat'),

6
sagemath-fes.patch
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@ -1,7 +1,7 @@
diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig 2017-03-04 13:33:14.446490840 -0500
+++ src/module_list.py 2017-03-04 13:33:23.046491170 -0500
@@ -555,11 +555,11 @@ ext_modules = [
--- src/module_list.py.orig 2017-04-11 10:00:15.271271687 -0400
+++ src/module_list.py 2017-04-11 10:00:26.344272111 -0400
@@ -522,11 +522,11 @@ ext_modules = [
sources = ["sage/libs/ecl.pyx"],
libraries = ["ecl"]),

6
sagemath-gcc6.patch
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@ -1,7 +1,7 @@
diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig 2017-03-29 18:45:52.972009314 -0400
+++ src/module_list.py 2017-03-29 18:46:02.855009693 -0400
@@ -880,7 +880,7 @@ ext_modules = [
--- src/module_list.py.orig 2017-04-11 10:02:15.848276304 -0400
+++ src/module_list.py 2017-04-11 10:02:24.616276640 -0400
@@ -855,7 +855,7 @@ ext_modules = [
library_dirs = m4ri_library_dirs,
include_dirs = m4ri_include_dirs,
depends = [SAGE_INC + "/m4rie/m4rie.h"],

34
sagemath-includes.patch
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@ -1,7 +1,7 @@
diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig 2017-03-29 18:42:35.820001764 -0400
+++ src/module_list.py 2017-03-29 18:43:56.158004841 -0400
@@ -63,6 +63,7 @@ linbox_cflags = pkgconfig.cflags('linbox
--- src/module_list.py.orig 2017-04-11 10:01:47.513275219 -0400
+++ src/module_list.py 2017-04-11 10:02:00.105275701 -0400
@@ -62,6 +62,7 @@ linbox_cflags = pkgconfig.cflags('linbox
# Singular
singular_pc = pkgconfig.parse('Singular')
singular_libs = singular_pc['libraries']
@ -9,7 +9,7 @@ diff -up src/module_list.py.orig src/module_list.py
singular_library_dirs = singular_pc['library_dirs']
singular_cflags = pkgconfig.cflags('Singular').split()
@@ -188,7 +189,8 @@ ext_modules = [
@@ -187,7 +188,8 @@ ext_modules = [
language='c++',
libraries = ["gmp", "m", "ntl"]),
@ -19,7 +19,7 @@ diff -up src/module_list.py.orig src/module_list.py
Extension('sage.algebras.quatalg.quaternion_algebra_cython',
sources = ['sage/algebras/quatalg/quaternion_algebra_cython.pyx'],
@@ -607,7 +609,8 @@ ext_modules = [
@@ -574,7 +576,8 @@ ext_modules = [
[])),
Extension('sage.libs.lrcalc.lrcalc',
@ -29,7 +29,7 @@ diff -up src/module_list.py.orig src/module_list.py
Extension('*', ['sage/libs/cypari2/*.pyx']),
Extension('*', ['sage/libs/pari/*.pyx']),
@@ -625,7 +628,8 @@ ext_modules = [
@@ -592,7 +595,8 @@ ext_modules = [
sources = ['sage/libs/readline.pyx'],
libraries = ['readline']),
@ -39,7 +39,7 @@ diff -up src/module_list.py.orig src/module_list.py
Extension('sage.libs.symmetrica.symmetrica',
sources = ["sage/libs/symmetrica/symmetrica.pyx"],
@@ -633,17 +637,21 @@ ext_modules = [
@@ -600,17 +604,21 @@ ext_modules = [
Extension('sage.libs.mpmath.utils',
sources = ["sage/libs/mpmath/utils.pyx"],
@ -65,7 +65,7 @@ diff -up src/module_list.py.orig src/module_list.py
###################################
##
@@ -651,7 +659,8 @@ ext_modules = [
@@ -618,7 +626,8 @@ ext_modules = [
##
###################################
@ -75,7 +75,7 @@ diff -up src/module_list.py.orig src/module_list.py
###################################
##
@@ -824,6 +833,7 @@ ext_modules = [
@@ -799,6 +808,7 @@ ext_modules = [
Extension("sage.matrix.matrix_complex_ball_dense",
["sage/matrix/matrix_complex_ball_dense.pyx"],
libraries=['arb', 'mpfi', 'mpfr'],
