Merge commit 'cd0b7cec80' into f22

- Update to sagemath 6.5
- Add new Catalan and Hungarian doc subpackages
- Add customizations to not need a patched pari
- Add "with docs" test build option
- Convert build conditionals to use bcond
- Correct deprecated warning when loading sagenb
- Rebuild for NTL 9.1.0

.gitignore

@@ -7,3 +7,4 @@
 /sage-6.2.tar.gz
 /sage-6.3.tar.gz
 /sage-6.4.1.tar.gz
+/sage-6.5.tar.gz

sagemath-cbc.patch

@@ -1,7 +1,7 @@
 diff -up src/module_list.py.orig src/module_list.py
---- src/module_list.py.orig	2014-11-18 15:28:48.952130767 -0200
+--- src/module_list.py.orig	2015-04-03 15:09:20.200406141 -0300
-+++ src/module_list.py	2014-11-18 15:28:57.040130873 -0200
++++ src/module_list.py	2015-04-03 15:09:39.744406890 -0300
-@@ -2168,7 +2168,7 @@ if (os.path.isfile(SAGE_INC + "/cplex.h"
+@@ -2187,7 +2187,7 @@ if (os.path.isfile(SAGE_INC + "/cplex.h"
                    libraries = ["stdc++", "cplex"])
          )
  

sagemath-cremona.patch

@@ -1,7 +1,7 @@
 diff -up src/sage/databases/cremona.py.orig src/sage/databases/cremona.py
---- src/sage/databases/cremona.py.orig	2014-11-18 15:26:03.247128579 -0200
+--- src/sage/databases/cremona.py.orig	2015-04-03 15:06:14.304399023 -0300
-+++ src/sage/databases/cremona.py	2014-11-18 15:26:16.920128759 -0200
++++ src/sage/databases/cremona.py	2015-04-03 15:06:26.792399501 -0300
-@@ -819,14 +819,9 @@ class MiniCremonaDatabase(SQLDatabase):
+@@ -820,14 +820,9 @@ class MiniCremonaDatabase(SQLDatabase):
              if N < self.largest_conductor():
                  message = "There is no elliptic curve with label " + label \
                      + " in the database"
@@ -17,7 +17,7 @@ diff -up src/sage/databases/cremona.py.orig src/sage/databases/cremona.py
              raise ValueError(message)
          ainvs = eval(c[0])
          data = {'cremona_label': label,
-@@ -1669,10 +1664,12 @@ def CremonaDatabase(name=None,mini=None,
+@@ -1670,10 +1665,12 @@ def CremonaDatabase(name=None,mini=None,
      if name is None and not set_global:
          return _db
      if set_global and name is None:

sagemath-cryptominisat.patch

@@ -1,7 +1,7 @@
 diff -up src/module_list.py.orig src/module_list.py
---- src/module_list.py.orig	2014-11-18 15:30:01.952131730 -0200
+--- src/module_list.py.orig	2015-04-03 15:11:09.304410319 -0300
-+++ src/module_list.py	2014-11-18 15:30:08.968131823 -0200
++++ src/module_list.py	2015-04-03 15:11:18.304410664 -0300
-@@ -2177,7 +2177,7 @@ if 1:
+@@ -2196,7 +2196,7 @@ if 1:
          )
  
  

sagemath-extensions.patch

@@ -1,7 +1,7 @@
 diff -up src/module_list.py.orig src/module_list.py
---- src/module_list.py.orig	2014-11-18 13:23:35.915031576 -0200
+--- src/module_list.py.orig	2015-04-03 14:55:11.184373629 -0300
-+++ src/module_list.py	2014-11-18 13:23:46.515031716 -0200
++++ src/module_list.py	2015-04-03 14:55:20.536373988 -0300
-@@ -2126,7 +2126,8 @@ ext_modules = [
+@@ -2145,7 +2145,8 @@ ext_modules = [
  # These extensions are to be compiled only if the
  # corresponding packages have been installed
  

sagemath-fes.patch

@@ -1,7 +1,7 @@
 diff -up src/module_list.py.orig src/module_list.py
---- src/module_list.py.orig	2014-11-18 15:29:30.360131313 -0200
+--- src/module_list.py.orig	2015-04-03 15:10:36.432409060 -0300
-+++ src/module_list.py	2014-11-18 15:29:37.432131407 -0200
++++ src/module_list.py	2015-04-03 15:10:46.240409436 -0300
-@@ -2130,7 +2130,7 @@ ext_modules = [
+@@ -2149,7 +2149,7 @@ ext_modules = [
  def is_package_installed(name):
      return False
  

sagemath-gap-hap.patch

@@ -1,7 +1,7 @@
 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	2014-11-18 15:27:46.545129943 -0200
+--- src/sage/groups/perm_gps/permgroup.py.orig	2015-04-03 15:08:05.769403291 -0300
-+++ src/sage/groups/perm_gps/permgroup.py	2014-11-18 15:27:53.760130038 -0200
++++ src/sage/groups/perm_gps/permgroup.py	2015-04-03 15:08:15.296403656 -0300
-@@ -180,8 +180,7 @@ def hap_decorator(f):
+@@ -181,8 +181,7 @@ def hap_decorator(f):
      """
      @wraps(f)
      def wrapped(self, n, p=0):
@@ -11,7 +11,7 @@ diff -up src/sage/groups/perm_gps/permgroup.py.orig src/sage/groups/perm_gps/per
          load_hap()
          from sage.rings.arith import is_prime
          if not (p == 0 or is_prime(p)):
-@@ -3979,8 +3978,7 @@ class PermutationGroup_generic(group.Gro
+@@ -3943,8 +3942,7 @@ class PermutationGroup_generic(group.Gro
  
          - David Joyner and Graham Ellis
          """

sagemath-libgap.patch

@@ -1,7 +1,7 @@
 diff -up src/sage/libs/gap/util.pyx.orig src/sage/libs/gap/util.pyx
---- src/sage/libs/gap/util.pyx.orig	2014-02-07 12:44:48.769857619 -0200
+--- src/sage/libs/gap/util.pyx.orig	2015-04-03 15:10:03.911407815 -0300
-+++ src/sage/libs/gap/util.pyx	2014-02-07 12:45:27.743859112 -0200
++++ src/sage/libs/gap/util.pyx	2015-04-03 15:10:13.247408173 -0300
-@@ -155,18 +155,9 @@ def gap_root():
+@@ -153,18 +153,9 @@ def gap_root():
  
          sage: from sage.libs.gap.util import gap_root
          sage: gap_root()   # random output

sagemath-lrcalc.patch

@@ -1,7 +1,7 @@
 diff -up src/module_list.py.orig src/module_list.py
---- src/module_list.py.orig	2014-11-18 15:28:17.313130349 -0200
+--- src/module_list.py.orig	2015-04-03 15:08:44.096404759 -0300
-+++ src/module_list.py	2014-11-18 15:28:24.520130444 -0200
++++ src/module_list.py	2015-04-03 15:08:56.856405247 -0300
-@@ -2210,7 +2210,7 @@ if UNAME[0] == "Darwin" and not UNAME[2]
+@@ -2229,7 +2229,7 @@ if UNAME[0] == "Darwin" and not UNAME[2]
          )
  
