[sagemath] Update to sagemath 6.4.1
pcpa
pcpa at fedoraproject.org
Sat Dec 13 23:05:36 UTC 2014
commit 738094a8d8f11fefc709f3c19eb08d8b461504d9
Author: pcpa <paulo.cesar.pereira.de.andrade at gmail.com>
Date: Sat Dec 13 21:05:42 2014 -0200
Update to sagemath 6.4.1
.gitignore | 1 +
Jmol.js | 1663 ---------
JmolHelp.html | 79 -
sagemath-4ti2.patch | 8 +-
sagemath-cbc.patch | 6 +-
sagemath-cremona.patch | 8 +-
sagemath-cryptominisat.patch | 6 +-
sagemath-ecl-unicode.patch | 100 -
sagemath-extensions.patch | 6 +-
sagemath-fes.patch | 6 +-
sagemath-gap-hap.patch | 6 +-
sagemath-lrcalc.patch | 6 +-
sagemath-lrslib.patch | 6 +-
sagemath-nauty.patch | 6 +-
sagemath-ntl6.patch | 1422 -------
sagemath-pari.patch | 12 +-
sagemath-pari2.7.patch | 8511 ------------------------------------------
sagemath-png.patch | 10 +-
sagemath-readonly.patch | 6 +-
sagemath-rpmbuild.patch | 24 +-
sagemath-sagedoc.patch | 38 +-
sagemath-sagenb.patch | 125 +-
sagemath-scons.patch | 6 +-
sagemath-scripts.patch | 187 +-
sagemath-sphinx.patch | 139 -
sagemath.spec | 130 +-
sources | 2 +-
27 files changed, 276 insertions(+), 12243 deletions(-)
---
diff --git a/.gitignore b/.gitignore
index 941e8c6..3c23a60 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,4 @@
/sage-6.1.1.tar.gz
/sage-6.2.tar.gz
/sage-6.3.tar.gz
+/sage-6.4.1.tar.gz
diff --git a/sagemath-4ti2.patch b/sagemath-4ti2.patch
index f4dc6dc..a5cf30f 100644
--- a/sagemath-4ti2.patch
+++ b/sagemath-4ti2.patch
@@ -1,7 +1,7 @@
diff -up src/sage/sandpiles/sandpile.py.orig src/sage/sandpiles/sandpile.py
---- src/sage/sandpiles/sandpile.py.orig 2014-01-28 16:01:55.841188856 -0200
-+++ src/sage/sandpiles/sandpile.py 2014-01-28 16:02:07.914189318 -0200
-@@ -24,8 +24,6 @@ packages. An alternative is to install
+--- src/sage/sandpiles/sandpile.py.orig 2014-11-18 15:24:27.192127311 -0200
++++ src/sage/sandpiles/sandpile.py 2014-11-18 15:24:38.049127454 -0200
+@@ -23,8 +23,6 @@ packages. An alternative is to install
following variable to the correct path.
"""
@@ -10,7 +10,7 @@ diff -up src/sage/sandpiles/sandpile.py.orig src/sage/sandpiles/sandpile.py
r"""
Sage Sandpiles
-@@ -4097,7 +4095,7 @@ class SandpileDivisor(dict):
+@@ -4096,7 +4094,7 @@ class SandpileDivisor(dict):
sign_file.close()
# compute
try:
diff --git a/sagemath-cbc.patch b/sagemath-cbc.patch
index 4d3b132..da1ab8a 100644
--- a/sagemath-cbc.patch
+++ b/sagemath-cbc.patch
@@ -1,7 +1,7 @@
diff -up src/module_list.py.orig src/module_list.py
---- src/module_list.py.orig 2014-08-12 14:22:43.914983839 -0300
-+++ src/module_list.py 2014-08-12 14:22:55.283984274 -0300
-@@ -2148,7 +2148,7 @@ if (os.path.isfile(SAGE_INC + "/cplex.h"
+--- src/module_list.py.orig 2014-11-18 15:28:48.952130767 -0200
++++ src/module_list.py 2014-11-18 15:28:57.040130873 -0200
+@@ -2168,7 +2168,7 @@ if (os.path.isfile(SAGE_INC + "/cplex.h"
libraries = ["stdc++", "cplex"])
)
diff --git a/sagemath-cremona.patch b/sagemath-cremona.patch
index 6548aa1..f230daa 100644
--- a/sagemath-cremona.patch
+++ b/sagemath-cremona.patch
@@ -1,7 +1,7 @@
diff -up src/sage/databases/cremona.py.orig src/sage/databases/cremona.py
---- src/sage/databases/cremona.py.orig 2014-08-12 14:17:40.563972222 -0300
-+++ src/sage/databases/cremona.py 2014-08-12 14:17:51.891972656 -0300
-@@ -814,14 +814,9 @@ class MiniCremonaDatabase(SQLDatabase):
+--- src/sage/databases/cremona.py.orig 2014-11-18 15:26:03.247128579 -0200
++++ src/sage/databases/cremona.py 2014-11-18 15:26:16.920128759 -0200
+@@ -819,14 +819,9 @@ class MiniCremonaDatabase(SQLDatabase):
if N < self.largest_conductor():
message = "There is no elliptic curve with label " + label \
+ " in the database"
@@ -17,7 +17,7 @@ diff -up src/sage/databases/cremona.py.orig src/sage/databases/cremona.py
raise ValueError(message)
ainvs = eval(c[0])
data = {'cremona_label': label,
-@@ -1656,10 +1651,12 @@ def CremonaDatabase(name=None,mini=None,
+@@ -1669,10 +1664,12 @@ def CremonaDatabase(name=None,mini=None,
if name is None and not set_global:
return _db
if set_global and name is None:
diff --git a/sagemath-cryptominisat.patch b/sagemath-cryptominisat.patch
index e937762..a5e9ffd 100644
--- a/sagemath-cryptominisat.patch
+++ b/sagemath-cryptominisat.patch
@@ -1,7 +1,7 @@
diff -up src/module_list.py.orig src/module_list.py
---- src/module_list.py.orig 2014-08-12 14:24:04.771986935 -0300
-+++ src/module_list.py 2014-08-12 14:24:13.962987287 -0300
-@@ -2158,7 +2158,7 @@ if 1:
+--- src/module_list.py.orig 2014-11-18 15:30:01.952131730 -0200
++++ src/module_list.py 2014-11-18 15:30:08.968131823 -0200
+@@ -2177,7 +2177,7 @@ if 1:
)
diff --git a/sagemath-extensions.patch b/sagemath-extensions.patch
index 5d6e824..c94f202 100644
--- a/sagemath-extensions.patch
+++ b/sagemath-extensions.patch
@@ -1,7 +1,7 @@
diff -up src/module_list.py.orig src/module_list.py
---- src/module_list.py.orig 2014-08-12 14:02:16.914936853 -0300
-+++ src/module_list.py 2014-08-12 14:02:26.626937225 -0300
-@@ -2103,7 +2103,8 @@ ext_modules = [
+--- src/module_list.py.orig 2014-11-18 13:23:35.915031576 -0200
++++ src/module_list.py 2014-11-18 13:23:46.515031716 -0200
+@@ -2126,7 +2126,8 @@ ext_modules = [
# These extensions are to be compiled only if the
# corresponding packages have been installed
diff --git a/sagemath-fes.patch b/sagemath-fes.patch
index 870cb18..4d8c859 100644
--- a/sagemath-fes.patch
+++ b/sagemath-fes.patch
@@ -1,7 +1,7 @@
diff -up src/module_list.py.orig src/module_list.py
---- src/module_list.py.orig 2014-08-12 14:23:31.642985666 -0300
-+++ src/module_list.py 2014-08-12 14:23:39.051985950 -0300
-@@ -2107,7 +2107,7 @@ ext_modules = [
+--- src/module_list.py.orig 2014-11-18 15:29:30.360131313 -0200
++++ src/module_list.py 2014-11-18 15:29:37.432131407 -0200
+@@ -2130,7 +2130,7 @@ ext_modules = [
def is_package_installed(name):
return False
diff --git a/sagemath-gap-hap.patch b/sagemath-gap-hap.patch
index 778bedd..46540af 100644
--- a/sagemath-gap-hap.patch
+++ b/sagemath-gap-hap.patch
@@ -1,6 +1,6 @@
diff -up src/sage/groups/perm_gps/permgroup.py.orig src/sage/groups/perm_gps/permgroup.py
---- src/sage/groups/perm_gps/permgroup.py.orig 2014-08-12 14:19:36.779976673 -0300
-+++ src/sage/groups/perm_gps/permgroup.py 2014-08-12 14:19:44.435976966 -0300
+--- src/sage/groups/perm_gps/permgroup.py.orig 2014-11-18 15:27:46.545129943 -0200
++++ src/sage/groups/perm_gps/permgroup.py 2014-11-18 15:27:53.760130038 -0200
@@ -180,8 +180,7 @@ def hap_decorator(f):
"""
@wraps(f)
@@ -11,7 +11,7 @@ diff -up src/sage/groups/perm_gps/permgroup.py.orig src/sage/groups/perm_gps/per
load_hap()
from sage.rings.arith import is_prime
if not (p == 0 or is_prime(p)):
-@@ -3934,8 +3933,7 @@ class PermutationGroup_generic(group.Gro
+@@ -3979,8 +3978,7 @@ class PermutationGroup_generic(group.Gro
- David Joyner and Graham Ellis
"""
diff --git a/sagemath-lrcalc.patch b/sagemath-lrcalc.patch
index 2e0c369..640fd2d 100644
--- a/sagemath-lrcalc.patch
+++ b/sagemath-lrcalc.patch
@@ -1,7 +1,7 @@
diff -up src/module_list.py.orig src/module_list.py
---- src/module_list.py.orig 2014-08-12 14:22:06.954982423 -0300
-+++ src/module_list.py 2014-08-12 14:22:15.018982732 -0300
-@@ -2191,7 +2191,7 @@ if UNAME[0] == "Darwin" and not UNAME[2]
+--- src/module_list.py.orig 2014-11-18 15:28:17.313130349 -0200
++++ src/module_list.py 2014-11-18 15:28:24.520130444 -0200
+@@ -2210,7 +2210,7 @@ if UNAME[0] == "Darwin" and not UNAME[2]
)
diff --git a/sagemath-lrslib.patch b/sagemath-lrslib.patch
index 988d923..d7ad0ad 100644
--- a/sagemath-lrslib.patch
+++ b/sagemath-lrslib.patch
@@ -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 2014-08-12 14:18:21.763973800 -0300
-+++ src/sage/geometry/polyhedron/base.py 2014-08-12 14:18:29.539974098 -0300
-@@ -3494,11 +3494,6 @@ class Polyhedron_base(Element):
+--- src/sage/geometry/polyhedron/base.py.orig 2014-11-18 15:26:45.817129141 -0200
++++ src/sage/geometry/polyhedron/base.py 2014-11-18 15:26:53.185129238 -0200
+@@ -3515,11 +3515,6 @@ class Polyhedron_base(Element):
David Avis's lrs program.
