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Update to sagemath 6.3

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This commit is contained in:
pcpa 2014-08-15 13:30:04 -03:00
parent 86aa0a3b29
commit 886f9fabef
22 changed files with 1019 additions and 1023 deletions
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1
.gitignore vendored
View file

@ -5,3 +5,4 @@
/sage-5.13.tar
/sage-6.1.1.tar.gz
/sage-6.2.tar.gz
/sage-6.3.tar.gz

7
sagemath-cbc.patch
View file

@ -1,6 +1,7 @@
--- src/module_list.py.orig 2014-05-10 16:02:43.371125667 -0300
+++ src/module_list.py 2014-05-10 16:02:58.362124591 -0300
@@ -2115,7 +2115,7 @@ if (os.path.isfile(SAGE_INC + "/cplex.h"
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"
libraries = ["stdc++", "cplex"])
)

12
sagemath-cremona.patch
View file

@ -1,7 +1,7 @@
diff -up src/sage/databases/cremona.py.orig src/sage/databases/cremona.py
--- src/sage/databases/cremona.py.orig 2014-02-07 12:35:15.971835685 -0200
+++ src/sage/databases/cremona.py 2014-02-07 12:35:25.242836040 -0200
@@ -886,14 +886,9 @@ class MiniCremonaDatabase(SQLDatabase):
--- 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):
if N < self.largest_conductor():
message = "There is no elliptic curve with label " + label \
+ " in the database"
@ -15,9 +15,9 @@ diff -up src/sage/databases/cremona.py.orig src/sage/databases/cremona.py
- + "contains the complete Cremona database"
+ + label + " in the default database"
raise ValueError(message)
def iter(self, conductors):
@@ -1591,10 +1586,12 @@ def CremonaDatabase(name=None,mini=None,
ainvs = eval(c[0])
data = {'cremona_label': label,
@@ -1656,10 +1651,12 @@ def CremonaDatabase(name=None,mini=None,
if name is None and not set_global:
return _db
if set_global and name is None:

7
sagemath-cryptominisat.patch
View file

@ -1,6 +1,7 @@
--- src/module_list.py.orig 2014-05-10 15:59:50.979138032 -0300
+++ src/module_list.py 2014-05-10 16:00:00.142137375 -0300
@@ -2125,7 +2125,7 @@ if is_package_installed('cbc'):
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:
)

6
sagemath-extensions.patch
View file

@ -1,7 +1,7 @@
diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig 2014-05-26 13:34:05.597783829 -0300
+++ src/module_list.py 2014-05-26 13:34:15.908784224 -0300
@@ -2070,7 +2070,8 @@ ext_modules = [
--- 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 = [
# These extensions are to be compiled only if the
# corresponding packages have been installed

7
sagemath-fes.patch
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@ -1,6 +1,7 @@
--- src/module_list.py.orig 2014-05-10 15:58:00.155145981 -0300
+++ src/module_list.py 2014-05-10 15:58:09.742145293 -0300
@@ -2074,7 +2074,7 @@ ext_modules = [
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 = [
def is_package_installed(name):
return False

7
sagemath-gap-hap.patch
View file

@ -1,5 +1,6 @@
--- src/sage/groups/perm_gps/permgroup.py.orig 2014-05-10 15:53:23.284165840 -0300
+++ src/sage/groups/perm_gps/permgroup.py 2014-05-10 15:54:59.829158915 -0300
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
@@ -180,8 +180,7 @@ def hap_decorator(f):
"""
@wraps(f)
@ -10,7 +11,7 @@
load_hap()
from sage.rings.arith import is_prime
if not (p == 0 or is_prime(p)):
@@ -3933,8 +3932,7 @@ class PermutationGroup_generic(group.Gro
@@ -3934,8 +3933,7 @@ class PermutationGroup_generic(group.Gro
- David Joyner and Graham Ellis
"""