@ -83,15 +83,15 @@ diff -up src/module_list.py.orig src/module_list.py
language = "c++"),
Extension('sage.matrix.matrix_complex_double_dense',
@@ -891,6 +901,7 @@ ext_modules = [
@@ -866,6 +876,7 @@ ext_modules = [
sources = ['sage/matrix/matrix_modn_sparse.pyx']),
Extension('sage.matrix.matrix_mpolynomial_dense',
+ include_dirs = singular_incs,
sources = ['sage/matrix/matrix_mpolynomial_dense.pyx']),
Extension('sage.matrix.matrix_rational_dense',
@@ -1203,6 +1214,7 @@ ext_modules = [
Extension('sage.matrix.matrix_polynomial_dense',
@@ -1189,6 +1200,7 @@ ext_modules = [
Extension("sage.rings.complex_arb",
["sage/rings/complex_arb.pyx"],
libraries=['mpfi', 'mpfr', 'gmp'],
@ -99,7 +99,7 @@ diff -up src/module_list.py.orig src/module_list.py
language = 'c++'),
Extension('sage.rings.complex_double',
@@ -1275,6 +1287,7 @@ ext_modules = [
@@ -1264,6 +1276,7 @@ ext_modules = [
Extension("sage.rings.real_arb",
["sage/rings/real_arb.pyx"],
libraries = ['mpfi', 'mpfr'],
@ -107,7 +107,7 @@ diff -up src/module_list.py.orig src/module_list.py
language = 'c++'),
Extension('sage.rings.real_lazy',
@@ -1473,12 +1486,15 @@ ext_modules = [
@@ -1462,12 +1475,15 @@ ext_modules = [
sources = ['sage/rings/polynomial/multi_polynomial.pyx']),
Extension('sage.rings.polynomial.multi_polynomial_ideal_libsingular',
@ -123,7 +123,7 @@ diff -up src/module_list.py.orig src/module_list.py
sources = ['sage/rings/polynomial/multi_polynomial_libsingular.pyx']),
Extension('sage.rings.polynomial.multi_polynomial_ring_generic',
@@ -1492,6 +1508,7 @@ ext_modules = [
@@ -1481,6 +1497,7 @@ ext_modules = [
Extension('sage.rings.polynomial.polynomial_complex_arb',
sources = ['sage/rings/polynomial/polynomial_complex_arb.pyx'],
@ -132,8 +132,8 @@ diff -up src/module_list.py.orig src/module_list.py
Extension('sage.rings.polynomial.polynomial_compiled',
diff -up src/setup.py.orig src/setup.py
--- src/setup.py.orig 2017-03-29 18:42:34.196001702 -0400
+++ src/setup.py 2017-03-29 18:42:39.088001890 -0400
--- src/setup.py.orig 2017-04-11 10:01:57.270275593 -0400
+++ src/setup.py 2017-04-11 10:02:00.107275701 -0400
@@ -83,6 +83,7 @@ except KeyError:
# search for dependencies and add to gcc -I<path>
# this depends on SAGE_CYTHONIZED

10
sagemath-libgap.patch
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@ -1,6 +1,6 @@
diff -up src/sage/libs/gap/test/main.c.orig src/sage/libs/gap/test/main.c
--- src/sage/libs/gap/test/main.c.orig 2017-03-04 13:30:35.525484755 -0500
+++ src/sage/libs/gap/test/main.c 2017-03-04 13:30:58.662485641 -0500
--- src/sage/libs/gap/test/main.c.orig 2017-04-11 09:59:37.166270228 -0400
+++ src/sage/libs/gap/test/main.c 2017-04-11 09:59:39.063270300 -0400
@@ -22,7 +22,7 @@ void eval(char* cmd) {
libgap_start_interaction(cmd);
@ -11,9 +11,9 @@ diff -up src/sage/libs/gap/test/main.c.orig src/sage/libs/gap/test/main.c
char* out = libgap_get_output();
libgap_exit();
diff -up src/sage/libs/gap/util.pyx.orig src/sage/libs/gap/util.pyx
--- src/sage/libs/gap/util.pyx.orig 2017-03-04 13:31:07.509485979 -0500
+++ src/sage/libs/gap/util.pyx 2017-03-04 13:31:44.126487382 -0500
@@ -154,17 +154,9 @@ def gap_root():
--- src/sage/libs/gap/util.pyx.orig 2017-04-11 09:59:20.424269587 -0400
+++ src/sage/libs/gap/util.pyx 2017-04-11 09:59:39.065270300 -0400
@@ -158,17 +158,9 @@ def gap_root():
sage: from sage.libs.gap.util import gap_root
sage: gap_root() # random output