"""
diff --git a/sagemath-nauty.patch b/sagemath-nauty.patch
index 76f5350..c810d40 100644
--- a/sagemath-nauty.patch
+++ b/sagemath-nauty.patch
@@ -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 2014-08-12 14:19:00.906975299 -0300
-+++ src/sage/graphs/graph_generators.py 2014-08-12 14:19:08.986975608 -0300
-@@ -830,7 +830,7 @@ class GraphGenerators():
+--- src/sage/graphs/graph_generators.py.orig 2014-11-18 15:27:15.584129534 -0200
++++ src/sage/graphs/graph_generators.py 2014-11-18 15:27:23.352129636 -0200
+@@ -833,7 +833,7 @@ class GraphGenerators():
"""
import subprocess
from sage.misc.package import is_package_installed
diff --git a/sagemath-pari.patch b/sagemath-pari.patch
index ed7c40b..4ce8923 100644
--- a/sagemath-pari.patch
+++ b/sagemath-pari.patch
@@ -1,6 +1,7 @@
---- src/sage/libs/pari/pari_instance.pxd.orig 2014-05-10 15:49:08.954184083 -0300
-+++ src/sage/libs/pari/pari_instance.pxd 2014-05-10 15:49:13.304183771 -0300
-@@ -5,6 +5,10 @@ cimport cython
+diff -up src/sage/libs/pari/pari_instance.pxd.orig src/sage/libs/pari/pari_instance.pxd
+--- src/sage/libs/pari/pari_instance.pxd.orig 2014-11-18 15:25:03.591127791 -0200
++++ src/sage/libs/pari/pari_instance.pxd 2014-11-18 15:25:18.999127995 -0200
+@@ -6,6 +6,10 @@ cimport cython
from sage.libs.pari.gen cimport gen
@@ -11,8 +12,9 @@
cpdef long prec_bits_to_words(unsigned long prec_in_bits)
@cython.final
---- src/sage/libs/pari/pari_instance.pyx.orig 2014-05-10 15:49:06.437184263 -0300
-+++ src/sage/libs/pari/pari_instance.pyx 2014-05-10 15:49:13.307183771 -0300
+diff -up src/sage/libs/pari/pari_instance.pyx.orig src/sage/libs/pari/pari_instance.pyx
+--- src/sage/libs/pari/pari_instance.pyx.orig 2014-11-18 15:25:16.287127959 -0200
++++ src/sage/libs/pari/pari_instance.pyx 2014-11-18 15:25:19.000127995 -0200
@@ -437,7 +437,12 @@ cdef class PariInstance(sage.structure.p
# The size here doesn't really matter, because we will allocate
# our own stack anyway. We ask PARI not to set up signal and
diff --git a/sagemath-png.patch b/sagemath-png.patch
index d7cc39a..2288e21 100644
--- a/sagemath-png.patch
+++ b/sagemath-png.patch
@@ -1,7 +1,7 @@
diff -up src/module_list.py.orig src/module_list.py
---- src/module_list.py.orig 2014-08-12 14:10:45.498956328 -0300
-+++ src/module_list.py 2014-08-12 14:10:53.082956619 -0300
-@@ -1065,7 +1065,7 @@ ext_modules = [
+--- src/module_list.py.orig 2014-11-18 15:23:33.184126598 -0200
++++ src/module_list.py 2014-11-18 15:23:42.856126725 -0200
+@@ -1081,7 +1081,7 @@ ext_modules = [
Extension('sage.matrix.matrix_mod2_dense',
sources = ['sage/matrix/matrix_mod2_dense.pyx'],
@@ -10,7 +10,7 @@ diff -up src/module_list.py.orig src/module_list.py
extra_compile_args = m4ri_extra_compile_args,
depends = [SAGE_INC + "/png.h", SAGE_INC + "/m4ri/m4ri.h"]),
-@@ -1360,7 +1360,7 @@ ext_modules = [
+@@ -1379,7 +1379,7 @@ ext_modules = [
Extension('sage.modules.vector_mod2_dense',
sources = ['sage/modules/vector_mod2_dense.pyx'],
@@ -19,7 +19,7 @@ diff -up src/module_list.py.orig src/module_list.py
extra_compile_args = m4ri_extra_compile_args,
depends = [SAGE_INC + "/png.h", SAGE_INC + "/m4ri/m4ri.h"]),
-@@ -1876,7 +1876,7 @@ ext_modules = [
+@@ -1893,7 +1893,7 @@ ext_modules = [
Extension('sage.rings.polynomial.pbori',
sources = ['sage/rings/polynomial/pbori.pyx'],
libraries=['polybori-' + polybori_major_version,
diff --git a/sagemath-readonly.patch b/sagemath-readonly.patch
index aac8360..cf6f0e0 100644
--- a/sagemath-readonly.patch
+++ b/sagemath-readonly.patch
@@ -1,7 +1,7 @@
diff -up src/sage/all.py.orig src/sage/all.py
---- src/sage/all.py.orig 2014-08-12 14:10:06.778954845 -0300
-+++ src/sage/all.py 2014-08-12 14:10:14.402955137 -0300
-@@ -316,11 +316,11 @@ def _write_started_file():
+--- src/sage/all.py.orig 2014-11-18 15:20:50.327124447 -0200
++++ src/sage/all.py 2014-11-18 15:20:58.279124552 -0200
+@@ -307,11 +307,11 @@ def _write_started_file():
Check that the file exists when Sage is running::
diff --git a/sagemath-rpmbuild.patch b/sagemath-rpmbuild.patch
index 3a602b3..f3992e4 100644
--- a/sagemath-rpmbuild.patch
+++ b/sagemath-rpmbuild.patch
@@ -1,16 +1,16 @@
diff -up src/module_list.py.orig src/module_list.py
---- src/module_list.py.orig 2014-08-13 11:34:14.739202143 -0300
-+++ src/module_list.py 2014-08-13 11:34:18.828202300 -0300
-@@ -5,7 +5,7 @@ from distutils.core import setup
+--- src/module_list.py.orig 2014-11-18 13:25:41.898033239 -0200
++++ src/module_list.py 2014-11-18 13:27:10.616034410 -0200
+@@ -4,7 +4,7 @@ import os
from distutils.extension import Extension
- from sage.env import *
+ from sage.env import SAGE_LOCAL
-SAGE_INC = os.path.join(SAGE_LOCAL, 'include')
+SAGE_INC = '/usr/include'
#########################################################
### BLAS setup
-@@ -36,10 +36,11 @@ else:
+@@ -35,10 +35,11 @@ else:
### Commonly used definitions
#########################################################
@@ -24,7 +24,7 @@ diff -up src/module_list.py.orig src/module_list.py
flint_depends = [SAGE_INC + '/flint/flint.h']
singular_depends = [SAGE_INC + '/libsingular.h']
-@@ -70,7 +71,7 @@ givaro_extra_compile_args =['-D__STDC_LI
+@@ -71,7 +72,7 @@ givaro_extra_compile_args =['-D__STDC_LI
### PolyBoRi settings
#########################################################
@@ -33,7 +33,7 @@ diff -up src/module_list.py.orig src/module_list.py
polybori_major_version = '0.8'
-@@ -710,7 +711,7 @@ ext_modules = [
+@@ -730,7 +731,7 @@ ext_modules = [
sources = ['sage/libs/lcalc/lcalc_Lfunction.pyx'],
libraries = ['m', 'ntl', 'mpfr', 'gmp', 'gmpxx',
'Lfunction'],
@@ -43,13 +43,13 @@ diff -up src/module_list.py.orig src/module_list.py
language = 'c++'),
diff -up src/setup.py.orig src/setup.py
---- src/setup.py.orig 2014-08-13 11:34:14.742202143 -0300
-+++ src/setup.py 2014-08-13 11:34:55.082203688 -0300
+--- src/setup.py.orig 2014-11-18 13:25:47.434033312 -0200
++++ src/setup.py 2014-11-18 13:28:52.152035751 -0200
@@ -36,11 +36,11 @@ except KeyError:
compile_result_dir = None
keep_going = False
--SAGE_INC = os.path.join(SAGE_LOCAL,'include')
+-SAGE_INC = os.path.join(SAGE_LOCAL, 'include')
+SAGE_INC = '/usr/include'
# search for dependencies and add to gcc -I<path>
@@ -70,10 +70,10 @@ diff -up src/setup.py.orig src/setup.py
m.extra_link_args = m.extra_link_args + extra_link_args
- m.library_dirs = m.library_dirs + [os.path.join(SAGE_LOCAL, "lib")]
+ m.library_dirs += ['c_lib', '%s/lib' % SAGE_LOCAL]
+ m.include_dirs = m.include_dirs + include_dirs
- #############################################
-@@ -556,20 +558,6 @@ print "Discovered Python source, time: %
+@@ -579,20 +581,6 @@ print "Discovered Python source, time: %
#########################################################
diff --git a/sagemath-sagedoc.patch b/sagemath-sagedoc.patch
index db6ec03..ed775af 100644
--- a/sagemath-sagedoc.patch
