Update to sagemath 8.6.

Also:
- Install an SVG icon instead of a fixed size (128x128) icon.
- Require hicolor-icon-theme since we install an icon.
- Drop obsolete Obsolete.

sagemath-escape.patch

@@ -1,6 +1,5 @@
-diff -up src/sage/combinat/crystals/alcove_path.py.orig src/sage/combinat/crystals/alcove_path.py
+--- src/sage/combinat/crystals/alcove_path.py.orig	2019-01-14 17:16:01.000000000 -0700
---- src/sage/combinat/crystals/alcove_path.py.orig	2018-12-22 16:37:07.000000000 -0700
++++ src/sage/combinat/crystals/alcove_path.py	2019-02-07 15:43:21.188614487 -0700
-+++ src/sage/combinat/crystals/alcove_path.py	2019-01-04 11:16:55.320833974 -0700
 @@ -383,7 +383,7 @@ class CrystalOfAlcovePaths(UniqueReprese
  
          One can compute all vertices of the crystal by finding all the
@@ -10,9 +9,39 @@ diff -up src/sage/combinat/crystals/alcove_path.py.orig src/sage/combinat/crysta
          search algorithm.
  
          .. WARNING::
-diff -up src/sage/homology/homology_group.py.orig src/sage/homology/homology_group.py
+--- src/sage/combinat/crystals/kirillov_reshetikhin.py.orig	2019-01-14 17:16:01.000000000 -0700
---- src/sage/homology/homology_group.py.orig	2018-12-22 16:37:08.000000000 -0700
++++ src/sage/combinat/crystals/kirillov_reshetikhin.py	2019-02-07 15:44:37.612978369 -0700
-+++ src/sage/homology/homology_group.py	2019-01-04 11:17:37.136047323 -0700
+@@ -3443,7 +3443,7 @@ class CrystalOfTableaux_E7(CrystalOfTabl
+     <sage.combinat.crystals.kirillov_reshetikhin.KR_type_E7>` `B^{7,s}`.
+     """
+     def module_generator(self, shape):
+-        """
++        r"""
+         Return the module generator of ``self`` with shape ``shape``.
+ 
+         .. NOTE::
+@@ -3496,7 +3496,7 @@ class KR_type_E7(KirillovReshetikhinGene
+ 
+     @cached_method
+     def A7_decomposition(self):
+-        """
++        r"""
+         Return the decomposition of ``self`` into `A_7` highest
+         weight crystals.
+ 
+--- src/sage/groups/perm_gps/permgroup_named.py.orig	2019-01-14 17:16:02.000000000 -0700
++++ src/sage/groups/perm_gps/permgroup_named.py	2019-02-07 15:51:38.530055246 -0700
+@@ -3027,7 +3027,7 @@ class SuzukiGroup(PermutationGroup_uniqu
+         return "The Suzuki group over %s" % self.base_ring()
+ 
+ class ComplexReflectionGroup(PermutationGroup_unique):
+-    """
++    r"""
+     A finite complex reflection group as a permutation group.
+ 
+     We can realize `G(m,1,n)` as `m` copies of the symmetric group
+--- src/sage/homology/homology_group.py.orig	2019-01-14 17:16:03.000000000 -0700
++++ src/sage/homology/homology_group.py	2019-02-07 15:43:21.197614413 -0700
 @@ -109,7 +109,7 @@ class HomologyGroup_class(AdditiveAbelia
              sage: from sage.homology.homology_group import HomologyGroup
              sage: H = HomologyGroup(7, ZZ, [4,4,4,4,4,7,7])
@@ -22,10 +51,9 @@ diff -up src/sage/homology/homology_group.py.orig src/sage/homology/homology_gro
              sage: latex(HomologyGroup(6, ZZ))
              \ZZ^{6}
          """
-diff -up src/sage/rings/number_field/number_field.py.orig src/sage/rings/number_field/number_field.py
+--- src/sage/rings/number_field/number_field.py.orig	2019-01-14 17:16:04.000000000 -0700
---- src/sage/rings/number_field/number_field.py.orig	2018-12-22 16:37:10.000000000 -0700
++++ src/sage/rings/number_field/number_field.py	2019-02-07 15:43:21.220614222 -0700
-+++ src/sage/rings/number_field/number_field.py	2019-01-08 16:25:39.730547708 -0700
+@@ -6622,7 +6622,7 @@ class NumberField_generic(WithEqualityBy
-@@ -6613,7 +6613,7 @@ class NumberField_generic(WithEqualityBy
          return U
  
      def S_unit_solutions(self, S=[], prec=106, include_exponents=False, include_bound=False, proof=None):

