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Update to sagemath 6.4.1

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pcpa 2014-12-13 21:05:42 -02:00
parent 3e866bf86e
commit 738094a8d8
27 changed files with 276 additions and 12243 deletions
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1
.gitignore vendored
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@ -6,3 +6,4 @@
/sage-6.1.1.tar.gz /sage-6.1.1.tar.gz
/sage-6.2.tar.gz /sage-6.2.tar.gz
/sage-6.3.tar.gz /sage-6.3.tar.gz
/sage-6.4.1.tar.gz

1663
Jmol.js
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79
JmolHelp.html
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@ -1,79 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html><head>
<meta content="text/html; charset=ISO-8859-1" http-equiv="content-type"><title>JmolHelp</title>
<meta content="J. Gutow" name="author">
<meta content="Brief Jmol instructions for SAGE math" name="description"></head><body>
<div style="text-align: center;">
<h3>Brief Help for the Jmol 3-D viewer</h3>
<div style="text-align: left;">
<dl>
<dt>Reorient View</dt>
<dd>To reorient the view&nbsp;place cursor over the image, hold down
the mouse button and drag.</dd>
<dt>Zoom View</dt>
<dd>To
zoom place the cursor over the image hold down the shift key and the
mouse button while dragging down to zoom in or up to zoom out.</dd><dt>Change Applet Size</dt>
<dd>Select the desired size from the pop-up menu in the "Display" tab
available in the "Advanced Controls" or click on the "Open in own
window" button.&nbsp; The resulting window's size can be adjusted.<br>
</dd>
<dt>Adjust Colors and Mesh</dt>
<dd>Select desired colors and translucency using the menus and
checkboxes in the "Colors &amp; Mesh" tab available in the "Advanced
Controls".<br>
</dd>
<dt>Save as Static Image</dt>
<dd>Click on the "Get Static Image to Save" button in the "Display" tab available in the "Advanced Controls".<br>
</dd>
<dt>Download to open in Jmol Application</dt>
<dd>Click on the "Download View" button in the "Display" tab
available in the "Advanced Controls".&nbsp; The file you download can
be opened using the Jmol application.&nbsp; Using the application the
view can be further adjusted and web pages with the live view embedded
can be created (<a href="#Embedding">see below</a>).<br>
</dd>
<dt>Start/Stop Spinning</dt>
<dd>Use the "Spin" checkbox in the "Display" tab available in the "Advanced Controls".</dd>
<dt>High/Low Quality Display</dt>
<dd>Use the "High Quality" checkbox in the "Display" tab available in
the "Advanced Controls".&nbsp; Note memory requirements are
significantly more for the better display.&nbsp; This can slow the
applets response and sometimes causes blank displays.</dd><dt><br>
</dt>
<dt><a name="Embedding"></a>Embedding the live image in another web page, adding annotation
and advanced control of view<br>
</dt>
</dl>
<ol>
<li>Download the view to your computer using the download button in
the Display tab.&nbsp; You can then open the file in the Jmol
application available from the <a href="http://www.jmol.org/">Jmol web
site</a>.&nbsp;</li>
<li>Simple examples of adding annotation are provided in the <a href="http://www.uwosh.edu/faculty_staff/gutow/Jmol_Web_Page_Maker/Export_to_web_tutorial.shtml">Export-to-Web
tutorial</a>, which also describes how to use the downloaded document to
embed the live image in an arbitrary web page.</li>
<li>More detailed information on changing the way Jmol displays
things using Jmol commands is available in the <a href="http://chemapps.stolaf.edu/jmol/docs/"><span style="text-decoration: underline;">J</span></a><a href="http://chemapps.stolaf.edu/jmol/docs/">mol scripting
documentation</a>, the <a href="http://www.jmol.org/">Jmol web site</a>
and the <a href="http://wiki.jmol.org/">Jmol wiki</a>.</li>
<li>It is also possible to use Jmol commands to adjust the display
within Sage.&nbsp; To do this
right-click (control-click) in the applet window to get the applet
pop-up menu. &nbsp;In the advanced submenu select "Console". &nbsp;You
can type Jmol script commands into the console.</li>
</ol>
<div style="text-align: right;"><small><small>By Jonathan Gutow<br>
June 2011<br>
</small></small></div>
</div>
</div>
</body></html>

8
sagemath-4ti2.patch
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@ -1,7 +1,7 @@
diff -up src/sage/sandpiles/sandpile.py.orig src/sage/sandpiles/sandpile.py 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.orig 2014-11-18 15:24:27.192127311 -0200
+++ src/sage/sandpiles/sandpile.py 2014-01-28 16:02:07.914189318 -0200 +++ src/sage/sandpiles/sandpile.py 2014-11-18 15:24:38.049127454 -0200
@@ -24,8 +24,6 @@ packages. An alternative is to install @@ -23,8 +23,6 @@ packages. An alternative is to install
following variable to the correct path. following variable to the correct path.
""" """
@ -10,7 +10,7 @@ diff -up src/sage/sandpiles/sandpile.py.orig src/sage/sandpiles/sandpile.py
r""" r"""
Sage Sandpiles Sage Sandpiles
@@ -4097,7 +4095,7 @@ class SandpileDivisor(dict): @@ -4096,7 +4094,7 @@ class SandpileDivisor(dict):
sign_file.close() sign_file.close()
# compute # compute
try: try:

6
sagemath-cbc.patch
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@ -1,7 +1,7 @@
diff -up src/module_list.py.orig src/module_list.py 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.orig 2014-11-18 15:28:48.952130767 -0200
+++ src/module_list.py 2014-08-12 14:22:55.283984274 -0300 +++ src/module_list.py 2014-11-18 15:28:57.040130873 -0200
@@ -2148,7 +2148,7 @@ if (os.path.isfile(SAGE_INC + "/cplex.h" @@ -2168,7 +2168,7 @@ if (os.path.isfile(SAGE_INC + "/cplex.h"
libraries = ["stdc++", "cplex"]) libraries = ["stdc++", "cplex"])
) )

8
sagemath-cremona.patch
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@ -1,7 +1,7 @@
diff -up src/sage/databases/cremona.py.orig src/sage/databases/cremona.py 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.orig 2014-11-18 15:26:03.247128579 -0200
+++ src/sage/databases/cremona.py 2014-08-12 14:17:51.891972656 -0300 +++ src/sage/databases/cremona.py 2014-11-18 15:26:16.920128759 -0200
@@ -814,14 +814,9 @@ class MiniCremonaDatabase(SQLDatabase): @@ -819,14 +819,9 @@ class MiniCremonaDatabase(SQLDatabase):
if N < self.largest_conductor(): if N < self.largest_conductor():
message = "There is no elliptic curve with label " + label \ message = "There is no elliptic curve with label " + label \
+ " in the database" + " in the database"
@ -17,7 +17,7 @@ diff -up src/sage/databases/cremona.py.orig src/sage/databases/cremona.py
raise ValueError(message) raise ValueError(message)
ainvs = eval(c[0]) ainvs = eval(c[0])
data = {'cremona_label': label, 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: if name is None and not set_global:
return _db return _db
if set_global and name is None: if set_global and name is None:

6
sagemath-cryptominisat.patch
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@ -1,7 +1,7 @@
diff -up src/module_list.py.orig src/module_list.py 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.orig 2014-11-18 15:30:01.952131730 -0200
+++ src/module_list.py 2014-08-12 14:24:13.962987287 -0300 +++ src/module_list.py 2014-11-18 15:30:08.968131823 -0200
@@ -2158,7 +2158,7 @@ if 1: @@ -2177,7 +2177,7 @@ if 1:
) )