8
sagemath-lrslib.patch
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@ -1,7 +1,7 @@
diff -up src/sage/geometry/polyhedron/base.py.orig src/sage/geometry/polyhedron/base.py
--- src/sage/geometry/polyhedron/base.py.orig 2017-03-04 13:27:41.267478082 -0500
+++ src/sage/geometry/polyhedron/base.py 2017-03-04 13:27:49.646478403 -0500
@@ -21,7 +21,6 @@ import six
--- src/sage/geometry/polyhedron/base.py.orig 2017-04-11 09:57:57.498266411 -0400
+++ src/sage/geometry/polyhedron/base.py 2017-04-11 09:58:07.176266782 -0400
@@ -22,7 +22,6 @@ import six
from sage.structure.element import Element, coerce_binop, is_Vector
from sage.misc.all import cached_method, prod
@ -9,7 +9,7 @@ diff -up src/sage/geometry/polyhedron/base.py.orig src/sage/geometry/polyhedron/
from sage.rings.all import QQ, ZZ
from sage.rings.real_double import RDF
@@ -3680,10 +3679,6 @@ class Polyhedron_base(Element):
@@ -3988,10 +3987,6 @@ class Polyhedron_base(Element):
David Avis's lrs program.
"""

6
sagemath-nauty.patch
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@ -1,7 +1,7 @@
diff -up src/sage/graphs/graph_generators.py.orig src/sage/graphs/graph_generators.py
--- src/sage/graphs/graph_generators.py.orig 2017-03-04 13:28:37.640480240 -0500
+++ src/sage/graphs/graph_generators.py 2017-03-04 13:28:47.287480610 -0500
@@ -874,7 +874,7 @@ class GraphGenerators():
--- src/sage/graphs/graph_generators.py.orig 2017-04-11 09:58:45.689268257 -0400
+++ src/sage/graphs/graph_generators.py 2017-04-11 09:58:53.297268548 -0400
@@ -875,7 +875,7 @@ class GraphGenerators():
>A geng -d0D3 n=4 e=0-6
"""
import subprocess

24
sagemath-pari.patch
View file

@ -1,7 +1,7 @@
diff -up src/sage/libs/cypari2/paridecl.pxd.orig src/sage/libs/cypari2/paridecl.pxd
--- src/sage/libs/cypari2/paridecl.pxd.orig 2017-03-04 14:37:56.976639516 -0500
+++ src/sage/libs/cypari2/paridecl.pxd 2017-03-04 14:38:09.953640013 -0500
@@ -77,7 +77,7 @@ cdef extern from "sage/libs/cypari2/cypa
--- src/sage/libs/cypari2/paridecl.pxd.orig 2017-04-18 07:41:28.165058343 -0400
+++ src/sage/libs/cypari2/paridecl.pxd 2017-04-18 07:45:56.847068632 -0400
@@ -84,7 +84,7 @@ cdef extern from *: # PARI headers a
int PARI_SIGINT_block, PARI_SIGINT_pending
void NEXT_PRIME_VIADIFF(long, byteptr)
void PREC_PRIME_VIADIFF(long, byteptr)
@ -11,14 +11,14 @@ diff -up src/sage/libs/cypari2/paridecl.pxd.orig src/sage/libs/cypari2/paridecl.
int precdl
# The "except 0" here is to ensure compatibility with
diff -up src/sage/libs/cypari2/pari_instance.pyx.orig src/sage/libs/cypari2/pari_instance.pyx
--- src/sage/libs/cypari2/pari_instance.pyx.orig 2017-03-04 14:38:30.535640801 -0500
+++ src/sage/libs/cypari2/pari_instance.pyx 2017-03-04 14:38:39.680641151 -0500
@@ -510,7 +510,7 @@ cdef class PariInstance(PariInstance_aut
# As a simple heuristic, we set the virtual stack to 1/4 of the
# virtual memory.
--- src/sage/libs/cypari2/pari_instance.pyx.orig 2017-04-18 07:46:04.924068941 -0400
+++ src/sage/libs/cypari2/pari_instance.pyx 2017-04-18 07:46:41.870070356 -0400
@@ -461,7 +461,7 @@ cdef class Pari(Pari_auto):
- pari_init_opts(size, maxprime, INIT_DFTm)
+ pari_init_opts(size, maxprime, INIT_DFTm|INIT_noINTGMPm)
from sage.misc.getusage import virtual_memory_limit
# Take 1MB as minimal stack. Use maxprime=0, which PARI will
# internally increase to some small value like 65537.
- pari_init_opts(1000000, 0, INIT_DFTm)
+ pari_init_opts(1000000, 0, INIT_DFTm|INIT_noINTGMPm)
# Disable PARI's stack overflow checking which is incompatible
# with multi-threading.

