[arch-commits] Commit in sagemath/repos (34 files)
Antonio Rojas
arojas at archlinux.org
Thu Aug 4 23:02:50 UTC 2016
Date: Thursday, August 4, 2016 @ 23:02:50
Author: arojas
Revision: 185159
archrelease: copy trunk to community-staging-i686, community-staging-x86_64
Added:
sagemath/repos/community-staging-i686/
sagemath/repos/community-staging-i686/PKGBUILD
(from rev 185158, sagemath/trunk/PKGBUILD)
sagemath/repos/community-staging-i686/anal.h
(from rev 185158, sagemath/trunk/anal.h)
sagemath/repos/community-staging-i686/clean.patch
(from rev 185158, sagemath/trunk/clean.patch)
sagemath/repos/community-staging-i686/cython-sys-path.patch
(from rev 185158, sagemath/trunk/cython-sys-path.patch)
sagemath/repos/community-staging-i686/disable-fes.patch
(from rev 185158, sagemath/trunk/disable-fes.patch)
sagemath/repos/community-staging-i686/ecm-7.patch
(from rev 185158, sagemath/trunk/ecm-7.patch)
sagemath/repos/community-staging-i686/env.patch
(from rev 185158, sagemath/trunk/env.patch)
sagemath/repos/community-staging-i686/is-package-installed.patch
(from rev 185158, sagemath/trunk/is-package-installed.patch)
sagemath/repos/community-staging-i686/jupyter-path.patch
(from rev 185158, sagemath/trunk/jupyter-path.patch)
sagemath/repos/community-staging-i686/linbox-1.4.patch
(from rev 185158, sagemath/trunk/linbox-1.4.patch)
sagemath/repos/community-staging-i686/package.patch
(from rev 185158, sagemath/trunk/package.patch)
sagemath/repos/community-staging-i686/paths.patch
(from rev 185158, sagemath/trunk/paths.patch)
sagemath/repos/community-staging-i686/python-2.7.11.patch
(from rev 185158, sagemath/trunk/python-2.7.11.patch)
sagemath/repos/community-staging-i686/sagemath-ipython5.patch
(from rev 185158, sagemath/trunk/sagemath-ipython5.patch)
sagemath/repos/community-staging-i686/skip-check.patch
(from rev 185158, sagemath/trunk/skip-check.patch)
sagemath/repos/community-staging-i686/test-optional.patch
(from rev 185158, sagemath/trunk/test-optional.patch)
sagemath/repos/community-staging-x86_64/
sagemath/repos/community-staging-x86_64/PKGBUILD
(from rev 185158, sagemath/trunk/PKGBUILD)
sagemath/repos/community-staging-x86_64/anal.h
(from rev 185158, sagemath/trunk/anal.h)
sagemath/repos/community-staging-x86_64/clean.patch
(from rev 185158, sagemath/trunk/clean.patch)
sagemath/repos/community-staging-x86_64/cython-sys-path.patch
(from rev 185158, sagemath/trunk/cython-sys-path.patch)
sagemath/repos/community-staging-x86_64/disable-fes.patch
(from rev 185158, sagemath/trunk/disable-fes.patch)
sagemath/repos/community-staging-x86_64/ecm-7.patch
(from rev 185158, sagemath/trunk/ecm-7.patch)
sagemath/repos/community-staging-x86_64/env.patch
(from rev 185158, sagemath/trunk/env.patch)
sagemath/repos/community-staging-x86_64/is-package-installed.patch
(from rev 185158, sagemath/trunk/is-package-installed.patch)
sagemath/repos/community-staging-x86_64/jupyter-path.patch
(from rev 185158, sagemath/trunk/jupyter-path.patch)
sagemath/repos/community-staging-x86_64/linbox-1.4.patch
(from rev 185158, sagemath/trunk/linbox-1.4.patch)
sagemath/repos/community-staging-x86_64/package.patch
(from rev 185158, sagemath/trunk/package.patch)