17
sagemath-jmol.patch
View file

@ -1,16 +1,7 @@
diff -up src/sage/interfaces/jmoldata.py.orig src/sage/interfaces/jmoldata.py
--- src/sage/interfaces/jmoldata.py.orig 2014-02-07 12:31:50.599827821 -0200
+++ src/sage/interfaces/jmoldata.py 2014-02-07 12:34:31.334833976 -0200
@@ -64,7 +64,7 @@ class JmolData(SageObject):
sage_makedirs(jmolscratch)
scratchout = os.path.join(jmolscratch,"jmolout.txt")
jout=open(scratchout,'w')
- testjavapath = os.path.join(SAGE_LOCAL, "share", "jmol", "testjava.sh")
+ testjavapath = os.path.join(SAGE_LOCAL, "bin", "testjava.sh")
result = subprocess.call([testjavapath],stdout=jout)
jout.close()
if (result == 0):
@@ -144,8 +144,6 @@ class JmolData(SageObject):
--- src/sage/interfaces/jmoldata.py.orig 2014-08-12 14:13:57.189963669 -0300
+++ src/sage/interfaces/jmoldata.py 2014-08-12 14:16:21.359969189 -0300
@@ -139,8 +139,6 @@ class JmolData(SageObject):
True
"""
@ -19,7 +10,7 @@ diff -up src/sage/interfaces/jmoldata.py.orig src/sage/interfaces/jmoldata.py
launchscript = ""
if (datafile_cmd!='script'):
launchscript = "load "
@@ -157,9 +155,8 @@ class JmolData(SageObject):
@@ -152,9 +150,8 @@ class JmolData(SageObject):
scratchout = tmp_filename(ext=".txt")
with open(scratchout, 'w') as jout:
# Now call the java application and write the file.

7
sagemath-lrcalc.patch
View file

@ -1,6 +1,7 @@
--- src/module_list.py.orig 2014-05-10 15:57:18.343148980 -0300
+++ src/module_list.py 2014-05-10 15:57:28.082148282 -0300
@@ -2150,7 +2150,7 @@ if UNAME[0] == "Darwin" and not UNAME[2]
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]
)

6
sagemath-lrslib.patch
View file

@ -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 2014-02-07 12:36:06.514837620 -0200
+++ src/sage/geometry/polyhedron/base.py 2014-02-07 12:36:16.918838019 -0200
@@ -3406,11 +3406,6 @@ class Polyhedron_base(Element):
--- 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):
David Avis's lrs program.
"""

10
sagemath-maxima.patch
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@ -1,6 +1,6 @@
diff -up src/bin/sage-maxima.lisp.orig src/bin/sage-maxima.lisp
--- src/bin/sage-maxima.lisp.orig 2014-02-07 11:52:01.751736343 -0200
+++ src/bin/sage-maxima.lisp 2014-02-07 11:52:17.429736944 -0200
--- src/bin/sage-maxima.lisp.orig 2014-08-12 14:11:32.329958121 -0300
+++ src/bin/sage-maxima.lisp 2014-08-12 14:11:38.922958374 -0300
@@ -3,4 +3,8 @@
;(setf *general-display-prefix* "<sage-display>")
@ -12,8 +12,8 @@ diff -up src/bin/sage-maxima.lisp.orig src/bin/sage-maxima.lisp
+ *standard-input* (open "/dev/stdin" :direction :input)
+ *standard-output* (open "/dev/stdout" :direction :output))
diff -up src/sage/interfaces/maxima.py.orig src/sage/interfaces/maxima.py
--- src/sage/interfaces/maxima.py.orig 2014-02-07 11:50:56.989733863 -0200
+++ src/sage/interfaces/maxima.py 2014-02-07 11:51:45.174735709 -0200
--- src/sage/interfaces/maxima.py.orig 2014-08-12 14:11:20.722957677 -0300
+++ src/sage/interfaces/maxima.py 2014-08-12 14:11:38.923958374 -0300
@@ -544,7 +544,7 @@ class Maxima(MaximaAbstract, Expect):
Expect.__init__(self,
name = 'maxima',
@ -23,7 +23,7 @@ diff -up src/sage/interfaces/maxima.py.orig src/sage/interfaces/maxima.py
maxread = 10000,
script_subdirectory = script_subdirectory,
restart_on_ctrlc = False,
@@ -593,7 +593,8 @@ class Maxima(MaximaAbstract, Expect):
@@ -594,7 +594,8 @@ class Maxima(MaximaAbstract, Expect):
# Remove limit on the max heapsize (since otherwise it defaults
# to 256MB with ECL).

7
sagemath-nauty.patch
View file

@ -1,6 +1,7 @@
--- src/sage/graphs/graph_generators.py.orig 2014-05-10 15:51:24.250174378 -0300
+++ src/sage/graphs/graph_generators.py 2014-05-10 15:51:36.224173519 -0300
@@ -824,7 +824,7 @@ class GraphGenerators():
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():
"""
import subprocess
from sage.misc.package import is_package_installed

1628
sagemath-pari2.7.patch
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File diff suppressed because it is too large Load diff