  

sagemath-lrslib.patch

@@ -1,7 +1,7 @@
 diff -up src/sage/geometry/polyhedron/base.py.orig src/sage/geometry/polyhedron/base.py
---- src/sage/geometry/polyhedron/base.py.orig	2014-11-18 15:26:45.817129141 -0200
+--- src/sage/geometry/polyhedron/base.py.orig	2015-04-03 15:06:44.704400187 -0300
-+++ src/sage/geometry/polyhedron/base.py	2014-11-18 15:26:53.185129238 -0200
++++ src/sage/geometry/polyhedron/base.py	2015-04-03 15:06:59.632400758 -0300
-@@ -3515,11 +3515,6 @@ class Polyhedron_base(Element):
+@@ -3242,11 +3242,6 @@ class Polyhedron_base(Element):
  
               David Avis's lrs program.
          """

sagemath-maxima.patch

@@ -1,6 +1,6 @@
 diff -up src/bin/sage-maxima.lisp.orig src/bin/sage-maxima.lisp
---- src/bin/sage-maxima.lisp.orig	2014-08-12 14:11:32.329958121 -0300
+--- src/bin/sage-maxima.lisp.orig	2015-04-03 15:04:30.952395065 -0300
-+++ src/bin/sage-maxima.lisp	2014-08-12 14:11:38.922958374 -0300
++++ src/bin/sage-maxima.lisp	2015-04-03 15:04:43.255395536 -0300
 @@ -3,4 +3,8 @@
  ;(setf *general-display-prefix* "<sage-display>")
  
@@ -12,9 +12,9 @@ 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	2014-08-12 14:11:20.722957677 -0300
+--- src/sage/interfaces/maxima.py.orig	2015-04-03 15:04:24.152394805 -0300
-+++ src/sage/interfaces/maxima.py	2014-08-12 14:11:38.923958374 -0300
++++ src/sage/interfaces/maxima.py	2015-04-03 15:04:43.256395536 -0300
-@@ -544,7 +544,7 @@ class Maxima(MaximaAbstract, Expect):
+@@ -551,7 +551,7 @@ class Maxima(MaximaAbstract, Expect):
          Expect.__init__(self,
                          name = 'maxima',
                          prompt = '\(\%i[0-9]+\) ',
@@ -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,
-@@ -594,7 +594,8 @@ class Maxima(MaximaAbstract, Expect):
+@@ -601,7 +601,8 @@ class Maxima(MaximaAbstract, Expect):
  
          # Remove limit on the max heapsize (since otherwise it defaults
          # to 256MB with ECL).

sagemath-nauty.patch

@@ -1,7 +1,7 @@
 diff -up src/sage/graphs/graph_generators.py.orig src/sage/graphs/graph_generators.py
---- src/sage/graphs/graph_generators.py.orig	2014-11-18 15:27:15.584129534 -0200
+--- src/sage/graphs/graph_generators.py.orig	2015-04-03 15:07:35.008402113 -0300
-+++ src/sage/graphs/graph_generators.py	2014-11-18 15:27:23.352129636 -0200
++++ src/sage/graphs/graph_generators.py	2015-04-03 15:07:44.816402489 -0300
-@@ -833,7 +833,7 @@ class GraphGenerators():
+@@ -827,7 +827,7 @@ class GraphGenerators():
          """
          import subprocess
          from sage.misc.package import is_package_installed

sagemath-parallel.patch

@@ -0,0 +1,15 @@
+diff -up src/module_list.py.orig src/module_list.py
+--- src/module_list.py.orig	2015-04-03 15:39:22.360475152 -0300
++++ src/module_list.py	2015-04-03 15:39:37.470475731 -0300
+@@ -2110,11 +2110,6 @@ ext_modules = [
+     Extension('sage.tests.interrupt',
+               sources = ['sage/tests/interrupt.pyx', 'sage/tests/c_lib.c']),
+ 
+-    Extension('sage.tests.parallel',
+-              sources = ['sage/tests/parallel.pyx'],
+-              extra_compile_args=["-fopenmp"],
+-              extra_link_args=["-fopenmp"]),
+-
+     Extension('sage.tests.stl_vector',
+               sources = ['sage/tests/stl_vector.pyx'],
+               libraries = ['gmp'],

sagemath-pari.patch

@@ -1,6 +1,68 @@
+diff -up src/sage/libs/pari/decl.pxi.orig src/sage/libs/pari/decl.pxi
+--- src/sage/libs/pari/decl.pxi.orig	2015-04-03 17:09:59.840683372 -0300
++++ src/sage/libs/pari/decl.pxi	2015-04-03 17:10:10.876683795 -0300
+@@ -165,7 +165,6 @@ cdef extern from 'parisage.h':
+     extern int new_galois_format, precdl
+     # The "except 0" here is to ensure compatibility with
+     # _pari_err_handle() in handle_error.pyx
+-    extern int (*cb_pari_err_handle)(GEN) except 0
+     extern int (*cb_pari_handle_exception)(long) except 0
+     extern void (*cb_pari_err_recover)(long)
+ 
+@@ -3757,6 +3756,3 @@ cdef extern from 'pari/paripriv.h':
+         unsigned long flags
+     
+     extern gp_data* GP_DATA
+-
+-cdef extern from 'pari/anal.h':
+-    char* closure_func_err()
+diff -up src/sage/libs/pari/handle_error.pyx.orig src/sage/libs/pari/handle_error.pyx
+--- src/sage/libs/pari/handle_error.pyx.orig	2015-04-03 17:09:59.842683372 -0300
++++ src/sage/libs/pari/handle_error.pyx	2015-04-03 17:10:10.876683795 -0300
+@@ -131,13 +131,13 @@ cdef void _pari_init_error_handling():
+         sage: pari('warning("test")')
+           ***   user warning: test
+     """
+-    global cb_pari_err_handle
++    global cb_pari_handle_exception
+     global cb_pari_err_recover
+-    cb_pari_err_handle = _pari_err_handle
++    cb_pari_handle_exception = _pari_handle_exception
+     cb_pari_err_recover = _pari_err_recover
+ 
+ 
+-cdef int _pari_err_handle(GEN E) except 0:
++cdef int _pari_handle_exception(long errnum_unused) except 0:
+     """
+     Convert a PARI error into a Sage exception, unless the error was
+     a stack overflow, in which case we enlarge the stack.
+@@ -156,6 +156,7 @@ cdef int _pari_err_handle(GEN E) except
+         PariError: impossible inverse in gdiv: 0
+ 
+     """
++    cdef GEN E = pari_err_last()
+     cdef long errnum = E[1]
+     if errnum == e_STACK:
+         # PARI is out of memory.  We double the size of the PARI stack
+@@ -165,15 +166,10 @@ cdef int _pari_err_handle(GEN E) except
+ 
+     sig_block()
+     cdef char* errstr
+-    cdef char* s
+     try:
+         errstr = pari_err2str(E)
+         pari_error_string = errstr.decode('ascii')
+ 
+-        s = closure_func_err()
+-        if s is not NULL:
+-            pari_error_string = s.decode('ascii') + ": " + pari_error_string
+-
+         raise PariError(errnum, pari_error_string, pari_instance.new_gen_noclear(E))
+     finally:
+         pari_free(errstr)
 diff -up src/sage/libs/pari/pari_instance.pxd.orig src/sage/libs/pari/pari_instance.pxd
---- src/sage/libs/pari/pari_instance.pxd.orig	2014-11-18 15:25:03.591127791 -0200
+--- src/sage/libs/pari/pari_instance.pxd.orig	2015-04-03 17:09:59.834683372 -0300
-+++ src/sage/libs/pari/pari_instance.pxd	2014-11-18 15:25:18.999127995 -0200
++++ src/sage/libs/pari/pari_instance.pxd	2015-04-03 17:10:10.874683795 -0300
 @@ -6,6 +6,10 @@ cimport cython
  
  from sage.libs.pari.gen cimport gen
@@ -13,9 +75,9 @@ diff -up src/sage/libs/pari/pari_instance.pxd.orig src/sage/libs/pari/pari_insta
  