sagemath/repos/community-staging-x86_64/paths.patch
(from rev 185158, sagemath/trunk/paths.patch)
sagemath/repos/community-staging-x86_64/python-2.7.11.patch
(from rev 185158, sagemath/trunk/python-2.7.11.patch)
sagemath/repos/community-staging-x86_64/sagemath-ipython5.patch
(from rev 185158, sagemath/trunk/sagemath-ipython5.patch)
sagemath/repos/community-staging-x86_64/skip-check.patch
(from rev 185158, sagemath/trunk/skip-check.patch)
sagemath/repos/community-staging-x86_64/test-optional.patch
(from rev 185158, sagemath/trunk/test-optional.patch)
-----------------------------------------------------+
community-staging-i686/PKGBUILD | 157 ++++++
community-staging-i686/anal.h | 65 ++
community-staging-i686/clean.patch | 24
community-staging-i686/cython-sys-path.patch | 10
community-staging-i686/disable-fes.patch | 19
community-staging-i686/ecm-7.patch | 79 +++
community-staging-i686/env.patch | 150 +++++
community-staging-i686/is-package-installed.patch | 387 ++++++++++++++
community-staging-i686/jupyter-path.patch | 31 +
community-staging-i686/linbox-1.4.patch | 470 ++++++++++++++++++
community-staging-i686/package.patch | 11
community-staging-i686/paths.patch | 32 +
community-staging-i686/python-2.7.11.patch | 11
community-staging-i686/sagemath-ipython5.patch | 120 ++++
community-staging-i686/skip-check.patch | 22
community-staging-i686/test-optional.patch | 11
community-staging-x86_64/PKGBUILD | 157 ++++++
community-staging-x86_64/anal.h | 65 ++
community-staging-x86_64/clean.patch | 24
community-staging-x86_64/cython-sys-path.patch | 10
community-staging-x86_64/disable-fes.patch | 19
community-staging-x86_64/ecm-7.patch | 79 +++
community-staging-x86_64/env.patch | 150 +++++
community-staging-x86_64/is-package-installed.patch | 387 ++++++++++++++
community-staging-x86_64/jupyter-path.patch | 31 +
community-staging-x86_64/linbox-1.4.patch | 470 ++++++++++++++++++
community-staging-x86_64/package.patch | 11
community-staging-x86_64/paths.patch | 32 +
community-staging-x86_64/python-2.7.11.patch | 11
community-staging-x86_64/sagemath-ipython5.patch | 120 ++++
community-staging-x86_64/skip-check.patch | 22
community-staging-x86_64/test-optional.patch | 11
32 files changed, 3198 insertions(+)
Copied: sagemath/repos/community-staging-i686/PKGBUILD (from rev 185158, sagemath/trunk/PKGBUILD)
===================================================================
--- community-staging-i686/PKGBUILD (rev 0)
+++ community-staging-i686/PKGBUILD 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,157 @@
+# $Id$
+# Maintainer: Evgeniy Alekseev <arcanis.arch at gmail dot com>
+# Maintainer: Antonio Rojas <arojas at archlinux.org>
+# Contributor: Daniel Wallace <danielwallace at gtmanfred dot com>
+# Contributor: Thomas Dziedzic <gostrc at gmail dot com>
+# Contributor: Osman Ugus <ugus11 at yahoo dot com>
+# Contributor: Stefan Husmann <stefan-husmann at t-online dot de>
+# Special thanks to Nareto for moving the compile from the .install to the PKGBUILD
+
+pkgname=sagemath
+pkgver=7.3
+pkgrel=1
+pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab"
+arch=(i686 x86_64)