100
sagemath-ecl-unicode.patch
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@ -1,100 +0,0 @@
diff -up src/sage/libs/ecl.pxd.orig src/sage/libs/ecl.pxd
--- src/sage/libs/ecl.pxd.orig 2014-03-12 13:06:42.944532214 -0300
+++ src/sage/libs/ecl.pxd 2014-03-12 13:06:45.560532100 -0300
@@ -134,6 +134,7 @@ cdef extern from "ecl/ecl.h":
cl_object ecl_read_from_cstring_safe(char *s, cl_object err)
cl_object cl_write_to_string(cl_narg narg, cl_object o)
cl_object ecl_cstring_to_base_string_or_nil(char *s)
+ cl_object si_coerce_to_base_string(cl_object x)
# S-expr evaluation and function calls
diff -up src/sage/libs/ecl.pyx.orig src/sage/libs/ecl.pyx
--- src/sage/libs/ecl.pyx.orig 2014-03-12 13:06:42.949532214 -0300
+++ src/sage/libs/ecl.pyx 2014-03-12 13:07:55.483529040 -0300
@@ -329,17 +329,19 @@ cdef cl_object ecl_safe_eval(cl_object f
...
RuntimeError: ECL says: Console interrupt.
"""
+ cdef cl_object s
ecl_sig_on()
cl_funcall(2,safe_eval_clobj,form)
ecl_sig_off()
if ecl_nvalues > 1:
- raise RuntimeError, "ECL says: "+ecl_base_string_pointer_safe(ecl_values(1))
+ s = si_coerce_to_base_string(ecl_values(1))
+ raise RuntimeError, "ECL says: "+ecl_base_string_pointer_safe(s)
else:
return ecl_values(0)
cdef cl_object ecl_safe_funcall(cl_object func, cl_object arg) except NULL:
- cdef cl_object l
+ cdef cl_object l, s
l = cl_cons(func,cl_cons(arg,Cnil));
ecl_sig_on()
@@ -347,17 +349,20 @@ cdef cl_object ecl_safe_funcall(cl_objec
ecl_sig_off()
if ecl_nvalues > 1:
- raise RuntimeError, "ECL says: "+ecl_base_string_pointer_safe(ecl_values(1))
+ s = si_coerce_to_base_string(ecl_values(1))
+ raise RuntimeError, "ECL says: "+ecl_base_string_pointer_safe(s)
else:
return ecl_values(0)
cdef cl_object ecl_safe_apply(cl_object func, cl_object args) except NULL:
+ cdef cl_object s
ecl_sig_on()
cl_funcall(3,safe_apply_clobj,func,args)
ecl_sig_off()
if ecl_nvalues > 1:
- raise RuntimeError, "ECL says: "+ecl_base_string_pointer_safe(ecl_values(1))
+ s = si_coerce_to_base_string(ecl_values(1))
+ raise RuntimeError, "ECL says: "+ecl_base_string_pointer_safe(s)
else:
return ecl_values(0)
@@ -407,10 +412,11 @@ def print_objects():
HELLO
"""
- cdef cl_object c
+ cdef cl_object c, s
c = list_of_objects
while True:
- print ecl_base_string_pointer_safe(cl_write_to_string(1,cl_car(c)))
+ s = si_coerce_to_base_string(cl_write_to_string(1,cl_car(c)))
+ print ecl_base_string_pointer_safe(s)
c=cl_cadr(c)
if c == Cnil:
break
@@ -485,6 +491,7 @@ cdef cl_object python_to_ecl(pyobj) exce
raise TypeError,"Unimplemented type for python_to_ecl"
cdef ecl_to_python(cl_object o):
+ cdef cl_object s
cdef Integer N
# conversions from an ecl object to a python object.
@@ -519,7 +526,8 @@ cdef ecl_to_python(cl_object o):
return tuple(L)
return L
else:
- return ecl_base_string_pointer_safe(cl_write_to_string(1,o))
+ s = si_coerce_to_base_string(cl_write_to_string(1,o))
+ return ecl_base_string_pointer_safe(s)
#Maxima's BFLOAT multiprecision float type can be read with:
#def bfloat_to_python(e):
@@ -735,7 +743,7 @@ cdef class EclObject:
"""
cdef cl_object s
- s = cl_write_to_string(1,self.obj)
+ s = si_coerce_to_base_string(cl_write_to_string(1,self.obj))
return ecl_base_string_pointer_safe(s)
def __hash__(self):

6
sagemath-extensions.patch
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@ -1,7 +1,7 @@
diff -up src/module_list.py.orig src/module_list.py 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.orig 2014-11-18 13:23:35.915031576 -0200
+++ src/module_list.py 2014-08-12 14:02:26.626937225 -0300 +++ src/module_list.py 2014-11-18 13:23:46.515031716 -0200
@@ -2103,7 +2103,8 @@ ext_modules = [ @@ -2126,7 +2126,8 @@ ext_modules = [
# These extensions are to be compiled only if the # These extensions are to be compiled only if the
# corresponding packages have been installed # corresponding packages have been installed

6
sagemath-fes.patch
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@ -1,7 +1,7 @@
diff -up src/module_list.py.orig src/module_list.py 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.orig 2014-11-18 15:29:30.360131313 -0200
+++ src/module_list.py 2014-08-12 14:23:39.051985950 -0300 +++ src/module_list.py 2014-11-18 15:29:37.432131407 -0200
@@ -2107,7 +2107,7 @@ ext_modules = [ @@ -2130,7 +2130,7 @@ ext_modules = [
def is_package_installed(name): def is_package_installed(name):
return False return False

6
sagemath-gap-hap.patch
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@ -1,6 +1,6 @@
diff -up src/sage/groups/perm_gps/permgroup.py.orig src/sage/groups/perm_gps/permgroup.py 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.orig 2014-11-18 15:27:46.545129943 -0200
+++ src/sage/groups/perm_gps/permgroup.py 2014-08-12 14:19:44.435976966 -0300 +++ src/sage/groups/perm_gps/permgroup.py 2014-11-18 15:27:53.760130038 -0200
@@ -180,8 +180,7 @@ def hap_decorator(f): @@ -180,8 +180,7 @@ def hap_decorator(f):
""" """
@wraps(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() load_hap()
from sage.rings.arith import is_prime from sage.rings.arith import is_prime
if not (p == 0 or is_prime(p)): 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 - David Joyner and Graham Ellis
""" """

6
sagemath-lrcalc.patch
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@ -1,7 +1,7 @@
diff -up src/module_list.py.orig src/module_list.py 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.orig 2014-11-18 15:28:17.313130349 -0200
+++ src/module_list.py 2014-08-12 14:22:15.018982732 -0300 +++ src/module_list.py 2014-11-18 15:28:24.520130444 -0200
@@ -2191,7 +2191,7 @@ if UNAME[0] == "Darwin" and not UNAME[2] @@ -2210,7 +2210,7 @@ if UNAME[0] == "Darwin" and not UNAME[2]
) )

6
sagemath-lrslib.patch
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@ -1,7 +1,7 @@
diff -up src/sage/geometry/polyhedron/base.py.orig src/sage/geometry/polyhedron/base.py 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.orig 2014-11-18 15:26:45.817129141 -0200
+++ src/sage/geometry/polyhedron/base.py 2014-08-12 14:18:29.539974098 -0300 +++ src/sage/geometry/polyhedron/base.py 2014-11-18 15:26:53.185129238 -0200
@@ -3494,11 +3494,6 @@ class Polyhedron_base(Element): @@ -3515,11 +3515,6 @@ class Polyhedron_base(Element):
David Avis's lrs program. David Avis's lrs program.
""" """

6
sagemath-nauty.patch
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@ -1,7 +1,7 @@
diff -up src/sage/graphs/graph_generators.py.orig src/sage/graphs/graph_generators.py 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.orig 2014-11-18 15:27:15.584129534 -0200
+++ src/sage/graphs/graph_generators.py 2014-08-12 14:19:08.986975608 -0300 +++ src/sage/graphs/graph_generators.py 2014-11-18 15:27:23.352129636 -0200
@@ -830,7 +830,7 @@ class GraphGenerators(): @@ -833,7 +833,7 @@ class GraphGenerators():
""" """
import subprocess import subprocess
from sage.misc.package import is_package_installed from sage.misc.package import is_package_installed