  @cython.final
 diff -up src/sage/libs/pari/pari_instance.pyx.orig src/sage/libs/pari/pari_instance.pyx
---- src/sage/libs/pari/pari_instance.pyx.orig	2014-11-18 15:25:16.287127959 -0200
+--- src/sage/libs/pari/pari_instance.pyx.orig	2015-04-03 17:09:59.835683372 -0300
-+++ src/sage/libs/pari/pari_instance.pyx	2014-11-18 15:25:19.000127995 -0200
++++ src/sage/libs/pari/pari_instance.pyx	2015-04-03 17:10:10.874683795 -0300
-@@ -437,7 +437,12 @@ cdef class PariInstance(sage.structure.p
+@@ -417,7 +417,12 @@ cdef class PariInstance(sage.structure.p
          # The size here doesn't really matter, because we will allocate
          # our own stack anyway. We ask PARI not to set up signal and
          # error handlers.
@@ -28,3 +90,13 @@ diff -up src/sage/libs/pari/pari_instance.pyx.orig src/sage/libs/pari/pari_insta
  
          _pari_init_error_handling()
  
+diff -up src/sage/libs/pari/handle_error.pxd.orig src/sage/libs/pari/handle_error.pxd
+--- src/sage/libs/pari/handle_error.pxd.orig	2015-04-03 17:14:16.506693201 -0300
++++ src/sage/libs/pari/handle_error.pxd	2015-04-03 17:14:44.287694265 -0300
+@@ -1,5 +1,5 @@
+ include 'sage/libs/pari/decl.pxi'
+ 
+ cdef void _pari_init_error_handling()
+-cdef int _pari_err_handle(GEN E) except 0
++cdef int _pari_handle_exception(long errnum_unused) except 0
+ cdef void _pari_err_recover(long errnum)

sagemath-png.patch

@@ -1,7 +1,7 @@
 diff -up src/module_list.py.orig src/module_list.py
---- src/module_list.py.orig	2014-11-18 15:23:33.184126598 -0200
+--- src/module_list.py.orig	2015-04-03 15:03:27.647392641 -0300
-+++ src/module_list.py	2014-11-18 15:23:42.856126725 -0200
++++ src/module_list.py	2015-04-03 15:03:57.589393787 -0300
-@@ -1081,7 +1081,7 @@ ext_modules = [
+@@ -1097,7 +1097,7 @@ ext_modules = [
  
      Extension('sage.matrix.matrix_mod2_dense',
                sources = ['sage/matrix/matrix_mod2_dense.pyx'],
@@ -10,7 +10,7 @@ diff -up src/module_list.py.orig src/module_list.py
                extra_compile_args = m4ri_extra_compile_args,
                depends = [SAGE_INC + "/png.h", SAGE_INC + "/m4ri/m4ri.h"]),
  
-@@ -1379,7 +1379,7 @@ ext_modules = [
+@@ -1398,7 +1398,7 @@ ext_modules = [
  
      Extension('sage.modules.vector_mod2_dense',
                sources = ['sage/modules/vector_mod2_dense.pyx'],
@@ -19,12 +19,12 @@ diff -up src/module_list.py.orig src/module_list.py
                extra_compile_args = m4ri_extra_compile_args,
                depends = [SAGE_INC + "/png.h", SAGE_INC + "/m4ri/m4ri.h"]),
  
-@@ -1893,7 +1893,7 @@ ext_modules = [
+@@ -1912,7 +1912,7 @@ ext_modules = [
      Extension('sage.rings.polynomial.pbori',
                sources = ['sage/rings/polynomial/pbori.pyx'],
                libraries=['polybori-' + polybori_major_version,
--                         'polybori_groebner-' + polybori_major_version, 'm4ri', 'png12'],
+-                         'polybori_groebner-' + polybori_major_version, 'm4ri', 'gd', 'png12'],
-+                         'polybori_groebner-' + polybori_major_version, 'm4ri', 'png'],
++                         'polybori_groebner-' + polybori_major_version, 'm4ri', 'gd', 'png'],
                include_dirs = [SAGE_INC, "sage/libs/polybori"],
                depends = [SAGE_INC + "/polybori/" + hd + ".h" for hd in ["polybori", "config"] ] + \
                          [SAGE_INC + '/m4ri/m4ri.h'],

sagemath-readonly.patch

@@ -1,7 +1,7 @@
 diff -up src/sage/all.py.orig src/sage/all.py
---- src/sage/all.py.orig	2014-11-18 15:20:50.327124447 -0200
+--- src/sage/all.py.orig	2015-04-03 15:01:52.463388996 -0300
-+++ src/sage/all.py	2014-11-18 15:20:58.279124552 -0200
++++ src/sage/all.py	2015-04-03 15:02:06.559389536 -0300
-@@ -307,11 +307,11 @@ def _write_started_file():
+@@ -296,11 +296,11 @@ def _write_started_file():
  
      Check that the file exists when Sage is running::
  

sagemath-rpmbuild.patch

@@ -1,6 +1,6 @@
 diff -up src/module_list.py.orig src/module_list.py
---- src/module_list.py.orig	2014-11-18 13:25:41.898033239 -0200
+--- src/module_list.py.orig	2015-04-03 14:55:44.607374909 -0300
-+++ src/module_list.py	2014-11-18 13:27:10.616034410 -0200
++++ src/module_list.py	2015-04-03 14:56:03.416375630 -0300
 @@ -4,7 +4,7 @@ import os
  from distutils.extension import Extension
  from sage.env import SAGE_LOCAL
@@ -33,7 +33,7 @@ diff -up src/module_list.py.orig src/module_list.py
  polybori_major_version = '0.8'
  
  
-@@ -730,7 +731,7 @@ ext_modules = [
+@@ -746,7 +747,7 @@ ext_modules = [
                sources = ['sage/libs/lcalc/lcalc_Lfunction.pyx'],
                libraries = ['m', 'ntl', 'mpfr', 'gmp', 'gmpxx',
                             'Lfunction'],
@@ -43,8 +43,8 @@ diff -up src/module_list.py.orig src/module_list.py
                language = 'c++'),
  
 diff -up src/setup.py.orig src/setup.py
---- src/setup.py.orig	2014-11-18 13:25:47.434033312 -0200
+--- src/setup.py.orig	2015-04-03 14:56:00.033375500 -0300
-+++ src/setup.py	2014-11-18 13:28:52.152035751 -0200
++++ src/setup.py	2015-04-03 14:56:03.416375630 -0300
 @@ -36,11 +36,11 @@ except KeyError:
      compile_result_dir = None
      keep_going = False

