Update to sagemath 7.5.1

2025-04-18 18:29:01 -04:00 · 2017-04-06 08:02:52 -04:00 · 2017-04-06 08:02:52 -04:00 · 056e08d023
commit 056e08d023
parent ac3aa7f6b7
24 changed files with 481 additions and 439 deletions
--- a/.gitignore
+++ b/.gitignore
@ -11,3 +11,4 @@
 /sage-6.8.tar.gz
 /sage-7.3.tar.gz
 /sage-7.4.tar.gz
+/sage-7.5.1.tar.gz
--- a/sagemath-4ti2.patch
+++ b/sagemath-4ti2.patch
@ -1,6 +1,6 @@
 diff -up src/sage/sandpiles/sandpile.py.orig src/sage/sandpiles/sandpile.py
--- src/sage/sandpiles/sandpile.py.orig	2016-10-20 08:05:08.805531352 -0400
-+++ src/sage/sandpiles/sandpile.py	2016-10-20 08:05:17.107531669 -0400
+--- src/sage/sandpiles/sandpile.py.orig	2017-03-04 13:25:45.385473644 -0500
+++ src/sage/sandpiles/sandpile.py	2017-03-04 13:25:53.872473969 -0500
@@ -346,9 +346,6 @@ from sage.arith.all import falling_facto
 from sage.rings.all import Integer, PolynomialRing, QQ, ZZ
 from sage.symbolic.all import I, pi
@ -11,7 +11,7 @@ diff -up src/sage/sandpiles/sandpile.py.orig src/sage/sandpiles/sandpile.py
 class Sandpile(DiGraph):
     """
     Class for Dhar's abelian sandpile model.
-@@ -5203,7 +5200,7 @@ class SandpileDivisor(dict):
+@@ -5197,7 +5194,7 @@ class SandpileDivisor(dict):
         sign_file.close()
         # compute
         try:
--- a/sagemath-arb.patch
+++ b/sagemath-arb.patch
@ -91,3 +91,63 @@ diff -up src/sage/libs/arb/bernoulli.pxd.orig src/sage/libs/arb/bernoulli.pxd
 -cdef extern from "bernoulli.h":
 +cdef extern from "arb/bernoulli.h":
     void bernoulli_fmpq_ui(fmpq_t b, ulong n)
+diff -up src/sage/libs/arb/acb_poly.pxd.orig src/sage/libs/arb/acb_poly.pxd
+--- src/sage/libs/arb/acb_poly.pxd.orig	2017-03-29 18:10:08.675927202 -0400
+++ src/sage/libs/arb/acb_poly.pxd	2017-03-29 18:10:13.934927403 -0400
+@@ -3,7 +3,7 @@
+ from sage.libs.arb.types cimport *
+ from sage.libs.flint.types cimport fmpz_poly_t, fmpq_poly_t
+ 
+-cdef extern from "acb_poly.h":
+cdef extern from "arb/acb_poly.h":
+     void acb_poly_init(acb_poly_t poly)
+     void acb_poly_clear(acb_poly_t poly)
+     void acb_poly_fit_length(acb_poly_t poly, long len)
+diff -up src/sage/libs/arb/types.pxd.orig src/sage/libs/arb/types.pxd
+--- src/sage/libs/arb/types.pxd.orig	2017-03-29 18:08:42.979923920 -0400
+++ src/sage/libs/arb/types.pxd	2017-03-29 18:09:18.413925277 -0400
+@@ -1,4 +1,4 @@
+-cdef extern from "mag.h":
+cdef extern from "arb/mag.h":
+     ctypedef struct mag_struct:
+         pass
+     ctypedef mag_struct mag_t[1]
+@@ -6,7 +6,7 @@ cdef extern from "mag.h":
+     ctypedef const mag_struct * mag_srcptr
+     long MAG_BITS
+ 
+-cdef extern from "arf.h":
+cdef extern from "arb/arf.h":
+     ctypedef struct arf_struct:
+         pass
+     ctypedef arf_struct arf_t[1]
+@@ -20,25 +20,25 @@ cdef extern from "arf.h":
+         ARF_RND_NEAR
+     long ARF_PREC_EXACT
+ 
+-cdef extern from "arb.h":
+cdef extern from "arb/arb.h":
+     ctypedef struct arb_struct:
+         pass
+     ctypedef arb_struct arb_t[1]
+     ctypedef arb_struct * arb_ptr
+ 
+-cdef extern from "acb.h":
+cdef extern from "arb/acb.h":
+     ctypedef struct acb_struct:
+         pass
+     ctypedef acb_struct[1] acb_t
+     ctypedef acb_struct * acb_ptr
+     ctypedef const acb_struct * acb_srcptr
+ 
+-cdef extern from "acb_mat.h":
+cdef extern from "arb/acb_mat.h":
+     ctypedef struct acb_mat_struct:
+         pass
+     ctypedef acb_mat_struct[1] acb_mat_t
+ 
+-cdef extern from "acb_poly.h":
+cdef extern from "arb/acb_poly.h":
+     ctypedef struct acb_poly_struct:
+         pass
+     ctypedef acb_poly_struct[1] acb_poly_t
--- a/sagemath-atlas.patch
+++ b/sagemath-atlas.patch
@ -1,15 +1,15 @@
 diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig	2016-10-20 09:16:23.105695029 -0400
-+++ src/module_list.py	2016-10-20 09:17:17.868697126 -0400
+--- src/module_list.py.orig	2017-03-29 19:33:34.149118879 -0400
+++ src/module_list.py	2017-03-29 19:34:09.520120233 -0400
@@ -12,20 +12,14 @@ SAGE_INC = '/usr/include'
 import pkgconfig
 
 # CBLAS can be one of multiple implementations
 -cblas_pc = pkgconfig.parse('cblas')
 +cblas_pc = pkgconfig.parse('atlas')
- cblas_libs = list(cblas_pc['libraries'])
- cblas_library_dirs = list(cblas_pc['library_dirs'])
- cblas_include_dirs = list(cblas_pc['include_dirs'])
+ cblas_libs = cblas_pc['libraries']
+ cblas_library_dirs = cblas_pc['library_dirs']
+ cblas_include_dirs = cblas_pc['include_dirs']
 
 -# TODO: Remove Cygwin hack by installing a suitable cblas.pc
 -if os.path.exists('/usr/lib/libblas.dll.a'):
@ -17,27 +17,28 @@ diff -up src/module_list.py.orig src/module_list.py
 -
 -# LAPACK can be one of multiple implementations
 -lapack_pc = pkgconfig.parse('lapack')
-lapack_libs = list(lapack_pc['libraries'])
-lapack_library_dirs = list(lapack_pc['library_dirs'])
-lapack_include_dirs = list(lapack_pc['include_dirs'])
+-lapack_libs = lapack_pc['libraries']
+-lapack_library_dirs = lapack_pc['library_dirs']
+-lapack_include_dirs = lapack_pc['include_dirs']
 +lapack_libs = [ 'lapack' ]
 +lapack_library_dirs = []
 +lapack_include_dirs = [ SAGE_INC + '/lapack' ]
 
 # FFLAS-FFPACK
 fflas_ffpack_pc = pkgconfig.parse('fflas-ffpack')
-@@ -43,7 +37,7 @@ givaro_cflags = pkgconfig.cflags('givaro
- # Note we replace the built-in gslcblas with the above cblas
+@@ -45,7 +39,8 @@ givaro_cflags = pkgconfig.cflags('givaro
 gsl_pc = pkgconfig.parse('gsl')
- gsl_libs = list(gsl_pc['libraries'].difference(['gslcblas']).union(cblas_libs))
-gsl_library_dirs = list(gsl_pc['library_dirs'])
+ gsl_libs = gsl_pc['libraries']
+ gsl_libs.remove('gslcblas')
+-gsl_library_dirs = gsl_pc['library_dirs']
+gsl_libs.extend(cblas_libs)
 +gsl_library_dirs = list(cblas_pc['library_dirs'])
- gsl_include_dirs = list(gsl_pc['include_dirs'])
+ gsl_include_dirs = gsl_pc['include_dirs']
 
 # GD image library
 diff -up src/sage/misc/cython.py.orig src/sage/misc/cython.py
--- src/sage/misc/cython.py.orig	2016-10-20 09:17:25.057697402 -0400
-+++ src/sage/misc/cython.py	2016-10-20 09:17:43.339698102 -0400
+--- src/sage/misc/cython.py.orig	2017-03-29 19:33:27.181118612 -0400
+++ src/sage/misc/cython.py	2017-03-29 19:33:36.568118971 -0400
@@ -30,15 +30,11 @@ import pkgconfig
 
 
--- a/sagemath-extensions.patch
+++ b/sagemath-extensions.patch
@ -1,7 +1,7 @@
 diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig	2016-10-20 07:59:58.978519487 -0400
-+++ src/module_list.py	2016-10-20 08:00:12.330519999 -0400
-@@ -167,7 +167,6 @@ library_order["stdc++"] = 1000
+--- src/module_list.py.orig	2017-03-04 13:10:19.482438188 -0500
+++ src/module_list.py	2017-03-04 13:13:17.345444999 -0500
+@@ -166,7 +166,6 @@ library_order["stdc++"] = 1000
 ###
 #############################################################
 
@ -9,8 +9,8 @@ diff -up src/module_list.py.orig src/module_list.py
 UNAME = os.uname()
 
 def uname_specific(name, value, alternative):
-@@ -398,21 +397,21 @@ ext_modules = [
-               libraries = ['flint'],
+@@ -382,21 +381,21 @@ ext_modules = [
+               sources = ['sage/graphs/matchpoly.pyx'],
               extra_compile_args = ['-std=c99']),
 
 -    OptionalExtension("sage.graphs.mcqd",
@ -46,7 +46,7 @@ diff -up src/module_list.py.orig src/module_list.py
 
     Extension('sage.graphs.planarity',
               sources = ['sage/graphs/planarity.pyx'],
-@@ -431,10 +430,10 @@ ext_modules = [
+@@ -415,10 +414,10 @@ ext_modules = [
     Extension('sage.graphs.graph_decompositions.cutwidth',
               sources = ['sage/graphs/graph_decompositions/cutwidth.pyx']),
 