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sagemath-ntl6.patch
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12
sagemath-pari.patch
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@ -1,6 +1,7 @@
--- src/sage/libs/pari/pari_instance.pxd.orig 2014-05-10 15:49:08.954184083 -0300 diff -up src/sage/libs/pari/pari_instance.pxd.orig src/sage/libs/pari/pari_instance.pxd
+++ src/sage/libs/pari/pari_instance.pxd 2014-05-10 15:49:13.304183771 -0300 --- src/sage/libs/pari/pari_instance.pxd.orig 2014-11-18 15:25:03.591127791 -0200
@@ -5,6 +5,10 @@ cimport cython +++ 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 from sage.libs.pari.gen cimport gen
@ -11,8 +12,9 @@
cpdef long prec_bits_to_words(unsigned long prec_in_bits) cpdef long prec_bits_to_words(unsigned long prec_in_bits)
@cython.final @cython.final
--- src/sage/libs/pari/pari_instance.pyx.orig 2014-05-10 15:49:06.437184263 -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 2014-05-10 15:49:13.307183771 -0300 --- 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 @@ -437,7 +437,12 @@ cdef class PariInstance(sage.structure.p
# The size here doesn't really matter, because we will allocate # The size here doesn't really matter, because we will allocate
# our own stack anyway. We ask PARI not to set up signal and # our own stack anyway. We ask PARI not to set up signal and

8511
sagemath-pari2.7.patch
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10
sagemath-png.patch
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@ -1,7 +1,7 @@
diff -up src/module_list.py.orig src/module_list.py 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.orig 2014-11-18 15:23:33.184126598 -0200
+++ src/module_list.py 2014-08-12 14:10:53.082956619 -0300 +++ src/module_list.py 2014-11-18 15:23:42.856126725 -0200
@@ -1065,7 +1065,7 @@ ext_modules = [ @@ -1081,7 +1081,7 @@ ext_modules = [
Extension('sage.matrix.matrix_mod2_dense', Extension('sage.matrix.matrix_mod2_dense',
sources = ['sage/matrix/matrix_mod2_dense.pyx'], 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, extra_compile_args = m4ri_extra_compile_args,
depends = [SAGE_INC + "/png.h", SAGE_INC + "/m4ri/m4ri.h"]), 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', Extension('sage.modules.vector_mod2_dense',
sources = ['sage/modules/vector_mod2_dense.pyx'], 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, extra_compile_args = m4ri_extra_compile_args,
depends = [SAGE_INC + "/png.h", SAGE_INC + "/m4ri/m4ri.h"]), 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', Extension('sage.rings.polynomial.pbori',
sources = ['sage/rings/polynomial/pbori.pyx'], sources = ['sage/rings/polynomial/pbori.pyx'],
libraries=['polybori-' + polybori_major_version, libraries=['polybori-' + polybori_major_version,

6
sagemath-readonly.patch
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@ -1,7 +1,7 @@
diff -up src/sage/all.py.orig src/sage/all.py 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.orig 2014-11-18 15:20:50.327124447 -0200
+++ src/sage/all.py 2014-08-12 14:10:14.402955137 -0300 +++ src/sage/all.py 2014-11-18 15:20:58.279124552 -0200
@@ -316,11 +316,11 @@ def _write_started_file(): @@ -307,11 +307,11 @@ def _write_started_file():
Check that the file exists when Sage is running:: Check that the file exists when Sage is running::

22
sagemath-rpmbuild.patch
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@ -1,16 +1,16 @@
diff -up src/module_list.py.orig src/module_list.py 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.orig 2014-11-18 13:25:41.898033239 -0200
+++ src/module_list.py 2014-08-13 11:34:18.828202300 -0300 +++ src/module_list.py 2014-11-18 13:27:10.616034410 -0200
@@ -5,7 +5,7 @@ from distutils.core import setup @@ -4,7 +4,7 @@ import os
from distutils.extension import Extension 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 = os.path.join(SAGE_LOCAL, 'include')
+SAGE_INC = '/usr/include' +SAGE_INC = '/usr/include'
######################################################### #########################################################
### BLAS setup ### BLAS setup
@@ -36,10 +36,11 @@ else: @@ -35,10 +35,11 @@ else:
### Commonly used definitions ### 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'] flint_depends = [SAGE_INC + '/flint/flint.h']
singular_depends = [SAGE_INC + '/libsingular.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 ### PolyBoRi settings
######################################################### #########################################################
@ -33,7 +33,7 @@ diff -up src/module_list.py.orig src/module_list.py
polybori_major_version = '0.8' polybori_major_version = '0.8'
@@ -710,7 +711,7 @@ ext_modules = [ @@ -730,7 +731,7 @@ ext_modules = [
sources = ['sage/libs/lcalc/lcalc_Lfunction.pyx'], sources = ['sage/libs/lcalc/lcalc_Lfunction.pyx'],
libraries = ['m', 'ntl', 'mpfr', 'gmp', 'gmpxx', libraries = ['m', 'ntl', 'mpfr', 'gmp', 'gmpxx',
'Lfunction'], 'Lfunction'],
@ -43,8 +43,8 @@ diff -up src/module_list.py.orig src/module_list.py
language = 'c++'), language = 'c++'),
diff -up src/setup.py.orig src/setup.py diff -up src/setup.py.orig src/setup.py
--- src/setup.py.orig 2014-08-13 11:34:14.742202143 -0300 --- src/setup.py.orig 2014-11-18 13:25:47.434033312 -0200
+++ src/setup.py 2014-08-13 11:34:55.082203688 -0300 +++ src/setup.py 2014-11-18 13:28:52.152035751 -0200
@@ -36,11 +36,11 @@ except KeyError: @@ -36,11 +36,11 @@ except KeyError:
compile_result_dir = None compile_result_dir = None
keep_going = False keep_going = False
@ -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.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 = m.library_dirs + [os.path.join(SAGE_LOCAL, "lib")]
+ m.library_dirs += ['c_lib', '%s/lib' % SAGE_LOCAL] + m.library_dirs += ['c_lib', '%s/lib' % SAGE_LOCAL]
m.include_dirs = m.include_dirs + include_dirs
############################################# @@ -579,20 +581,6 @@ print "Discovered Python source, time: %
@@ -556,20 +558,6 @@ print "Discovered Python source, time: %
######################################################### #########################################################

38
sagemath-sagedoc.patch
View file

@ -1,18 +1,18 @@
diff -up src/doc/common/builder.py.orig src/doc/common/builder.py 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.orig 2014-11-18 13:30:43.238037217 -0200
+++ src/doc/common/builder.py 2014-08-12 14:06:47.943947231 -0300 +++ 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 @@ -32,7 +32,7 @@ from sage.env import SAGE_DOC, SAGE_SRC
# SAGE_DOC, LANGUAGES, SPHINXOPTS, PAPER, OMIT, # SAGE_DOC, LANGUAGES, SPHINXOPTS, PAPER, OMIT,
# PAPEROPTS, ALLSPHINXOPTS, NUM_THREADS, WEBSITESPHINXOPTS # PAPEROPTS, ALLSPHINXOPTS, NUM_THREADS, WEBSITESPHINXOPTS
# from build_options.py. # from build_options.py.
-execfile(os.path.join(SAGE_DOC, 'common' , 'build_options.py')) -fpath = 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(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 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.orig 2014-11-18 13:30:43.248037218 -0200
+++ src/doc/common/conf.py 2014-08-12 14:07:26.095948692 -0300 +++ src/doc/common/conf.py 2014-11-18 13:32:40.336038763 -0200
@@ -1,5 +1,5 @@ @@ -1,5 +1,5 @@
import sys, os, sphinx import sys, os, sphinx
-from sage.env import SAGE_DOC -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, # 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 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.orig 2014-11-18 13:30:43.259037218 -0200
+++ src/sage/doctest/control.py 2014-08-12 14:08:08.384950312 -0300 +++ src/sage/doctest/control.py 2014-11-18 13:33:27.185039382 -0200
@@ -89,7 +89,6 @@ class DocTestDefaults(SageObject): @@ -89,7 +89,6 @@ class DocTestDefaults(SageObject):
self.valgrind = False self.valgrind = False
self.massif = 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 # Non-interactive debuggers: 48 hours
options.timeout = int(os.getenv('SAGE_TIMEOUT_VALGRIND', 48 * 60 * 60)) options.timeout = int(os.getenv('SAGE_TIMEOUT_VALGRIND', 48 * 60 * 60))
elif options.long: elif options.long:
@@ -822,13 +821,8 @@ class DocTestController(SageObject): @@ -889,13 +888,8 @@ class DocTestController(SageObject):
elif opt.cachegrind: elif opt.cachegrind:
toolname = "cachegrind" toolname = "cachegrind"
flags = os.getenv("SAGE_CACHEGRIND_FLAGS", "") 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: if "%s" in flags:
flags %= toolname + ".%p" # replace %s with toolname flags %= toolname + ".%p" # replace %s with toolname
cmd += flags + sage_cmd cmd += flags + sage_cmd
@@ -888,10 +882,10 @@ class DocTestController(SageObject): @@ -955,10 +949,10 @@ class DocTestController(SageObject):
0 0
""" """
opt = self.options 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() return self.run_val_gdb()
else: else:
diff -up src/sage/interfaces/singular.py.orig src/sage/interfaces/singular.py 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.orig 2014-11-18 13:30:43.265037218 -0200
+++ src/sage/interfaces/singular.py 2014-08-12 14:08:26.055950988 -0300 +++ src/sage/interfaces/singular.py 2014-11-18 13:33:49.257039673 -0200
@@ -2147,7 +2147,7 @@ def generate_docstring_dictionary(): @@ -2147,7 +2147,7 @@ def generate_docstring_dictionary():
nodes.clear() nodes.clear()
node_names.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_node = re.compile("File: singular\.hlp, Node: ([^,]*),.*")
new_lookup = re.compile("\* ([^:]*):*([^.]*)\..*") 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