+++ b/sagemath-sagedoc.patch
@@ -1,18 +1,18 @@
diff -up src/doc/common/builder.py.orig src/doc/common/builder.py
---- src/doc/common/builder.py.orig 2014-08-12 14:06:23.374946290 -0300
-+++ src/doc/common/builder.py 2014-08-12 14:06:47.943947231 -0300
+--- src/doc/common/builder.py.orig 2014-11-18 13:30:43.238037217 -0200
++++ src/doc/common/builder.py 2014-11-18 13:32:05.097038298 -0200
@@ -32,7 +32,7 @@ from sage.env import SAGE_DOC, SAGE_SRC
# SAGE_DOC, LANGUAGES, SPHINXOPTS, PAPER, OMIT,
# PAPEROPTS, ALLSPHINXOPTS, NUM_THREADS, WEBSITESPHINXOPTS
# from build_options.py.
--execfile(os.path.join(SAGE_DOC, 'common' , 'build_options.py'))
-+execfile(os.path.join(os.getenv('SAGE_ROOT'), 'src', 'doc', 'common' , 'build_options.py'))
+-fpath = os.path.join(SAGE_DOC, 'common', 'build_options.py')
++fpath = os.path.join(os.getenv('SAGE_ROOT'), 'src', 'doc', 'common', 'build_options.py')
+ exec(compile(open(fpath).read(), fpath, 'exec'))
- def delete_empty_directories(root_dir, verbose=True):
diff -up src/doc/common/conf.py.orig src/doc/common/conf.py
---- src/doc/common/conf.py.orig 2014-08-12 14:06:23.376946291 -0300
-+++ src/doc/common/conf.py 2014-08-12 14:07:26.095948692 -0300
+--- src/doc/common/conf.py.orig 2014-11-18 13:30:43.248037218 -0200
++++ src/doc/common/conf.py 2014-11-18 13:32:40.336038763 -0200
@@ -1,5 +1,5 @@
import sys, os, sphinx
-from sage.env import SAGE_DOC
@@ -31,8 +31,8 @@ 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 2014-08-12 14:06:23.382946291 -0300
-+++ src/sage/doctest/control.py 2014-08-12 14:08:08.384950312 -0300
+--- src/sage/doctest/control.py.orig 2014-11-18 13:30:43.259037218 -0200
++++ src/sage/doctest/control.py 2014-11-18 13:33:27.185039382 -0200
@@ -89,7 +89,6 @@ class DocTestDefaults(SageObject):
self.valgrind = False
self.massif = False
@@ -50,7 +50,7 @@ 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:
-@@ -822,13 +821,8 @@ class DocTestController(SageObject):
+@@ -889,13 +888,8 @@ class DocTestController(SageObject):
elif opt.cachegrind:
toolname = "cachegrind"
flags = os.getenv("SAGE_CACHEGRIND_FLAGS", "")
@@ -64,7 +64,7 @@ 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
-@@ -888,10 +882,10 @@ class DocTestController(SageObject):
+@@ -955,10 +949,10 @@ class DocTestController(SageObject):
0
"""
opt = self.options
@@ -78,8 +78,8 @@ 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 2014-08-12 14:06:23.391946291 -0300
-+++ src/sage/interfaces/singular.py 2014-08-12 14:08:26.055950988 -0300
+--- src/sage/interfaces/singular.py.orig 2014-11-18 13:30:43.265037218 -0200
++++ src/sage/interfaces/singular.py 2014-11-18 13:33:49.257039673 -0200
@@ -2147,7 +2147,7 @@ def generate_docstring_dictionary():
nodes.clear()
node_names.clear()
@@ -89,15 +89,3 @@ 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/misc/latex_macros.py.orig src/sage/misc/latex_macros.py
---- src/sage/misc/latex_macros.py.orig 2014-08-12 14:06:23.402946292 -0300
-+++ src/sage/misc/latex_macros.py 2014-08-12 14:08:46.103951756 -0300
-@@ -142,7 +142,7 @@ def convert_latex_macro_to_mathjax(macro
- return name + ': ["' + defn + '",' + str(num_args) + ']'
-
- from superseded import deprecated_function_alias
--convert_latex_macro_to_jsmath = deprecated_function_alias(13508, convert_latex_macro_to_mathjax)
-+convert_latex_macro_to_jsmath = convert_latex_macro_to_mathjax
-
- # To add a new macro for use in the Sage documentation, add a list or
- # tuple to the following list. Each list (or tuple) should have the
diff --git a/sagemath-sagenb.patch b/sagemath-sagenb.patch
index 7785686..57d289b 100644
--- a/sagemath-sagenb.patch
+++ b/sagemath-sagenb.patch
@@ -1,6 +1,6 @@
-diff -up build/pkgs/sagenb/src/sagenb-0.10.8.2/flask_version/base.py.orig build/pkgs/sagenb/src/sagenb-0.10.8.2/flask_version/base.py
---- build/pkgs/sagenb/src/sagenb-0.10.8.2/flask_version/base.py.orig 2014-02-11 18:13:34.453086409 -0200
-+++ build/pkgs/sagenb/src/sagenb-0.10.8.2/flask_version/base.py 2014-02-11 18:14:30.976088573 -0200
+diff -up build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/flask_version/base.py.orig build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/flask_version/base.py
+--- build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/flask_version/base.py.orig 2014-12-06 17:45:36.063723826 -0200
++++ build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/flask_version/base.py 2014-12-06 17:49:09.074731983 -0200
@@ -4,8 +4,6 @@ from functools import partial
from flask import Flask, Module, url_for, render_template, request, session, redirect, g, make_response, current_app
from decorators import login_required, guest_or_login_required, with_lock
@@ -18,84 +18,55 @@ diff -up build/pkgs/sagenb/src/sagenb-0.10.8.2/flask_version/base.py.orig build/
self.config['SESSION_COOKIE_HTTPONLY'] = False
-@@ -36,7 +33,7 @@ class SageNBFlask(Flask):
+@@ -36,12 +33,12 @@ class SageNBFlask(Flask):
self.add_static_path('/javascript', DATA)
self.add_static_path('/static', DATA)
self.add_static_path('/java', DATA)
- self.add_static_path('/java/jmol', os.path.join(os.environ["SAGE_ROOT"],"local","share","jmol"))
-+ self.add_static_path('/java/jmol', os.path.join(DATA, "jmol"))
+- self.add_static_path('/jsmol', os.path.join(os.environ["SAGE_ROOT"],"local","share","jsmol"))
+- self.add_static_path('/jsmol/js', os.path.join(os.environ["SAGE_ROOT"],"local","share","jsmol","js"))
+- self.add_static_path('/j2s', os.path.join(os.environ["SAGE_ROOT"],"local","share","jsmol","j2s"))
+- self.add_static_path('/jsmol/j2s', os.path.join(os.environ["SAGE_ROOT"],"local","share","jsmol","j2s"))
+- self.add_static_path('/j2s/core', os.path.join(os.environ["SAGE_ROOT"],"local","share","jsmol","j2s","core"))
++ self.add_static_path('/java/jmol', os.path.join(os.environ["SAGE_ROOT"],"share","jmol"))
++ self.add_static_path('/jsmol', os.path.join(os.environ["SAGE_ROOT"],"share","jsmol"))
++ self.add_static_path('/jsmol/js', os.path.join(os.environ["SAGE_ROOT"],"share","jsmol","js"))
++ self.add_static_path('/j2s', os.path.join(os.environ["SAGE_ROOT"],"jsmol","j2s"))
++ self.add_static_path('/jsmol/j2s', os.path.join(os.environ["SAGE_ROOT"],"share","jsmol","j2s"))
++ self.add_static_path('/j2s/core', os.path.join(os.environ["SAGE_ROOT"],"share","jsmol","j2s","core"))
import mimetypes
mimetypes.add_type('text/plain','.jmol')
-diff -up build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/data/sage/html/notebook/base.html.orig build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/data/sage/html/notebook/base.html
---- build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/data/sage/html/notebook/base.html.orig 2014-02-11 18:13:34.468086409 -0200
-+++ build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/data/sage/html/notebook/base.html 2014-02-11 18:13:51.591087065 -0200
-@@ -46,7 +46,7 @@ INPUT:
- <!-- Jmol - embedded 3D graphics -->
- <script type="text/javascript" src="/java/jmol/appletweb/Jmol.js"></script>
- <!-- This must stay in head -->
--<script>jmolInitialize("/java/jmol");jmolSetCallback("menuFile","/java/jmol/appletweb/SageMenu.mnu");</script>
-+<script>jmolInitialize("/java/jmol", "JmolApplet.jar,Jmol.jar,vecmath.jar");</script>
-
- {% if JEDITABLE_TINYMCE and not worksheet.docbrowser() and not worksheet.is_published() %}
- <!-- TinyMCE and jEditable - in-place editing of text cells -->
-diff -up build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/data/sage/js/jmol_lib.js.orig build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/data/sage/js/jmol_lib.js
---- build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/data/sage/js/jmol_lib.js.orig 2014-02-11 18:13:34.422086407 -0200
-+++ build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/data/sage/js/jmol_lib.js 2014-02-11 18:13:51.576087064 -0200
-@@ -256,9 +256,6 @@ function makeCntrlPanels(url, n, functio
- panelHTML +='<button title="Move to own window" onClick="javascript:void(jmol_popup(\''+n+'\'))">Move to own window</button> arbitrarily resizable.<hr/>';
- //static image to save
- panelHTML +='<button onClick="sleepJmol('+n+',jmolStatus)"> Get Static Image to Save (Sleep) </button> Right-click or Cmd-click on image to get download options.<hr/>';
-- //save file to local disk
-- panelHTML += '<button title="Download View" onClick="javascript:void(jmolFileDownload('+n+'))">Download this view</button> will require loading signed applet if not already done.';
-- panelHTML +='<hr/>';
- //spin on
- panelHTML +='<input class="worksheet" type="checkbox" value="spin on" onchange="jmol_spin(this.checked,'+n+');" title="Enable/disable spin"/>Spin on';
- //antialaisdisplay (smoothing of objects)
-diff -up build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/flask_version/base.py.orig build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/flask_version/base.py
---- build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/flask_version/base.py.orig 2014-02-11 18:13:34.459086409 -0200
-+++ build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/flask_version/base.py 2014-02-11 18:13:51.590087065 -0200
-@@ -4,8 +4,6 @@ from functools import partial
- from flask import Flask, Module, url_for, render_template, request, session, redirect, g, make_response, current_app
- from decorators import login_required, guest_or_login_required, with_lock
- from decorators import global_lock
--# Make flask use the old session foo from <=flask-0.9
--from flask_oldsessions import OldSecureCookieSessionInterface
-
- from flask.ext.autoindex import AutoIndex
- try:
-@@ -25,7 +23,6 @@ class SageNBFlask(Flask):
- def __init__(self, *args, **kwds):
- self.startup_token = kwds.pop('startup_token', None)
- Flask.__init__(self, *args, **kwds)
-- self.session_interface = OldSecureCookieSessionInterface()
-
- self.config['SESSION_COOKIE_HTTPONLY'] = False
-
-@@ -36,7 +33,7 @@ class SageNBFlask(Flask):
- self.add_static_path('/javascript', DATA)
- self.add_static_path('/static', DATA)
- self.add_static_path('/java', DATA)
-- self.add_static_path('/java/jmol', os.path.join(os.environ["SAGE_ROOT"],"local","share","jmol"))
-+ self.add_static_path('/java/jmol', os.path.join(DATA, "jmol"))
- import mimetypes
- mimetypes.add_type('text/plain','.jmol')
+diff -up build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/misc/misc.py.orig build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/misc/misc.py
+--- build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/misc/misc.py.orig 2014-12-06 17:45:36.066723826 -0200
++++ build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/misc/misc.py 2014-12-06 17:45:38.853723933 -0200
+@@ -174,7 +174,8 @@ def pad_zeros(s, size=3):
-diff -up build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/notebook/cell.py.orig build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/notebook/cell.py
---- build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/notebook/cell.py.orig 2014-02-11 18:13:34.441086408 -0200
-+++ build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/notebook/cell.py 2014-02-11 18:13:51.583087065 -0200
-@@ -2369,7 +2369,7 @@ class Cell(Cell_generic):
- jmol_script = jmol_file.read()
- jmol_file.close()
+ SAGENB_ROOT = os.path.split(resource_filename(__name__, ''))[0]
-- jmol_script = jmol_script.replace('defaultdirectory "', 'defaultdirectory "' + self.url_to_self() + '/')
-+ jmol_script = jmol_script.replace('defaultdirectory "', 'defaultdirectory "/home/' + self.worksheet_filename() + '/')
+-DATA = os.path.join(SAGENB_ROOT, 'data')
++from sage.misc.misc import SAGE_SRC
++DATA = os.path.join(SAGE_SRC, 'sagenb', 'data')
- jmol_file = open(jmol_name, 'w')
- jmol_file.write(jmol_script)
-diff -up build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/notebook/run_notebook.py.orig build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/notebook/run_notebook.py
---- build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/notebook/run_notebook.py.orig 2014-02-11 18:13:34.447086408 -0200
-+++ build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/notebook/run_notebook.py 2014-02-11 18:13:51.586087065 -0200
+ if os.environ.has_key('DOT_SAGENB'):
+ DOT_SAGENB = os.environ['DOT_SAGENB']
+diff -up build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/notebook/cell.py.orig build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/notebook/cell.py
+--- build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/notebook/cell.py.orig 2014-12-06 17:45:36.067723826 -0200
++++ build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/notebook/cell.py 2014-12-06 17:45:38.854723933 -0200
+@@ -2338,8 +2338,8 @@ class Cell(Cell_generic):
+ with open(jmol_name, 'r') as f:
+ jmol_script = f.read()
+ jmol_script = jmol_script.replace(
+- 'defaultdirectory "',
+- 'defaultdirectory "{0}/'.format(self.url_to_worksheet()))
++ 'defaultdirectory "',
++ 'defaultdirectory "/home/' + self.worksheet_filename() + '/')
+ with open(jmol_name, 'w') as f:
+ f.write(jmol_script)
+
+diff -up build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/notebook/run_notebook.py.orig build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/notebook/run_notebook.py
+--- build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/notebook/run_notebook.py.orig 2014-12-06 17:45:36.069723826 -0200
++++ build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/notebook/run_notebook.py 2014-12-06 17:45:38.854723933 -0200
@@ -46,12 +46,14 @@ sagenb.notebook.misc.DIR = %(cwd)r #We s
# Flask #
#########
@@ -113,15 +84,3 @@ diff -up build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/notebook/run_notebook.py.o
def save_notebook(notebook):
print "Quitting all running worksheets..."