11
sagemath-png.patch
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@ -1,6 +1,7 @@
--- src/module_list.py.orig 2014-05-10 15:46:32.570195300 -0300
+++ src/module_list.py 2014-05-10 15:46:44.964194411 -0300
@@ -1058,7 +1058,7 @@ ext_modules = [
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 = [
Extension('sage.matrix.matrix_mod2_dense',
sources = ['sage/matrix/matrix_mod2_dense.pyx'],
@ -9,7 +10,7 @@
extra_compile_args = m4ri_extra_compile_args,
depends = [SAGE_INC + "/png.h", SAGE_INC + "/m4ri/m4ri.h"]),
@@ -1354,7 +1354,7 @@ ext_modules = [
@@ -1360,7 +1360,7 @@ ext_modules = [
Extension('sage.modules.vector_mod2_dense',
sources = ['sage/modules/vector_mod2_dense.pyx'],
@ -18,7 +19,7 @@
extra_compile_args = m4ri_extra_compile_args,
depends = [SAGE_INC + "/png.h", SAGE_INC + "/m4ri/m4ri.h"]),
@@ -1860,7 +1860,7 @@ ext_modules = [
@@ -1876,7 +1876,7 @@ ext_modules = [
Extension('sage.rings.polynomial.pbori',
sources = ['sage/rings/polynomial/pbori.pyx'],
libraries=['polybori-' + polybori_major_version,

7
sagemath-readonly.patch
View file

@ -1,6 +1,7 @@
--- src/sage/all.py.orig 2014-05-10 15:45:46.934198573 -0300
+++ src/sage/all.py 2014-05-10 15:45:58.395197751 -0300
@@ -327,11 +327,11 @@ def _write_started_file():
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():
Check that the file exists when Sage is running::

35
sagemath-rpmbuild.patch
View file

@ -1,5 +1,6 @@
--- src/module_list.py.orig 2014-05-10 15:38:39.635229222 -0300
+++ src/module_list.py 2014-05-10 15:40:06.410222998 -0300
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
from distutils.extension import Extension
from sage.env import *
@ -22,7 +23,7 @@
+numpy_depends = [get_python_lib(1) + '/numpy/core/include/numpy/_numpyconfig.h']
flint_depends = [SAGE_INC + '/flint/flint.h']
singular_depends = [SAGE_INC + '/libsingular.h', SAGE_INC + '/givaro/givconfig.h']
singular_depends = [SAGE_INC + '/libsingular.h']
@@ -70,7 +71,7 @@ givaro_extra_compile_args =['-D__STDC_LI
### PolyBoRi settings
#########################################################
@ -32,7 +33,7 @@
polybori_major_version = '0.8'
@@ -702,7 +703,7 @@ ext_modules = [
@@ -710,7 +711,7 @@ ext_modules = [
sources = ['sage/libs/lcalc/lcalc_Lfunction.pyx'],
libraries = ['m', 'ntl', 'mpfr', 'gmp', 'gmpxx',
'Lfunction'],
@ -41,8 +42,9 @@
extra_compile_args=["-O3", "-ffast-math"],
language = 'c++'),
--- src/setup.py.orig 2014-05-10 15:40:24.650221690 -0300
+++ src/setup.py 2014-05-10 15:43:52.993206746 -0300
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
@@ -36,11 +36,11 @@ except KeyError:
compile_result_dir = None
keep_going = False
@ -71,3 +73,24 @@
#############################################
@@ -556,20 +558,6 @@ print "Discovered Python source, time: %
#########################################################
-### Clean
-#########################################################
-
-print('Cleaning up stale installed files....')
-t = time.time()
-from sage_setup.clean import clean_install_dir
-output_dirs = SITE_PACKAGES + glob.glob(os.path.join(SAGE_SRC, 'build', 'lib*'))
-for output_dir in output_dirs:
- print('- cleaning {0}'.format(output_dir))
- clean_install_dir(output_dir, python_packages, python_modules, ext_modules)
-print('Finished cleaning, time: %.2f seconds.' % (time.time() - t))
-
-
-#########################################################
### Distutils
#########################################################