123
sagemath-sagenb.patch
View file

@ -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 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-0.10.8.2/flask_version/base.py.orig 2014-02-11 18:13:34.453086409 -0200 --- 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-0.10.8.2/flask_version/base.py 2014-02-11 18:14:30.976088573 -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 @@ -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 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 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 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('/javascript', DATA)
self.add_static_path('/static', DATA) self.add_static_path('/static', DATA)
self.add_static_path('/java', 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(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 import mimetypes
mimetypes.add_type('text/plain','.jmol') 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 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-0.10.8.2/sagenb/data/sage/html/notebook/base.html.orig 2014-02-11 18:13:34.468086409 -0200 --- build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/misc/misc.py.orig 2014-12-06 17:45:36.066723826 -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 +++ build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/misc/misc.py 2014-12-06 17:45:38.853723933 -0200
@@ -46,7 +46,7 @@ INPUT: @@ -174,7 +174,8 @@ def pad_zeros(s, size=3):
<!-- 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() %} SAGENB_ROOT = os.path.split(resource_filename(__name__, ''))[0]
<!-- 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 -DATA = os.path.join(SAGENB_ROOT, 'data')
try: +from sage.misc.misc import SAGE_SRC
@@ -25,7 +23,6 @@ class SageNBFlask(Flask): +DATA = os.path.join(SAGE_SRC, 'sagenb', 'data')
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 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)
@@ -36,7 +33,7 @@ class SageNBFlask(Flask): 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
self.add_static_path('/javascript', DATA) --- build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/notebook/run_notebook.py.orig 2014-12-06 17:45:36.069723826 -0200
self.add_static_path('/static', DATA) +++ build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/notebook/run_notebook.py 2014-12-06 17:45:38.854723933 -0200
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-0.10.8.2/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()
- jmol_script = jmol_script.replace('defaultdirectory "', 'defaultdirectory "' + self.url_to_self() + '/')
+ jmol_script = jmol_script.replace('defaultdirectory "', 'defaultdirectory "/home/' + self.worksheet_filename() + '/')
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
@@ -46,12 +46,14 @@ sagenb.notebook.misc.DIR = %(cwd)r #We s @@ -46,12 +46,14 @@ sagenb.notebook.misc.DIR = %(cwd)r #We s
# Flask # # 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): def save_notebook(notebook):
print "Quitting all running worksheets..." 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']

6
sagemath-scons.patch
View file

@ -1,6 +1,6 @@
diff -up src/c_lib/SConstruct.orig src/c_lib/SConstruct 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.orig 2014-11-17 17:41:32.525922611 -0200
+++ src/c_lib/SConstruct 2014-05-26 13:25:26.593763955 -0300 +++ src/c_lib/SConstruct 2014-11-17 17:41:41.486922954 -0200
@@ -126,8 +126,8 @@ env['PYV']=platform.python_version().rsp @@ -126,8 +126,8 @@ env['PYV']=platform.python_version().rsp
# The SCons convenience function Split is the only strange thing # The SCons convenience function Split is the only strange thing
# to python programmers. It just makes a list by splitting on # 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" ) cppFiles = Split( "ZZ_pylong.cpp ntl_wrap.cpp" )
@@ -136,9 +136,22 @@ incFiles = Split( "ccobject.h convert.h @@ -136,9 +136,22 @@ incFiles = Split( "ccobject.h convert.h
Split( "interrupt.h memory.h mpn_pylong.h mpz_longlong.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(CFLAGS='@@optflags@@')
+env.Append(CXXFLAGS='@@optflags@@') +env.Append(CXXFLAGS='@@optflags@@')