sagemath-sagedoc.patch

@@ -1,6 +1,6 @@
 diff -up src/doc/common/builder.py.orig src/doc/common/builder.py
---- src/doc/common/builder.py.orig	2014-11-18 13:30:43.238037217 -0200
+--- src/doc/common/builder.py.orig	2015-04-03 14:56:53.775377558 -0300
-+++ src/doc/common/builder.py	2014-11-18 13:32:05.097038298 -0200
++++ src/doc/common/builder.py	2015-04-03 14:56:58.208377728 -0300
 @@ -32,7 +32,7 @@ from sage.env import SAGE_DOC, SAGE_SRC
  #     SAGE_DOC, LANGUAGES, SPHINXOPTS, PAPER, OMIT,
  #     PAPEROPTS, ALLSPHINXOPTS, NUM_THREADS, WEBSITESPHINXOPTS
@@ -11,8 +11,8 @@ diff -up src/doc/common/builder.py.orig src/doc/common/builder.py
  
  
 diff -up src/doc/common/conf.py.orig src/doc/common/conf.py
---- src/doc/common/conf.py.orig	2014-11-18 13:30:43.248037218 -0200
+--- src/doc/common/conf.py.orig	2015-04-03 14:56:53.777377558 -0300
-+++ src/doc/common/conf.py	2014-11-18 13:32:40.336038763 -0200
++++ src/doc/common/conf.py	2015-04-03 14:56:58.208377728 -0300
 @@ -1,5 +1,5 @@
  import sys, os, sphinx
 -from sage.env import SAGE_DOC
@@ -31,8 +31,8 @@ diff -up src/doc/common/conf.py.orig src/doc/common/conf.py
  
      # It would be really nice if sphinx would copy the entire mathjax directory,
 diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
---- src/sage/doctest/control.py.orig	2014-11-18 13:30:43.259037218 -0200
+--- src/sage/doctest/control.py.orig	2015-04-03 14:56:32.065376727 -0300
-+++ src/sage/doctest/control.py	2014-11-18 13:33:27.185039382 -0200
++++ src/sage/doctest/control.py	2015-04-03 14:56:58.209377728 -0300
 @@ -89,7 +89,6 @@ class DocTestDefaults(SageObject):
          self.valgrind = False
          self.massif = False
@@ -50,7 +50,7 @@ diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
                  # Non-interactive debuggers: 48 hours
                  options.timeout = int(os.getenv('SAGE_TIMEOUT_VALGRIND', 48 * 60 * 60))
              elif options.long:
-@@ -889,13 +888,8 @@ class DocTestController(SageObject):
+@@ -890,13 +889,8 @@ class DocTestController(SageObject):
              elif opt.cachegrind:
                  toolname = "cachegrind"
                  flags = os.getenv("SAGE_CACHEGRIND_FLAGS", "")
@@ -64,7 +64,7 @@ diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
              if "%s" in flags:
                  flags %= toolname + ".%p" # replace %s with toolname
          cmd += flags + sage_cmd
-@@ -955,10 +949,10 @@ class DocTestController(SageObject):
+@@ -956,10 +950,10 @@ class DocTestController(SageObject):
              0
          """
          opt = self.options
@@ -78,9 +78,9 @@ diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
              return self.run_val_gdb()
          else:
 diff -up src/sage/interfaces/singular.py.orig src/sage/interfaces/singular.py
---- src/sage/interfaces/singular.py.orig	2014-11-18 13:30:43.265037218 -0200
+--- src/sage/interfaces/singular.py.orig	2015-04-03 14:56:32.066376727 -0300
-+++ src/sage/interfaces/singular.py	2014-11-18 13:33:49.257039673 -0200
++++ src/sage/interfaces/singular.py	2015-04-03 14:56:58.210377728 -0300
-@@ -2147,7 +2147,7 @@ def generate_docstring_dictionary():
+@@ -2149,7 +2149,7 @@ def generate_docstring_dictionary():
      nodes.clear()
      node_names.clear()
  

sagemath-sagenb.patch

@@ -1,6 +1,6 @@
-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
+diff -up build/pkgs/sagenb/src/sagenb-0.11.4/sagenb/flask_version/base.py.orig build/pkgs/sagenb/src/sagenb-0.11.4/sagenb/flask_version/base.py
---- build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/flask_version/base.py.orig	2014-12-06 17:45:36.063723826 -0200
+--- build/pkgs/sagenb/src/sagenb-0.11.4/sagenb/flask_version/base.py.orig	2015-04-03 14:57:55.335379915 -0300
-+++ build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/flask_version/base.py	2014-12-06 17:49:09.074731983 -0200
++++ build/pkgs/sagenb/src/sagenb-0.11.4/sagenb/flask_version/base.py	2015-04-03 14:59:22.805383265 -0300
 @@ -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
@@ -37,23 +37,23 @@ diff -up build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/flask_version/base.py.orig b
          import mimetypes
          mimetypes.add_type('text/plain','.jmol')
  
-diff -up build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/misc/misc.py.orig build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/misc/misc.py
+diff -up build/pkgs/sagenb/src/sagenb-0.11.4/sagenb/misc/misc.py.orig build/pkgs/sagenb/src/sagenb-0.11.4/sagenb/misc/misc.py
---- build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/misc/misc.py.orig	2014-12-06 17:45:36.066723826 -0200
+--- build/pkgs/sagenb/src/sagenb-0.11.4/sagenb/misc/misc.py.orig	2015-04-03 14:58:07.335380375 -0300
-+++ build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/misc/misc.py	2014-12-06 17:45:38.853723933 -0200
++++ build/pkgs/sagenb/src/sagenb-0.11.4/sagenb/misc/misc.py	2015-04-03 14:59:36.461383788 -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
++import sage.env
-+DATA = os.path.join(SAGE_SRC, 'sagenb', 'data')
++DATA = os.path.join(sage.env.SAGE_SRC, 'sagenb', 'data')
  
  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
+diff -up build/pkgs/sagenb/src/sagenb-0.11.4/sagenb/notebook/cell.py.orig build/pkgs/sagenb/src/sagenb-0.11.4/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-0.11.4/sagenb/notebook/cell.py.orig	2015-04-03 14:58:19.246380831 -0300
-+++ build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/notebook/cell.py	2014-12-06 17:45:38.854723933 -0200
++++ build/pkgs/sagenb/src/sagenb-0.11.4/sagenb/notebook/cell.py	2015-04-03 15:00:09.605385057 -0300
-@@ -2338,8 +2338,8 @@ class Cell(Cell_generic):
+@@ -2340,8 +2340,8 @@ class Cell(Cell_generic):
              with open(jmol_name, 'r') as f:
                  jmol_script = f.read()
              jmol_script = jmol_script.replace(
@@ -64,9 +64,9 @@ diff -up build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/notebook/cell.py.orig build/
              with open(jmol_name, 'w') as f:
                  f.write(jmol_script)
   