6
sagemath-readonly.patch
View file

@ -1,7 +1,7 @@
diff -up src/sage/all.py.orig src/sage/all.py
--- src/sage/all.py.orig 2017-03-04 13:24:30.701470784 -0500
+++ src/sage/all.py 2017-03-04 13:24:50.878471557 -0500
@@ -300,11 +300,11 @@ def _write_started_file():
--- src/sage/all.py.orig 2017-04-11 09:56:17.559262584 -0400
+++ src/sage/all.py 2017-04-11 09:56:25.743262897 -0400
@@ -298,11 +298,11 @@ def _write_started_file():
Check that the file exists when Sage is running::

30
sagemath-sagedoc.patch
View file

@ -1,7 +1,7 @@
diff -up src/doc/common/conf.py.orig src/doc/common/conf.py
--- src/doc/common/conf.py.orig 2017-03-30 11:27:42.351311111 -0400
+++ src/doc/common/conf.py 2017-03-30 11:27:44.482311193 -0400
@@ -218,7 +218,7 @@ if (os.environ.get('SAGE_DOC_MATHJAX', '
--- src/doc/common/conf.py.orig 2017-04-11 09:55:23.607260518 -0400
+++ src/doc/common/conf.py 2017-04-11 09:55:52.327261618 -0400
@@ -220,7 +220,7 @@ if (os.environ.get('SAGE_DOC_MATHJAX', '
html_theme_options['mathjax_macros'] = sage_mathjax_macros()
from pkg_resources import Requirement, working_set
@ -11,8 +11,8 @@ diff -up src/doc/common/conf.py.orig src/doc/common/conf.py
# It would be really nice if sphinx would copy the entire mathjax directory,
diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
--- src/sage/doctest/control.py.orig 2017-03-30 11:27:42.358311112 -0400
+++ src/sage/doctest/control.py 2017-03-30 11:27:44.483311193 -0400
--- src/sage/doctest/control.py.orig 2017-04-11 09:55:23.610260518 -0400
+++ src/sage/doctest/control.py 2017-04-11 09:55:52.330261618 -0400
@@ -95,7 +95,6 @@ class DocTestDefaults(SageObject):
self.valgrind = False
self.massif = False
@ -30,7 +30,7 @@ diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
# Non-interactive debuggers: 48 hours
options.timeout = int(os.getenv('SAGE_TIMEOUT_VALGRIND', 48 * 60 * 60))
elif options.long:
@@ -1030,13 +1029,8 @@ class DocTestController(SageObject):
@@ -1034,13 +1033,8 @@ class DocTestController(SageObject):
elif opt.cachegrind:
toolname = "cachegrind"
flags = os.getenv("SAGE_CACHEGRIND_FLAGS", "")
@ -44,7 +44,7 @@ diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
if "%s" in flags:
flags %= toolname + ".%p" # replace %s with toolname
cmd += flags + sage_cmd
@@ -1096,10 +1090,10 @@ class DocTestController(SageObject):
@@ -1100,10 +1094,10 @@ class DocTestController(SageObject):
0
"""
opt = self.options
@ -58,8 +58,8 @@ diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
return self.run_val_gdb()
else:
diff -up src/sage/interfaces/singular.py.orig src/sage/interfaces/singular.py
--- src/sage/interfaces/singular.py.orig 2017-03-30 11:27:42.364311112 -0400
+++ src/sage/interfaces/singular.py 2017-03-30 11:27:44.486311193 -0400
--- src/sage/interfaces/singular.py.orig 2017-04-11 09:55:50.260261539 -0400
+++ src/sage/interfaces/singular.py 2017-04-11 09:55:52.332261618 -0400
@@ -2291,7 +2291,7 @@ def generate_docstring_dictionary():
nodes.clear()
node_names.clear()
@ -70,9 +70,9 @@ diff -up src/sage/interfaces/singular.py.orig src/sage/interfaces/singular.py
new_node = re.compile("File: singular\.hlp, Node: ([^,]*),.*")
new_lookup = re.compile("\* ([^:]*):*([^.]*)\..*")
diff -up src/sage_setup/docbuild/ext/multidocs.py.orig src/sage_setup/docbuild/ext/multidocs.py
--- src/sage_setup/docbuild/ext/multidocs.py.orig 2017-03-30 11:27:42.371311112 -0400
+++ src/sage_setup/docbuild/ext/multidocs.py 2017-03-30 11:27:44.487311193 -0400
@@ -83,8 +83,11 @@ def merge_environment(app, env):
--- src/sage_setup/docbuild/ext/multidocs.py.orig 2017-04-11 09:55:23.612260518 -0400
+++ src/sage_setup/docbuild/ext/multidocs.py 2017-04-11 09:55:52.332261618 -0400
@@ -84,8 +84,11 @@ def merge_environment(app, env):
for ind in newalldoc:
# treat subdocument source as orphaned file and don't complain
md = env.metadata.get(ind, dict())
@ -85,10 +85,10 @@ diff -up src/sage_setup/docbuild/ext/multidocs.py.orig src/sage_setup/docbuild/e
+ env.metadata[ind] = {'orphan'}
# merge the citations
newcite = {}
for ind, (path, tag) in docenv.citations.iteritems():
for ind, (path, tag) in six.iteritems(docenv.citations):
diff -up src/sage_setup/docbuild/__init__.py.orig src/sage_setup/docbuild/__init__.py
--- src/sage_setup/docbuild/__init__.py.orig 2017-03-30 11:27:42.379311112 -0400
+++ src/sage_setup/docbuild/__init__.py 2017-03-30 11:29:25.179315049 -0400
--- src/sage_setup/docbuild/__init__.py.orig 2017-04-11 09:55:50.272261539 -0400
+++ src/sage_setup/docbuild/__init__.py 2017-04-11 09:55:52.333261618 -0400
@@ -248,13 +248,14 @@ if NUM_THREADS > 1:
# map_async handles KeyboardInterrupt correctly. Plain map and
# apply_async does not, so don't use it.