---- build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/misc/misc.py.orig 2014-02-19 12:22:25.360997774 -0300
-+++ build/pkgs/sagenb/src/sagenb-0.10.8.2/sagenb/misc/misc.py 2014-02-19 12:26:01.260011849 -0300
-@@ -174,7 +174,8 @@ def pad_zeros(s, size=3):
-
- SAGENB_ROOT = os.path.split(resource_filename(__name__, ''))[0]
-
--DATA = os.path.join(SAGENB_ROOT, 'data')
-+from sage.misc.misc import SAGE_SRC
-+DATA = os.path.join(SAGE_SRC, 'sagenb', 'data')
-
- if os.environ.has_key('DOT_SAGENB'):
- DOT_SAGENB = os.environ['DOT_SAGENB']
diff --git a/sagemath-scons.patch b/sagemath-scons.patch
index 6e254fa..01558fa 100644
--- a/sagemath-scons.patch
+++ b/sagemath-scons.patch
@@ -1,6 +1,6 @@
diff -up src/c_lib/SConstruct.orig src/c_lib/SConstruct
---- src/c_lib/SConstruct.orig 2014-05-26 13:24:15.242761223 -0300
-+++ src/c_lib/SConstruct 2014-05-26 13:25:26.593763955 -0300
+--- src/c_lib/SConstruct.orig 2014-11-17 17:41:32.525922611 -0200
++++ src/c_lib/SConstruct 2014-11-17 17:41:41.486922954 -0200
@@ -126,8 +126,8 @@ env['PYV']=platform.python_version().rsp
# The SCons convenience function Split is the only strange thing
# to python programmers. It just makes a list by splitting on
@@ -14,7 +14,7 @@ diff -up src/c_lib/SConstruct.orig src/c_lib/SConstruct
cppFiles = Split( "ZZ_pylong.cpp ntl_wrap.cpp" )
@@ -136,9 +136,22 @@ incFiles = Split( "ccobject.h convert.h
Split( "interrupt.h memory.h mpn_pylong.h mpz_longlong.h" ) + \
- Split( "mpz_pylong.h ntl_wrap.h stdsage.h ZZ_pylong.h" )
+ Split( "mpz_pylong.h ntl_wrap.h parisage.h stdsage.h ZZ_pylong.h" )
+env.Append(CFLAGS='@@optflags@@')
+env.Append(CXXFLAGS='@@optflags@@')
diff --git a/sagemath-scripts.patch b/sagemath-scripts.patch
index 0f8778f..78d0cb0 100644
--- a/sagemath-scripts.patch
+++ b/sagemath-scripts.patch
@@ -1,8 +1,8 @@
diff -up src/bin/sage.orig src/bin/sage
---- src/bin/sage.orig 2014-08-12 13:51:14.714911495 -0300
-+++ src/bin/sage 2014-08-12 13:59:39.911930840 -0300
-@@ -13,17 +13,14 @@ usage() {
- echo " file.<sage|py|spyx> -- run given .sage, .py or .spyx files"
+--- src/bin/sage.orig 2014-11-17 17:42:48.321925514 -0200
++++ src/bin/sage 2014-11-17 17:55:52.524955544 -0200
+@@ -13,11 +13,9 @@ usage() {
+ echo " file.[sage|py|spyx] -- run given .sage, .py or .spyx file"
echo " -advanced -- list all command line options"
echo " -c <cmd> -- Evaluates cmd as sage code"
- echo " -experimental -- list all experimental packages that can be installed"
@@ -10,16 +10,18 @@ diff -up src/bin/sage.orig src/bin/sage
echo " -gp [...] -- run Sage's PARI/GP calculator with given arguments"
echo " -h, -? -- print this help message"
- echo " -i [packages] -- install the given Sage packages"
- echo " -inotebook [...] -- start the *insecure* Sage notebook"
+ echo " -pip [...] -- invoke pip, the Python package manager"
+ echo " -inotebook [...] -- start the *insecure* Sage notebook (deprecated)"
echo " -maxima [...] -- run Sage's Maxima with given arguments"
- echo " -mwrank [...] -- run Sage's mwrank with given arguments"
- echo " -n, -notebook [...] -- start the Sage notebook (options are the same"
- echo " as for the notebook command in Sage)"
+@@ -25,7 +23,6 @@ usage() {
+ echo " --notebook=[...] -- start the Sage notebook (valid options are"
+ echo " 'default', 'sagenb', and 'ipython')"
+ echo " -n, --notebook -- shortcut for --notebook=default"
- echo " -optional -- list all optional packages that can be installed"
echo " -python [...] -- run the Python interpreter"
echo " -R [...] -- run Sage's R with given arguments"
echo " -singular [...] -- run Sage's singular with given arguments"
-@@ -39,10 +36,6 @@ usage() {
+@@ -41,10 +38,6 @@ usage() {
echo " --optional - controls which optional tests are run"
echo " --sagenb - test all sagenb files"
echo " --help - show all testing options"
@@ -30,32 +32,31 @@ diff -up src/bin/sage.orig src/bin/sage
echo " -v, -version -- print the Sage version"
exit 0
}
-@@ -61,16 +54,14 @@ usage_advanced() {
+@@ -63,8 +56,6 @@ usage_advanced() {
echo " -preparse <file.sage> -- preparse file.sage and produce corresponding file.sage.py"
echo " -q -- quiet; start with no banner"
echo " -root -- print the Sage root directory"
- echo " -gthread, -qthread, -q4thread, -wthread, -pylab"
- echo " -- pass the option through to ipython"
-+ echo " -testall [options] -- test all source files, docs, and examples. options"
-+ echo " like -t"
echo " -v, -version -- print the Sage version"
echo
- #### 1.......................26..................................................78
- #### |.....................--.|...................................................|
- echo "Running the notebook:"
+@@ -75,8 +66,6 @@ usage_advanced() {
+ echo " 'default', 'sagenb', and 'ipython'). See the output"
+ echo " of sage --notebook --help for more details and"
+ echo " examples of how to pass optional arguments"
- echo " -bn, -build-and-notebook [...] -- build the Sage library then start"
- echo " the Sage notebook"
- echo " -inotebook [...] -- start the *insecure* Sage notebook"
- echo " -n, -notebook [...] -- start the Sage notebook (options are the same"
- echo " as for the notebook command in Sage)"
-@@ -87,13 +78,8 @@ usage_advanced() {
+ echo " -inotebook [...] -- start the *insecure* Sage notebook (deprecated)"
+ echo " -n, -notebook [...] -- start the default Sage notebook (options are the"
+ echo " same as for the notebook command in Sage). See the"
+@@ -94,13 +83,9 @@ usage_advanced() {
echo " -gp [...] -- run Sage's PARI/GP calculator with given arguments"
echo " -ipython [...] -- run Sage's IPython using the default environment (not"
echo " Sage), passing additional options to IPython"
- echo " -kash [...] -- run Sage's Kash with given arguments"
- command -v kash &>/dev/null || \
-- echo " (not installed currently, run sage -i kash)"
+ echo " (not installed currently, run sage -i kash)"
echo " -lisp [...] -- run Lisp interpreter included with Sage"
echo " -M2 [...] -- run Sage's Macaulay2 with given arguments"
- command -v M2 &>/dev/null || \
@@ -63,7 +64,7 @@ diff -up src/bin/sage.orig src/bin/sage
echo " -maxima [...] -- run Sage's Maxima with given arguments"
echo " -mwrank [...] -- run Sage's mwrank with given arguments"
echo " -python [...] -- run the Python interpreter"
-@@ -107,75 +93,10 @@ usage_advanced() {
+@@ -114,74 +99,10 @@ usage_advanced() {
echo
#### 1.......................26..................................................78
#### |.....................--.|...................................................|
@@ -82,6 +83,7 @@ diff -up src/bin/sage.orig src/bin/sage
- echo " -info [packages] -- print the SPKG.txt of the given packages"
- echo " -optional -- list all optional packages that can be installed"
- echo " -standard -- list all standard packages that can be installed"
+- echo " -installed -- list all installed packages"
- #echo " -update -- download latest non-optional Sage packages (do not build them)"
- #echo " -update-build -- build and install all downloaded non-optional Sage packages"
- echo " -upgrade [version] -- download, build and install the given version. Here,"
@@ -93,20 +95,17 @@ diff -up src/bin/sage.orig src/bin/sage
- #### 1.......................26..................................................78
- #### |.....................--.|...................................................|
- echo "Building and testing the Sage library:"
-- echo " -b [branch] -- build Sage library. If branch is given, switch to"
-- echo " branch in devel/sage-branch and build that branch"
-- echo " -ba [branch] -- same as -b and rebuild all Cython code"
-- echo " -ba-force [branch] -- same as -ba, but don't query before rebuilding"
-- echo " -br [branch] -- switch to, build, and run Sage given branch"
+- echo " -b -- build Sage library."