-diff -up build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/notebook/run_notebook.py.orig build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/notebook/run_notebook.py
+diff -up build/pkgs/sagenb/src/sagenb-0.11.4/sagenb/notebook/run_notebook.py.orig build/pkgs/sagenb/src/sagenb-0.11.4/sagenb/notebook/run_notebook.py
---- build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/notebook/run_notebook.py.orig	2014-12-06 17:45:36.069723826 -0200
+--- build/pkgs/sagenb/src/sagenb-0.11.4/sagenb/notebook/run_notebook.py.orig	2015-04-03 14:58:32.839381352 -0300
-+++ build/pkgs/sagenb/src/sagenb-0.11.1/sagenb/notebook/run_notebook.py	2014-12-06 17:45:38.854723933 -0200
++++ build/pkgs/sagenb/src/sagenb-0.11.4/sagenb/notebook/run_notebook.py	2015-04-03 15:01:22.725387857 -0300
 @@ -46,12 +46,14 @@ sagenb.notebook.misc.DIR = %(cwd)r #We s
  # Flask #
  #########

sagemath-scons.patch

@@ -1,6 +1,6 @@
 diff -up src/c_lib/SConstruct.orig src/c_lib/SConstruct
---- src/c_lib/SConstruct.orig	2014-11-17 17:41:32.525922611 -0200
+--- src/c_lib/SConstruct.orig	2015-04-03 14:44:19.695348682 -0300
-+++ src/c_lib/SConstruct	2014-11-17 17:41:41.486922954 -0200
++++ src/c_lib/SConstruct	2015-04-03 14:44:30.359349090 -0300
 @@ -126,8 +126,8 @@ env['PYV']=platform.python_version().rsp
  # The SCons convenience function Split is the only strange thing
  # to python programmers. It just makes a list by splitting on
@@ -10,7 +10,7 @@ diff -up src/c_lib/SConstruct.orig src/c_lib/SConstruct
 +includes = ['@@includedir@@', '@@includedir@@/python$PYV/',
 +            '@@includedir@@/NTL/', 'include']
  cFiles = Split( "convert.c  interrupt.c  memory.c  mpn_pylong.c  mpz_pylong.c") + \
-          Split( "mpz_longlong.c stdsage.c  gmp_globals.c" )
+          Split( "mpz_longlong.c stdsage.c" )
  cppFiles = Split( "ZZ_pylong.cpp  ntl_wrap.cpp" )
 @@ -136,9 +136,22 @@ incFiles = Split( "ccobject.h  convert.h
             Split( "interrupt.h  memory.h  mpn_pylong.h  mpz_longlong.h" ) + \

sagemath-scripts.patch

@@ -1,6 +1,6 @@
 diff -up src/bin/sage.orig src/bin/sage
---- src/bin/sage.orig	2014-11-17 17:42:48.321925514 -0200
+--- src/bin/sage.orig	2015-04-03 14:45:35.718351593 -0300
-+++ src/bin/sage	2014-11-17 17:55:52.524955544 -0200
++++ src/bin/sage	2015-04-03 14:54:09.029371249 -0300
 @@ -13,11 +13,9 @@ usage() {
      echo "  file.[sage|py|spyx] -- run given .sage, .py or .spyx file"
      echo "  -advanced           -- list all command line options"
@@ -32,16 +32,18 @@ diff -up src/bin/sage.orig src/bin/sage
      echo "  -v, -version        -- print the Sage version"
      exit 0
  }
-@@ -63,8 +56,6 @@ usage_advanced() {
+@@ -63,10 +56,7 @@ 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 "  -v, -version        -- print the Sage version"
+-    echo "  -git-branch         -- print the current git branch"
  
      echo
-@@ -75,8 +66,6 @@ usage_advanced() {
+     ####  1.......................26..................................................78
+@@ -76,8 +66,6 @@ usage_advanced() {
      echo "                         'default', 'sagenb', and 'ipython'). See the output"
      echo "                         of sage --notebook --help for more details and"
      echo "                         examples of how to pass optional arguments"
@@ -50,7 +52,7 @@ diff -up src/bin/sage.orig src/bin/sage
      echo "  -inotebook [...]    -- start the *insecure* Sage notebook (deprecated)"
      echo "  -n, -notebook [...] -- start the default Sage notebook (options are the"
      echo "                         same as for the notebook command in Sage).  See the"
-@@ -94,13 +83,9 @@ usage_advanced() {
+@@ -95,13 +83,9 @@ usage_advanced() {
      echo "  -gp [...]           -- run Sage's PARI/GP calculator with given arguments"
      echo "  -ipython [...]      -- run Sage's IPython using the default environment (not"
      echo "                         Sage), passing additional options to IPython"
@@ -64,7 +66,7 @@ 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"
-@@ -114,74 +99,10 @@ usage_advanced() {
+@@ -115,44 +99,7 @@ usage_advanced() {
      echo
      ####  1.......................26..................................................78
      ####  |.....................--.|...................................................|
@@ -106,32 +108,19 @@ diff -up src/bin/sage.orig src/bin/sage
 -    echo "                      -- replace failing doctests with the actual output. With"
 -    echo "                         optional output_file: redirect there. With the --long"
 -    echo "                         option: include #long time tests."
--    echo "  -startuptime [module] -- display how long each component of Sage takes to"
++    echo "Testing the Sage library:"
--    echo "                         start up; optionally specify a module to get more"
+     echo "  -startuptime [module] -- display how long each component of Sage takes to"
--    echo "                         details about that particular module"
+     echo "                         start up; optionally specify a module to get more"
--    echo "  -t [options] <--all|files|dir>"
+     echo "                         details about that particular module"
--    echo "                      -- test examples in .py, .pyx, .sage, .tex or .rst files"
+@@ -163,7 +110,6 @@ usage_advanced() {
--    echo "                         selected options:"
+     echo "                           --verbose - print debugging output during the test"
--    echo "                           --long - include lines with the phrase 'long time'"
+     echo "                           --optional - controls which optional tests are run"
--    echo "                           --verbose - print debugging output during the test"
+     echo "                           --randorder[=seed] - randomize order of tests"
--    echo "                           --optional - controls which optional tests are run"
--    echo "                           --randorder[=seed] - randomize order of tests"
 -    echo "                           --new - only test files modified since last commit"
--    echo "                           --initial - only show the first failure per block"
+     echo "                           --initial - only show the first failure per block"
--    echo "                           --debug - drop into PDB after an unexpected error"
+     echo "                           --debug - drop into PDB after an unexpected error"
--    echo "                           --failed - only test files that failed last test"
+     echo "                           --failed - only test files that failed last test"
--    echo "                           --sagenb - test all sagenb files"
+@@ -182,7 +128,6 @@ usage_advanced() {
--    echo "                           --help - show all testing options"
--    echo "                           --warn-long [timeout] - warning if doctest is slow"
--    echo "  -tp <N> [...]       -- like -t above, but tests in parallel using N threads"
--    echo "                         with 0 interpreted as a sensible default"
--    echo "  -testall [options]  -- test all source files, docs, and examples.  options"
--    echo "                         like -t"
--
--    echo
--    ####  1.......................26..................................................78
--    ####  |.....................--.|...................................................|
-     echo "Documentation:"
      echo "  -coverage <files>   -- give info about doctest coverage of files"
      echo "  -coverageall        -- give summary info about doctest coverage of all"
      echo "                         files in the Sage library"
@@ -139,13 +128,12 @@ 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"
-@@ -201,16 +122,6 @@ usage_advanced() {
+@@ -202,15 +147,6 @@ usage_advanced() {
      echo
      ####  1.......................26..................................................78
      ####  |.....................--.|...................................................|
 -    echo "Making Sage packages or distributions:"
 -    echo "  -bdist VER          -- build a binary distribution of Sage"
--    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"
 -    echo "  -sdist              -- build a source distribution of Sage"
@@ -156,7 +144,7 @@ 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 +135,6 @@ usage_advanced() {
+@@ -224,9 +160,6 @@ usage_advanced() {
      echo "  -memcheck           -- run Sage using Valgrind's memcheck tool.  The log"
      echo "                         files are named sage-memcheck.PID can be found in"
      echo "                         $DOT_SAGE"
@@ -166,7 +154,7 @@ diff -up src/bin/sage.orig src/bin/sage
      echo "  -valgrind           -- this is an alias for -memcheck"
      echo
      echo "You can also use -- before a long option, e.g., 'sage --optional'."
-@@ -246,65 +154,14 @@ if [ "$1" = '--nodotsage' ]; then
+@@ -246,34 +179,6 @@ if [ "$1" = '--nodotsage' ]; then
      exit $status
  fi
  