37
sagemath-sagedoc.patch
View file

@ -1,5 +1,6 @@
--- src/doc/common/builder.py.orig 2014-05-10 15:44:39.046203443 -0300
+++ src/doc/common/builder.py 2014-05-10 15:45:03.225201708 -0300
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
@@ -32,7 +32,7 @@ from sage.env import SAGE_DOC, SAGE_SRC
# SAGE_DOC, LANGUAGES, SPHINXOPTS, PAPER, OMIT,
# PAPEROPTS, ALLSPHINXOPTS, NUM_THREADS, WEBSITESPHINXOPTS
@ -8,17 +9,18 @@
+execfile(os.path.join(os.getenv('SAGE_ROOT'), 'src', 'doc', 'common' , 'build_options.py'))
def print_build_error():
--- src/doc/common/conf.py.orig 2014-05-10 15:44:59.936201944 -0300
+++ src/doc/common/conf.py 2014-05-10 15:45:03.229201708 -0300
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
@@ -1,5 +1,5 @@
import sys, os, sphinx
-from sage.env import SAGE_DOC
+from sage.env import SAGE_DOC, SAGE_SRC
from datetime import date
def get_doc_abspath(path):
"""
@@ -202,8 +202,7 @@ if (os.environ.get('SAGE_DOC_MATHJAX', '
@@ -203,8 +203,7 @@ if (os.environ.get('SAGE_DOC_MATHJAX', '
from sage.misc.latex_macros import sage_mathjax_macros
html_theme_options['mathjax_macros'] = sage_mathjax_macros()
@ -28,8 +30,9 @@
mathjax_relative = os.path.join('sagenb','data','mathjax')
# It would be really nice if sphinx would copy the entire mathjax directory,
--- src/sage/doctest/control.py.orig 2014-05-10 15:44:59.940201944 -0300
+++ src/sage/doctest/control.py 2014-05-10 15:45:03.230201708 -0300
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
@@ -89,7 +89,6 @@ class DocTestDefaults(SageObject):
self.valgrind = False
self.massif = False
@ -47,7 +50,7 @@
# Non-interactive debuggers: 48 hours
options.timeout = int(os.getenv('SAGE_TIMEOUT_VALGRIND', 48 * 60 * 60))
elif options.long:
@@ -821,13 +820,8 @@ class DocTestController(SageObject):
@@ -822,13 +821,8 @@ class DocTestController(SageObject):
elif opt.cachegrind:
toolname = "cachegrind"
flags = os.getenv("SAGE_CACHEGRIND_FLAGS", "")
@ -61,7 +64,7 @@
if "%s" in flags:
flags %= toolname + ".%p" # replace %s with toolname
cmd += flags + sage_cmd
@@ -887,10 +881,10 @@ class DocTestController(SageObject):
@@ -888,10 +882,10 @@ class DocTestController(SageObject):
0
"""
opt = self.options
@ -74,9 +77,10 @@
return 2
return self.run_val_gdb()
else:
--- src/sage/interfaces/singular.py.orig 2014-05-10 15:44:59.940201944 -0300
+++ src/sage/interfaces/singular.py 2014-05-10 15:45:03.230201708 -0300
@@ -2149,7 +2149,7 @@ def generate_docstring_dictionary():
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
@@ -2147,7 +2147,7 @@ def generate_docstring_dictionary():
nodes.clear()
node_names.clear()
@ -85,8 +89,9 @@
new_node = re.compile("File: singular\.hlp, Node: ([^,]*),.*")
new_lookup = re.compile("\* ([^:]*):*([^.]*)\..*")
--- src/sage/misc/latex_macros.py.orig 2014-05-10 15:44:59.940201944 -0300
+++ src/sage/misc/latex_macros.py 2014-05-10 15:45:03.232201708 -0300
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) + ']'