@ -61,7 +61,7 @@ diff -up src/module_list.py.orig src/module_list.py
 
     Extension('sage.graphs.spanning_tree',
               sources = ['sage/graphs/spanning_tree.pyx']),
-@@ -573,18 +572,18 @@ ext_modules = [
+@@ -545,18 +544,18 @@ ext_modules = [
     ##
     ################################
 
@ -87,9 +87,9 @@ diff -up src/module_list.py.orig src/module_list.py
              ["sage/libs/fes.pyx"],
              language = "c",
              libraries = ['fes'],
-@@ -614,17 +613,17 @@ ext_modules = [
-     Extension('sage.libs.gmp.rational_reconstruction',
-               sources = ['sage/libs/gmp/rational_reconstruction.pyx']),
+@@ -580,17 +579,17 @@ ext_modules = [
+     Extension('sage.libs.gmp.pylong',
+               sources = ['sage/libs/gmp/pylong.pyx']),
 
 -    OptionalExtension('sage.libs.braiding',
 -                      sources = ["sage/libs/braiding.pyx"],
@ -112,9 +112,9 @@ diff -up src/module_list.py.orig src/module_list.py
 +#                      libraries = ["homfly", "gc"],
 +#                      package="libhomfly"),
 
-  #    Extension('sage.libs.linbox.linbox',
-  #             sources = ['sage/libs/linbox/linbox.pyx']),
-@@ -997,10 +996,10 @@ ext_modules = [
+     Extension('*', ['sage/libs/linbox/*.pyx']),
+ 
+@@ -917,10 +916,10 @@ ext_modules = [
     Extension('sage.matrix.matrix_window',
               sources = ['sage/matrix/matrix_window.pyx']),
 
@ -129,20 +129,7 @@ diff -up src/module_list.py.orig src/module_list.py
 
     Extension('sage.matrix.misc',
               sources = ['sage/matrix/misc.pyx'],
-@@ -1033,12 +1032,6 @@ ext_modules = [
- 
-     Extension('*', ['sage/misc/*.pyx']),
- 
-    # Only include darwin_utilities on OS_X >= 10.5
-    OptionalExtension('sage.misc.darwin_utilities',
-        sources = ['sage/misc/darwin_memory_usage.c',
-                   'sage/misc/darwin_utilities.pyx'],
-        condition = (UNAME[0] == "Darwin" and not UNAME[2].startswith('8.'))),
-
-     ################################
-     ##
-     ## sage.modular
-@@ -1190,19 +1183,19 @@ ext_modules = [
+@@ -1099,19 +1098,19 @@ ext_modules = [
     Extension("sage.numerical.backends.interactivelp_backend",
               ["sage/numerical/backends/interactivelp_backend.pyx"]),
 
@ -174,7 +161,7 @@ diff -up src/module_list.py.orig src/module_list.py
               ["sage/numerical/backends/coin_backend.pyx"],
               language = 'c++',
               libraries = ["Cbc", "CbcSolver", "Cgl", "Clp", "CoinUtils",
-@@ -1681,7 +1674,7 @@ ext_modules = [
+@@ -1583,7 +1582,7 @@ ext_modules = [
     ##
     ################################
 
@ -183,7 +170,7 @@ diff -up src/module_list.py.orig src/module_list.py
               sources = ["sage/sat/solvers/cryptominisat/cryptominisat.pyx"],
               include_dirs = [os.path.join(SAGE_INC, "cmsat")] + zlib_include_dirs,
               language = "c++",
-@@ -1689,7 +1682,7 @@ ext_modules = [
+@@ -1591,7 +1590,7 @@ ext_modules = [
               library_dirs = zlib_library_dirs,
               package = 'cryptominisat'),
 
--- a/sagemath-fes-build.patch
+++ b/sagemath-fes-build.patch
@ -1,7 +1,7 @@
 diff -up src/sage/libs/fes.pyx.orig src/sage/libs/fes.pyx
--- src/sage/libs/fes.pyx.orig	2016-08-08 13:44:21.919554511 -0400
-+++ src/sage/libs/fes.pyx	2016-08-08 13:44:36.618555074 -0400
-@@ -90,8 +90,8 @@ from sage.rings.polynomial.pbori import
+--- src/sage/libs/fes.pyx.orig	2017-03-04 13:32:40.457489539 -0500
+++ src/sage/libs/fes.pyx	2017-03-04 13:32:50.717489932 -0500
+@@ -84,8 +84,8 @@ from sage.rings.polynomial.pbori import
 from sage.arith.all import binomial
 from sage.combinat.subset import Subsets
 
--- a/sagemath-fes.patch
+++ b/sagemath-fes.patch
@ -1,7 +1,7 @@
 diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig	2016-10-20 08:12:42.137548711 -0400
-+++ src/module_list.py	2016-10-20 08:12:55.836549236 -0400
-@@ -583,11 +583,11 @@ ext_modules = [
+--- src/module_list.py.orig	2017-03-04 13:33:14.446490840 -0500
+++ src/module_list.py	2017-03-04 13:33:23.046491170 -0500
+@@ -555,11 +555,11 @@ ext_modules = [
               sources = ["sage/libs/ecl.pyx"],
               libraries = ["ecl"]),
 
--- a/sagemath-ftbfs.patch
+++ b/sagemath-ftbfs.patch
@ -1,28 +0,0 @@
-diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig	2016-12-21 12:24:59.301116425 -0500
-+++ src/module_list.py	2016-12-21 12:25:33.927117751 -0500
-@@ -36,7 +36,7 @@ givaro_cflags = pkgconfig.cflags('givaro
- # GNU Scientific Library
- # Note we replace the built-in gslcblas with the above cblas
- gsl_pc = pkgconfig.parse('gsl')
-gsl_libs = list(gsl_pc['libraries'].difference(['gslcblas']).union(cblas_libs))
-+gsl_libs = list(set(gsl_pc['libraries']).difference(['gslcblas']).union(cblas_libs))
- gsl_library_dirs = list(cblas_pc['library_dirs'])
- gsl_include_dirs = list(gsl_pc['include_dirs'])
- 
-diff -up src/setup.py.orig src/setup.py
--- src/setup.py.orig	2016-12-21 12:26:52.909120775 -0500
-+++ src/setup.py	2016-12-21 12:27:00.759121076 -0500
-@@ -565,9 +565,9 @@ def run_cythonize():
- 
-     # Sage uses these directives (mostly for historical reasons).
-     Cython.Compiler.Options.embed_pos_in_docstring = True
-    Cython.Compiler.Options.directive_defaults['autotestdict'] = False
-    Cython.Compiler.Options.directive_defaults['cdivision'] = True
-    Cython.Compiler.Options.directive_defaults['fast_getattr'] = True
-+    Cython.Compiler.Options._directive_defaults['autotestdict'] = False
-+    Cython.Compiler.Options._directive_defaults['cdivision'] = True
-+    Cython.Compiler.Options._directive_defaults['fast_getattr'] = True
-     # The globals() builtin in Cython was fixed to return to the current scope,
-     # but Sage relies on the broken behavior of returning to the nearest
-     # enclosing Python scope (e.g. to perform variable injection).
--- a/sagemath-gcc6.patch
+++ b/sagemath-gcc6.patch
@ -1,7 +1,7 @@
 diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig	2016-10-20 08:30:33.400589734 -0400
-+++ src/module_list.py	2016-10-20 08:32:10.570593455 -0400
-@@ -964,7 +964,7 @@ ext_modules = [
+--- src/module_list.py.orig	2017-03-29 18:45:52.972009314 -0400
+++ src/module_list.py	2017-03-29 18:46:02.855009693 -0400
+@@ -880,7 +880,7 @@ ext_modules = [
               library_dirs = m4ri_library_dirs,
               include_dirs = m4ri_include_dirs,
               depends = [SAGE_INC + "/m4rie/m4rie.h"],
--- a/sagemath-givaro.patch
+++ b/sagemath-givaro.patch
@ -1,7 +1,7 @@
 diff -up src/sage/libs/singular/singular.pyx.orig src/sage/libs/singular/singular.pyx
--- src/sage/libs/singular/singular.pyx.orig	2016-10-20 08:19:08.767563517 -0400
-+++ src/sage/libs/singular/singular.pyx	2016-10-20 08:19:15.138563761 -0400
-@@ -21,6 +21,8 @@ cdef extern from "limits.h":
+--- src/sage/libs/singular/singular.pyx.orig	2017-03-04 13:34:53.241494624 -0500
+++ src/sage/libs/singular/singular.pyx	2017-03-04 13:35:03.289495008 -0500
+@@ -23,6 +23,8 @@ cdef extern from "limits.h":
     long INT_MAX
     long INT_MIN
 
--- a/sagemath-includes.patch
+++ b/sagemath-includes.patch
@ -1,35 +1,25 @@
 diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig	2016-10-20 08:21:43.948569459 -0400
-+++ src/module_list.py	2016-10-20 08:28:34.226585170 -0400
-@@ -116,6 +116,7 @@ except ValueError:
- #########################################################
- 
- singular_libs = ['singular', 'flint', 'ntl', 'gmpxx', 'gmp', 'readline', 'm']
+--- src/module_list.py.orig	2017-03-29 18:42:35.820001764 -0400
+++ src/module_list.py	2017-03-29 18:43:56.158004841 -0400
+@@ -63,6 +63,7 @@ linbox_cflags = pkgconfig.cflags('linbox
+ # Singular
+ singular_pc = pkgconfig.parse('Singular')
+ singular_libs = singular_pc['libraries']
 +singular_incs = [SAGE_INC + '/singular', SAGE_INC + '/factory']
+ singular_library_dirs = singular_pc['library_dirs']
+ singular_cflags = pkgconfig.cflags('Singular').split()
 
- #########################################################
- ### Library order
-@@ -192,16 +193,19 @@ ext_modules = [
-     Extension('sage.algebras.letterplace.free_algebra_letterplace',
-               sources = ['sage/algebras/letterplace/free_algebra_letterplace.pyx'],
-               libraries = singular_libs,
-+              include_dirs = singular_incs,
-               language="c++"),
+@@ -188,7 +189,8 @@ ext_modules = [
+                language='c++',
+                libraries = ["gmp", "m", "ntl"]),
 