187
sagemath-scripts.patch
View file

@ -1,8 +1,8 @@
diff -up src/bin/sage.orig src/bin/sage diff -up src/bin/sage.orig src/bin/sage
--- src/bin/sage.orig 2014-08-12 13:51:14.714911495 -0300 --- src/bin/sage.orig 2014-11-17 17:42:48.321925514 -0200
+++ src/bin/sage 2014-08-12 13:59:39.911930840 -0300 +++ src/bin/sage 2014-11-17 17:55:52.524955544 -0200
@@ -13,17 +13,14 @@ usage() { @@ -13,11 +13,9 @@ usage() {
echo " file.<sage|py|spyx> -- run given .sage, .py or .spyx files" echo " file.[sage|py|spyx] -- run given .sage, .py or .spyx file"
echo " -advanced -- list all command line options" echo " -advanced -- list all command line options"
echo " -c <cmd> -- Evaluates cmd as sage code" echo " -c <cmd> -- Evaluates cmd as sage code"
- echo " -experimental -- list all experimental packages that can be installed" - 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 " -gp [...] -- run Sage's PARI/GP calculator with given arguments"
echo " -h, -? -- print this help message" echo " -h, -? -- print this help message"
- echo " -i [packages] -- install the given Sage packages" - 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 " -maxima [...] -- run Sage's Maxima with given arguments"
echo " -mwrank [...] -- run Sage's mwrank with given arguments" @@ -25,7 +23,6 @@ usage() {
echo " -n, -notebook [...] -- start the Sage notebook (options are the same" echo " --notebook=[...] -- start the Sage notebook (valid options are"
echo " as for the notebook command in Sage)" echo " 'default', 'sagenb', and 'ipython')"
echo " -n, --notebook -- shortcut for --notebook=default"
- echo " -optional -- list all optional packages that can be installed" - echo " -optional -- list all optional packages that can be installed"
echo " -python [...] -- run the Python interpreter" echo " -python [...] -- run the Python interpreter"
echo " -R [...] -- run Sage's R with given arguments" echo " -R [...] -- run Sage's R with given arguments"
echo " -singular [...] -- run Sage's singular 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 " --optional - controls which optional tests are run"
echo " --sagenb - test all sagenb files" echo " --sagenb - test all sagenb files"
echo " --help - show all testing options" 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" echo " -v, -version -- print the Sage version"
exit 0 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 " -preparse <file.sage> -- preparse file.sage and produce corresponding file.sage.py"
echo " -q -- quiet; start with no banner" echo " -q -- quiet; start with no banner"
echo " -root -- print the Sage root directory" echo " -root -- print the Sage root directory"
- echo " -gthread, -qthread, -q4thread, -wthread, -pylab" - echo " -gthread, -qthread, -q4thread, -wthread, -pylab"
- echo " -- pass the option through to ipython" - 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 " -v, -version -- print the Sage version"
echo echo
#### 1.......................26..................................................78 @@ -75,8 +66,6 @@ usage_advanced() {
#### |.....................--.|...................................................| echo " 'default', 'sagenb', and 'ipython'). See the output"
echo "Running the notebook:" 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 " -bn, -build-and-notebook [...] -- build the Sage library then start"
- echo " the Sage notebook" - echo " the Sage notebook"
echo " -inotebook [...] -- start the *insecure* Sage notebook" echo " -inotebook [...] -- start the *insecure* Sage notebook (deprecated)"
echo " -n, -notebook [...] -- start the Sage notebook (options are the same" echo " -n, -notebook [...] -- start the default Sage notebook (options are the"
echo " as for the notebook command in Sage)" echo " same as for the notebook command in Sage). See the"
@@ -87,13 +78,8 @@ usage_advanced() { @@ -94,13 +83,9 @@ usage_advanced() {
echo " -gp [...] -- run Sage's PARI/GP calculator with given arguments" echo " -gp [...] -- run Sage's PARI/GP calculator with given arguments"
echo " -ipython [...] -- run Sage's IPython using the default environment (not" echo " -ipython [...] -- run Sage's IPython using the default environment (not"
echo " Sage), passing additional options to IPython" echo " Sage), passing additional options to IPython"
- echo " -kash [...] -- run Sage's Kash with given arguments" - echo " -kash [...] -- run Sage's Kash with given arguments"
- command -v kash &>/dev/null || \ - 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 " -lisp [...] -- run Lisp interpreter included with Sage"
echo " -M2 [...] -- run Sage's Macaulay2 with given arguments" echo " -M2 [...] -- run Sage's Macaulay2 with given arguments"
- command -v M2 &>/dev/null || \ - 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 " -maxima [...] -- run Sage's Maxima with given arguments"
echo " -mwrank [...] -- run Sage's mwrank with given arguments" echo " -mwrank [...] -- run Sage's mwrank with given arguments"
echo " -python [...] -- run the Python interpreter" echo " -python [...] -- run the Python interpreter"
@@ -107,75 +93,10 @@ usage_advanced() { @@ -114,74 +99,10 @@ usage_advanced() {
echo echo
#### 1.......................26..................................................78 #### 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 " -info [packages] -- print the SPKG.txt of the given packages"
- echo " -optional -- list all optional packages that can be installed" - echo " -optional -- list all optional packages that can be installed"
- echo " -standard -- list all standard 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 -- download latest non-optional Sage packages (do not build them)"
- #echo " -update-build -- build and install all downloaded non-optional Sage packages" - #echo " -update-build -- build and install all downloaded non-optional Sage packages"
- echo " -upgrade [version] -- download, build and install the given version. Here," - 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 - #### 1.......................26..................................................78
- #### |.....................--.|...................................................| - #### |.....................--.|...................................................|
- echo "Building and testing the Sage library:" - echo "Building and testing the Sage library:"
- echo " -b [branch] -- build Sage library. If branch is given, switch to" - echo " -b -- build Sage library."
- echo " branch in devel/sage-branch and build that branch" - echo " -ba -- same as -b and rebuild all Cython code"
- echo " -ba [branch] -- same as -b and rebuild all Cython code" - echo " -ba-force -- same as -ba, but don't query before rebuilding"
- echo " -ba-force [branch] -- same as -ba, but don't query before rebuilding" - echo " -br -- build and run Sage"
- echo " -br [branch] -- switch to, build, and run Sage given branch"
- echo " -bt [...] -- build and test, options like -t below" - echo " -bt [...] -- build and test, options like -t below"
- echo " -btp <N> [...] -- build and test parallel, options like -tp below" - echo " -btp <N> [...] -- build and test parallel, options like -tp below"
- echo " -btnew [...] -- build and test modified files, options like -tnew" - echo " -btnew [...] -- build and test modified files, options like -tnew"
- echo " -fixdoctests <file.py> [output_file] [--long]" - echo " -fixdoctests <file.py> [output_file] [--long]"
- echo " -- writes a new version of file.py to output_file" - echo " -- replace failing doctests with the actual output. With"
- echo " (defaults: to file.py.out) that will pass the doctests." - echo " optional output_file: redirect there. With the --long"
- echo " With the optional --long argument the long time tests" - echo " option: include #long time tests."
- echo " are also checked."
- echo " A patch for the new file is printed to stdout."
- echo " -startuptime [module] -- display how long each component of Sage takes to" - echo " -startuptime [module] -- display how long each component of Sage takes to"
- echo " start up; optionally specify a module to get more" - echo " start up; optionally specify a module to get more"
- echo " details about that particular module" - 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 " --failed - only test files that failed last test"
- echo " --sagenb - test all sagenb files" - echo " --sagenb - test all sagenb files"
- echo " --help - show all testing options" - 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 " -tp <N> [...] -- like -t above, but tests in parallel using N threads"
- echo " with 0 interpreted as a sensible default" - echo " with 0 interpreted as a sensible default"
- echo " -testall [options] -- test all source files, docs, and examples. options" - 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_src <string> -- search through all the Sage library code for string"
echo " -search_doc <string> -- search through the Sage documentation for string" echo " -search_doc <string> -- search through the Sage documentation for string"