160
sagemath-scripts.patch
View file

@ -1,6 +1,6 @@
diff -up src/bin/sage.orig src/bin/sage
--- src/bin/sage.orig 2014-05-26 13:29:30.741773304 -0300
+++ src/bin/sage 2014-05-26 13:29:50.173774048 -0300
--- 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"
echo " -advanced -- list all command line options"
@ -30,10 +30,12 @@ diff -up src/bin/sage.orig src/bin/sage
echo " -v, -version -- print the Sage version"
exit 0
}
@@ -63,14 +56,14 @@ usage_advanced() {
@@ -61,16 +54,14 @@ 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 " -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"
@ -47,13 +49,13 @@ diff -up src/bin/sage.orig src/bin/sage
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 +80,9 @@ usage_advanced() {
@@ -87,13 +78,8 @@ 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 || \
@ -61,7 +63,7 @@ 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"
@@ -107,80 +96,10 @@ usage_advanced() {
@@ -107,75 +93,10 @@ usage_advanced() {
echo
#### 1.......................26..................................................78
#### |.....................--.|...................................................|
@ -93,11 +95,6 @@ diff -up src/bin/sage.orig src/bin/sage
- 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 " -sync-build -- delete old code and other files in the Sage library"
- echo " that have already been deleted from devel/sage but"
- echo " remain in the build directory. This is sometimes"
- echo " necessary because \`sage -b\` merely copies new or"
- echo " modified files to the target directory."
- 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"
@ -142,13 +139,12 @@ 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"
@@ -200,17 +119,6 @@ usage_advanced() {
@@ -195,16 +116,6 @@ usage_advanced() {
echo
#### 1.......................26..................................................78
#### |.....................--.|...................................................|
- echo "Making Sage packages or distributions:"
- echo " -bdist VER -- build a binary distribution of Sage"
- echo " -combinat [...] -- run sage-combinat patch management script"
- echo " -crap sage-ver.tar -- detect suspicious garbage in sage source tarball"
- echo " -pkg <dir> -- create Sage package dir.spkg from a given directory"
- echo " -pkg_nc <dir> -- as -pkg, but do not compress the package"
@ -160,7 +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"
@@ -224,9 +132,6 @@ usage_advanced() {
@@ -218,9 +129,6 @@ 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"
@ -170,10 +166,27 @@ 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'."
@@ -255,17 +160,6 @@ if [ "$1" = '-upgrade' -o "$1" = "--upgr
@@ -240,34 +148,6 @@ if [ "$1" = '--nodotsage' ]; then
exit $status
fi
-# Check for '--patchbot' before sourcing sage-env: patchbot needs
-# an unclobbered environment before testing unsafe tickets.
-if [ "$1" = '-patchbot' -o "$1" = "--patchbot" ]; then
- shift
- cd "$SAGE_ROOT"
- exec local/bin/patchbot/patchbot.py "$@"
-fi
-
-# Check for '--upgrade' before sourcing sage-env: the top-level "make"
-# should be run outside of the Sage shell, see #15517.
-if [ "$1" = '-upgrade' -o "$1" = "--upgrade" ]; then
- shift
- cd "$SAGE_ROOT"
- exec local/bin/sage-upgrade "$@"
-fi
-
-
-# Source sage-env ($0 is the name of this "sage" script, so we can just
-# append -env to that). We redirect stdout to stderr, which is safer
-# for scripts.
@ -188,8 +201,11 @@ 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
@@ -278,25 +172,11 @@ fi
@@ -277,28 +157,13 @@ if [ $# -gt 0 ]; then
fi
fi
-
# Prepare for running Sage, either interactively or non-interactively.
sage_setup() {
- # Check that we're not in a source tarball which hasn't been built yet (#13561).
@ -214,10 +230,11 @@ diff -up src/bin/sage.orig src/bin/sage
if [ ! -d "$IPYTHONDIR" ]; then
# make sure that $DOT_SAGE exists so that ipython will happily
# create its config directories there. If DOT_SAGE doesn't
@@ -307,20 +187,6 @@ sage_setup() {
@@ -308,21 +173,6 @@ sage_setup() {
sage-cleaner &>/dev/null &
}
-
-# 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
@ -235,19 +252,7 @@ diff -up src/bin/sage.orig src/bin/sage
# Start an interactive Sage session, this function never returns.
interactive_sage() {
sage_setup
@@ -370,11 +236,6 @@ if [ "$1" = '-axiom' -o "$1" = '--axiom'
exec axiom "$@"
fi
-if [ "$1" = '-combinat' -o "$1" = '--combinat' ]; then
- shift
- exec sage-combinat "$@"
-fi
-
if [ "$1" = '-gap' -o "$1" = '--gap' ]; then
shift
exec gap "$@"
@@ -387,7 +248,7 @@ fi
@@ -384,7 +234,7 @@ fi
if [ "$1" = '-singular' -o "$1" = '--singular' ]; then
shift
@ -256,7 +261,7 @@ diff -up src/bin/sage.orig src/bin/sage