-     Extension('sage.algebras.letterplace.free_algebra_element_letterplace',
-               sources = ['sage/algebras/letterplace/free_algebra_element_letterplace.pyx'],
-               libraries = singular_libs,
-+              include_dirs = singular_incs,
-               language="c++"),
- 
-     Extension('sage.algebras.letterplace.letterplace_ideal',
-               sources = ['sage/algebras/letterplace/letterplace_ideal.pyx'],
-               libraries = singular_libs,
-+              include_dirs = singular_incs,
-               language="c++"),
+-    Extension('*', sources = ['sage/algebras/letterplace/*.pyx']),
+    Extension('*', sources = ['sage/algebras/letterplace/*.pyx'],
+              include_dirs = singular_incs),
 
     Extension('sage.algebras.quatalg.quaternion_algebra_cython',
-@@ -644,7 +648,8 @@ ext_modules = [
+                sources = ['sage/algebras/quatalg/quaternion_algebra_cython.pyx'],
+@@ -607,7 +609,8 @@ ext_modules = [
                                                         [])),
 
     Extension('sage.libs.lrcalc.lrcalc',
@ -37,47 +27,19 @@ diff -up src/module_list.py.orig src/module_list.py
 +              sources = ["sage/libs/lrcalc/lrcalc.pyx"],
 +              include_dirs = [os.path.join(SAGE_INC, 'lrcalc')]),
 
-     Extension('sage.libs.pari.closure',
-               sources = ["sage/libs/pari/closure.pyx"]),
-@@ -677,31 +682,37 @@ ext_modules = [
-     Extension('sage.libs.singular.singular',
-               sources = ['sage/libs/singular/singular.pyx'],
-               libraries = singular_libs,
-+              include_dirs = singular_incs,
-               language="c++"),
+     Extension('*', ['sage/libs/cypari2/*.pyx']),
+     Extension('*', ['sage/libs/pari/*.pyx']),
+@@ -625,7 +628,8 @@ ext_modules = [
+               sources = ['sage/libs/readline.pyx'],
+               libraries = ['readline']),
 
-     Extension('sage.libs.singular.polynomial',
-               sources = ['sage/libs/singular/polynomial.pyx'],
-               libraries = singular_libs,
-+              include_dirs = singular_incs,
-               language="c++"),
- 
-     Extension('sage.libs.singular.ring',
-               sources = ['sage/libs/singular/ring.pyx'],
-               libraries = singular_libs,
-+              include_dirs = singular_incs,
-               language="c++"),
- 
-     Extension('sage.libs.singular.groebner_strategy',
-               sources = ['sage/libs/singular/groebner_strategy.pyx'],
-               libraries = singular_libs,
-+              include_dirs = singular_incs,
-               language="c++"),
- 
-     Extension('sage.libs.singular.function',
-               sources = ['sage/libs/singular/function.pyx'],
-               libraries = singular_libs,
-+              include_dirs = singular_incs,
-               language="c++"),
- 
-     Extension('sage.libs.singular.option',
-               sources = ['sage/libs/singular/option.pyx'],
-               libraries = singular_libs,
-+              include_dirs = singular_incs,
-               language="c++"),
+-    Extension('*', sources = ['sage/libs/singular/*.pyx']),
+    Extension('*', sources = ['sage/libs/singular/*.pyx'],
+              include_dirs = singular_incs),
 
     Extension('sage.libs.symmetrica.symmetrica',
-@@ -710,17 +721,21 @@ ext_modules = [
+               sources = ["sage/libs/symmetrica/symmetrica.pyx"],
+@@ -633,17 +637,21 @@ ext_modules = [
 
     Extension('sage.libs.mpmath.utils',
               sources = ["sage/libs/mpmath/utils.pyx"],
@ -103,7 +65,7 @@ diff -up src/module_list.py.orig src/module_list.py
 
     ###################################
     ##
-@@ -728,7 +743,8 @@ ext_modules = [
+@@ -651,7 +659,8 @@ ext_modules = [
     ##
     ###################################
 
@ -113,24 +75,23 @@ diff -up src/module_list.py.orig src/module_list.py
 
     ###################################
     ##
-@@ -901,7 +917,7 @@ ext_modules = [
+@@ -824,6 +833,7 @@ ext_modules = [
     Extension("sage.matrix.matrix_complex_ball_dense",
               ["sage/matrix/matrix_complex_ball_dense.pyx"],
               libraries=['arb', 'mpfi', 'mpfr'],
-              include_dirs=[SAGE_INC + '/flint'],
 +              include_dirs=[SAGE_INC + '/flint', SAGE_INC + '/arb'],
               language = "c++"),
 
     Extension('sage.matrix.matrix_complex_double_dense',
-@@ -971,6 +987,7 @@ ext_modules = [
+@@ -891,6 +901,7 @@ ext_modules = [
+               sources = ['sage/matrix/matrix_modn_sparse.pyx']),
+ 
     Extension('sage.matrix.matrix_mpolynomial_dense',
-               sources = ['sage/matrix/matrix_mpolynomial_dense.pyx'],
-               libraries = singular_libs,
 +              include_dirs = singular_incs,
-               language="c++"),
+               sources = ['sage/matrix/matrix_mpolynomial_dense.pyx']),
 
     Extension('sage.matrix.matrix_rational_dense',
-@@ -1288,6 +1305,7 @@ ext_modules = [
+@@ -1203,6 +1214,7 @@ ext_modules = [
     Extension("sage.rings.complex_arb",
               ["sage/rings/complex_arb.pyx"],
               libraries=['mpfi', 'mpfr', 'gmp'],
@ -138,7 +99,7 @@ diff -up src/module_list.py.orig src/module_list.py
               language = 'c++'),
 
     Extension('sage.rings.complex_double',
-@@ -1360,6 +1378,7 @@ ext_modules = [
+@@ -1275,6 +1287,7 @@ ext_modules = [
     Extension("sage.rings.real_arb",
               ["sage/rings/real_arb.pyx"],
               libraries = ['mpfi', 'mpfr'],
@ -146,30 +107,34 @@ diff -up src/module_list.py.orig src/module_list.py
               language = 'c++'),
 
     Extension('sage.rings.real_lazy',
-@@ -1564,16 +1583,19 @@ ext_modules = [
+@@ -1473,12 +1486,15 @@ ext_modules = [
+               sources = ['sage/rings/polynomial/multi_polynomial.pyx']),
+ 
     Extension('sage.rings.polynomial.multi_polynomial_ideal_libsingular',
-               sources = ['sage/rings/polynomial/multi_polynomial_ideal_libsingular.pyx'],
-               libraries = singular_libs,
 +              include_dirs = singular_incs,
-               language="c++"),
+               sources = ['sage/rings/polynomial/multi_polynomial_ideal_libsingular.pyx']),
 
     Extension('sage.rings.polynomial.plural',
-               sources = ['sage/rings/polynomial/plural.pyx'],
-               libraries = ['m', 'readline', 'singular', 'givaro', 'gmpxx', 'gmp'],
 +              include_dirs = singular_incs,
-               language="c++"),
+               sources = ['sage/rings/polynomial/plural.pyx']),
 
     Extension('sage.rings.polynomial.multi_polynomial_libsingular',
-               sources = ['sage/rings/polynomial/multi_polynomial_libsingular.pyx'],
-               libraries = singular_libs,
 +              include_dirs = singular_incs,
-               language="c++"),
+               sources = ['sage/rings/polynomial/multi_polynomial_libsingular.pyx']),
 
     Extension('sage.rings.polynomial.multi_polynomial_ring_generic',
+@@ -1492,6 +1508,7 @@ ext_modules = [
+ 
+     Extension('sage.rings.polynomial.polynomial_complex_arb',
+                sources = ['sage/rings/polynomial/polynomial_complex_arb.pyx'],
+               include_dirs=[SAGE_INC + '/flint', SAGE_INC + '/arb'],
+                language="c++"),
+ 
+     Extension('sage.rings.polynomial.polynomial_compiled',
 diff -up src/setup.py.orig src/setup.py
--- src/setup.py.orig	2016-10-20 08:28:56.912586039 -0400
-+++ src/setup.py	2016-10-20 08:29:26.634587177 -0400
-@@ -78,6 +78,7 @@ except KeyError:
+--- src/setup.py.orig	2017-03-29 18:42:34.196001702 -0400
+++ src/setup.py	2017-03-29 18:42:39.088001890 -0400
+@@ -83,6 +83,7 @@ except KeyError:
 # search for dependencies and add to gcc -I<path>
 # this depends on SAGE_CYTHONIZED
 include_dirs = sage_include_directories(use_sources=True)
--- a/sagemath-libgap.patch
+++ b/sagemath-libgap.patch
@ -1,6 +1,6 @@
 diff -up src/sage/libs/gap/test/main.c.orig src/sage/libs/gap/test/main.c
--- src/sage/libs/gap/test/main.c.orig	2016-08-08 13:43:32.376552613 -0400
-+++ src/sage/libs/gap/test/main.c	2016-08-08 13:43:38.209552837 -0400
+--- src/sage/libs/gap/test/main.c.orig	2017-03-04 13:30:35.525484755 -0500
+++ src/sage/libs/gap/test/main.c	2017-03-04 13:30:58.662485641 -0500
@@ -22,7 +22,7 @@ void eval(char* cmd) {
   libgap_start_interaction(cmd);
 