@@ -198,19 +186,13 @@ diff -up src/bin/sage.orig src/bin/sage
 -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
--  fi
+@@ -286,24 +191,11 @@ fi
--  if [ "$1" = "-advanced" -o "$1" = "--advanced" ]; then
--     usage_advanced
--  fi
--fi
--
- 
  # Prepare for running Sage, either interactively or non-interactively.
  sage_setup() {
--    # Check that we're not in a source tarball which hasn't been built yet (#13561).
+     # Check that we're not in a source tarball which hasn't been built yet (#13561).
 -    if [ ! -d "$SAGE_LOCAL/lib/python/site-packages/sage" ]; then
 -        echo >&2 '************************************************************************'
 -        echo >&2 'It seems that you are attempting to run Sage from an unpacked source'
@@ -232,10 +214,11 @@ 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
-@@ -315,20 +172,6 @@ sage_setup() {
+@@ -313,21 +205,6 @@ 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
@@ -253,7 +236,7 @@ diff -up src/bin/sage.orig src/bin/sage
  # Start an interactive Sage session, this function never returns.
  interactive_sage() {
      sage_setup
-@@ -390,7 +233,7 @@ fi
+@@ -389,7 +266,7 @@ fi
  
  if [ "$1" = '-singular' -o "$1" = '--singular' ]; then
      shift
@@ -262,10 +245,15 @@ diff -up src/bin/sage.orig src/bin/sage
  fi
  
  if [ "$1" = '-sqlite3' -o "$1" = '--sqlite3' ]; then
-@@ -423,11 +266,6 @@ if [ "$1" = '-kash' -o "$1" = '--kash' ]
+@@ -417,16 +294,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
-     exec kash "$@"
+     exec ecl "$@"
  fi
  
+-if [ "$1" = '-kash' -o "$1" = '--kash' ]; then
+-    shift
+-    exec kash "$@"
+-fi
+-
 -if [ "$1" = '-fixdoctests' -o "$1" = '--fixdoctests' ]; then
 -    shift
 -    exec sage-fixdoctests "$@"
@@ -274,15 +262,11 @@ diff -up src/bin/sage.orig src/bin/sage
  if [ "$1" = '-maxima' -o "$1" = '--maxima' ]; then
      shift
      exec maxima "$@"
-@@ -448,15 +286,6 @@ if [ "$1" = '-scons' -o "$1" = '--scons'
+@@ -447,11 +314,6 @@ 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
@@ -290,7 +274,24 @@ diff -up src/bin/sage.orig src/bin/sage
  if [ "$1" = '-python' -o "$1" = '--python' ]; then
      shift
      exec python "$@"
-@@ -596,20 +425,6 @@ EOF
+@@ -467,16 +329,6 @@ if [ "$1" = '-ipython' -o "$1" = '--ipyt
+     exec ipython "$@"
+ fi
+ 
+-if [ "$1" = '-git' -o "$1" = '--git' ]; then
+-    shift
+-    exec git "$@"
+-fi
+-
+-if [ "$1" = '-git-branch' -o "$1" = '--git-branch' ]; then
+-    shift
+-    exec git --git-dir="$SAGE_ROOT"/.git rev-parse --abbrev-ref HEAD
+-fi
+-
+ if [ "$1" = '-sh' -o "$1" = '--sh' ]; then
+     # AUTHORS:
+     # - Carl Witty and William Stein: initial version
+@@ -596,20 +448,6 @@ EOF
  fi
  
  #####################################################################
@@ -311,19 +312,7 @@ diff -up src/bin/sage.orig src/bin/sage
  # File conversion
  #####################################################################
  
-@@ -624,23 +439,9 @@ if [ "$1" = '-rst2sws' -o "$1" = '--rst2
+@@ -627,11 +465,6 @@ fi
- fi
- 
- #####################################################################
--# Crap
--#####################################################################
--
--if [ "$1" = "-crap" -o "$1" = "--crap" ]; then
--    shift
--    exec sage-crap $@
--fi
--
--#####################################################################
  # Run Sage's versions of the standard Algebra/Geometry etc. software
  #####################################################################
  
@@ -332,11 +321,11 @@ diff -up src/bin/sage.orig src/bin/sage
 -    sage-build "$@" || exit $?
 -}
 -
- if [[ "$1" =~ "--notebook="* || "$1" =~ "-n="* || "$1" =~ "-notebook="* ]]; then
+ if [[ "$1" =~ ^--notebook=.* || "$1" =~ ^-n=.* || "$1" =~ ^-notebook=.* ]] ; then
      sage-cleaner &>/dev/null &
      exec sage-notebook "$@"
-@@ -652,13 +453,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
+@@ -642,13 +475,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
-     exec sage-notebook --notebook=default "$@"
+     exec sage-notebook "$@"
  fi
  
 -if [ "$1" = "-bn" -o "$1" = "--build-and-notebook" ]; then
@@ -349,7 +338,7 @@ diff -up src/bin/sage.orig src/bin/sage
  if [ "$1" = "-inotebook" -o "$1" = '--inotebook' ]; then
      shift
      sage-cleaner &>/dev/null &
-@@ -677,40 +471,19 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
+@@ -667,40 +493,19 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
     exit 0
  fi
  
@@ -392,7 +381,7 @@ diff -up src/bin/sage.orig src/bin/sage
          shift
          exec sage-runtests -p "$@"
      else
-@@ -719,10 +492,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
+@@ -709,16 +514,6 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
      fi
  fi
  
@@ -400,11 +389,16 @@ diff -up src/bin/sage.orig src/bin/sage
 -    if [ "$1" = '-btnew' ]; then
 -        build_sage
 -    fi
-+if [ "$1" = '-tnew' ]; then
+-    shift
+-    SAGE_BANNER="no"
+-    sage_setup
+-    exec sage-runtests --new "$@"
+-fi
+-
+ if [ "$1" = '-testall' -o "$1" = "--testall" ]; then
      shift
      SAGE_BANNER="no"
-     sage_setup
+@@ -734,136 +529,6 @@ if [ "$1" = '-c' ]; then
-@@ -744,136 +514,6 @@ if [ "$1" = '-c' ]; then
      exec sage-eval "$@"
  fi
  
@@ -541,7 +535,7 @@ diff -up src/bin/sage.orig src/bin/sage
  if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then
      shift
      sage_setup
-@@ -922,26 +562,10 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
+@@ -912,26 +577,10 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
      exec sage-callgrind "$@"
  fi
  