fi
if [ "$1" = '-sqlite3' -o "$1" = '--sqlite3' ]; then
@@ -415,16 +276,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
@@ -412,16 +262,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
exec ecl "$@"
fi
@ -273,7 +278,7 @@ diff -up src/bin/sage.orig src/bin/sage
if [ "$1" = '-maxima' -o "$1" = '--maxima' ]; then
shift
exec maxima "$@"
@@ -584,20 +435,6 @@ EOF
@@ -581,20 +421,6 @@ EOF
fi
#####################################################################
@ -294,7 +299,7 @@ diff -up src/bin/sage.orig src/bin/sage
# File conversion
#####################################################################
@@ -612,36 +449,15 @@ if [ "$1" = '-rst2sws' -o "$1" = '--rst2
@@ -609,36 +435,15 @@ if [ "$1" = '-rst2sws' -o "$1" = '--rst2
fi
#####################################################################
@ -331,7 +336,7 @@ diff -up src/bin/sage.orig src/bin/sage
if [ "$1" = "-inotebook" -o "$1" = '--inotebook' ]; then
shift
sage-cleaner &>/dev/null &
@@ -660,58 +476,12 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
@@ -657,40 +462,19 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
exit 0
fi
@ -352,37 +357,12 @@ diff -up src/bin/sage.orig src/bin/sage
interactive_sage
fi
-if [ "$1" = '-ba' ]; then
- shift
- echo " *** WARNING ***"
- echo " You are about to rebuild the entire Sage library."
- echo " This will take a significant amount of time."
- echo " (Use --ba-force instead of -ba to skip this prompt.)"
- echo -n " Do you want to proceed? [y/n] "
- read CHOICE
- while [ "$CHOICE" != "y" -a "$CHOICE" != "n" ]; do
- echo -n " Choose one of y, n: "
- read CHOICE
- done
- if [ $CHOICE = 'n' ]; then
- exit 0
- fi
- build_sage -b "$@"
- exit $?
-fi
-
-if [ "$1" = '-ba-force' -o "$1" = '--ba-force' ]; then
-if [ "$1" = '-ba' -o "$1" = '-ba-force' -o "$1" = '--ba-force' ]; then
- shift
- build_sage -b "$@"
- exit $?
-fi
-
-if [ "$1" = '-sync-build' -o "$1" = '--sync-build' ]; then
- shift
- cd "$SAGE_ROOT"
- exec sage-sync-build.py "$@"
-fi
-
-if [ "$1" = '-t' -o "$1" = '-bt' -o "$1" = '-tp' -o "$1" = '-btp' ]; then
- if [ "$1" = '-bt' -o "$1" = '-btp' ]; then
- build_sage
@ -391,7 +371,15 @@ diff -up src/bin/sage.orig src/bin/sage
if [ ! -f "$DOT_SAGE"/init.sage ]; then
echo >&2 "init.sage does not exist ... creating"
touch "$DOT_SAGE"/init.sage
@@ -727,10 +497,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
fi
SAGE_BANNER="no"
sage_setup
- if [ "$1" = '-tp' -o "$1" = '-btp' ]; then
+ if [ "$1" = '-tp' ]; then
shift
exec sage-runtests -p "$@"
else
@@ -699,10 +483,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
fi
fi
@ -403,20 +391,7 @@ diff -up src/bin/sage.orig src/bin/sage
shift
SAGE_BANNER="no"
sage_setup
@@ -744,12 +511,6 @@ if [ "$1" = '-testall' -o "$1" = "--test
exec sage-runtests -a "$@"
fi
-if [ "$1" = '-patchbot' -o "$1" = "--patchbot" ]; then
- shift
- cd "$SAGE_ROOT"
- exec "$SAGE_LOCAL/bin/patchbot/patchbot.py" "$@"
-fi
-
if [ "$1" = '-c' ]; then
shift
SAGE_BANNER="no"
@@ -758,124 +519,6 @@ if [ "$1" = '-c' ]; then
@@ -724,132 +505,6 @@ if [ "$1" = '-c' ]; then
exec sage-eval "$@"
fi
@ -458,6 +433,14 @@ diff -up src/bin/sage.orig src/bin/sage
- exit 1
- fi
- done
- # Display a message if we actually installed something (using this
- # file, generated by sage-spkg, is a bit of a hack though)
- if [ -f "$SAGE_LOCAL/lib/sage-force-relocate.txt" ]; then
- echo
- echo "Warning: it might be needed to update the Sage library before"
- echo "installed packages work: you should run 'make' from \$SAGE_ROOT"
- echo "before running Sage."
- fi
- exit 0
-}
-
@ -541,7 +524,7 @@ diff -up src/bin/sage.orig src/bin/sage
if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then
shift
sage_setup
@@ -924,12 +567,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
@@ -898,21 +553,10 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
exec sage-callgrind "$@"
fi
@ -554,9 +537,18 @@ diff -up src/bin/sage.orig src/bin/sage
if [ "$1" = '-startuptime' -o "$1" = '--startuptime' ]; then
exec sage-startuptime.py "$@"
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 [ "$1" = '-dev' -o "$1" = "--dev" ]; then
shift
exec sage-dev "$@"
diff -up src/bin/sage-runtests.orig src/bin/sage-runtests
--- src/bin/sage-runtests.orig 2014-05-26 13:29:46.150773894 -0300
+++ src/bin/sage-runtests 2014-05-26 13:29:50.174774048 -0300
--- 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
@@ -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 " +
@ -569,8 +561,8 @@ 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 2014-05-26 13:29:46.152773894 -0300
+++ src/bin/sage-valgrind 2014-05-26 13:29:50.174774048 -0300
--- 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"