@ -11,9 +11,9 @@ diff -up src/sage/libs/gap/test/main.c.orig src/sage/libs/gap/test/main.c
   char* out = libgap_get_output();
   libgap_exit();
 diff -up src/sage/libs/gap/util.pyx.orig src/sage/libs/gap/util.pyx
--- src/sage/libs/gap/util.pyx.orig	2016-08-08 13:41:46.176548547 -0400
-+++ src/sage/libs/gap/util.pyx	2016-08-08 13:42:26.594550094 -0400
-@@ -154,18 +154,9 @@ def gap_root():
+--- src/sage/libs/gap/util.pyx.orig	2017-03-04 13:31:07.509485979 -0500
+++ src/sage/libs/gap/util.pyx	2017-03-04 13:31:44.126487382 -0500
+@@ -154,17 +154,9 @@ def gap_root():
 
         sage: from sage.libs.gap.util import gap_root
         sage: gap_root()   # random output
@ -21,9 +21,8 @@ diff -up src/sage/libs/gap/util.pyx.orig src/sage/libs/gap/util.pyx
 +        '/usr/lib/gap'
     """
 -    import os.path
-    gapdir = os.path.join(SAGE_LOCAL, 'gap', 'latest')
-    if os.path.exists(gapdir):
-        return gapdir
+-    if os.path.exists(GAP_ROOT_DIR):
+-        return GAP_ROOT_DIR
 -    print('The gap-4.5.5.spkg (or later) seems to be not installed!')
 -    gap_sh = open(os.path.join(SAGE_LOCAL, 'bin', 'gap')).read().splitlines()
 -    gapdir = filter(lambda dir:dir.strip().startswith('GAP_DIR'), gap_sh)[0]
--- a/sagemath-lrslib.patch
+++ b/sagemath-lrslib.patch
@ -1,6 +1,6 @@
 diff -up src/sage/geometry/polyhedron/base.py.orig src/sage/geometry/polyhedron/base.py
--- src/sage/geometry/polyhedron/base.py.orig	2016-08-08 13:38:11.144540312 -0400
-+++ src/sage/geometry/polyhedron/base.py	2016-08-08 13:38:26.707540908 -0400
+--- src/sage/geometry/polyhedron/base.py.orig	2017-03-04 13:27:41.267478082 -0500
+++ src/sage/geometry/polyhedron/base.py	2017-03-04 13:27:49.646478403 -0500
@@ -21,7 +21,6 @@ import six
 from sage.structure.element import Element, coerce_binop, is_Vector
 
@ -9,7 +9,7 @@ diff -up src/sage/geometry/polyhedron/base.py.orig src/sage/geometry/polyhedron/
 
 from sage.rings.all import QQ, ZZ
 from sage.rings.real_double import RDF
-@@ -3691,10 +3690,6 @@ class Polyhedron_base(Element):
+@@ -3680,10 +3679,6 @@ class Polyhedron_base(Element):
 
              David Avis's lrs program.
         """
--- a/sagemath-nauty.patch
+++ b/sagemath-nauty.patch
@ -1,7 +1,7 @@
 diff -up src/sage/graphs/graph_generators.py.orig src/sage/graphs/graph_generators.py
--- src/sage/graphs/graph_generators.py.orig	2016-08-08 13:38:51.824541870 -0400
-+++ src/sage/graphs/graph_generators.py	2016-08-08 13:39:20.460542967 -0400
-@@ -872,7 +872,7 @@ class GraphGenerators():
+--- src/sage/graphs/graph_generators.py.orig	2017-03-04 13:28:37.640480240 -0500
+++ src/sage/graphs/graph_generators.py	2017-03-04 13:28:47.287480610 -0500
+@@ -874,7 +874,7 @@ class GraphGenerators():
             >A geng -d0D3 n=4 e=0-6
         """
         import subprocess
--- a/sagemath-nofstring.patch
+++ b/sagemath-nofstring.patch
@ -1,6 +1,6 @@
 diff -up src/sage/arith/multi_modular.pyx.orig src/sage/arith/multi_modular.pyx
--- src/sage/arith/multi_modular.pyx.orig	2016-10-20 08:20:20.321566257 -0400
-+++ src/sage/arith/multi_modular.pyx	2016-10-20 08:20:45.522567222 -0400
+--- src/sage/arith/multi_modular.pyx.orig	2017-03-04 13:36:01.148497224 -0500
+++ src/sage/arith/multi_modular.pyx	2017-03-04 13:36:03.202497303 -0500
@@ -172,9 +172,9 @@ cdef class MultiModularBasis_base(object
             ArithmeticError: The inverse of 6 modulo 10 is not defined.
         """
@ -23,8 +23,8 @@ diff -up src/sage/arith/multi_modular.pyx.orig src/sage/arith/multi_modular.pyx
 
         cdef Py_ssize_t i
 diff -up src/sage/rings/finite_rings/integer_mod.pyx.orig src/sage/rings/finite_rings/integer_mod.pyx
--- src/sage/rings/finite_rings/integer_mod.pyx.orig	2016-10-20 08:20:40.398567026 -0400
-+++ src/sage/rings/finite_rings/integer_mod.pyx	2016-10-20 08:20:45.526567222 -0400
+--- src/sage/rings/finite_rings/integer_mod.pyx.orig	2017-03-04 13:36:01.155497224 -0500
+++ src/sage/rings/finite_rings/integer_mod.pyx	2017-03-04 13:36:03.204497303 -0500
@@ -392,7 +392,7 @@ cdef class IntegerMod_abstract(FiniteRin
         from integer_mod_ring import IntegerModRing
         R = IntegerModRing(modulus)
@ -35,9 +35,9 @@ diff -up src/sage/rings/finite_rings/integer_mod.pyx.orig src/sage/rings/finite_
 
     def is_nilpotent(self):
 diff -up src/sage/structure/parent.pyx.orig src/sage/structure/parent.pyx
--- src/sage/structure/parent.pyx.orig	2016-10-20 08:20:20.325566257 -0400
-+++ src/sage/structure/parent.pyx	2016-10-20 08:20:45.529567222 -0400
-@@ -733,7 +733,7 @@ cdef class Parent(category_object.Catego
+--- src/sage/structure/parent.pyx.orig	2017-03-04 13:35:36.771496290 -0500
+++ src/sage/structure/parent.pyx	2017-03-04 13:36:03.205497303 -0500
+@@ -735,7 +735,7 @@ cdef class Parent(category_object.Catego
     cdef int init_coerce(self, bint warn=True) except -1:
         if self._coerce_from_hash is None:
             if warn:
@ -47,9 +47,9 @@ diff -up src/sage/structure/parent.pyx.orig src/sage/structure/parent.pyx
             self._initial_action_list = []
             self._initial_convert_list = []
 diff -up src/sage/symbolic/ring.pyx.orig src/sage/symbolic/ring.pyx
--- src/sage/symbolic/ring.pyx.orig	2016-10-20 08:20:20.327566257 -0400
-+++ src/sage/symbolic/ring.pyx	2016-10-20 08:20:45.531567222 -0400
-@@ -355,7 +355,7 @@ cdef class SymbolicRing(CommutativeRing)
+--- src/sage/symbolic/ring.pyx.orig	2017-03-04 13:35:36.772496290 -0500
+++ src/sage/symbolic/ring.pyx	2017-03-04 13:36:03.206497303 -0500
+@@ -379,7 +379,7 @@ cdef class SymbolicRing(CommutativeRing)
             from sage.misc.all import prod
             return prod([SR(p)**e for p,e in x], SR(x.unit()))
         else:
--- a/sagemath-ntl.patch
+++ b/sagemath-ntl.patch
@ -1,13 +1,7 @@
-NTL 8.x introduces a new class, NTL::WrappedPtr<T>.  Unfortunately, Cython
-does not add a namespace identifier to the name of the existing WrappedPtr
-class, generated from the patched files below, resulting in ambiguous
-references to that name.  This patch simply changes the name of the existing
-class to avoid the name collision.
-
 diff -up src/sage/libs/polybori/decl.pxd.orig src/sage/libs/polybori/decl.pxd
--- src/sage/libs/polybori/decl.pxd.orig	2015-10-11 18:10:28.994844062 -0300
-+++ src/sage/libs/polybori/decl.pxd	2015-10-11 18:11:16.004845863 -0300
-@@ -289,10 +289,10 @@ cdef extern from "sage/libs/polybori/pb_
+--- src/sage/libs/polybori/decl.pxd.orig	2017-03-04 13:33:54.155492361 -0500
+++ src/sage/libs/polybori/decl.pxd	2017-03-04 13:34:09.926492965 -0500
+@@ -291,10 +291,10 @@ cdef extern from "sage/libs/polybori/pb_
         int (* size)()
         PBPolyEntry (* get "operator[]")(int)
 
@ -21,8 +15,8 @@ diff -up src/sage/libs/polybori/decl.pxd.orig src/sage/libs/polybori/decl.pxd
 
     cdef cppclass PBGBStrategy "GroebnerStrategy":
 diff -up src/sage/libs/polybori/pb_wrap.h.orig src/sage/libs/polybori/pb_wrap.h
--- src/sage/libs/polybori/pb_wrap.h.orig	2015-10-11 18:10:35.738844321 -0300
-+++ src/sage/libs/polybori/pb_wrap.h	2015-10-11 18:12:42.724849183 -0300
+--- src/sage/libs/polybori/pb_wrap.h.orig	2017-03-04 13:34:07.773492882 -0500
+++ src/sage/libs/polybori/pb_wrap.h	2017-03-04 13:34:09.928492965 -0500
@@ -177,23 +177,23 @@ PyObject* preallocated_to_PyString(const
 
 
--- a/sagemath-pari.patch
+++ b/sagemath-pari.patch
@ -1,77 +1,24 @@
-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	2016-10-20 08:06:47.720535139 -0400
-+++ src/sage/libs/pari/handle_error.pxd	2016-10-20 08:07:01.459535665 -0400
-@@ -1,5 +1,5 @@
- from .types cimport GEN
+diff -up src/sage/libs/cypari2/paridecl.pxd.orig src/sage/libs/cypari2/paridecl.pxd
+--- src/sage/libs/cypari2/paridecl.pxd.orig	2017-03-04 14:37:56.976639516 -0500
+++ src/sage/libs/cypari2/paridecl.pxd	2017-03-04 14:38:09.953640013 -0500
+@@ -77,7 +77,7 @@ cdef extern from "sage/libs/cypari2/cypa
+     int     PARI_SIGINT_block, PARI_SIGINT_pending
+     void    NEXT_PRIME_VIADIFF(long, byteptr)
+     void    PREC_PRIME_VIADIFF(long, byteptr)
+-    int     INIT_JMPm, INIT_SIGm, INIT_DFTm, INIT_noPRIMEm, INIT_noIMTm
+    int     INIT_JMPm, INIT_SIGm, INIT_DFTm, INIT_noPRIMEm, INIT_noIMTm, INIT_noINTGMPm
+     int     new_galois_format, factor_add_primes, factor_proven
+     int     precdl
+     # The "except 0" here is to ensure compatibility with
+diff -up src/sage/libs/cypari2/pari_instance.pyx.orig src/sage/libs/cypari2/pari_instance.pyx
+--- src/sage/libs/cypari2/pari_instance.pyx.orig	2017-03-04 14:38:30.535640801 -0500
+++ src/sage/libs/cypari2/pari_instance.pyx	2017-03-04 14:38:39.680641151 -0500
+@@ -510,7 +510,7 @@ cdef class PariInstance(PariInstance_aut
+         # As a simple heuristic, we set the virtual stack to 1/4 of the
+         # virtual memory.
 