139
sagemath-scripts.patch
View file

@ -1,6 +1,6 @@
diff -up src/bin/sage.orig src/bin/sage
--- src/bin/sage.orig 2017-03-04 12:58:43.035411519 -0500
+++ src/bin/sage 2017-03-04 13:08:11.111433272 -0500
--- src/bin/sage.orig 2017-04-11 09:46:27.981240007 -0400
+++ src/bin/sage 2017-04-11 09:53:04.143255178 -0400
@@ -1,5 +1,16 @@
#!/usr/bin/env bash
@ -154,7 +154,7 @@ diff -up src/bin/sage.orig src/bin/sage
echo " -search_src <string> -- search through all the Sage library code for string"
echo " -search_doc <string> -- search through the Sage documentation for string"
echo " -grep <string> -- same as -search_src"
@@ -220,16 +165,6 @@ usage_advanced() {
@@ -222,16 +167,6 @@ usage_advanced() {
echo
#### 1.......................26..................................................78
#### |.....................--.|...................................................|
@ -171,7 +171,7 @@ diff -up src/bin/sage.orig src/bin/sage
echo "Valgrind memory debugging:"
echo " -cachegrind -- run Sage using Valgrind's cachegrind tool. The log"
echo " files are named sage-cachegrind.PID can be found in"
@@ -243,9 +178,6 @@ usage_advanced() {
@@ -245,9 +180,6 @@ usage_advanced() {
echo " -memcheck -- run Sage using Valgrind's memcheck tool. The log"
echo " files are named sage-memcheck.PID can be found in"
echo " $DOT_SAGE"
@ -181,11 +181,10 @@ diff -up src/bin/sage.orig src/bin/sage
echo " -valgrind -- this is an alias for -memcheck"
echo
echo "You can also use -- before a long option, e.g., 'sage --optional'."
@@ -253,104 +185,6 @@ usage_advanced() {
exit 0
@@ -256,121 +188,6 @@ usage_advanced() {
}
-
-#####################################################################
-# Special options to be processed without sage-env
-#####################################################################
@ -206,8 +205,26 @@ diff -up src/bin/sage.orig src/bin/sage
-# an unclobbered environment before testing unsafe tickets.
-if [ "$1" = '-patchbot' -o "$1" = "--patchbot" ]; then
- shift
- cd "$SAGE_ROOT"
- exec local/bin/patchbot/patchbot.py "$@"
- # We ask the Python from Sage where the patchbot is installed.
- # We set PYTHONPATH to that directory such that the system Python
- # should also find the sage_patchbot package.
- cmd='import sage_patchbot as p; import os; print(os.path.dirname(p.__path__[0]))'
- export PYTHONPATH=`"$SAGE_ROOT/sage" --python -c "$cmd"`
- if [ -z "$PYTHONPATH" ]; then
- # Something went wrong, assume that the patchbot is not installed
- echo >&2 "Error: cannot find installation path for sage_patchbot"
- echo >&2 "See https://wiki.sagemath.org/buildbot for instructions"
- exit 1
- fi
-
- # Try "python2.7", then "python2", then "python"
- shopt -s execfail # Do not exit if "exec" fails
- exec python2.7 -m sage_patchbot.patchbot "$@"
- exec python2 -m sage_patchbot.patchbot "$@"
- exec python -m sage_patchbot.patchbot "$@"
- echo >&2 "Error: cannot find a suitable Python program."
- echo >&2 "The SageMath patchbot requires a system Python installation."
- exit 127
-fi
-
-# Check for '--upgrade' before sourcing sage-env: the top-level "make"
@ -286,7 +303,7 @@ diff -up src/bin/sage.orig src/bin/sage
if [ $# -gt 0 ]; then
if [ "$1" = '-h' -o "$1" = '-?' -o "$1" = '-help' -o "$1" = '--help' ]; then
usage
@@ -362,23 +196,9 @@ fi
@@ -382,23 +199,9 @@ fi
# Prepare for running Sage, either interactively or non-interactively.
sage_setup() {