28
sagemath-sphinx.patch
View file

@ -1,7 +1,7 @@
diff -up src/sage/graphs/generic_graph.py.orig src/sage/graphs/generic_graph.py
--- src/sage/graphs/generic_graph.py.orig 2014-05-26 15:38:33.169069789 -0300
+++ src/sage/graphs/generic_graph.py 2014-05-26 15:41:55.071077520 -0300
@@ -9222,7 +9222,7 @@ class GenericGraph(GenericGraph_pyx):
--- src/sage/graphs/generic_graph.py.orig 2014-08-12 14:58:26.408065882 -0300
+++ src/sage/graphs/generic_graph.py 2014-08-12 14:58:29.914066017 -0300
@@ -9275,7 +9275,7 @@ class GenericGraph(GenericGraph_pyx):
.. SEEALSO::
@ -10,7 +10,7 @@ diff -up src/sage/graphs/generic_graph.py.orig src/sage/graphs/generic_graph.py
"""
for e in edges:
self.subdivide_edge(e, k)
@@ -11504,10 +11504,10 @@ class GenericGraph(GenericGraph_pyx):
@@ -11557,10 +11557,10 @@ class GenericGraph(GenericGraph_pyx):
.. SEEALSO::
@ -24,7 +24,7 @@ diff -up src/sage/graphs/generic_graph.py.orig src/sage/graphs/generic_graph.py
"""
self._scream_if_not_simple()
@@ -13369,13 +13369,13 @@ class GenericGraph(GenericGraph_pyx):
@@ -13429,13 +13429,13 @@ class GenericGraph(GenericGraph_pyx):
.. SEEALSO::
@ -43,7 +43,7 @@ diff -up src/sage/graphs/generic_graph.py.orig src/sage/graphs/generic_graph.py
EXAMPLES::
@@ -13494,13 +13494,13 @@ class GenericGraph(GenericGraph_pyx):
@@ -13554,13 +13554,13 @@ class GenericGraph(GenericGraph_pyx):
.. SEEALSO::
@ -63,9 +63,9 @@ diff -up src/sage/graphs/generic_graph.py.orig src/sage/graphs/generic_graph.py
EXAMPLES::
diff -up src/sage/graphs/graph.py.orig src/sage/graphs/graph.py
--- src/sage/graphs/graph.py.orig 2014-05-26 15:42:17.579078382 -0300
+++ src/sage/graphs/graph.py 2014-05-26 16:04:45.519129999 -0300
@@ -2704,9 +2704,9 @@ class Graph(GenericGraph):
--- src/sage/graphs/graph.py.orig 2014-08-12 14:58:26.410065882 -0300
+++ src/sage/graphs/graph.py 2014-08-12 14:58:29.917066017 -0300
@@ -3023,9 +3023,9 @@ class Graph(GenericGraph):
.. SEEALSO::
@ -78,7 +78,7 @@ diff -up src/sage/graphs/graph.py.orig src/sage/graphs/graph.py
EXAMPLES::
@@ -2751,9 +2751,9 @@ class Graph(GenericGraph):
@@ -3070,9 +3070,9 @@ class Graph(GenericGraph):
.. SEEALSO::
@ -91,7 +91,7 @@ diff -up src/sage/graphs/graph.py.orig src/sage/graphs/graph.py
EXAMPLES::
@@ -2788,9 +2788,9 @@ class Graph(GenericGraph):
@@ -3107,9 +3107,9 @@ class Graph(GenericGraph):
.. SEEALSO::
@ -104,7 +104,7 @@ diff -up src/sage/graphs/graph.py.orig src/sage/graphs/graph.py
EXAMPLES:
@@ -2827,9 +2827,9 @@ class Graph(GenericGraph):
@@ -3146,9 +3146,9 @@ class Graph(GenericGraph):
.. SEEALSO::
@ -117,7 +117,7 @@ diff -up src/sage/graphs/graph.py.orig src/sage/graphs/graph.py
EXAMPLES:
@@ -5751,8 +5751,8 @@ class Graph(GenericGraph):
@@ -6114,8 +6114,8 @@ class Graph(GenericGraph):
.. SEEALSO::
@ -128,7 +128,7 @@ diff -up src/sage/graphs/graph.py.orig src/sage/graphs/graph.py
REFERENCE:
@@ -5937,7 +5937,7 @@ class Graph(GenericGraph):
@@ -6300,7 +6300,7 @@ class Graph(GenericGraph):
.. SEEALSO::