- 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)
-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	2016-10-20 08:07:12.336536082 -0400
-+++ src/sage/libs/pari/handle_error.pyx	2016-10-20 08:08:23.089538791 -0400
-@@ -139,7 +139,7 @@ cdef void _pari_init_error_handling():
-     cb_pari_err_recover = _pari_err_recover
+-        pari_init_opts(size, maxprime, INIT_DFTm)
+        pari_init_opts(size, maxprime, INIT_DFTm|INIT_noINTGMPm)
 
- 
-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.
-@@ -158,11 +158,11 @@ 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]
- 
-     sig_block()
-     cdef char* errstr
-    cdef char* s
-     try:
-         if errnum == e_STACK:
-             # Custom error message for PARI stack overflow
-@@ -173,11 +173,6 @@ cdef int _pari_err_handle(GEN E) except
-             errstr = pari_err2str(E)
-             pari_error_string = errstr.decode('ascii')
-             pari_free(errstr)
-
-        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:
-         sig_unblock()
-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	2016-10-20 08:08:33.152539177 -0400
-+++ src/sage/libs/pari/pari_instance.pxd	2016-10-20 08:08:51.209539868 -0400
-@@ -5,6 +5,10 @@ cimport cython
- 
- from sage.libs.pari.gen cimport gen
- 
-+cdef extern from "gmp.h":
-+    cdef void mp_get_memory_functions(void**, void**, void**)
-+    cdef void mp_set_memory_functions(void*, void*, void*)
-+
- cpdef long prec_bits_to_words(unsigned long prec_in_bits)
- cpdef long prec_words_to_bits(long prec_in_words)
- cpdef long default_bitprec()
-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	2016-10-20 08:09:05.632540421 -0400
-+++ src/sage/libs/pari/pari_instance.pyx	2016-10-20 08:10:25.322543472 -0400
-@@ -475,7 +475,12 @@ cdef class PariInstance(PariInstance_aut
-         from sage.misc.memory_info import MemoryInfo
-         mem = MemoryInfo()
- 
-+        cdef void *_gmp_malloc
-+        cdef void *_gmp_realloc
-+        cdef void *_gmp_free
-+        mp_get_memory_functions(&_gmp_malloc, &_gmp_realloc, &_gmp_free)
-         pari_init_opts(size, maxprime, INIT_DFTm)
-+        mp_set_memory_functions(_gmp_malloc, _gmp_realloc, _gmp_free)
-         
-         sizemax = mem.virtual_memory_limit() // 4
+         from sage.misc.getusage import virtual_memory_limit
 
--- a/sagemath-readonly.patch
+++ b/sagemath-readonly.patch
@ -1,7 +1,7 @@
 diff -up src/sage/all.py.orig src/sage/all.py
--- src/sage/all.py.orig	2016-08-08 13:29:42.192520823 -0400
-+++ src/sage/all.py	2016-08-08 13:30:18.601522217 -0400
-@@ -305,11 +305,11 @@ def _write_started_file():
+--- src/sage/all.py.orig	2017-03-04 13:24:30.701470784 -0500
+++ src/sage/all.py	2017-03-04 13:24:50.878471557 -0500
+@@ -300,11 +300,11 @@ def _write_started_file():
 
     Check that the file exists when Sage is running::
 
--- a/sagemath-rpmbuild.patch
+++ b/sagemath-rpmbuild.patch
@ -1,6 +1,6 @@
 diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig	2016-10-20 08:01:32.743523078 -0400
-+++ src/module_list.py	2016-10-20 08:01:43.593523493 -0400
+--- src/module_list.py.orig	2017-03-04 13:14:34.197447942 -0500
+++ src/module_list.py	2017-03-04 13:14:58.646448878 -0500
@@ -3,7 +3,7 @@ from glob import glob
 from distutils.extension import Extension
 from sage.env import SAGE_LOCAL
@ -11,9 +11,9 @@ diff -up src/module_list.py.orig src/module_list.py
 #########################################################
 ### pkg-config setup
 diff -up src/sage/misc/cython.py.orig src/sage/misc/cython.py
--- src/sage/misc/cython.py.orig	2016-10-20 08:03:03.079526537 -0400
-+++ src/sage/misc/cython.py	2016-10-20 08:03:18.761527138 -0400
-@@ -433,7 +433,7 @@ extra_compile_args = %s
+--- src/sage/misc/cython.py.orig	2017-03-04 13:15:11.022449352 -0500
+++ src/sage/misc/cython.py	2017-03-04 13:15:43.031450578 -0500
+@@ -432,7 +432,7 @@ extra_compile_args = %s
 
 ext_modules = [Extension('%s', sources=['%s.%s', %s],
                      libraries=%s,
@ -23,41 +23,70 @@ diff -up src/sage/misc/cython.py.orig src/sage/misc/cython.py
                      language = '%s' )]
 
 diff -up src/setup.py.orig src/setup.py
--- src/setup.py.orig	2016-10-20 08:01:54.264523902 -0400
-+++ src/setup.py	2016-10-20 08:02:33.449525402 -0400
-@@ -584,11 +584,9 @@ def run_cythonize():
-         print('Enabling Cython profiling support')
-         profile = True
- 
-    # Disable Cython caching (the cache is stored in ~/.cycache which is
+--- src/setup.py.orig	2017-03-04 13:15:50.884450879 -0500
+++ src/setup.py	2017-03-04 13:18:14.831456391 -0500
+@@ -412,9 +412,8 @@ class sage_build_ext(build_ext):
+             # Debugging
+             gdb_debug=debug,
+             output_dir=SAGE_CYTHONIZED,
+-            # Disable Cython caching, which is currently too broken to
+-            # use reliably: http://trac.sagemath.org/ticket/17851
+-            cache=False,
 +            # Enable Cython caching (the cache is stored in ~/.cycache which is
-     # Cython's default).
-    # Cycache is currently too broken to use reliably:
-    # http://trac.sagemath.org/ticket/17851
-    Cython.Compiler.Main.default_options['cache'] = False
-+    Cython.Compiler.Main.default_options['cache'] = True
+            cache=True,
+             )
 
-     force = True
-     version_file = os.path.join(SAGE_CYTHONIZED, '.cython_version')
-@@ -641,21 +639,6 @@ print("Discovered Python/Cython sources,
- 
- 
- #########################################################
-### Clean
-#########################################################
-
-print('Cleaning up stale installed files....')
+         open(version_file, 'w').write(version_stamp)
+@@ -699,9 +698,6 @@ class sage_install(install):
+         install.run(self)
+         self.install_kernel_spec()
+         log.warn('Cleaning up stale installed files....')
 -        t = time.time()
-from sage_setup.clean import clean_install_dir
-output_dirs = SITE_PACKAGES + glob.glob(os.path.join(build_base, 'lib*'))
-for output_dir in output_dirs:
-    print('- cleaning {0}'.format(output_dir))
-    clean_install_dir(output_dir, python_packages, python_modules,
-            ext_modules, python_data_files)
-print('Finished cleaning, time: %.2f seconds.' % (time.time() - t))
-
-
-#########################################################
- ### Install also Jupyter kernel spec
- #########################################################
+-        self.clean_stale_files()
+-        log.warn('Finished cleaning, time: %.2f seconds.' % (time.time() - t))
 
+     def install_kernel_spec(self):
+         """
+@@ -715,42 +711,6 @@ class sage_install(install):
+         from sage.repl.ipython_kernel.install import SageKernelSpec
+         SageKernelSpec.update()
+ 
+-    def clean_stale_files(self):
+-        """
+-        Remove stale installed files.
+-
+-        This removes files which are built/installed but which do not
+-        exist in the Sage sources (typically because some source file
+-        has been deleted). Files are removed from the build directory
+-        ``build/lib-*`` and from the install directory ``site-packages``.
+-        """
+-        dist = self.distribution
+-        cmd_build_py = dist.get_command_obj("build_py")
+-        cmd_build_py.ensure_finalized()
+-        cmd_build_ext = dist.get_command_obj("build_ext")
+-        cmd_build_ext.ensure_finalized()
+-
+-        # Determine all Python modules inside all packages
+-        py_modules = []
+-        for package in dist.packages:
+-            package_dir = cmd_build_py.get_package_dir(package)
+-            py_modules += cmd_build_py.find_package_modules(package, package_dir)
+-        # modules is a list of triples (package, module, module_file).
+-        # Construct the complete module name from this.
+-        py_modules = ["{0}.{1}".format(*m) for m in py_modules]
+-
+-        # Clean install directory (usually, purelib and platlib are the same)
+-        # and build directory.
+-        output_dirs = [self.install_purelib, self.install_platlib, self.build_lib]
+-        from sage_setup.clean import clean_install_dir
+-        for output_dir in set(output_dirs):
+-            log.warn('- cleaning {0}'.format(output_dir))
+-            clean_install_dir(output_dir,
+-                    dist.packages,
+-                    py_modules,
+-                    dist.ext_modules,
+-                    cmd_build_ext.cythonized_files)
+-
+ 
+ #########################################################
+ ### Distutils
--- a/sagemath-sagedoc.patch
+++ b/sagemath-sagedoc.patch
@ -1,7 +1,7 @@
 diff -up src/doc/common/conf.py.orig src/doc/common/conf.py
--- src/doc/common/conf.py.orig	2016-10-20 08:03:49.618528319 -0400
-+++ src/doc/common/conf.py	2016-10-20 08:04:20.281529493 -0400
-@@ -217,7 +217,7 @@ if (os.environ.get('SAGE_DOC_MATHJAX', '
+--- src/doc/common/conf.py.orig	2017-03-30 11:27:42.351311111 -0400
+++ src/doc/common/conf.py	2017-03-30 11:27:44.482311193 -0400
+@@ -218,7 +218,7 @@ if (os.environ.get('SAGE_DOC_MATHJAX', '
     html_theme_options['mathjax_macros'] = sage_mathjax_macros()
 
     from pkg_resources import Requirement, working_set
@ -11,8 +11,8 @@ diff -up src/doc/common/conf.py.orig src/doc/common/conf.py
 