sagemath-fes-build.patch

@@ -1,14 +1,30 @@
 diff -up src/sage/libs/fes.pyx.orig src/sage/libs/fes.pyx
---- src/sage/libs/fes.pyx.orig	2018-12-22 16:37:08.000000000 -0700
+--- src/sage/libs/fes.pyx.orig	2019-01-14 17:16:03.000000000 -0700
-+++ src/sage/libs/fes.pyx	2019-01-17 09:46:02.925523575 -0700
++++ src/sage/libs/fes.pyx	2019-02-07 08:30:50.024227599 -0700
-@@ -86,8 +86,8 @@ from sage.rings.polynomial.pbori import
+@@ -11,7 +11,7 @@ variables. Performing a full exhaustive
- from sage.arith.all import binomial
+ take a **long** time. The number of variables can be artificially
- from sage.combinat.subset import Subsets
+ reduced to 64 by specializing some of them.
  
--from sage.matrix.all import *
+-Note that the FES library **requires** at least of the equations to be
--from sage.modules.all import *
++Note that the FES library **requires** at least one of the equations to be
-+from sage.matrix.all import identity_matrix, matrix
+ non-linear.
-+from sage.modules.all import vector
+ 
+ AUTHORS:
+@@ -71,7 +71,7 @@ from cysignals.signals cimport sig_on, s
+ cdef extern from "fes_interface.h":
+     ctypedef int (*solution_callback_t)(void *, uint64_t)
+ 
+-    void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose)
++    void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose, int T)
  
  
+ from sage.rings.integer import Integer
+@@ -217,7 +217,7 @@ def exhaustive_search(eqs,  max_sols=Inf
  
+     # ------- runs the library
+     sig_on()
+-    exhaustive_search_wrapper(n, len(eqs), degree, coeffs, report_solution, <void *> internal_state, verbose)
++    exhaustive_search_wrapper(n, len(eqs), degree, coeffs, report_solution, <void *> internal_state, verbose, 0)
+     sig_off()
+ 
+     # ------- frees memory occupied by the dense representation of the equations

sagemath-libgap.patch

@@ -1,53 +1,51 @@
 diff -up src/sage/env.py.orig src/sage/env.py
---- src/sage/env.py.orig	2018-12-22 16:37:08.000000000 -0700
+--- src/sage/env.py.orig	2019-01-14 17:16:02.000000000 -0700
-+++ src/sage/env.py	2019-01-04 11:08:22.825475344 -0700
++++ src/sage/env.py	2019-02-07 16:11:38.887417503 -0700
 @@ -164,7 +164,7 @@ _add_variable_or_fallback('CONWAY_POLYNO
  _add_variable_or_fallback('GRAPHS_DATA_DIR',  opj('$SAGE_SHARE','graphs'))
  _add_variable_or_fallback('ELLCURVE_DATA_DIR',opj('$SAGE_SHARE','ellcurves'))
  _add_variable_or_fallback('POLYTOPE_DATA_DIR',opj('$SAGE_SHARE','reflexive_polytopes'))
--_add_variable_or_fallback('GAP_ROOT_DIR',     opj('$SAGE_LOCAL','gap','latest'))
+-_add_variable_or_fallback('GAP_ROOT_DIR',     opj('$SAGE_SHARE','gap'))
 +_add_variable_or_fallback('GAP_ROOT_DIR',     opj('/usr','lib','gap'))
  _add_variable_or_fallback('THEBE_DIR',        opj('$SAGE_SHARE','thebe'))
  _add_variable_or_fallback('COMBINATORIAL_DESIGN_DATA_DIR', opj('$SAGE_SHARE', 'combinatorial_designs'))
  _add_variable_or_fallback('CREMONA_MINI_DATA_DIR', opj('$SAGE_SHARE', 'cremona'))
-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	2018-12-22 16:37:08.000000000 -0700
-+++ src/sage/libs/gap/test/main.c	2019-01-04 11:08:22.842475024 -0700
-@@ -22,7 +22,7 @@ void eval(char* cmd) {
-   libgap_start_interaction(cmd);
- 
-   libgap_enter();
--  libGAP_ReadEvalCommand(libGAP_BottomLVars);
-+  libGAP_ReadEvalCommand(libGAP_BottomLVars, NULL);
-   libGAP_ViewObjHandler(libGAP_ReadEvalResult);
-   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	2018-12-22 16:37:08.000000000 -0700
+--- src/sage/libs/gap/util.pyx.orig	2019-01-14 17:16:03.000000000 -0700
-+++ src/sage/libs/gap/util.pyx	2019-01-04 11:08:22.843475005 -0700
++++ src/sage/libs/gap/util.pyx	2019-02-07 16:13:52.658939819 -0700
-@@ -27,6 +27,8 @@ from sage.cpython.string cimport str_to_
+@@ -18,6 +18,7 @@ import os
- from sage.interfaces.gap_workspace import prepare_workspace_dir
+ import signal
- from sage.env import SAGE_LOCAL, GAP_ROOT_DIR
+ import warnings
  