+url="http://www.sagemath.org"
+license=(GPL)
+depends=(ipython2 cysignals ppl palp brial singular cliquer maxima-ecl gfan sympow tachyon python2-rpy2 nauty
+ python2-matplotlib python2-scipy python2-sympy python2-networkx python2-pillow libgap flintqs lcalc lrcalc arb
+ eclib gmp-ecm zn_poly gd python2-cvxopt pynac linbox rubiks pari-galdata pari-seadata-small planarity rankwidth
+ sage-data-combinatorial_designs sage-data-elliptic_curves sage-data-graphs sage-data-polytopes_db sage-data-conway_polynomials)
+optdepends=('cython2: to compile cython code' 'python2-pkgconfig: to compile cython code'
+ 'jmol: 3D plots' 'sage-notebook: Browser-based (flask) notebook interface'
+ 'sagemath-doc: Documentation and inline help' 'ipython2-notebook: Jupyter notebook interface' 'mathjax: Jupyter notebook interface'
+ 'coin-or-cbc: COIN backend for numerical computations' 'coin-or-csdp: for computing Lovász theta-function of graphs'
+ 'buckygen: for generating fullerene graphs' 'plantri: for generating some classes of graphs' 'benzene: for generating fusenes and benzenoids'
+ 'modular_decomposition: modular decomposition of graphs' 'ffmpeg: to export animations to video' 'imagemagick: to show animations'
+ 'coxeter3: Coxeter groups implementation' 'cryptominisat: SAT solver' 'gap-data: for computing Galois groups'
+ 'lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes'
+ 'libhomfly: for computing the homfly polynomial of links' 'libbraiding: for computing in braid groups'
+ 'python2-igraph: igraph backend for graph theory' 'sage-notebook-export: convert flask notebooks to jupyter'
+ 'jupyter-notebook: Jupyter notebook interface')
+makedepends=(cython2 boost ratpoints symmetrica fflas-ffpack python2-jinja coin-or-cbc libhomfly libbraiding
+ mcqd coxeter3 cryptominisat modular_decomposition bliss-graphs tdlib python2-pkgconfig meataxe) # libfes
+conflicts=(sage-mathematics)
+replaces=(sage-mathematics)
+provides=(sage-mathematics)
+source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"
+ anal.h env.patch paths.patch clean.patch skip-check.patch cython-sys-path.patch is-package-installed.patch package.patch
+ disable-fes.patch jupyter-path.patch test-optional.patch python-2.7.11.patch linbox-1.4.patch ecm-7.patch sagemath-ipython5.patch)
+md5sums=('cb2aed3d24de7b2228a9b34e81a27870'
+ 'a906a180d198186a39820b0a2f9a9c63'
+ '4c8ddf07861abe703816e045e9e22de0'
+ '6f4dd6ec97affa2ce9a00ddf7e35db4c'
+ '6d9ae0978ce6a05a0da2cafdfb178a09'
+ '6cafcb381437d4751fd55b25d5090987'
+ 'a1bcdd3fe620dbae60ed8b0e98b2ece7'
+ 'b3ecf7c93a90e0afccbc686af9fdc85f'
+ '9ba81f717ffd4e20b8b2f2a318307488'
+ '06a67e611d10aa2381efe1f08ea4ffd9'
+ '16b529194c6105c3364127bd8f1efa83'
+ 'cdcabd475b80afe0534a5621e972736e'
+ 'ef927896f2071b442b1d07d7e69f5f3a'
+ 'a276f0fbbff6eade409d0569ebd728d4'
+ '0c9a57d35de80c2cd418ebec912efbbb'
+ 'abf4a70811d4f19191348202a923fe4b')
+
+prepare(){
+ cd sage-$pkgver
+
+# Arch-specific patches
+# assume all optional packages are installed
+ patch -p0 -i ../package.patch
+# find L.h header
+ sed -e 's|libLfunction|Lfunction|' -i src/sage/libs/lcalc/lcalc_sage.h
+# don't try to link against libpng 1.2