     # It would be really nice if sphinx would copy the entire mathjax directory,
 diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
--- src/sage/doctest/control.py.orig	2016-10-20 08:03:49.619528319 -0400
-+++ src/sage/doctest/control.py	2016-10-20 08:04:20.283529494 -0400
+--- src/sage/doctest/control.py.orig	2017-03-30 11:27:42.358311112 -0400
+++ src/sage/doctest/control.py	2017-03-30 11:27:44.483311193 -0400
@@ -95,7 +95,6 @@ class DocTestDefaults(SageObject):
         self.valgrind = False
         self.massif = False
@ -30,15 +30,7 @@ diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
                 # Non-interactive debuggers: 48 hours
                 options.timeout = int(os.getenv('SAGE_TIMEOUT_VALGRIND', 48 * 60 * 60))
             elif options.long:
-@@ -635,7 +634,6 @@ class DocTestController(SageObject):
-         from sage.env import SAGE_SRC, SAGE_DOC_SRC, SAGE_ROOT
-         def all_files():
-             self.files.append(opj(SAGE_SRC, 'sage'))
-            self.files.append(opj(SAGE_SRC, 'sage_setup'))
-             self.files.append(SAGE_DOC_SRC)
-             self.options.sagenb = True
-         DOT_GIT= opj(SAGE_ROOT, '.git')
-@@ -1030,13 +1028,8 @@ class DocTestController(SageObject):
+@@ -1030,13 +1029,8 @@ class DocTestController(SageObject):
             elif opt.cachegrind:
                 toolname = "cachegrind"
                 flags = os.getenv("SAGE_CACHEGRIND_FLAGS", "")
@ -52,7 +44,7 @@ diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
             if "%s" in flags:
                 flags %= toolname + ".%p" # replace %s with toolname
         cmd += flags + sage_cmd
-@@ -1096,10 +1089,10 @@ class DocTestController(SageObject):
+@@ -1096,10 +1090,10 @@ class DocTestController(SageObject):
             0
         """
         opt = self.options
@ -66,20 +58,20 @@ 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	2016-10-20 08:03:49.621528319 -0400
-+++ src/sage/interfaces/singular.py	2016-10-20 08:04:20.286529494 -0400
-@@ -2258,7 +2258,7 @@ def generate_docstring_dictionary():
+--- src/sage/interfaces/singular.py.orig	2017-03-30 11:27:42.364311112 -0400
+++ src/sage/interfaces/singular.py	2017-03-30 11:27:44.486311193 -0400
+@@ -2291,7 +2291,7 @@ def generate_docstring_dictionary():
     nodes.clear()
     node_names.clear()
 
-    singular_docdir = os.environ["SAGE_LOCAL"]+"/share/singular/"
+-    singular_docdir = SAGE_LOCAL+"/share/info/"
 +    singular_docdir = os.environ["SINGULAR_BIN_DIR"]+"/info/"
 
     new_node = re.compile("File: singular\.hlp,  Node: ([^,]*),.*")
     new_lookup = re.compile("\* ([^:]*):*([^.]*)\..*")
 diff -up src/sage_setup/docbuild/ext/multidocs.py.orig src/sage_setup/docbuild/ext/multidocs.py
--- src/sage_setup/docbuild/ext/multidocs.py.orig	2016-10-20 08:03:49.622528319 -0400
-+++ src/sage_setup/docbuild/ext/multidocs.py	2016-10-20 08:04:20.287529494 -0400
+--- src/sage_setup/docbuild/ext/multidocs.py.orig	2017-03-30 11:27:42.371311112 -0400
+++ src/sage_setup/docbuild/ext/multidocs.py	2017-03-30 11:27:44.487311193 -0400
@@ -83,8 +83,11 @@ def merge_environment(app, env):
             for ind in newalldoc:
                 # treat subdocument source as orphaned file and don't complain
@ -95,14 +87,16 @@ diff -up src/sage_setup/docbuild/ext/multidocs.py.orig src/sage_setup/docbuild/e
             newcite = {}
             for ind, (path, tag) in docenv.citations.iteritems():
 diff -up src/sage_setup/docbuild/__init__.py.orig src/sage_setup/docbuild/__init__.py
--- src/sage_setup/docbuild/__init__.py.orig	2016-10-20 08:04:16.858529362 -0400
-+++ src/sage_setup/docbuild/__init__.py	2016-10-20 08:04:20.288529494 -0400
-@@ -295,12 +295,12 @@ class AllBuilder(object):
+--- src/sage_setup/docbuild/__init__.py.orig	2017-03-30 11:27:42.379311112 -0400
+++ src/sage_setup/docbuild/__init__.py	2017-03-30 11:29:25.179315049 -0400
+@@ -248,13 +248,14 @@ if NUM_THREADS > 1:
+         # map_async handles KeyboardInterrupt correctly. Plain map and
         # apply_async does not, so don't use it.
-         x = pool.map_async(build_other_doc, L, 1)
+         x = pool.map_async(target, args, 1)
+        ret = []
         try:
-            x.get(99999)
-+            x.get(3600)
+-            ret = x.get(99999)
+            ret = x.get(3600)
             pool.close()
             pool.join()
         except Exception:
@ -110,20 +104,5 @@ diff -up src/sage_setup/docbuild/__init__.py.orig src/sage_setup/docbuild/__init
             if ABORT_ON_ERROR:
 +                pool.terminate()
                 raise
-         logger.warning("Elapsed time: %.1f seconds."%(time.time()-start))
-         logger.warning("Done building the documentation!")
-@@ -492,12 +492,12 @@ class ReferenceBuilder(AllBuilder):
-             # (See comment in AllBuilder._wrapper about using map instead of apply.)
-             x = pool.map_async(build_ref_doc, L, 1)
-             try:
-                x.get(99999)
-+                x.get(3600)
-                 pool.close()
-                 pool.join()
-             except Exception:
-                pool.terminate()
-                 if ABORT_ON_ERROR:
-+                    pool.terminate()
-                     raise
-             # The html refman must be build at the end to ensure correct
-             # merging of indexes and inventories.
+         return ret
+ else:
--- a/sagemath-scripts.patch
+++ b/sagemath-scripts.patch
@ -1,6 +1,6 @@
 diff -up src/bin/sage.orig src/bin/sage
--- src/bin/sage.orig	2016-12-30 06:31:16.930949819 -0500
-+++ src/bin/sage	2016-12-30 06:31:50.812950266 -0500
+--- src/bin/sage.orig	2017-03-04 12:58:43.035411519 -0500
+++ src/bin/sage	2017-03-04 13:08:11.111433272 -0500
@@ -1,5 +1,16 @@
 #!/usr/bin/env bash
 
@ -62,16 +62,16 @@ diff -up src/bin/sage.orig src/bin/sage
 
     echo
     ####  1.......................26..................................................78
-@@ -78,8 +78,6 @@ usage_advanced() {
-     echo "                         'default', 'sagenb', and 'jupyter'). See the output"
-     echo "                         of sage --notebook --help for more details and"
-     echo "                         examples of how to pass optional arguments"
+@@ -79,8 +79,6 @@ usage_advanced() {
+     echo "                         See the output of sage --notebook --help"
+     echo "                         for more details and examples of how to pass"
+     echo "                         optional arguments"
 -    echo "  -bn, -build-and-notebook [...] -- build the Sage library then start"
 -    echo "                         the Sage notebook"
     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"
-@@ -98,18 +96,12 @@ usage_advanced() {
+@@ -99,17 +97,13 @@ 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"
@ -81,16 +81,15 @@ diff -up src/bin/sage.orig src/bin/sage
     echo "  -lisp [...]         -- run Lisp interpreter included with Sage"
     echo "  -M2 [...]           -- run Sage's Macaulay2 with given arguments"
 -    command -v M2 &>/dev/null || \
-    echo "                         (not installed currently, run sage -i macaulay2)"
+     echo "                         (not installed currently, run sage -i macaulay2)"
     echo "  -maxima [...]       -- run Sage's Maxima with given arguments"
     echo "  -mwrank [...]       -- run Sage's mwrank with given arguments"
     echo "  -polymake [...]     -- run Sage's Polymake with given arguments"
 -    command -v polymake &>/dev/null || \
-    echo "                         (not installed currently, run sage -i polymake)"
+     echo "                         (not installed currently, run sage -i polymake)"
     echo "  -python [...]       -- run the Python interpreter"
     echo "  -R [...]            -- run Sage's R with given arguments"
-     echo "  -scons [...]        -- run Sage's scons"
-@@ -121,49 +113,7 @@ usage_advanced() {
+@@ -122,55 +116,7 @@ usage_advanced() {
     echo
     ####  1.......................26..................................................78
     ####  |.....................--.|...................................................|
@ -107,6 +106,12 @@ diff -up src/bin/sage.orig src/bin/sage
 -    echo "                                 if they are already installed"
 -    echo "                           -s -- do not delete the temporary build directories"
 -    echo "                                 after a successful build"
+-    echo "                           -y -- reply yes to prompts about experimental"
+-    echo "                                 and old-style packages; warning: there"
+-    echo "                                 is no guarantee that these packages will"
+-    echo "                                 build correctly; use at your own risk"
+-    echo "                           -n -- reply no to prompts about experimental"
+-    echo "                                 and old-style packages"
 -    echo "  -p [opts] [packages]-- install the given Sage packages, without dependency"
 -    echo "                         checking and with support for old-style spkgs."
 -    echo "                         Options are -c, -d and -s with the same meaning as"
@ -141,7 +146,7 @@ diff -up src/bin/sage.orig src/bin/sage
     echo "  -startuptime [module] -- display how long each component of Sage takes to"
     echo "                         start up; optionally specify a module to get more"
     echo "                         details about that particular module"
-@@ -193,7 +143,6 @@ usage_advanced() {
+@@ -200,7 +146,6 @@ usage_advanced() {
     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"
@ -149,7 +154,7 @@ diff -up src/bin/sage.orig src/bin/sage
     echo "  -search_src <string> -- search through all the Sage library code for string"
     echo "  -search_doc <string> -- search through the Sage documentation for string"
     echo "  -grep <string>      -- same as -search_src"
-@@ -213,16 +162,6 @@ usage_advanced() {
+@@ -220,16 +165,6 @@ usage_advanced() {
     echo
     ####  1.......................26..................................................78
     ####  |.....................--.|...................................................|
@ -166,7 +171,7 @@ diff -up src/bin/sage.orig src/bin/sage
     echo "Valgrind memory debugging:"
     echo "  -cachegrind         -- run Sage using Valgrind's cachegrind tool.  The log"
     echo "                         files are named sage-cachegrind.PID can be found in"
-@@ -236,9 +175,6 @@ usage_advanced() {
+@@ -243,9 +178,6 @@ 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"
@ -176,10 +181,27 @@ diff -up src/bin/sage.orig src/bin/sage
     echo "  -valgrind           -- this is an alias for -memcheck"
     echo
     echo "You can also use -- before a long option, e.g., 'sage --optional'."
-@@ -263,87 +199,6 @@ if [ "$1" = '--nodotsage' ]; then
-     exit $status
- fi
+@@ -253,104 +185,6 @@ usage_advanced() {
+     exit 0
+ }
 