+- echo " -ba -- same as -b and rebuild all Cython code"
+- echo " -ba-force -- same as -ba, but don't query before rebuilding"
+- echo " -br -- build and run Sage"
- echo " -bt [...] -- build and test, options like -t below"
- echo " -btp <N> [...] -- build and test parallel, options like -tp below"
- echo " -btnew [...] -- build and test modified files, options like -tnew"
- echo " -fixdoctests <file.py> [output_file] [--long]"
-- echo " -- writes a new version of file.py to output_file"
-- echo " (defaults: to file.py.out) that will pass the doctests."
-- echo " With the optional --long argument the long time tests"
-- echo " are also checked."
-- echo " A patch for the new file is printed to stdout."
+- echo " -- replace failing doctests with the actual output. With"
+- echo " optional output_file: redirect there. With the --long"
+- echo " option: include #long time tests."
- echo " -startuptime [module] -- display how long each component of Sage takes to"
- echo " start up; optionally specify a module to get more"
- echo " details about that particular module"
@@ -123,6 +122,7 @@ diff -up src/bin/sage.orig src/bin/sage
- echo " --failed - only test files that failed last test"
- echo " --sagenb - test all sagenb files"
- echo " --help - show all testing options"
+- echo " --warn-long [timeout] - warning if doctest is slow"
- echo " -tp <N> [...] -- like -t above, but tests in parallel using N threads"
- echo " with 0 interpreted as a sensible default"
- echo " -testall [options] -- test all source files, docs, and examples. options"
@@ -139,7 +139,7 @@ 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"
-@@ -195,16 +116,6 @@ usage_advanced() {
+@@ -201,16 +122,6 @@ usage_advanced() {
echo
#### 1.......................26..................................................78
#### |.....................--.|...................................................|
@@ -156,7 +156,7 @@ 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"
-@@ -218,9 +129,6 @@ usage_advanced() {
+@@ -224,9 +135,6 @@ 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"
@@ -166,7 +166,7 @@ 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'."
-@@ -240,34 +148,6 @@ if [ "$1" = '--nodotsage' ]; then
+@@ -246,65 +154,14 @@ if [ "$1" = '--nodotsage' ]; then
exit $status
fi
@@ -198,14 +198,16 @@ diff -up src/bin/sage.orig src/bin/sage
-fi
-
-
- if [ $# -gt 0 ]; then
- if [ "$1" = '-h' -o "$1" = '-?' -o "$1" = '-help' -o "$1" = '--help' ]; then
- usage
-@@ -277,28 +157,13 @@ if [ $# -gt 0 ]; then
- fi
- fi
-
+-if [ $# -gt 0 ]; then
+- if [ "$1" = '-h' -o "$1" = '-?' -o "$1" = '-help' -o "$1" = '--help' ]; then
+- usage
+- fi
+- if [ "$1" = "-advanced" -o "$1" = "--advanced" ]; then
+- usage_advanced
+- fi
+-fi
-
+
# Prepare for running Sage, either interactively or non-interactively.
sage_setup() {
- # Check that we're not in a source tarball which hasn't been built yet (#13561).
@@ -230,11 +232,10 @@ diff -up src/bin/sage.orig src/bin/sage
if [ ! -d "$IPYTHONDIR" ]; then
# make sure that $DOT_SAGE exists so that ipython will happily
# create its config directories there. If DOT_SAGE doesn't
-@@ -308,21 +173,6 @@ sage_setup() {
- sage-cleaner &>/dev/null &
+@@ -315,20 +172,6 @@ sage_setup() {
}
--
+
-# Check to see if the whole Sage install tree has moved. If so,
-# change various hardcoded paths. Skip this if we don't have write
-# access to $SAGE_LOCAL (e.g. when running as a different user) or
@@ -252,7 +253,7 @@ diff -up src/bin/sage.orig src/bin/sage
# Start an interactive Sage session, this function never returns.
interactive_sage() {
sage_setup
-@@ -384,7 +234,7 @@ fi
+@@ -390,7 +233,7 @@ fi
if [ "$1" = '-singular' -o "$1" = '--singular' ]; then
shift
@@ -261,15 +262,10 @@ diff -up src/bin/sage.orig src/bin/sage
fi
if [ "$1" = '-sqlite3' -o "$1" = '--sqlite3' ]; then
-@@ -412,16 +262,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
- exec ecl "$@"
+@@ -423,11 +266,6 @@ if [ "$1" = '-kash' -o "$1" = '--kash' ]
+ exec kash "$@"
fi
--if [ "$1" = '-kash' -o "$1" = '--kash' ]; then
-- shift
-- exec kash "$@"
--fi
--
-if [ "$1" = '-fixdoctests' -o "$1" = '--fixdoctests' ]; then
- shift
- exec sage-fixdoctests "$@"
@@ -278,7 +274,23 @@ diff -up src/bin/sage.orig src/bin/sage
if [ "$1" = '-maxima' -o "$1" = '--maxima' ]; then
shift
exec maxima "$@"
-@@ -581,20 +421,6 @@ EOF
+@@ -448,15 +286,6 @@ if [ "$1" = '-scons' -o "$1" = '--scons'
+ exec scons "$@"
+ fi
+
+-if [ "$1" = '-pip' -o "$1" = '--pip' ]; then
+- if [ ! -x "$SAGE_LOCAL/bin/pip" ]; then
+- echo "Pip is not installed. Run \"sage -i pip\" to install it."
+- exit 1
+- fi
+- shift
+- exec pip "$@"
+-fi
+-
+ if [ "$1" = '-python' -o "$1" = '--python' ]; then
+ shift
+ exec python "$@"
+@@ -596,20 +425,6 @@ EOF
fi
#####################################################################
@@ -299,7 +311,7 @@ diff -up src/bin/sage.orig src/bin/sage
# File conversion
#####################################################################
-@@ -609,36 +435,15 @@ if [ "$1" = '-rst2sws' -o "$1" = '--rst2
+@@ -624,23 +439,9 @@ if [ "$1" = '-rst2sws' -o "$1" = '--rst2
fi
#####################################################################
@@ -320,23 +332,24 @@ diff -up src/bin/sage.orig src/bin/sage
- sage-build "$@" || exit $?