@ -310,7 +327,7 @@ diff -up src/bin/sage.orig src/bin/sage
if [ ! -d "$IPYTHONDIR" ]; then
# make sure that $DOT_SAGE exists so that ipython will happily
# create its config directories there. If DOT_SAGE doesn't
@@ -389,20 +209,6 @@ sage_setup() {
@@ -409,20 +212,6 @@ sage_setup() {
}
@ -331,7 +348,7 @@ diff -up src/bin/sage.orig src/bin/sage
# Start an interactive Sage session, this function never returns.
interactive_sage() {
sage_setup
@@ -507,16 +313,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
@@ -527,16 +316,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
exec ecl "$@"
fi
@ -348,8 +365,8 @@ diff -up src/bin/sage.orig src/bin/sage
if [ "$1" = '-maxima' -o "$1" = '--maxima' ]; then
shift
exec maxima "$@"
@@ -542,11 +338,6 @@ if [ "$1" = '-pip' -o "$1" = '--pip' ];
exec pip-lock "$@"
@@ -562,11 +341,6 @@ if [ "$1" = '-pip' -o "$1" = '--pip' ];
exec pip "$@"
fi
-if [ "$1" = '-fix-pkg-checksums' -o "$1" = '--fix-pkg-checksums' ]; then
@ -360,7 +377,7 @@ diff -up src/bin/sage.orig src/bin/sage
if [ "$1" = '-python' -o "$1" = '--python' ]; then
shift
exec python "$@"
@@ -562,16 +353,6 @@ if [ "$1" = '-ipython' -o "$1" = '--ipyt
@@ -582,16 +356,6 @@ if [ "$1" = '-ipython' -o "$1" = '--ipyt
exec ipython "$@"
fi
@ -377,11 +394,10 @@ diff -up src/bin/sage.orig src/bin/sage
if [ "$1" = '-sh' -o "$1" = '--sh' ]; then
# AUTHORS:
# - Carl Witty and William Stein: initial version
@@ -690,19 +471,6 @@ EOF
exit $status
@@ -711,20 +475,6 @@ EOF
fi
-#####################################################################
#####################################################################
-# Test coverage of a module?
-#####################################################################
-
@ -394,10 +410,12 @@ diff -up src/bin/sage.orig src/bin/sage
- shift
- exec sage-coverageall "$@"
-fi
#####################################################################
-
-#####################################################################
# File conversion
@@ -722,11 +490,6 @@ fi
#####################################################################
@@ -747,11 +497,6 @@ fi
# Run Sage's versions of the standard Algebra/Geometry etc. software
#####################################################################
@ -409,7 +427,7 @@ diff -up src/bin/sage.orig src/bin/sage
if [[ "$1" =~ ^--notebook=.* || "$1" =~ ^-n=.* || "$1" =~ ^-notebook=.* ]] ; then
sage-cleaner &>/dev/null &
exec sage-notebook "$@"
@@ -737,13 +500,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
@@ -762,13 +507,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
exec sage-notebook "$@"
fi
@ -423,7 +441,7 @@ diff -up src/bin/sage.orig src/bin/sage
if [ "$1" = "-inotebook" -o "$1" = '--inotebook' ]; then
shift
sage-cleaner &>/dev/null &
@@ -762,31 +518,12 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
@@ -787,38 +525,19 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
exit 0
fi
@ -456,7 +474,15 @@ diff -up src/bin/sage.orig src/bin/sage
if [ ! -f "$DOT_SAGE"/init.sage ]; then
echo >&2 "init.sage does not exist ... creating"
touch "$DOT_SAGE"/init.sage
@@ -802,10 +539,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
fi
SAGE_BANNER=no sage_setup
export PYTHONIOENCODING="utf-8" # Fix encoding for doctests
- if [ "$1" = '-tp' -o "$1" = '-btp' ]; then
+ if [ "$1" = '-tp' ]; then
shift
exec sage-runtests -p "$@"