-+import re
++from posix.dlfcn cimport dlopen, dlclose, RTLD_NOW, RTLD_GLOBAL
-+
+ from libc.string cimport strcpy, strlen
  
- ############################################################################
+ from cpython.exc cimport PyErr_SetObject, PyErr_Occurred, PyErr_Fetch
- ### Hooking into the GAP memory management #################################
+@@ -181,7 +182,7 @@ def gap_root():
-@@ -185,7 +187,7 @@ def gap_root():
  
          sage: from sage.libs.gap.util import gap_root
          sage: gap_root()   # random output
 -        '/home/vbraun/opt/sage-5.3.rc0/local/gap/latest'
 +        '/usr/lib/gap'
      """
-     try:
+     if os.path.exists(sage.env.GAP_ROOT_DIR):
-         if os.path.exists(GAP_ROOT_DIR):
+         return sage.env.GAP_ROOT_DIR
-@@ -251,6 +253,7 @@ cdef initialize():
+@@ -259,6 +260,18 @@ cdef initialize():
-     libgap_initialize(argc, argv)
+     global _gap_is_initialized, environ
-     gap_error_msg = char_to_str(libgap_get_output())
+     if _gap_is_initialized: return
-     libgap_finish_interaction()
-+    gap_error_msg = re.sub(r'#I.*\n?', '', gap_error_msg, flags=re.MULTILINE)
-     if gap_error_msg:
-         raise RuntimeError('libGAP initialization failed\n' + gap_error_msg)
  
++    # Hack to ensure that all symbols provided by libgap are loaded into the
++    # global symbol table
++    # Note: we could use RTLD_NOLOAD and avoid the subsequent dlclose() but
++    # this isn't portable
++    cdef void* handle
++    handle = dlopen("libgap.so", RTLD_NOW | RTLD_GLOBAL)
++    if handle == NULL:
++        raise RuntimeError(
++                "Could not dlopen() libgap.so even though it should already "
++                "be loaded!")
++    dlclose(handle)
++
+     # Define argv and environ variables, which we will pass in to
+     # initialize GAP. Note that we must pass define the memory pool
+     # size!

sagemath.spec

@@ -21,13 +21,13 @@
 # not functional due to missing jar dependencies
 %bcond_with sage3d
 
-# use an workaround to match upstream sagemath patched sphinx
+# use a workaround to match upstream sagemath patched sphinx
 %bcond_without sphinx_hack
 
 # use workaround to match upstream sagemath patched cython
 %bcond_with cython_hack
 
-%ifarch x86_64
+%ifarch %{ix86} x86_64
 %bcond_without fes
 %else
 %bcond_with fes
@@ -73,7 +73,7 @@
 # Spkg equivalents of required rpms; we pretend they are installed as spkgs.
 # The version numbers shown are those of the latest released spkg, if the Fedora
 # version is not behind.
-%global SAGE_REQUIRED_PKGS 4ti2-1.6.7 cbc-2.9.4 CoCoALib-0.99564 cryptominisat-5.0.1 gap_packages-4.8.6new2.p0 gmp-6.1.2 gmpy2-2.1.0a4.p0 lrslib-062+autotools-2017-03-03 qepcad-B.1.71 saclib-2.2.7 sirocco-2.0 surf-1.0.6-gcc6
+%global SAGE_REQUIRED_PKGS 4ti2-1.6.7 cbc-2.9.4 CoCoALib-0.99564 cryptominisat-5.0.1 gap_packages-4.10.0 gmp-6.1.2 gmpy2-2.1.0a4.p0 lrslib-062+autotools-2017-03-03 qepcad-B.1.71 saclib-2.2.7 sirocco-2.0 surf-1.0.6-gcc6
 
 %global SAGE_ROOT		%{_libdir}/sagemath
 %global SAGE_LOCAL		%{SAGE_ROOT}/local
@@ -86,8 +86,8 @@
 
 Name:		sagemath
 Summary:	A free open-source mathematics software system
-Version:	8.5
+Version:	8.6
-Release:	4%{?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
@@ -356,7 +356,6 @@ Requires:	cddlib-tools
 Requires:	ecl
 Requires:	gap
 Requires:	GAPDoc
-Requires:	gap-libs
 Requires:	gap-pkg-atlasrep
 Requires:	gap-pkg-crime
 Requires:	gap-pkg-design
@@ -366,6 +365,7 @@ Requires:	gap-pkg-sonata
 Requires:	gap-pkg-toric
 Requires:	gfan
 Requires:	gmp-ecm
+Requires:	hicolor-icon-theme
 Requires:	jmol
 Requires:	jsmol
 Requires:	jsmath-fonts
@@ -467,7 +467,6 @@ packages into a common Python-based interface.
 %package	core
 Summary:	Open Source Mathematics Software
 Requires:	%{name}%{?_isa} = %{version}-%{release}
-Obsoletes:	%{name}-devel < 6.8-1
 %if %{with bundled_ipython}
 Provides:	bundled(ipython) = %(cut -d- -f2- <<< %{ipython_pkg})
 Provides:	bundled(prompt_toolkit) = %(cut -d- -f2- <<< %{prompt_tookit_pkg})
@@ -535,7 +534,6 @@ Includes two databases:
 %package	data-etc
 Summary:	Extcode for Sagemath
 Requires:	%{name}-data = %{version}-%{release}
-Obsoletes:      %{name}-data-extcode < %{version}
 BuildArch:	noarch
 