6
sagemath-sympy.patch
View file

@ -1,7 +1,7 @@
diff -up src/sage/env.py.orig src/sage/env.py
--- src/sage/env.py.orig 2014-02-07 12:50:28.534870630 -0200
+++ src/sage/env.py 2014-02-07 12:51:07.014872104 -0200
@@ -85,7 +85,7 @@ _add_variable_or_fallback('HOSTNAME',
--- src/sage/env.py.orig 2014-08-12 14:24:55.730988886 -0300
+++ src/sage/env.py 2014-08-12 14:25:03.802989196 -0300
@@ -86,7 +86,7 @@ _add_variable_or_fallback('HOSTNAME',
_add_variable_or_fallback('LOCAL_IDENTIFIER','$HOSTNAME.%s'%os.getpid())
# bunch of sage directories and files

34
sagemath.spec
View file

@ -38,8 +38,8 @@
Name: sagemath
Group: Applications/Engineering
Summary: A free open-source mathematics software system
Version: 6.2
Release: 2%{?dist}
Version: 6.3
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
@ -51,8 +51,6 @@ Source2: makecmds.sty
# not installed by jmol package, use one in sagemath jmol spkg
Source3: Jmol.js
Source4: JmolHelp.html
# from jmol-12.3.27.p2 spkg
Source5: testjava.sh
# 1. scons ignores most environment variables
# 2. scons 2.2* does not have soname support (expected for scons 2.3*)
@ -156,7 +154,7 @@ Patch24: %{name}-sympy.patch
# -k (keep-going)
Patch25: %{name}-sphinx.patch
# Edited latest version from http://trac.sagemath.org/ticket/15767
# Rediffed latest version from http://trac.sagemath.org/ticket/15767
Patch26: %{name}-pari2.7.patch
BuildRequires: 4ti2
@ -440,6 +438,16 @@ BuildArch: noarch
%description doc-fr
This package contains the French %{name} documentation.
#------------------------------------------------------------------------
%package doc-it
Summary: Italian documentation files for %{name}
Group: Documentation
Requires: %{name}-doc = %{version}-%{release}
BuildArch: noarch
%description doc-it
This package contains the Italian %{name} documentation.
#------------------------------------------------------------------------
%package doc-pt
Summary: Portuguese documentation files for %{name}
@ -614,7 +622,7 @@ popd
%patch24
%patch25
%patch26 -p1
%patch26
sed -e 's|@@SAGE_ROOT@@|%{SAGE_ROOT}|' \
-e 's|@@SAGE_DOC@@|%{SAGE_DOC}|' \
@ -749,7 +757,6 @@ 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}
install -p -m0755 %{SOURCE5} $SAGE_LOCAL/bin/testjava.sh
# jmol
rm -fr %{buildroot}%{python_sitearch}/sagenb/data/jmol
mkdir -p %{buildroot}%{python_sitearch}/sagenb/data/jmol/appletweb
@ -1077,6 +1084,9 @@ rm -r %{buildroot}%{python_sitearch}/sagenb/data/sage3d
# remove cache files
rm -r %{buildroot}%{python_sitearch}/sagenb/data/.webassets-cache
# remove sage_setup
rm -r %{buildroot}%{python_sitearch}/sage_setup
# last install command
rm -fr $DOT_SAGE
@ -1127,7 +1137,6 @@ exit 0
%{SAGE_LOCAL}/bin/ecm
%{SAGE_LOCAL}/bin/gap_stamp
%{SAGE_LOCAL}/bin/sage*
%{SAGE_LOCAL}/bin/testjava.sh
%{SAGE_LOCAL}/include
%{SAGE_LOCAL}/lib
%{SAGE_LOCAL}/share
@ -1223,6 +1232,11 @@ exit 0
%{SAGE_DOC}/fr
%{SAGE_DOC}/output/html/fr
#------------------------------------------------------------------------
%files doc-it
# GPLv2+
%{SAGE_DOC}/output/html/it
#------------------------------------------------------------------------
%files doc-pt
# GPLv2+
@ -1327,6 +1341,10 @@ exit 0
########################################################################
%changelog
* Wed Aug 13 2014 pcpa <paulo.cesar.pereira.de.andrade@gmail.com> - 6.3-1
- Update to sagemath 6.3 (#1095282)
- Add new doc-it Italian documentation subpackage
* Sun Jun 08 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 6.2-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild

2
sources
View file

@ -1 +1 @@
71aa49875797c001ce0a31409f5a1762 sage-6.2.tar.gz
668f080be70ffea8d67592ca00d161eb sage-6.3.tar.gz