@@ -569,8 +563,8 @@ diff -up src/bin/sage.orig src/bin/sage
      T=`echo "$1" | sed -e "s/.*\.//"`
      if [ "$T" = "spkg" ]; then
 diff -up src/bin/sage-runtests.orig src/bin/sage-runtests
---- src/bin/sage-runtests.orig	2014-11-17 17:43:03.195926083 -0200
+--- src/bin/sage-runtests.orig	2015-04-03 14:45:48.439352080 -0300
-+++ src/bin/sage-runtests	2014-11-17 17:48:39.236938952 -0200
++++ src/bin/sage-runtests	2015-04-03 14:54:20.773371699 -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 " +
@@ -583,8 +577,8 @@ 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	2014-11-17 17:43:14.588926520 -0200
+--- src/bin/sage-valgrind.orig	2015-04-03 14:45:55.318352343 -0300
-+++ src/bin/sage-valgrind	2014-11-17 17:48:18.884938172 -0200
++++ src/bin/sage-valgrind	2015-04-03 14:54:41.525372494 -0300
 @@ -1,16 +1,6 @@
  #!/usr/bin/env bash
  

sagemath.spec

@@ -1,30 +1,33 @@
 %global __provides_exclude_from	.*/site-packages/.*\\.so
 
+# for faster full rpm test builds
+%bcond_without docs
+
 # not functional due to missing jar dependencies
-%global with_sage3d		0
+%bcond_with sage3d
 
 # use an workaround to match upstream sagemath patched sphinx
-%global with_sphinx_hack	1
+%bcond_without sphinx_hack
 
 %ifarch x86_64
-%global have_fes		1
+%bcond_without fes
 %else
-%global have_fes		0
+%bcond_with fes
 %endif
 
 # set to run sage -testall in %%install
-%global with_check		0
+%bcond_with check
 %global SAGE_TIMEOUT		60
 %global SAGE_TIMEOUT_LONG	180
 
 %global conway_polynomials_pkg	conway_polynomials-0.4
 %global	elliptic_curves_pkg	elliptic_curves-0.7
 %global	flintqs_pkg		flintqs-20070817
-%global graphs_pkg		graphs-20120404
+%global graphs_pkg		graphs-20130920
 %global pexpect_pkg		pexpect-2.0
 %global polytopes_db_pkg	polytopes_db-20120220
 %global rubiks_pkg		rubiks-20070912
-%global	sagenb_pkg		sagenb-0.11.1
+%global	sagenb_pkg		sagenb-0.11.4
 %global sagetex_pkg		sagetex-2.3.4
 
 %global SAGE_ROOT		%{_libdir}/sagemath
@@ -38,8 +41,8 @@
 Name:		sagemath
 Group:		Applications/Engineering
 Summary:	A free open-source mathematics software system
-Version:	6.4.1
+Version:	6.5
-Release:	5%{?dist}
+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
@@ -142,6 +145,9 @@ Patch22:	%{name}-sympy.patch
 # Fix a name clash with NTL
 Patch23:	%{name}-ntl.patch
 
+# Temporary patch: http://trac.sagemath.org/ticket/17657
+Patch24:	%{name}-parallel.patch
+
 BuildRequires:	4ti2
 BuildRequires:	atlas-devel
 BuildRequires:	cddlib-tools
@@ -155,7 +161,7 @@ BuildRequires:	dvipng
 BuildRequires:	ecl
 BuildRequires:	eclib-devel
 BuildRequires:	factory-devel
-%if %{have_fes}
+%if %{with fes}
 BuildRequires:	fes-devel
 %endif
 BuildRequires:	flint-devel >= 2.3
@@ -208,16 +214,10 @@ BuildRequires:	polybori-devel
 BuildRequires:	R
 BuildRequires:	ratpoints-devel
 BuildRequires:	readline-devel
-%if 0%{?fedora} > 18
 BuildRequires:	rpy
-%endif
 BuildRequires:	scons
 BuildRequires:	Singular-devel
-%if 0%{?fedora} >= 18
 BuildRequires:	stix-math-fonts
-%else
-BuildRequires:	stix-fonts
-%endif
 BuildRequires:	sympow
 BuildRequires:	sympy
 BuildRequires:	symmetrica-devel
@@ -273,11 +273,7 @@ Requires:	%{name}-notebook
 Requires:	%{name}-rubiks
 Requires:	%{name}-sagetex
 Requires:	Singular
-%if 0%{?fedora} >= 18
 Requires:	stix-math-fonts
-%else
-Requires:	stix-fonts
-%endif
 Requires:	sympow
 Requires:	sympy
 Requires:	tachyon
@@ -387,6 +383,7 @@ Requires:	%{name}%{?_isa} = %{version}-%{release}
 This package contains the header files and development documentation
 for %{name}.
 
+%if %{with docs}
 #------------------------------------------------------------------------
 %package	doc
 Summary:	Documentation infrastructure files for %{name}
@@ -396,6 +393,16 @@ BuildArch:	noarch
 %description	doc
 This package contains the documentation infrastructure for %{name}.
 
+#------------------------------------------------------------------------
+%package	doc-ca
+Summary:	Catalan documentation files for %{name}
+Group:		Documentation
+Requires:	%{name}-doc = %{version}-%{release}
+BuildArch:	noarch
+
+%description	doc-ca
+This package contains the Catalan %{name} documentation.
+
 #------------------------------------------------------------------------
 %package	doc-de
 Summary:	German documentation files for %{name}
@@ -426,6 +433,16 @@ BuildArch:	noarch
 %description	doc-fr
 This package contains the French %{name} documentation.
 
+#------------------------------------------------------------------------
+%package	doc-hu
+Summary:	Hungarian documentation files for %{name}
+Group:		Documentation
+Requires:	%{name}-doc = %{version}-%{release}
+BuildArch:	noarch
+
+%description	doc-hu
+This package contains the Hungarian %{name} documentation.
+
 #------------------------------------------------------------------------
 %package	doc-it
 Summary:	Italian documentation files for %{name}
@@ -465,6 +482,8 @@ BuildArch:	noarch
 
 %description	doc-tr
 This package contains the Turkish %{name} documentation.
+# with docs
+%endif
 
 #------------------------------------------------------------------------
 %package	notebook
@@ -587,6 +606,7 @@ popd
 %patch5
 %patch6
 %patch7
+
 %patch8
 %patch9
 %patch10
@@ -600,13 +620,14 @@ popd
 %patch18
 %patch19
 
-%if %{have_fes}
+%if %{with fes}
 %patch20
 %endif
 
 %patch21
 %patch22
 %patch23
+%patch24
 
 sed -e 's|@@SAGE_ROOT@@|%{SAGE_ROOT}|' \
     -e 's|@@SAGE_DOC@@|%{SAGE_DOC}|' \
@@ -697,6 +718,14 @@ pushd build/pkgs/rubiks/src
     make %{?_smp_mflags} CC="gcc -fPIC" CXX="g++ -fPIC" CFLAGS="%{optflags}" CXXFLAGS="%{optflags}"
 popd
 
+# Remove buildroot reference from cython comments
+perl -pi -e 's|%{buildroot}||g;' `find src/build/cythonized -type f`
+# Try hard to remove buildroot from binaries
+rm -f `grep -lr "%{buildroot}" src/build/lib.linux-*/`
+pushd src
+    python ./setup.py build
+popd
+
 # last build command
 rm -fr $DOT_SAGE
 
@@ -734,9 +763,11 @@ pushd src
     python setup.py install --root=%{buildroot}
     cp -fa c_lib/libcsage.so.0 %{buildroot}%{_libdir}
     ln -sf libcsage.so.0 %{buildroot}%{_libdir}/libcsage.so
+%if %{with docs}
     # install documentation sources
     rm -fr $SAGE_DOC/{common,en,fr}
-    cp -far doc/{common,de,en,fr,pt,ru,tr} $SAGE_DOC
+    cp -far doc/{common,ca,de,en,fr,hu,it,pt,ru,tr} $SAGE_DOC
+%endif
 popd
 