 %description	data-etc
@@ -674,7 +672,7 @@ Summary:	Several programs for working with Rubik's cubes
 Requires:	%{name}%{?_isa} = %{version}-%{release}
 
 %description	rubiks
-Several programs for working with Rubik's cubes, by three  different people.
+Several programs for working with Rubik's cubes, by three different people.
 In summary the three contributors are:
 
 Michael Reid (GPL) http://www.math.ucf.edu/~reid/Rubik/optimal_solver.html
@@ -698,12 +696,15 @@ Requires:	%{name}%{?_isa} = %{version}-%{release}
 Requires:	tex(color.sty)
 Requires:	tex(fancyvrb.sty)
 Requires:	tex(graphicx.sty)
+Requires:	tex(hyperref.sty)
 Requires:	tex(ifpdf.sty)
 Requires:	tex(ifthen.sty)
 Requires:	tex(ifxetex.sty)
 Requires:	tex(listings.sty)
 Requires:	tex(makecmds.sty)
+Requires:	tex(tikz.sty)
 Requires:	tex(verbatim.sty)
+Requires:	tex(xspace.sty)
 
 %description	sagetex
 This is the SageTeX package. It allows you to embed code, results of
@@ -935,8 +936,9 @@ sed -i 's/64m/128m/' src/sage/libs/gap/util.pyx
 
 ########################################################################
 %build
-%set_build_flags
 export CC=%{__cc}
+export CFLAGS="%{optflags}"
+export CXXFLAGS="%{optflags}"
 export SAGE_PYTHON_VERSION=3
 export SAGE_ROOT=%{buildroot}%{SAGE_ROOT}
 export SAGE_LOCAL=%{buildroot}%{SAGE_LOCAL}
@@ -1435,9 +1437,8 @@ ln -sf %{SAGE_SHARE} $SAGE_ROOT/share
 ln -sf src $SAGE_ROOT/devel
 
 # Install menu and icons
-pushd build/pkgs/sagenb/src/sagenb/data
+install -p -m644 -D src/ext/notebook-ipython/logo.svg \
-    install -p -m644 -D sage/images/icon128x128.png %{buildroot}%{_datadir}/pixmaps/%{name}.png
+  %{buildroot}%{_datadir}/icons/hicolor/scalable/apps/sagemath.svg
-popd
 mkdir -p %{buildroot}%{_datadir}/applications
 cat > %{buildroot}%{_datadir}/applications/%{name}.desktop << EOF
 [Desktop Entry]
@@ -1587,7 +1588,7 @@ rm -fr $DOT_SAGE
 %dir %{SAGE_PYTHONPATH}
 # GPLv2+
 %{_bindir}/sage
-%{_datadir}/pixmaps/%{name}.png
+%{_datadir}/icons/hicolor/scalable/apps/%{name}.svg
 %{_datadir}/applications/%{name}.desktop
 %if %{with bundled_thebe}
 # MIT
@@ -1825,6 +1826,12 @@ rm -fr $DOT_SAGE
 
 ########################################################################
 %changelog
+* Mon Feb 18 2019 Jerry James <loganjerry@gmail.com> - 8.6-1
+- Update to sagemath 8.6
+- Install an SVG icon instead of a fixed size (128x128) icon
+- Require hicolor-icon-theme since we install an icon
+- Drop obsolete Obsoletes
+
 * Sun Feb 17 2019 Igor Gnatenko <ignatenkobrain@fedoraproject.org> - 8.5-4
 - Rebuild for readline 8.0
 

sources

@@ -1 +1 @@
-SHA512 (sage-8.5.tar.gz) = ebe373c7be50dc1df96de8a26ce41455869d79159eb584570525bc8a886d95c2605985bdecfa3e5d0ca50248d6bef605e3b8006266eafb39c4fb351bdc3510f4
+SHA512 (sage-8.6.tar.gz) = cbadb485e645ac44e9f55defc011e934e9d89d82058312c69ae6e87bb5a30228d484d3e54d99a088bf5b8d9b2b464e8b59fdd63d9cc575a519cab5734950c1f1