-}
-
- if [ "$1" = "-notebook" -o "$1" = '--notebook' -o "$1" = '-n' ]; then
- shift
+ if [[ "$1" =~ "--notebook="* || "$1" =~ "-n="* || "$1" =~ "-notebook="* ]]; then
sage-cleaner &>/dev/null &
exec sage-notebook "$@"
+@@ -652,13 +453,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
+ exec sage-notebook --notebook=default "$@"
fi
-if [ "$1" = "-bn" -o "$1" = "--build-and-notebook" ]; then
- shift
- build_sage
- sage-cleaner &>/dev/null &
-- exec sage-notebook "$@"
+- exec sage-notebook --notebook=default "$@"
-fi
-
if [ "$1" = "-inotebook" -o "$1" = '--inotebook' ]; then
shift
sage-cleaner &>/dev/null &
-@@ -657,40 +462,19 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
+@@ -677,40 +471,19 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
exit 0
fi
@@ -379,7 +392,7 @@ diff -up src/bin/sage.orig src/bin/sage
shift
exec sage-runtests -p "$@"
else
-@@ -699,10 +483,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
+@@ -719,10 +492,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
fi
fi
@@ -391,7 +404,7 @@ diff -up src/bin/sage.orig src/bin/sage
shift
SAGE_BANNER="no"
sage_setup
-@@ -724,132 +505,6 @@ if [ "$1" = '-c' ]; then
+@@ -744,136 +514,6 @@ if [ "$1" = '-c' ]; then
exec sage-eval "$@"
fi
@@ -445,15 +458,19 @@ diff -up src/bin/sage.orig src/bin/sage
-}
-
-if [ "$1" = '-optional' -o "$1" = "--optional" ]; then
-- exec sage-list-optional
+- exec sage-list-packages optional
-fi
-
-if [ "$1" = '-experimental' -o "$1" = "--experimental" ]; then
-- exec sage-list-experimental
+- exec sage-list-packages experimental
-fi
-
-if [ "$1" = '-standard' -o "$1" = "--standard" ]; then
-- exec sage-list-standard
+- exec sage-list-packages standard
+-fi
+-
+-if [ "$1" = '-installed' -o "$1" = "--installed" ]; then
+- exec sage-list-packages installed
-fi
-
-if [ "$1" = '-i' ]; then
@@ -524,7 +541,7 @@ diff -up src/bin/sage.orig src/bin/sage
if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then
shift
sage_setup
-@@ -898,21 +553,10 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
+@@ -922,26 +562,10 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
exec sage-callgrind "$@"
fi
@@ -543,12 +560,17 @@ diff -up src/bin/sage.orig src/bin/sage
- interactive_sage "$@"
-fi
-
- if [ "$1" = '-dev' -o "$1" = "--dev" ]; then
- shift
- exec sage-dev "$@"
+-if [ "$1" = '-dev' -o "$1" = "--dev" ]; then
+- shift
+- exec sage-dev "$@"
+-fi
+-
+ if [ $# -ge 1 ]; then
+ T=`echo "$1" | sed -e "s/.*\.//"`
+ if [ "$T" = "spkg" ]; then
diff -up src/bin/sage-runtests.orig src/bin/sage-runtests
---- src/bin/sage-runtests.orig 2014-08-12 14:00:18.705932326 -0300
-+++ src/bin/sage-runtests 2014-08-12 14:00:31.543932818 -0300
+--- src/bin/sage-runtests.orig 2014-11-17 17:43:03.195926083 -0200
++++ src/bin/sage-runtests 2014-11-17 17:48:39.236938952 -0200
@@ -54,10 +54,6 @@ if __name__ == "__main__":
help="run doctests using Valgrind's cachegrind tool. The log "
"files are named sage-cachegrind.PID and can be found in " +
@@ -561,14 +583,23 @@ 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 2014-08-12 14:00:41.666933205 -0300
-+++ src/bin/sage-valgrind 2014-08-12 14:01:14.983934481 -0300
-@@ -11,7 +11,7 @@ fi
- LOG="$DOT_SAGE"/valgrind/sage-memcheck.%p
- echo "Log file is $LOG"
+--- src/bin/sage-valgrind.orig 2014-11-17 17:43:14.588926520 -0200
++++ src/bin/sage-valgrind 2014-11-17 17:48:18.884938172 -0200
+@@ -1,16 +1,6 @@
+ #!/usr/bin/env bash
+
+-SUPP=""
+-if [ -f "$SAGE_EXTCODE/valgrind/python.supp" ]; then
+- SUPP+=" --suppressions=$SAGE_EXTCODE/valgrind/python.supp"
+-else
+- echo "Python suppressions not found (not installed?), skipping"
+-fi
+-SUPP+=" --suppressions=$SAGE_EXTCODE/valgrind/pyalloc.supp"
+-SUPP+=" --suppressions=$SAGE_EXTCODE/valgrind/sage.supp"
+-SUPP+=" --suppressions=$SAGE_EXTCODE/valgrind/sage-additional.supp"
+-
+-MEMCHECK_FLAGS="--leak-resolution=high --leak-check=full --num-callers=25 $SUPP"
++MEMCHECK_FLAGS="--leak-resolution=high --leak-check=full --num-callers=25"
--MEMCHECK_FLAGS="--leak-resolution=high --log-file=$LOG --leak-check=full --num-callers=25 --suppressions=$SAGE_LOCAL/lib/valgrind/sage.supp "; export MEMCHECK_FLAGS
-+MEMCHECK_FLAGS="--leak-resolution=high --log-file=$LOG --leak-check=full --num-callers=25 "; export MEMCHECK_FLAGS
if [ "$SAGE_MEMCHECK_FLAGS" ]; then
- echo "Overwriting memcheck flags with:"
- echo $SAGE_MEMCHECK_FLAGS
+ echo "Overwriting memcheck flags with: $SAGE_MEMCHECK_FLAGS"
diff --git a/sagemath.spec b/sagemath.spec
index 2555a02..a360633 100644
--- a/sagemath.spec
+++ b/sagemath.spec
@@ -24,7 +24,7 @@
%global pexpect_pkg pexpect-2.0
%global polytopes_db_pkg polytopes_db-20120220
%global rubiks_pkg rubiks-20070912
-%global sagenb_pkg sagenb-0.10.8.2
+%global sagenb_pkg sagenb-0.11.1
%global sagetex_pkg sagetex-2.3.4
%global SAGE_ROOT %{_libdir}/sagemath
@@ -38,8 +38,8 @@
Name: sagemath
Group: Applications/Engineering
Summary: A free open-source mathematics software system
-Version: 6.3
-Release: 4%{?dist}
+Version: 6.4.1
+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
# before files with that license
@@ -48,9 +48,6 @@ URL: http://www.sagemath.org
Source0: http://boxen.math.washington.edu/home/%{name}/sage-mirror/src/sage-%{version}.tar.gz
Source1: gprc.expect
Source2: makecmds.sty
-# not installed by jmol package, use one in sagemath jmol spkg
-Source3: Jmol.js
-Source4: JmolHelp.html
# 1. scons ignores most environment variables
# 2. scons 2.2* does not have soname support (expected for scons 2.3*)
@@ -67,13 +64,10 @@ Patch1: %{name}-gmp.patch
# Set of patches to work with system wide packages
Patch2: %{name}-scripts.patch
-# Adapt to ntl 6.0.0.