+-
+-#####################################################################
+-# Special options to be processed without sage-env
+-#####################################################################
+-
+-# Check for '--nodotsage' before sourcing sage-env; otherwise sage-env
+-# will already have set some environment variables with the old
+-# setting for DOT_SAGE.
+-if [ "$1" = '--nodotsage' ]; then
+-    export DOT_SAGE=`mktemp -d ${TMPDIR:-/tmp}/dotsageXXXXXX`
+-    shift
+-    command "$0" "$@"
+-    status=$?
+-    rm -rf "$DOT_SAGE"
+-    exit $status
+-fi
+-
 -# Check for '--patchbot' before sourcing sage-env: patchbot needs
 -# an unclobbered environment before testing unsafe tickets.
 -if [ "$1" = '-patchbot' -o "$1" = "--patchbot" ]; then
@ -264,7 +286,7 @@ diff -up src/bin/sage.orig src/bin/sage
 if [ $# -gt 0 ]; then
   if [ "$1" = '-h' -o "$1" = '-?' -o "$1" = '-help' -o "$1" = '--help' ]; then
      usage
-@@ -355,23 +210,10 @@ fi
+@@ -362,23 +196,9 @@ fi
 
 # Prepare for running Sage, either interactively or non-interactively.
 sage_setup() {
@ -279,7 +301,7 @@ diff -up src/bin/sage.orig src/bin/sage
 -        echo >&2 '************************************************************************'
 -        exit 1
 -    fi
- 
+-
     # Display the startup banner (unless SAGE_BANNER is explictly "no")
     sage_banner
 
@ -288,7 +310,7 @@ diff -up src/bin/sage.orig src/bin/sage
     if [ ! -d "$IPYTHONDIR" ]; then
         # make sure that $DOT_SAGE exists so that ipython will happily
         # create its config directories there.  If DOT_SAGE doesn't
-@@ -382,20 +224,6 @@ sage_setup() {
+@@ -389,20 +209,6 @@ sage_setup() {
 }
 
 
@ -309,16 +331,7 @@ diff -up src/bin/sage.orig src/bin/sage
 # Start an interactive Sage session, this function never returns.
 interactive_sage() {
     sage_setup
-@@ -472,7 +300,7 @@ fi
- 
- if [ "$1" = '-singular' -o "$1" = '--singular' ]; then
-     shift
-    exec singular "$@"
-+    exec Singular "$@"
- fi
- 
- if [ "$1" = '-sqlite3' -o "$1" = '--sqlite3' ]; then
-@@ -500,16 +328,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
+@@ -507,16 +313,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
     exec ecl "$@"
 fi
 
@ -335,10 +348,27 @@ diff -up src/bin/sage.orig src/bin/sage
 if [ "$1" = '-maxima' -o "$1" = '--maxima' ]; then
     shift
     exec maxima "$@"
-@@ -560,11 +378,6 @@ if [ "$1" = '-git' -o "$1" = '--git' ];
-     exec git "$@"
+@@ -542,11 +338,6 @@ if [ "$1" = '-pip' -o "$1" = '--pip' ];
+     exec pip-lock "$@"
 fi
 
+-if [ "$1" = '-fix-pkg-checksums' -o "$1" = '--fix-pkg-checksums' ]; then
+-    shift
+-    exec sage-fix-pkg-checksums "$@"
+-fi
+-
+ if [ "$1" = '-python' -o "$1" = '--python' ]; then
+     shift
+     exec python "$@"
+@@ -562,16 +353,6 @@ 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
@ -347,10 +377,11 @@ diff -up src/bin/sage.orig src/bin/sage
 if [ "$1" = '-sh' -o "$1" = '--sh' ]; then
     # AUTHORS:
     # - Carl Witty and William Stein: initial version
-@@ -684,20 +497,6 @@ EOF
+@@ -690,19 +471,6 @@ EOF
+     exit $status
 fi
 
- #####################################################################
+-#####################################################################
 -# Test coverage of a module?
 -#####################################################################
 -
@ -363,12 +394,10 @@ diff -up src/bin/sage.orig src/bin/sage
 -    shift
 -    exec sage-coverageall "$@"
 -fi
-
-#####################################################################
- # File conversion
- #####################################################################
 
-@@ -715,11 +514,6 @@ fi
+ #####################################################################
+ # File conversion
+@@ -722,11 +490,6 @@ fi
 # Run Sage's versions of the standard Algebra/Geometry etc. software
 #####################################################################
 
@ -380,7 +409,7 @@ diff -up src/bin/sage.orig src/bin/sage
 if [[ "$1" =~ ^--notebook=.* || "$1" =~ ^-n=.* || "$1" =~ ^-notebook=.* ]] ; then
     sage-cleaner &>/dev/null &
     exec sage-notebook "$@"
-@@ -730,13 +524,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
+@@ -737,13 +500,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
     exec sage-notebook "$@"
 fi
 
@ -394,7 +423,7 @@ diff -up src/bin/sage.orig src/bin/sage
 if [ "$1" = "-inotebook" -o "$1" = '--inotebook' ]; then
     shift
     sage-cleaner &>/dev/null &
-@@ -755,31 +542,12 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
+@@ -762,31 +518,12 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
    exit 0
 fi
 
@ -427,7 +456,7 @@ diff -up src/bin/sage.orig src/bin/sage
     if [ ! -f  "$DOT_SAGE"/init.sage ]; then
         echo >&2 "init.sage does not exist ... creating"
         touch "$DOT_SAGE"/init.sage
-@@ -795,10 +563,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
+@@ -802,10 +539,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
     fi
 fi
 
@ -439,7 +468,7 @@ diff -up src/bin/sage.orig src/bin/sage
     shift
     SAGE_BANNER=no sage_setup
     export PYTHONIOENCODING="utf-8"  # Fix encoding for doctests
-@@ -824,114 +589,6 @@ if [ "$1" = '--location' ]; then
+@@ -831,130 +565,6 @@ if [ "$1" = '--location' ]; then
     exit 0
 fi
 
@ -551,10 +580,26 @@ diff -up src/bin/sage.orig src/bin/sage
 -    exec python -m "sage_setup.docbuild" "$@"
 -fi
 -
- if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then
+-if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then
+-    shift
+-    sage_setup
+-    if [ "$SAGE_DEBUG" = "no" ]; then
+-        gdb -x "$SAGE_LOCAL/bin/sage-gdb-commands" \
+-            -args python "$SAGE_LOCAL/bin/sage-ipython" "$@" -i
+-    else
+-        # Location of cython_debug directory
+-        cygdb_dir="$SAGE_SRC/build/cythonized"
+-        cygdb "$cygdb_dir" "$SAGE_SRC/sage" \
+-            -- -x "$SAGE_LOCAL/bin/sage-gdb-commands" \
+-            -args python "$SAGE_LOCAL/bin/sage-ipython" "$@" -i
+-    fi
+-    exit $?
+-fi
+-
+ if [ "$1" = '-preparse' -o "$1" = "--preparse" ]; then
     shift
-     sage_setup
-@@ -980,26 +637,11 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
+     exec sage-preparse "$@"
+@@ -989,21 +599,10 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
     exec sage-callgrind "$@"
 fi
 
@ -574,16 +619,11 @@ diff -up src/bin/sage.orig src/bin/sage
 -fi
 -
 if [ $# -ge 1 ]; then
-    T=`echo "$1" | sed -e "s/.*\.//"`
-    if [ "$T" = "spkg" ]; then
-        install "$@"
-    fi
-     SAGE_BANNER=no sage_setup
-     unset TERM  # See Trac #12263
-     exec sage-run "$@"
+     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	2016-12-30 06:31:16.938949819 -0500
-+++ src/bin/sage-runtests	2016-12-30 06:31:21.902949885 -0500
+--- src/bin/sage-runtests.orig	2017-03-04 13:08:31.712434061 -0500
+++ src/bin/sage-runtests	2017-03-04 13:08:41.887434451 -0500
@@ -56,10 +56,6 @@ if __name__ == "__main__":
                       help="run doctests using Valgrind's cachegrind tool.  The log "
                          "files are named sage-cachegrind.PID and can be found in " +
@ -596,8 +636,8 @@ 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	2016-12-30 06:31:16.945949819 -0500
-+++ src/bin/sage-valgrind	2016-12-30 06:31:21.903949885 -0500
+--- src/bin/sage-valgrind.orig	2017-03-04 13:08:52.937434874 -0500
+++ src/bin/sage-valgrind	2017-03-04 13:09:13.143435648 -0500
@@ -1,16 +1,6 @@
 #!/usr/bin/env bash
 