else
@@ -827,16 +546,6 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
fi
fi
@ -464,14 +490,24 @@ diff -up src/bin/sage.orig src/bin/sage
- if [ "$1" = '-btnew' ]; then
- build_sage
- fi
+if [ "$1" = '-tnew' ]; then
- shift
- SAGE_BANNER=no sage_setup
- export PYTHONIOENCODING="utf-8" # Fix encoding for doctests
- exec sage-runtests --new "$@"
-fi
-
if [ "$1" = '-testall' -o "$1" = "--testall" ]; then
shift
SAGE_BANNER=no sage_setup
export PYTHONIOENCODING="utf-8" # Fix encoding for doctests
@@ -831,130 +565,6 @@ if [ "$1" = '--location' ]; then
exit 0
@@ -851,119 +560,6 @@ if [ "$1" = '-c' ]; then
exec sage-eval "$@"
fi
-if [ "$1" = '--location' ]; then
- maybe_sage_location
- exit 0
-fi
-
-
-install() {
- maybe_sage_location
@ -580,26 +616,10 @@ diff -up src/bin/sage.orig src/bin/sage
- exec python -m "sage_setup.docbuild" "$@"
-fi
-
-if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then
- shift
- sage_setup
- if [ "$SAGE_DEBUG" = "no" ]; then
- gdb -x "$SAGE_LOCAL/bin/sage-gdb-commands" \
- -args python "$SAGE_LOCAL/bin/sage-ipython" "$@" -i
- else
- # Location of cython_debug directory
- cygdb_dir="$SAGE_SRC/build/cythonized"
- cygdb "$cygdb_dir" "$SAGE_SRC/sage" \
- -- -x "$SAGE_LOCAL/bin/sage-gdb-commands" \
- -args python "$SAGE_LOCAL/bin/sage-ipython" "$@" -i
- fi
- exit $?
-fi
-
if [ "$1" = '-preparse' -o "$1" = "--preparse" ]; then
if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then
shift
exec sage-preparse "$@"
@@ -989,21 +599,10 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
sage_setup
@@ -1014,12 +610,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
exec sage-callgrind "$@"
fi
@ -612,18 +632,21 @@ diff -up src/bin/sage.orig src/bin/sage
if [ "$1" = '-startuptime' -o "$1" = '--startuptime' ]; then
exec sage-startuptime.py "$@"
fi
@@ -1030,11 +620,6 @@ if [ "$1" = '-gthread' -o "$1" = '-qthre
fi
-if [ "$1" = '-gthread' -o "$1" = '-qthread' -o "$1" = '-q4thread' -o "$1" = '-wthread' -o "$1" = '-pylab' ]; then
- # Intentionally no "shift" here
- interactive_sage "$@"
-fi
-
if [ $# -ge 1 ]; then
T=`echo "$1" | sed -e "s/.*\.//"`
if [ "$T" = "spkg" ]; then
- T=`echo "$1" | sed -e "s/.*\.//"`
- if [ "$T" = "spkg" ]; then
- install "$@"
- fi
- SAGE_BANNER=no sage_setup
unset TERM # See Trac #12263
exec sage-run "$@"
fi
diff -up src/bin/sage-runtests.orig src/bin/sage-runtests
--- src/bin/sage-runtests.orig 2017-03-04 13:08:31.712434061 -0500
+++ src/bin/sage-runtests 2017-03-04 13:08:41.887434451 -0500
--- src/bin/sage-runtests.orig 2017-04-11 09:53:17.222255678 -0400
+++ src/bin/sage-runtests 2017-04-11 09:53:31.631256230 -0400
@@ -56,10 +56,6 @@ if __name__ == "__main__":
help="run doctests using Valgrind's cachegrind tool. The log "
"files are named sage-cachegrind.PID and can be found in " +
@ -636,8 +659,8 @@ diff -up src/bin/sage-runtests.orig src/bin/sage-runtests
parser.add_option("-f", "--failed", action="store_true", default=False,
help="doctest only those files that failed in the previous run")
diff -up src/bin/sage-valgrind.orig src/bin/sage-valgrind
--- src/bin/sage-valgrind.orig 2017-03-04 13:08:52.937434874 -0500
+++ src/bin/sage-valgrind 2017-03-04 13:09:13.143435648 -0500
--- src/bin/sage-valgrind.orig 2017-04-11 09:53:45.006256742 -0400
+++ src/bin/sage-valgrind 2017-04-11 09:54:05.879257542 -0400
@@ -1,16 +1,6 @@
#!/usr/bin/env bash