 #------------------------------------------------------------------------
@@ -747,7 +778,7 @@ pushd build/pkgs/sagenb/src/%{sagenb_pkg}
     ln -sf %{_jsdir}/jsmol $SAGE_SHARE/jsmol
     # 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
 %endif
     ln -sf %{python_sitearch}/sagenb %{buildroot}%{SAGE_SRC}/sagenb
@@ -928,7 +959,7 @@ EOF
 chmod +x %{buildroot}%{_bindir}/sage
 
 #------------------------------------------------------------------------
-%if %{with_sage3d}
+%if %{with sage3d}
 cat > %{buildroot}%{SAGE_LOCAL}/bin/sage3d << EOF
 #!/bin/sh
 
@@ -953,6 +984,7 @@ pushd src
     touch %{buildroot}%{python_sitearch}/sage/libs/gmp/__init__.py
 popd
 
+%if %{with docs}
 #------------------------------------------------------------------------
 cp -f $SAGE_PYTHONPATH/{ANSI,FSM,pexpect,pxssh,screen}.py %{buildroot}%{python_sitearch}
 
@@ -965,7 +997,7 @@ pushd src/doc
     export LD_LIBRARY_PATH=%{buildroot}%{_libdir}:%{_libdir}/atlas:$LD_LIBRARY_PATH
     export PYTHONPATH=%{buildroot}%{python_sitearch}:$SAGE_PYTHONPATH:$SAGE_DOC
 
-%if %{with_sphinx_hack}
+%if %{with sphinx_hack}
     cp -far %{python_sitelib}/sphinx %{buildroot}%{python_sitearch}
     sed -i "s|\(source.startswith('>>>')\)|\1 or source.startswith('sage: ')|" \
 	%{buildroot}%{python_sitearch}/sphinx/highlighting.py
@@ -981,7 +1013,7 @@ pushd src/doc
     rm -fr $SAGE_DOC/output/doctrees
 popd
 
-%if %{with_check}
+%if %{with check}
 export SAGE_TIMEOUT=%{SAGE_TIMEOUT}
 export SAGE_TIMEOUT_LONG=%{SAGE_TIMEOUT_LONG}
 sage -testall --verbose || :
@@ -992,17 +1024,19 @@ sed -i 's|%{buildroot}||g' $SAGE_DOC/test.log
 
     rm -f %{buildroot}%{python_sitearch}/{ANSI,FSM,pexpect,pxssh,screen}.py{,c}
 
-%if %{with_sphinx_hack}
+%if %{with sphinx_hack}
     rm -fr %{buildroot}%{python_sitearch}/sphinx
 %endif
 
-# Script was used to build documentation 
-perl -pi -e 's|%{buildroot}||g;s|^##||g;' %{buildroot}%{_bindir}/sage
-
 # More wrong buildroot references
 perl -pi -e 's|%{buildroot}||g;' \
 	 -e "s|$PWD/src/doc|%{SAGE_DOC}|g;" \
     %{buildroot}%{SAGE_DOC}/output/html/en/reference/todolist.html
+# with docs
+%endif
+
+# Script was used to build documentation
+perl -pi -e 's|%{buildroot}||g;s|^##||g;' %{buildroot}%{_bindir}/sage
 
 #------------------------------------------------------------------------
 # Fix links
@@ -1044,12 +1078,15 @@ for file in `find %{buildroot} -name \*.py`; do
 	chmod +x $file
     fi
 done
+
+%if %{with docs}
 chmod -x %{buildroot}%{SAGE_DOC}/en/prep/media/Rplot001.png
 
 # Documentation is not rebuilt (also corrects rpmlint warning of hidden file)
 find %{buildroot}%{SAGE_DOC} -name .buildinfo -exec rm {} \;
 rm -fr %{buildroot}%{SAGE_DOC}/output/inventory
 find %{buildroot}%{SAGE_DOC} -type d -name _sources | xargs rm -fr
+%endif
 
 # remove bundles fonts
 rm -r %{buildroot}%{python_sitearch}/sagenb/data/mathjax/fonts
@@ -1057,7 +1094,7 @@ rm -r %{buildroot}%{python_sitearch}/sagenb/data/mathjax/fonts
 # remove .po files
 rm %{buildroot}%{python_sitearch}/sagenb/translations/*/LC_MESSAGES/*.po
 
-%if !%{with_sage3d}
+%if %{without sage3d}
 rm -r %{buildroot}%{python_sitearch}/sagenb/data/sage3d
 %endif
 
@@ -1165,6 +1202,7 @@ exit 0
 %{_includedir}/csage
 %{_libdir}/libcsage.so
 
+%if %{with docs}
 #------------------------------------------------------------------------
 %files		doc
 # GPLv2+
@@ -1173,6 +1211,12 @@ exit 0
 %dir %{SAGE_DOC}/output
 %dir %{SAGE_DOC}/output/html
 
+#------------------------------------------------------------------------
+%files		doc-ca
+# GPLv2+
+%{SAGE_DOC}/ca
+%{SAGE_DOC}/output/html/ca
+
 #------------------------------------------------------------------------
 %files		doc-de
 # GPLv2+
@@ -1191,9 +1235,16 @@ exit 0
 %{SAGE_DOC}/fr
 %{SAGE_DOC}/output/html/fr
 
+#------------------------------------------------------------------------
+%files		doc-hu
+# GPLv2+
+%{SAGE_DOC}/hu
+%{SAGE_DOC}/output/html/hu
+
 #------------------------------------------------------------------------
 %files		doc-it
 # GPLv2+
+%{SAGE_DOC}/it
 %{SAGE_DOC}/output/html/it
 
 #------------------------------------------------------------------------
@@ -1213,6 +1264,8 @@ exit 0
 # GPLv2+
 %{SAGE_DOC}/tr
 %{SAGE_DOC}/output/html/tr
+# with docs
+%endif
 
 #------------------------------------------------------------------------
 %files		notebook
@@ -1244,7 +1297,7 @@ exit 0
 %{python_sitearch}/sagenb/data/openid-realselector
 # GPLv2+
 %{python_sitearch}/sagenb/data/sage
-%if %{with_sage3d}
+%if %{with sage3d}
 # GPLv2+
 %{python_sitearch}/sagenb/data/sage3d
 %endif
@@ -1301,6 +1354,14 @@ exit 0
 
 ########################################################################
 %changelog
+* Thu May 14 2015 pcpa <paulo.cesar.pereira.de.andrade@gmail.com> - 6.5-1
+- Update to sagemath 6.5
+- Add new Catalan and Hungarian doc subpackages
+- Add customizations to not need a patched pari
+- Add "with docs" test build option
+- Convert build conditionals to use bcond
+- Correct deprecated warning when loading sagenb
+
 * Tue May  5 2015 Peter Robinson <pbrobinson@fedoraproject.org> 6.4.1-5
 - Build on ARMv7 (deps now provided)
 

sources

@@ -1 +1 @@
-9e64f198f791577555344b9aaa6768a9  sage-6.4.1.tar.gz
+ec9195561ffa2bcbc02391ac5af4e7ed  sage-6.5.tar.gz