echo " -grep <string> -- same as -search_src" echo " -grep <string> -- same as -search_src"
@@ -195,16 +116,6 @@ usage_advanced() { @@ -201,16 +122,6 @@ usage_advanced() {
echo echo
#### 1.......................26..................................................78 #### 1.......................26..................................................78
#### |.....................--.|...................................................| #### |.....................--.|...................................................|
@ -156,7 +156,7 @@ diff -up src/bin/sage.orig src/bin/sage
echo "Valgrind memory debugging:" echo "Valgrind memory debugging:"
echo " -cachegrind -- run Sage using Valgrind's cachegrind tool. The log" echo " -cachegrind -- run Sage using Valgrind's cachegrind tool. The log"
echo " files are named sage-cachegrind.PID can be found in" 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 " -memcheck -- run Sage using Valgrind's memcheck tool. The log"
echo " files are named sage-memcheck.PID can be found in" echo " files are named sage-memcheck.PID can be found in"
echo " $DOT_SAGE" 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 " -valgrind -- this is an alias for -memcheck"
echo echo
echo "You can also use -- before a long option, e.g., 'sage --optional'." 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 exit $status
fi fi
@ -198,14 +198,16 @@ diff -up src/bin/sage.orig src/bin/sage
-fi -fi
- -
- -
if [ $# -gt 0 ]; then -if [ $# -gt 0 ]; then
if [ "$1" = '-h' -o "$1" = '-?' -o "$1" = '-help' -o "$1" = '--help' ]; then - if [ "$1" = '-h' -o "$1" = '-?' -o "$1" = '-help' -o "$1" = '--help' ]; then
usage - usage
@@ -277,28 +157,13 @@ if [ $# -gt 0 ]; then - fi
fi - if [ "$1" = "-advanced" -o "$1" = "--advanced" ]; then
fi - usage_advanced
- fi
-fi
- -
# Prepare for running Sage, either interactively or non-interactively. # Prepare for running Sage, either interactively or non-interactively.
sage_setup() { sage_setup() {
- # Check that we're not in a source tarball which hasn't been built yet (#13561). - # Check that we're not in a source tarball which hasn't been built yet (#13561).
@ -230,11 +232,10 @@ diff -up src/bin/sage.orig src/bin/sage
if [ ! -d "$IPYTHONDIR" ]; then if [ ! -d "$IPYTHONDIR" ]; then
# make sure that $DOT_SAGE exists so that ipython will happily # make sure that $DOT_SAGE exists so that ipython will happily
# create its config directories there. If DOT_SAGE doesn't # create its config directories there. If DOT_SAGE doesn't
@@ -308,21 +173,6 @@ sage_setup() { @@ -315,20 +172,6 @@ sage_setup() {
sage-cleaner &>/dev/null &
} }
-
-# Check to see if the whole Sage install tree has moved. If so, -# 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 -# 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 -# 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. # Start an interactive Sage session, this function never returns.
interactive_sage() { interactive_sage() {
sage_setup sage_setup
@@ -384,7 +234,7 @@ fi @@ -390,7 +233,7 @@ fi
if [ "$1" = '-singular' -o "$1" = '--singular' ]; then if [ "$1" = '-singular' -o "$1" = '--singular' ]; then
shift shift
@ -261,15 +262,10 @@ diff -up src/bin/sage.orig src/bin/sage
fi fi
if [ "$1" = '-sqlite3' -o "$1" = '--sqlite3' ]; then if [ "$1" = '-sqlite3' -o "$1" = '--sqlite3' ]; then
@@ -412,16 +262,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ] @@ -423,11 +266,6 @@ if [ "$1" = '-kash' -o "$1" = '--kash' ]
exec ecl "$@" exec kash "$@"
fi fi
-if [ "$1" = '-kash' -o "$1" = '--kash' ]; then
- shift
- exec kash "$@"
-fi
-
-if [ "$1" = '-fixdoctests' -o "$1" = '--fixdoctests' ]; then -if [ "$1" = '-fixdoctests' -o "$1" = '--fixdoctests' ]; then
- shift - shift
- exec sage-fixdoctests "$@" - exec sage-fixdoctests "$@"
@ -278,7 +274,23 @@ diff -up src/bin/sage.orig src/bin/sage
if [ "$1" = '-maxima' -o "$1" = '--maxima' ]; then if [ "$1" = '-maxima' -o "$1" = '--maxima' ]; then
shift shift
exec maxima "$@" 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 fi
##################################################################### #####################################################################
@ -299,7 +311,7 @@ diff -up src/bin/sage.orig src/bin/sage
# File conversion # File conversion
##################################################################### #####################################################################
@@ -609,36 +435,15 @@ if [ "$1" = '-rst2sws' -o "$1" = '--rst2 @@ -624,23 +439,9 @@ if [ "$1" = '-rst2sws' -o "$1" = '--rst2
fi fi
##################################################################### #####################################################################
@ -320,23 +332,24 @@ diff -up src/bin/sage.orig src/bin/sage
- sage-build "$@" || exit $? - sage-build "$@" || exit $?
-} -}
- -
if [ "$1" = "-notebook" -o "$1" = '--notebook' -o "$1" = '-n' ]; then if [[ "$1" =~ "--notebook="* || "$1" =~ "-n="* || "$1" =~ "-notebook="* ]]; then
shift
sage-cleaner &>/dev/null & sage-cleaner &>/dev/null &
exec sage-notebook "$@" exec sage-notebook "$@"
@@ -652,13 +453,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
exec sage-notebook --notebook=default "$@"
fi fi
-if [ "$1" = "-bn" -o "$1" = "--build-and-notebook" ]; then -if [ "$1" = "-bn" -o "$1" = "--build-and-notebook" ]; then
- shift - shift
- build_sage - build_sage
- sage-cleaner &>/dev/null & - sage-cleaner &>/dev/null &
- exec sage-notebook "$@" - exec sage-notebook --notebook=default "$@"
-fi -fi
- -
if [ "$1" = "-inotebook" -o "$1" = '--inotebook' ]; then if [ "$1" = "-inotebook" -o "$1" = '--inotebook' ]; then
shift shift
sage-cleaner &>/dev/null & sage-cleaner &>/dev/null &
@@ -657,40 +462,19 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep @@ -677,40 +471,19 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
exit 0 exit 0
fi fi
@ -379,7 +392,7 @@ diff -up src/bin/sage.orig src/bin/sage
shift shift
exec sage-runtests -p "$@" exec sage-runtests -p "$@"
else 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
fi fi
@ -391,7 +404,7 @@ diff -up src/bin/sage.orig src/bin/sage
shift shift
SAGE_BANNER="no" SAGE_BANNER="no"
sage_setup sage_setup
@@ -724,132 +505,6 @@ if [ "$1" = '-c' ]; then @@ -744,136 +514,6 @@ if [ "$1" = '-c' ]; then
exec sage-eval "$@" exec sage-eval "$@"
fi fi
@ -445,15 +458,19 @@ diff -up src/bin/sage.orig src/bin/sage
-} -}
- -
-if [ "$1" = '-optional' -o "$1" = "--optional" ]; then -if [ "$1" = '-optional' -o "$1" = "--optional" ]; then
- exec sage-list-optional - exec sage-list-packages optional
-fi -fi
- -
-if [ "$1" = '-experimental' -o "$1" = "--experimental" ]; then -if [ "$1" = '-experimental' -o "$1" = "--experimental" ]; then
- exec sage-list-experimental - exec sage-list-packages experimental
-fi -fi
- -
-if [ "$1" = '-standard' -o "$1" = "--standard" ]; then -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 -fi
- -
-if [ "$1" = '-i' ]; then -if [ "$1" = '-i' ]; then
@ -524,7 +541,7 @@ diff -up src/bin/sage.orig src/bin/sage
if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then
shift shift
sage_setup sage_setup
@@ -898,21 +553,10 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca @@ -922,26 +562,10 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
exec sage-callgrind "$@" exec sage-callgrind "$@"
fi fi
@ -543,12 +560,17 @@ diff -up src/bin/sage.orig src/bin/sage
- interactive_sage "$@" - interactive_sage "$@"
-fi -fi
- -
if [ "$1" = '-dev' -o "$1" = "--dev" ]; then -if [ "$1" = '-dev' -o "$1" = "--dev" ]; then
shift - shift
exec sage-dev "$@" - 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 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.orig 2014-11-17 17:43:03.195926083 -0200
+++ src/bin/sage-runtests 2014-08-12 14:00:31.543932818 -0300 +++ src/bin/sage-runtests 2014-11-17 17:48:39.236938952 -0200
@@ -54,10 +54,6 @@ if __name__ == "__main__": @@ -54,10 +54,6 @@ if __name__ == "__main__":
help="run doctests using Valgrind's cachegrind tool. The log " help="run doctests using Valgrind's cachegrind tool. The log "
"files are named sage-cachegrind.PID and can be found in " + "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, parser.add_option("-f", "--failed", action="store_true", default=False,
help="doctest only those files that failed in the previous run") help="doctest only those files that failed in the previous run")
diff -up src/bin/sage-valgrind.orig src/bin/sage-valgrind 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.orig 2014-11-17 17:43:14.588926520 -0200
+++ src/bin/sage-valgrind 2014-08-12 14:01:14.983934481 -0300 +++ src/bin/sage-valgrind 2014-11-17 17:48:18.884938172 -0200
@@ -11,7 +11,7 @@ fi @@ -1,16 +1,6 @@
LOG="$DOT_SAGE"/valgrind/sage-memcheck.%p #!/usr/bin/env bash
echo "Log file is $LOG"
-SUPP=""
-if [ -f "$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 [ "$SAGE_MEMCHECK_FLAGS" ]; then if [ "$SAGE_MEMCHECK_FLAGS" ]; then
echo "Overwriting memcheck flags with:" echo "Overwriting memcheck flags with: $SAGE_MEMCHECK_FLAGS"
echo $SAGE_MEMCHECK_FLAGS