-Patch3: %{name}-ntl6.patch
-
# remove call to not implemented sagemath "is_package_installed" interfaces
# need to package coin-or solver in fedora
# remove check for non free solvers
-Patch4: %{name}-extensions.patch
+Patch3: %{name}-extensions.patch
# helper to:
# o respect a DESTDIR environment variable
@@ -81,81 +75,69 @@ Patch4: %{name}-extensions.patch
# o minor change to help in incremental builds by avoiding rebuilding
# files
# o do not assume there is an installed sagemath
-Patch5: %{name}-rpmbuild.patch
+Patch4: %{name}-rpmbuild.patch
# build documentation in buildroot environment
-Patch6: %{name}-sagedoc.patch
+Patch5: %{name}-sagedoc.patch
# sage notebook rpm and system environment adjustments
-Patch7: %{name}-sagenb.patch
+Patch6: %{name}-sagenb.patch
# do not attempt to create state files in system directories
-Patch8: %{name}-readonly.patch
-
-# force coercion of ecl t_string to ecl t_base_string
-# this is hackish and only required if ecl is built with unicode support
-Patch9: %{name}-ecl-unicode.patch
+Patch7: %{name}-readonly.patch
# do not link explicitly to png12
-Patch10: %{name}-png.patch
+Patch8: %{name}-png.patch
# work with all maxima-runtime lisp backend packages
-Patch11: %{name}-maxima.patch
+Patch9: %{name}-maxima.patch
# execute 4ti2 programs in $PATH not in $SAGE_ROOT/local/bin
-Patch12: %{name}-4ti2.patch
+Patch10: %{name}-4ti2.patch
# http://trac.sagemath.org/sage_trac/ticket/12992
# http://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=1317
-Patch13: %{name}-pari.patch
+Patch11: %{name}-pari.patch
# use jmol itself to export preview images
# FIXME besides not using X and told so, fails if DISPLAY is not set
-Patch14: %{name}-jmol.patch
+Patch12: %{name}-jmol.patch
# only cremona mini database built and installed
# FIXME add a package with the full cremona database
# FIXME actually it should be already available in pari-elldata
-Patch15: %{name}-cremona.patch
+Patch13: %{name}-cremona.patch
# lrslib is a requires
-Patch16: %{name}-lrslib.patch
+Patch14: %{name}-lrslib.patch
# nauty cannot be packaged due to license restrictions
# http://cs.anu.edu.au/~bdm/nauty/
# http://pallini.di.uniroma1.it/
-Patch17: %{name}-nauty.patch
+Patch15: %{name}-nauty.patch
# gap hap package not (yet) available
# http://www-gap.mcs.st-and.ac.uk/Packages/hap.html
-Patch18: %{name}-gap-hap.patch
+Patch16: %{name}-gap-hap.patch
# enable lrcalc
-Patch19: %{name}-lrcalc.patch
+Patch17: %{name}-lrcalc.patch
# enable cbc
-Patch20: %{name}-cbc.patch
+Patch18: %{name}-cbc.patch
# Use system gap directories
-Patch21: %{name}-libgap.patch
+Patch19: %{name}-libgap.patch
# enable fes
-Patch22: %{name}-fes.patch
+Patch20: %{name}-fes.patch
# enable cryptominisat
-Patch23: %{name}-cryptominisat.patch
+Patch21: %{name}-cryptominisat.patch
# Side effect of using distro packages
# https://bugzilla.redhat.com/show_bug.cgi?id=974769
-Patch24: %{name}-sympy.patch
-
-# Correct some warnings of newer sphinx that are treatead as errors
-# by default as of sagemath 6.2; other problems were fixed using
-# -k (keep-going)
-Patch25: %{name}-sphinx.patch
-
-# Rediffed latest version from http://trac.sagemath.org/ticket/15767
-Patch26: %{name}-pari2.7.patch
+Patch22: %{name}-sympy.patch
BuildRequires: 4ti2
BuildRequires: atlas-devel
@@ -163,7 +145,7 @@ BuildRequires: cddlib-tools
BuildRequires: cliquer-devel
BuildRequires: coin-or-Cbc-devel
BuildRequires: cryptominisat-devel
-BuildRequires: Cython
+BuildRequires: Cython >= 0.21.1
BuildRequires: desktop-file-utils
BuildRequires: dos2unix
BuildRequires: dvipng
@@ -611,18 +593,13 @@ popd
%patch17
%patch18
%patch19
-%patch20
-%patch21
%if %{have_fes}
-%patch22
+%patch20
%endif
-%patch23
-%patch24
-%patch25
-
-%patch26
+%patch21
+%patch22
sed -e 's|@@SAGE_ROOT@@|%{SAGE_ROOT}|' \
-e 's|@@SAGE_DOC@@|%{SAGE_DOC}|' \
@@ -687,7 +664,9 @@ pushd src/c_lib
-e 's|@@optflags@@|%{optflags}|g' \
-e "s|@@__global_ldflags@@|$ldflags|g" \
-i SConstruct
- CXX=g++ UNAME=Linux SAGE64=auto scons
+ # force building ntl_wrap.cpp with gcc otherwise other
+ # modules will not find mangled symbols.
+ CXX=gcc UNAME=Linux SAGE64=auto scons
ln -s libcsage.so.0 libcsage.so
popd
pushd src/sage/libs/mpmath
@@ -757,19 +736,22 @@ popd
pushd build/pkgs/sagenb/src/%{sagenb_pkg}
rm -f %{buildroot}%{python_sitearch}/sagenb/data/sage3d/sage3d
python setup.py install --root=%{buildroot} --install-purelib=%{python_sitearch}
+
# jmol
- rm -fr %{buildroot}%{python_sitearch}/sagenb/data/jmol
- mkdir -p %{buildroot}%{python_sitearch}/sagenb/data/jmol/appletweb
- pushd %{buildroot}%{python_sitearch}/sagenb/data/jmol
- cp -fa %{SOURCE3} %{SOURCE4} appletweb
- popd
+ ### FIXME waiting on https://bugzilla.redhat.com/show_bug.cgi?id=1108060
+ # To get it to work you need to get the sagemath jmol spkg or an
+ # upstream sagemath install, example:
+ # cp -fr ~/sage-6.4.1-x86_64-Linux/local/share/jmol /usr/share/sagemath
+ # cp -fr ~/sage-6.4.1-x86_64-Linux/local/share/jsmol /usr/share/sagemath
+
+ mkdir -p $SAGE_SHARE/jmol
+ mkdir -p $SAGE_SHARE/jsmol/
+
# sage3d
rm -f %{buildroot}%{_bindir}/sage3d
%if %{with_sage3d}
ln -sf %{SAGE_LOCAL}/bin/sage3d %{buildroot}%{python_sitearch}/sagenb/data/sage3d/sage3d
%endif
- # flask stuff not installed
- cp -ar flask_version %{buildroot}%{python_sitearch}/sagenb
ln -sf %{python_sitearch}/sagenb %{buildroot}%{SAGE_SRC}/sagenb
popd
@@ -1081,9 +1063,6 @@ rm %{buildroot}%{python_sitearch}/sagenb/translations/*/LC_MESSAGES/*.po
rm -r %{buildroot}%{python_sitearch}/sagenb/data/sage3d
%endif
-# remove cache files
-rm -r %{buildroot}%{python_sitearch}/sagenb/data/.webassets-cache
-
# remove sage_setup
rm -r %{buildroot}%{python_sitearch}/sage_setup
@@ -1099,23 +1078,6 @@ exit 0
/sbin/ldconfig
exit 0
-# Use symlinks and a minor patch to the notebook to not bundle jmol
-%post notebook
-ln -sf %{_javadir}/JmolApplet.jar %{python_sitearch}/sagenb/data/jmol/
-ln -sf %{_javadir}/Jmol.jar %{python_sitearch}/sagenb/data/jmol/
-ln -sf %{_javadir}/vecmath.jar %{python_sitearch}/sagenb/data/jmol/
-exit 0
-
-%postun notebook
-if [ $1 -eq 0 ] ; then
- rm -f %{python_sitearch}/sagenb/data/jmol/JmolApplet.jar
- rm -f %{python_sitearch}/sagenb/data/jmol/vecmath.jar
- rmdir %{python_sitearch}/sagenb/data/jmol &&
- rmdir %{python_sitearch}/sagenb/data &&
- rmdir %{python_sitearch}/sagenb
-fi
-exit 0
-
%post sagetex
%{_bindir}/mktexlsr
exit 0
@@ -1188,7 +1150,6 @@ exit 0
%{SAGE_ETC}/maxima
%{SAGE_ETC}/mwrank
%{SAGE_ETC}/pari
-%{SAGE_ETC}/singular
#------------------------------------------------------------------------
%files data-graphs
@@ -1270,7 +1231,8 @@ exit 0
# ASL 2.0
%{python_sitearch}/sagenb/data/highlight
# LGPLv2+
-%{python_sitearch}/sagenb/data/jmol
+%{SAGE_SHARE}/jmol/
+%{SAGE_SHARE}/jsmol/
# (MIT or GPLv2) and (MIT and BSD and GPL)
%{python_sitearch}/sagenb/data/jquery
# (MIT or GPLv2) and (MIT and BSD and GPL)
@@ -1291,8 +1253,6 @@ exit 0
%endif
# LGPLv2+
%{python_sitearch}/sagenb/data/tiny_mce
-# Auto generated files
-%{python_sitearch}/sagenb/data/webassets_generated
# LGPLv2+
%{python_sitearch}/sagenb/data/zorn
# GPLv2+
@@ -1317,6 +1277,9 @@ exit 0
%dir %{python_sitearch}/sagenb/translations
%lang(cs_CZ) %{python_sitearch}/sagenb/translations/cs_CZ
%lang(de_AT) %{python_sitearch}/sagenb/translations/de_AT
+%lang(de_AT) %{python_sitearch}/sagenb/translations/en_US
+%lang(de_AT) %{python_sitearch}/sagenb/translations/es_ES
+%lang(de_AT) %{python_sitearch}/sagenb/translations/fr_FR
%lang(pt_BR) %{python_sitearch}/sagenb/translations/pt_BR
%lang(ru_RU) %{python_sitearch}/sagenb/translations/ru_RU
@@ -1341,6 +1304,9 @@ exit 0
########################################################################
%changelog
+* Wed Nov 26 2014 pcpa <paulo.cesar.pereira.de.andrade at gmail.com> - 6.4.1-1
+- Update to sagemath 6.4.1 (#1095282)
+
* Sat Nov 1 2014 pcpa <paulo.cesar.pereira.de.andrade at gmail.com> - 6.3-4
- Install 128x128 icon (#1157575)
diff --git a/sources b/sources
index 9f2f5a2..cd5f6e4 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-668f080be70ffea8d67592ca00d161eb sage-6.3.tar.gz
+9e64f198f791577555344b9aaa6768a9 sage-6.4.1.tar.gz
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