--- a/sagemath-singular.patch
+++ b/sagemath-singular.patch
@ -0,0 +1,35 @@
+diff -up src/sage/libs/singular/decl.pxd.orig src/sage/libs/singular/decl.pxd
+--- src/sage/libs/singular/decl.pxd.orig	2017-03-29 14:40:18.119445065 -0400
+++ src/sage/libs/singular/decl.pxd	2017-03-29 14:42:36.153450351 -0400
+@@ -484,8 +484,8 @@ cdef extern from "singular/Singular/libs
+ 
+     ring *rDefault(int char , int nvars, char **names)
+     ring *rDefault(const n_Procs_s* cf, int nvars, char **names)
+-    ring *rDefault(int ch             , int nvars, char **names,int ord_size, int *ord, int *block0, int *block1, int **wvhdl)
+-    ring *rDefault(const n_Procs_s* cf, int nvars, char **names,int ord_size, int *ord, int *block0, int *block1, int **wvhdl)
+    ring *rDefault(int ch             , int nvars, char **names,int ord_size, rRingOrder_t *ord, int *block0, int *block1, int **wvhdl)
+    ring *rDefault(const n_Procs_s* cf, int nvars, char **names,int ord_size, rRingOrder_t *ord, int *block0, int *block1, int **wvhdl)
+ 
+ 
+ 
+diff -up src/sage/libs/singular/ring.pyx.orig src/sage/libs/singular/ring.pyx
+--- src/sage/libs/singular/ring.pyx.orig	2017-03-29 14:40:24.767445320 -0400
+++ src/sage/libs/singular/ring.pyx	2017-03-29 14:43:38.593452742 -0400
+@@ -21,7 +21,7 @@ from sage.libs.gmp.mpz cimport mpz_init_
+ from sage.libs.singular.decl cimport number, poly, ring, currRing
+ from sage.libs.singular.decl cimport rChangeCurrRing, rCopy0, rComplete, rDelete, idInit
+ from sage.libs.singular.decl cimport omAlloc0, omStrDup, omAlloc, omAlloc0Bin,  sip_sring_bin, rnumber_bin
+-from sage.libs.singular.decl cimport ringorder_dp, ringorder_Dp, ringorder_lp, ringorder_rp, ringorder_ds, ringorder_Ds, ringorder_ls, ringorder_M, ringorder_C, ringorder_wp, ringorder_Wp, ringorder_ws, ringorder_Ws, ringorder_a
+from sage.libs.singular.decl cimport rRingOrder_t, ringorder_dp, ringorder_Dp, ringorder_lp, ringorder_rp, ringorder_ds, ringorder_Ds, ringorder_ls, ringorder_M, ringorder_C, ringorder_wp, ringorder_Wp, ringorder_ws, ringorder_Ws, ringorder_a
+ from sage.libs.singular.decl cimport p_Copy, prCopyR
+ from sage.libs.singular.decl cimport n_unknown,  n_Zp,  n_Q,   n_R,   n_GF,  n_long_R,  n_algExt,n_transExt,n_long_C,   n_Z,   n_Zn,  n_Znm,  n_Z2m,  n_CF
+ from sage.libs.singular.decl cimport n_coeffType, cfInitCharProc
+@@ -165,7 +165,7 @@ cdef ring *singular_ring_new(base_ring,
+     ##         q    q : GF(q=p^n)       *names         TRUE              (todo)
+ 
+     _wvhdl  = <int **>omAlloc0((nblcks + 2) * sizeof(int *))
+-    _order  = <int *>omAlloc0((nblcks + 2) * sizeof(int))
+    _order  = <rRingOrder_t *>omAlloc0((nblcks + 2) * sizeof(rRingOrder_t))
+     _block0 = <int *>omAlloc0((nblcks + 2) * sizeof(int))
+     _block1 = <int *>omAlloc0((nblcks + 2) * sizeof(int))
+ 
--- a/sagemath.spec
+++ b/sagemath.spec
@ -34,12 +34,12 @@
 %global SAGE_TIMEOUT_LONG	180

 %global conway_polynomials_pkg	conway_polynomials-0.4
-%global cysignals_pkg		cysignals-1.1.1
+%global cysignals_pkg		cysignals-1.3.2
 %global	elliptic_curves_pkg	elliptic_curves-0.8
 %global	flintqs_pkg		flintqs-1.0
-%global graphs_pkg		graphs-20151224
+%global graphs_pkg		graphs-20161026
 %if %{with bundled_ipython}
-%global ipython_pkg		ipython-5.0.0
+%global ipython_pkg		ipython-5.1.0
 %endif
 %if %{with bundled_pari}
 %global pari_pkg		pari-2.8.0.alpha
@ -51,6 +51,7 @@
 %global rubiks_pkg		rubiks-20070912
 %global	sagenb_pkg		sagenb-0.13
 %global sagetex_pkg		sagetex-3.0
+%global Sphinx_pkg		Sphinx-1.4.4

 %global SAGE_ROOT		%{_libdir}/sagemath
 %global SAGE_LOCAL		%{SAGE_ROOT}/local
@ -64,8 +65,8 @@
 Name:		sagemath
 Group:		Applications/Engineering
 Summary:	A free open-source mathematics software system
-Version:	7.4
-Release:	4%{?dist}
+Version:	7.5.1
+Release:	1%{?dist}
 # The file ${SAGE_ROOT}/COPYING.txt is the upstream license breakdown file
 # Additionally, every $files section has a comment with the license name
 # before files with that license
@ -185,8 +186,8 @@ Patch29:	%{name}-atlas.patch
 # Update for python-flask-0.11.1
 Patch30:	%{name}-flask.patch

-# Corrections to build in latest f25 and rawhide
-Patch31:	%{name}-ftbfs.patch
+# Minor adaptation to latest singular
+Patch31:	%{name}-singular.patch

 BuildRequires:	4ti2
 BuildRequires:	arb-devel
@ -244,7 +245,9 @@ BuildRequires:	nauty
 BuildRequires:	ntl-devel
 BuildRequires:	numpy
 BuildRequires:	palp
-%if %{without bundled_pari}
+%if %{with bundled_pari}
+BuildConflicts:	pari-devel
+%else
 BuildRequires:	pari-devel
 BuildRequires:	pari-gp
 %endif
@ -266,6 +269,7 @@ BuildRequires:	python-networkx
 BuildRequires:	python-pexpect
 %endif
 BuildRequires:	python-pkgconfig
+BuildRequires:	python-psutil
 BuildRequires:	python-sphinx
 BuildRequires:	python-six
 BuildRequires:	python-twisted
@ -599,6 +603,11 @@ computations, and plots from the Sage mathematics software suite
 pushd build/pkgs/cysignals
    tar jxf ../../../upstream/%{cysignals_pkg}.tar.bz2
    mv %{cysignals_pkg} src
+    if [ %{__isa_bits} = "64" ]; then
+	for file in $(find . -name cysignals-CSI); do
+	    sed -i "s/'lib'/'%{_lib}'/" $file
+	done
+    fi
 popd

 pushd build/pkgs/conway_polynomials
@ -679,6 +688,20 @@ pushd build/pkgs/sagetex
    mv %{sagetex_pkg} src
 popd

+%if %{with docs}
+%if %{with sphinx_hack}
+pushd build/pkgs/sphinx
+    tar zxf ../../../upstream/%{Sphinx_pkg}.tar.gz
+    mv %{Sphinx_pkg} src
+    pushd src
+	for diff in `ls ../patches/*.patch`; do
+	    patch -p1 < $diff
+	done
+    popd
+popd
+%endif
+%endif
+
 %patch1
 %patch2
 %patch3
@ -714,6 +737,7 @@ popd
 %patch24
 %patch25
 %patch26
+
 %patch27
 %patch28
 %patch29
@ -1186,9 +1210,11 @@ pushd src/doc
    export PYTHONPATH=$SAGE_SETUP:%{buildroot}%{python_sitearch}:$SAGE_PYTHONPATH:$SAGE_DOC

 %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
+    pushd ../../build/pkgs/sphinx/src
+        %__python2 setup.py build
+        %__python2 setup.py install --root %{buildroot} --install-purelib=%{python_sitearch}
+        rm -f %{buildroot}%{_bindir}/sphinx*
+    popd
 %endif

    # there we go
@ -1198,7 +1224,7 @@ pushd src/doc
    # python -m sage_setup.docbuild
    # FIXME there is a 'ja' translation, but adding it to $LANGUAGES
    # does not get documentation built
-    LANGUAGES="ca de en fr hu it pt ru tr" \
+    SAGE_NUM_THREADS=2 LANGUAGES="ca de en fr hu it pt ru tr" \
 	%__python2 -m docbuild --no-pdf-links -k all html
    rm -f %{buildroot}%{SAGE_SRC}/doc
    ln -sf %{SAGE_DOC} %{buildroot}%{SAGE_SRC}/doc
@ -1221,7 +1247,8 @@ sed -i 's|%{buildroot}||g' $SAGE_DOC/test.log
 %endif

 %if %{with sphinx_hack}
-    rm -fr %{buildroot}%{python_sitearch}/sphinx
+    rm -fr %{buildroot}%{python_sitearch}/sphinx \
+	%{buildroot}%{python_sitearch}/Sphinx*
 %endif

 # More wrong buildroot references
@ -1233,6 +1260,8 @@ perl -pi -e 's|%{buildroot}||g;' \

 # Script was used to build documentation
 perl -pi -e 's|%{buildroot}||g;s|^##||g;' %{buildroot}%{_bindir}/sage
+perl -pi -e 's|%{buildroot}||;' \
+    %{buildroot}%{python_sitearch}/cysignals/__init__.pxd

 #------------------------------------------------------------------------
 # Fix links
@ -1282,6 +1311,7 @@ chmod -x %{buildroot}%{SAGE_DOC}/en/prep/media/Rplot001.png
 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
+find %{buildroot}%{SAGE_DOC} -name 'core.*' -exec rm {} \;
 %endif

 # remove .po files
@ -1662,6 +1692,9 @@ exit 0

 ########################################################################
 %changelog
+* Thu Apr  6 20176 pcpa <paulo.cesar.pereira.de.andrade@gmail.com> - 7.5.1-1
+- Update to sagemath 7.5.1
+
 * Fri Mar  3 2017 Jerry James <loganjerry@gmail.com> - 7.4-4
 - Rebuild for ppl 1.2

--- a/2
+++ b/2
@ -1 +1 @@
-SHA512 (sage-7.4.tar.gz) = e45d3b5617b190302e8fff9f281551d0b2c27710d860892d6511019272e2f80487e27ffe7dce6c1276da721817a8cbd7946fd5a2e32741e5cba1955496c1b041
+SHA512 (sage-7.5.1.tar.gz) = ef18951250573f4c04911757664e25f7e03332df36efd948e189009e62573b8f120a413b322947fee6e914cbcc64fbd99d5a960954a04ba5786660ecc0a6ee96