139
sagemath-sphinx.patch
View file

@ -1,139 +0,0 @@
diff -up src/sage/graphs/generic_graph.py.orig src/sage/graphs/generic_graph.py
--- 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::
- - :meth:`subdivide_edge` -- subdivides one edge
+ - :meth:`subdivide_edge` -- subdivides one edge
"""
for e in edges:
self.subdivide_edge(e, k)
@@ -11557,10 +11557,10 @@ class GenericGraph(GenericGraph_pyx):
.. SEEALSO::
- - :mod:`Interval Graph Recognition <sage.graphs.pq_trees>`.
+ - :mod:`Interval Graph Recognition <sage.graphs.pq_trees>`.
- - :meth:`PQ <sage.graphs.pq_trees.PQ>`
- -- Implementation of PQ-Trees.
+ - :meth:`PQ <sage.graphs.pq_trees.PQ>`
+ -- Implementation of PQ-Trees.
"""
self._scream_if_not_simple()
@@ -13429,13 +13429,13 @@ class GenericGraph(GenericGraph_pyx):
.. SEEALSO::
- - :meth:`breadth_first_search <sage.graphs.base.c_graph.CGraphBackend.breadth_first_search>`
- -- breadth-first search for fast compiled graphs.
+ - :meth:`breadth_first_search <sage.graphs.base.c_graph.CGraphBackend.breadth_first_search>`
+ -- breadth-first search for fast compiled graphs.
- - :meth:`depth_first_search <sage.graphs.base.c_graph.CGraphBackend.depth_first_search>`
- -- depth-first search for fast compiled graphs.
+ - :meth:`depth_first_search <sage.graphs.base.c_graph.CGraphBackend.depth_first_search>`
+ -- depth-first search for fast compiled graphs.
- - :meth:`depth_first_search` -- depth-first search for generic graphs.
+ - :meth:`depth_first_search` -- depth-first search for generic graphs.
EXAMPLES::
@@ -13554,13 +13554,13 @@ class GenericGraph(GenericGraph_pyx):
.. SEEALSO::
- - :meth:`breadth_first_search`
+ - :meth:`breadth_first_search`
- - :meth:`breadth_first_search <sage.graphs.base.c_graph.CGraphBackend.breadth_first_search>`
- -- breadth-first search for fast compiled graphs.
+ - :meth:`breadth_first_search <sage.graphs.base.c_graph.CGraphBackend.breadth_first_search>`
+ -- breadth-first search for fast compiled graphs.
- - :meth:`depth_first_search <sage.graphs.base.c_graph.CGraphBackend.depth_first_search>`
- -- depth-first search for fast compiled graphs.
+ - :meth:`depth_first_search <sage.graphs.base.c_graph.CGraphBackend.depth_first_search>`
+ -- depth-first search for fast compiled graphs.
EXAMPLES::
diff -up src/sage/graphs/graph.py.orig src/sage/graphs/graph.py
--- 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::
- - :meth:`~Graph.is_arc_transitive`
- - :meth:`~Graph.is_half_transitive`
- - :meth:`~Graph.is_semi_symmetric`
+ - :meth:`~Graph.is_arc_transitive`
+ - :meth:`~Graph.is_half_transitive`
+ - :meth:`~Graph.is_semi_symmetric`
EXAMPLES::
@@ -3070,9 +3070,9 @@ class Graph(GenericGraph):
.. SEEALSO::
- - :meth:`~Graph.is_edge_transitive`
- - :meth:`~Graph.is_half_transitive`
- - :meth:`~Graph.is_semi_symmetric`
+ - :meth:`~Graph.is_edge_transitive`
+ - :meth:`~Graph.is_half_transitive`
+ - :meth:`~Graph.is_semi_symmetric`
EXAMPLES::
@@ -3107,9 +3107,9 @@ class Graph(GenericGraph):
.. SEEALSO::
- - :meth:`~Graph.is_edge_transitive`
- - :meth:`~Graph.is_arc_transitive`
- - :meth:`~Graph.is_semi_symmetric`
+ - :meth:`~Graph.is_edge_transitive`
+ - :meth:`~Graph.is_arc_transitive`
+ - :meth:`~Graph.is_semi_symmetric`
EXAMPLES:
@@ -3146,9 +3146,9 @@ class Graph(GenericGraph):
.. SEEALSO::
- - :meth:`~Graph.is_edge_transitive`
- - :meth:`~Graph.is_arc_transitive`
- - :meth:`~Graph.is_half_transitive`
+ - :meth:`~Graph.is_edge_transitive`
+ - :meth:`~Graph.is_arc_transitive`
+ - :meth:`~Graph.is_half_transitive`
EXAMPLES:
@@ -6114,8 +6114,8 @@ class Graph(GenericGraph):
.. SEEALSO::
- * Graph cores is also a notion related to graph homomorphisms. For
- this second meaning, see :meth:`Graph.has_homomorphism_to`.
+ * Graph cores is also a notion related to graph homomorphisms. For
+ this second meaning, see :meth:`Graph.has_homomorphism_to`.
REFERENCE:
@@ -6300,7 +6300,7 @@ class Graph(GenericGraph):
.. SEEALSO::
- - :meth:`is_prime` -- Tests whether a graph is prime.
+ - :meth:`is_prime` -- Tests whether a graph is prime.
REFERENCE:

130
sagemath.spec
View file

@ -24,7 +24,7 @@
%global pexpect_pkg pexpect-2.0 %global pexpect_pkg pexpect-2.0
%global polytopes_db_pkg polytopes_db-20120220 %global polytopes_db_pkg polytopes_db-20120220
%global rubiks_pkg rubiks-20070912 %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 sagetex_pkg sagetex-2.3.4
%global SAGE_ROOT %{_libdir}/sagemath %global SAGE_ROOT %{_libdir}/sagemath
@ -38,8 +38,8 @@
Name: sagemath Name: sagemath
Group: Applications/Engineering Group: Applications/Engineering
Summary: A free open-source mathematics software system Summary: A free open-source mathematics software system
Version: 6.3 Version: 6.4.1
Release: 4%{?dist} Release: 1%{?dist}
# The file ${SAGE_ROOT}/COPYING.txt is the upstream license breakdown file # The file ${SAGE_ROOT}/COPYING.txt is the upstream license breakdown file
# Additionally, every $files section has a comment with the license name # Additionally, every $files section has a comment with the license name
# before files with that license # 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 Source0: http://boxen.math.washington.edu/home/%{name}/sage-mirror/src/sage-%{version}.tar.gz
Source1: gprc.expect Source1: gprc.expect
Source2: makecmds.sty 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 # 1. scons ignores most environment variables
# 2. scons 2.2* does not have soname support (expected for scons 2.3*) # 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 # Set of patches to work with system wide packages
Patch2: %{name}-scripts.patch Patch2: %{name}-scripts.patch
# Adapt to ntl 6.0.0.
Patch3: %{name}-ntl6.patch
# remove call to not implemented sagemath "is_package_installed" interfaces # remove call to not implemented sagemath "is_package_installed" interfaces
# need to package coin-or solver in fedora # need to package coin-or solver in fedora
# remove check for non free solvers # remove check for non free solvers
Patch4: %{name}-extensions.patch Patch3: %{name}-extensions.patch
# helper to: # helper to:
# o respect a DESTDIR environment variable # 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 # o minor change to help in incremental builds by avoiding rebuilding
# files # files
# o do not assume there is an installed sagemath # o do not assume there is an installed sagemath
Patch5: %{name}-rpmbuild.patch Patch4: %{name}-rpmbuild.patch
# build documentation in buildroot environment # build documentation in buildroot environment
Patch6: %{name}-sagedoc.patch Patch5: %{name}-sagedoc.patch
# sage notebook rpm and system environment adjustments # 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 # do not attempt to create state files in system directories
Patch8: %{name}-readonly.patch Patch7: %{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
# do not link explicitly to png12 # do not link explicitly to png12
Patch10: %{name}-png.patch Patch8: %{name}-png.patch
# work with all maxima-runtime lisp backend packages # 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 # 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://trac.sagemath.org/sage_trac/ticket/12992
# http://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=1317 # 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 # use jmol itself to export preview images
# FIXME besides not using X and told so, fails if DISPLAY is not set # 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 # only cremona mini database built and installed
# FIXME add a package with the full cremona database # FIXME add a package with the full cremona database
# FIXME actually it should be already available in pari-elldata # FIXME actually it should be already available in pari-elldata
Patch15: %{name}-cremona.patch Patch13: %{name}-cremona.patch
# lrslib is a requires # lrslib is a requires
Patch16: %{name}-lrslib.patch Patch14: %{name}-lrslib.patch
# nauty cannot be packaged due to license restrictions # nauty cannot be packaged due to license restrictions
# http://cs.anu.edu.au/~bdm/nauty/ # http://cs.anu.edu.au/~bdm/nauty/
# http://pallini.di.uniroma1.it/ # http://pallini.di.uniroma1.it/
Patch17: %{name}-nauty.patch Patch15: %{name}-nauty.patch
# gap hap package not (yet) available # gap hap package not (yet) available
# http://www-gap.mcs.st-and.ac.uk/Packages/hap.html # http://www-gap.mcs.st-and.ac.uk/Packages/hap.html
Patch18: %{name}-gap-hap.patch Patch16: %{name}-gap-hap.patch
# enable lrcalc # enable lrcalc
Patch19: %{name}-lrcalc.patch Patch17: %{name}-lrcalc.patch
# enable cbc # enable cbc
Patch20: %{name}-cbc.patch Patch18: %{name}-cbc.patch
# Use system gap directories # Use system gap directories
Patch21: %{name}-libgap.patch Patch19: %{name}-libgap.patch
# enable fes # enable fes
Patch22: %{name}-fes.patch Patch20: %{name}-fes.patch
# enable cryptominisat # enable cryptominisat
Patch23: %{name}-cryptominisat.patch Patch21: %{name}-cryptominisat.patch
# Side effect of using distro packages # Side effect of using distro packages
# https://bugzilla.redhat.com/show_bug.cgi?id=974769 # https://bugzilla.redhat.com/show_bug.cgi?id=974769
Patch24: %{name}-sympy.patch Patch22: %{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
BuildRequires: 4ti2 BuildRequires: 4ti2
BuildRequires: atlas-devel BuildRequires: atlas-devel
@ -163,7 +145,7 @@ BuildRequires: cddlib-tools
BuildRequires: cliquer-devel BuildRequires: cliquer-devel
BuildRequires: coin-or-Cbc-devel BuildRequires: coin-or-Cbc-devel
BuildRequires: cryptominisat-devel BuildRequires: cryptominisat-devel
BuildRequires: Cython BuildRequires: Cython >= 0.21.1
BuildRequires: desktop-file-utils BuildRequires: desktop-file-utils
BuildRequires: dos2unix BuildRequires: dos2unix
BuildRequires: dvipng BuildRequires: dvipng
@ -611,18 +593,13 @@ popd
%patch17 %patch17
%patch18 %patch18
%patch19 %patch19
%patch20
%patch21
%if %{have_fes} %if %{have_fes}
%patch22 %patch20
%endif %endif
%patch23 %patch21
%patch24 %patch22
%patch25
%patch26
sed -e 's|@@SAGE_ROOT@@|%{SAGE_ROOT}|' \ sed -e 's|@@SAGE_ROOT@@|%{SAGE_ROOT}|' \
-e 's|@@SAGE_DOC@@|%{SAGE_DOC}|' \ -e 's|@@SAGE_DOC@@|%{SAGE_DOC}|' \
@ -687,7 +664,9 @@ pushd src/c_lib
-e 's|@@optflags@@|%{optflags}|g' \ -e 's|@@optflags@@|%{optflags}|g' \
-e "s|@@__global_ldflags@@|$ldflags|g" \ -e "s|@@__global_ldflags@@|$ldflags|g" \
-i SConstruct -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 ln -s libcsage.so.0 libcsage.so
popd popd
pushd src/sage/libs/mpmath pushd src/sage/libs/mpmath
@ -757,19 +736,22 @@ popd
pushd build/pkgs/sagenb/src/%{sagenb_pkg} pushd build/pkgs/sagenb/src/%{sagenb_pkg}
rm -f %{buildroot}%{python_sitearch}/sagenb/data/sage3d/sage3d rm -f %{buildroot}%{python_sitearch}/sagenb/data/sage3d/sage3d
python setup.py install --root=%{buildroot} --install-purelib=%{python_sitearch} python setup.py install --root=%{buildroot} --install-purelib=%{python_sitearch}
# jmol # jmol
rm -fr %{buildroot}%{python_sitearch}/sagenb/data/jmol ### FIXME waiting on https://bugzilla.redhat.com/show_bug.cgi?id=1108060
mkdir -p %{buildroot}%{python_sitearch}/sagenb/data/jmol/appletweb # To get it to work you need to get the sagemath jmol spkg or an
pushd %{buildroot}%{python_sitearch}/sagenb/data/jmol # upstream sagemath install, example:
cp -fa %{SOURCE3} %{SOURCE4} appletweb # cp -fr ~/sage-6.4.1-x86_64-Linux/local/share/jmol /usr/share/sagemath
popd # 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 # sage3d
rm -f %{buildroot}%{_bindir}/sage3d rm -f %{buildroot}%{_bindir}/sage3d
%if %{with_sage3d} %if %{with_sage3d}
ln -sf %{SAGE_LOCAL}/bin/sage3d %{buildroot}%{python_sitearch}/sagenb/data/sage3d/sage3d ln -sf %{SAGE_LOCAL}/bin/sage3d %{buildroot}%{python_sitearch}/sagenb/data/sage3d/sage3d
%endif %endif
# flask stuff not installed
cp -ar flask_version %{buildroot}%{python_sitearch}/sagenb
ln -sf %{python_sitearch}/sagenb %{buildroot}%{SAGE_SRC}/sagenb ln -sf %{python_sitearch}/sagenb %{buildroot}%{SAGE_SRC}/sagenb
popd popd
@ -1081,9 +1063,6 @@ rm %{buildroot}%{python_sitearch}/sagenb/translations/*/LC_MESSAGES/*.po
rm -r %{buildroot}%{python_sitearch}/sagenb/data/sage3d rm -r %{buildroot}%{python_sitearch}/sagenb/data/sage3d
%endif %endif
# remove cache files
rm -r %{buildroot}%{python_sitearch}/sagenb/data/.webassets-cache
# remove sage_setup # remove sage_setup
rm -r %{buildroot}%{python_sitearch}/sage_setup rm -r %{buildroot}%{python_sitearch}/sage_setup
@ -1099,23 +1078,6 @@ exit 0
/sbin/ldconfig /sbin/ldconfig
exit 0 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 %post sagetex
%{_bindir}/mktexlsr %{_bindir}/mktexlsr
exit 0 exit 0
@ -1188,7 +1150,6 @@ exit 0
%{SAGE_ETC}/maxima %{SAGE_ETC}/maxima
%{SAGE_ETC}/mwrank %{SAGE_ETC}/mwrank
%{SAGE_ETC}/pari %{SAGE_ETC}/pari
%{SAGE_ETC}/singular
#------------------------------------------------------------------------ #------------------------------------------------------------------------
%files data-graphs %files data-graphs
@ -1270,7 +1231,8 @@ exit 0
# ASL 2.0 # ASL 2.0
%{python_sitearch}/sagenb/data/highlight %{python_sitearch}/sagenb/data/highlight
# LGPLv2+ # LGPLv2+
%{python_sitearch}/sagenb/data/jmol %{SAGE_SHARE}/jmol/
%{SAGE_SHARE}/jsmol/
# (MIT or GPLv2) and (MIT and BSD and GPL) # (MIT or GPLv2) and (MIT and BSD and GPL)
%{python_sitearch}/sagenb/data/jquery %{python_sitearch}/sagenb/data/jquery
# (MIT or GPLv2) and (MIT and BSD and GPL) # (MIT or GPLv2) and (MIT and BSD and GPL)
@ -1291,8 +1253,6 @@ exit 0
%endif %endif
# LGPLv2+ # LGPLv2+
%{python_sitearch}/sagenb/data/tiny_mce %{python_sitearch}/sagenb/data/tiny_mce
# Auto generated files
%{python_sitearch}/sagenb/data/webassets_generated
# LGPLv2+ # LGPLv2+
%{python_sitearch}/sagenb/data/zorn %{python_sitearch}/sagenb/data/zorn
# GPLv2+ # GPLv2+
@ -1317,6 +1277,9 @@ exit 0
%dir %{python_sitearch}/sagenb/translations %dir %{python_sitearch}/sagenb/translations
%lang(cs_CZ) %{python_sitearch}/sagenb/translations/cs_CZ %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/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(pt_BR) %{python_sitearch}/sagenb/translations/pt_BR
%lang(ru_RU) %{python_sitearch}/sagenb/translations/ru_RU %lang(ru_RU) %{python_sitearch}/sagenb/translations/ru_RU
@ -1341,6 +1304,9 @@ exit 0
######################################################################## ########################################################################
%changelog %changelog
* Wed Nov 26 2014 pcpa <paulo.cesar.pereira.de.andrade@gmail.com> - 6.4.1-1
- Update to sagemath 6.4.1 (#1095282)
* Sat Nov 1 2014 pcpa <paulo.cesar.pereira.de.andrade@gmail.com> - 6.3-4 * Sat Nov 1 2014 pcpa <paulo.cesar.pereira.de.andrade@gmail.com> - 6.3-4
- Install 128x128 icon (#1157575) - Install 128x128 icon (#1157575)

2
sources
View file

@ -1 +1 @@
668f080be70ffea8d67592ca00d161eb sage-6.3.tar.gz 9e64f198f791577555344b9aaa6768a9 sage-6.4.1.tar.gz