10
sagemath.spec
View file

@ -1,6 +1,6 @@
%global __provides_exclude_from .*/site-packages/.*\\.so
%bcond_without bundled_pari
%bcond_with bundled_pari
%bcond_with bundled_pexpect
%bcond_without bundled_ipython
@ -42,7 +42,7 @@
%global ipython_pkg ipython-5.1.0
%endif
%if %{with bundled_pari}
%global pari_pkg pari-2.8.0.alpha
%global pari_pkg pari-2.9.1
%endif
%if %{with bundled_pexpect}
%global pexpect_pkg pexpect-4.1.0
@ -65,7 +65,7 @@
Name: sagemath
Group: Applications/Engineering
Summary: A free open-source mathematics software system
Version: 7.5.1
Version: 7.6
Release: 1%{?dist}
# The file ${SAGE_ROOT}/COPYING.txt is the upstream license breakdown file
# Additionally, every $files section has a comment with the license name
@ -1692,6 +1692,10 @@ exit 0
########################################################################
%changelog
* Tue Apr 11 2017 pcpa <paulo.cesar.pereira.de.andrade@gmail.com> - 7.6-1
- Update to sagemath 7.6
- Switch back to system pari
* Thu Apr 6 2017 pcpa <paulo.cesar.pereira.de.andrade@gmail.com> - 7.5.1-1
- Update to sagemath 7.5.1

2
sources
View file

@ -1 +1 @@
SHA512 (sage-7.5.1.tar.gz) = ef18951250573f4c04911757664e25f7e03332df36efd948e189009e62573b8f120a413b322947fee6e914cbcc64fbd99d5a960954a04ba5786660ecc0a6ee96
SHA512 (sage-7.6.tar.gz) = d700a4e501f8883222b2456134c4983197c7d4216e88d94b6c01e94042baad9345c8a8383a08701c09b4fcad1b3b506413e406da3dad340428a76b6048500df3