+ sed -e 's|png12|png|' -i src/module_list.py
+# set env variables
+ patch -p0 -i ../env.patch
+# fix paths in python imports
+ patch -p0 -i ../paths.patch
+# don't try to remove installed files
+ patch -p0 -i ../clean.patch
+# skip checking build status
+ patch -p0 -i ../skip-check.patch
+# supress warning about GAP install dir
+ sed -e "s|gapdir = os.path.join(SAGE_LOCAL, 'gap', 'latest')|gapdir = '/usr/lib/gap'|" -i src/sage/libs/gap/util.pyx
+# find bliss headers
+ sed -e 's|graph.hh|bliss/graph.hh|' -i src/sage/graphs/bliss.pyx
+# don't list optional packages when running tests
+ patch -p0 -i ../test-optional.patch
+# set jupyter path
+ patch -p0 -i ../jupyter-path.patch
+# fix timeit with Python 2.7.11
+ patch -p0 -i ../python-2.7.11.patch
+# search system paths for cython includes
+ patch -p1 -i ../cython-sys-path.patch
+# fix regressions with ECM 7
+ patch -p1 -i ../ecm-7.patch
+
+# Upstream patches
+# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209
+# patch -p0 -i ../fes02.patch
+# disable fes module, fails to compile
+ patch -p0 -i ../disable-fes.patch
+# port to new givaro/fflas-ffpack/linbox http://trac.sagemath.org/ticket/17635
+ patch -p1 -i ../linbox-1.4.patch
+# port to ipython 5.0 https://trac.sagemath.org/ticket/21006
+ patch -p1 -i ../sagemath-ipython5.patch
+# replace is_package_installed usage http://trac.sagemath.org/ticket/20377
+ patch -p1 -i ../is-package-installed.patch
+
+# use python2
+ sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' -e 's|exec python|exec python2|' -i src/bin/*
+ sed -e 's|cython {OPT}|cython2 {OPT}|' -e 's|python setup.py|python2 setup.py|' -i src/sage/misc/cython.py
+ sed -e 's|exec ipython|exec ipython2|' -e 's|cygdb|cygdb2|' -i src/bin/sage
+ sed -e "s|'cython'|'cython2'|" -i src/bin/sage-cython
+ sed -e 's|python -c|python2 -c|' -i src/Makefile
+
+# copy required private PARI header
+ mkdir -p src/pari
+ cp "$srcdir"/anal.h src/pari/anal.h
+}
+
+
+build() {
+ cd sage-$pkgver/src
+
+ export SAGE_LOCAL="/usr"
+ export SAGE_SRC="$PWD"
+ export CC=gcc
+
+ make sage/libs/pari/auto_gen.pxi
+ make sage/ext/interpreters/__init__.py
+
+ python2 setup.py build
+}
+
+package() {
+ cd sage-$pkgver/src
+
+ export SAGE_ROOT="/usr"
+ export SAGE_LOCAL="$SAGE_ROOT"
+ export SAGE_SRC="$PWD"
+ export CC=gcc
+ export JUPYTER_PATH="$pkgdir"/usr/share/jupyter
+
+ python2 setup.py install --root="$pkgdir" --optimize=1 --skip-build
+
+ mkdir -p "$pkgdir"/usr/bin
+ cp bin/sage "$pkgdir"/usr/bin
+ for _i in arch-env banner cachegrind callgrind cleaner coverage coverageall cython env eval grep grepdoc inline-fortran ipython \
+ massif maxima.lisp native-execute notebook num-threads.py omega open preparse python rst2sws rst2txt run run-cython runtests startuptime.py \
+ sws2rst valgrind version.sh
+ do
+ cp bin/sage-$_i "$pkgdir"/usr/bin
+ done
+ cp bin/math-readline "$pkgdir"/usr/bin
+
+ mkdir -p "$pkgdir"/usr/share/sage
+ cp -r ext "$pkgdir"/usr/share/sage
+
+# Create SAGE_SRC, needed for the notebook
+ mkdir "$pkgdir"/usr/share/sage/source
+
+# Remove sage_setup
+ rm -r "$pkgdir"/usr/lib/python2.7/site-packages/sage_setup
+}
Copied: sagemath/repos/community-staging-i686/anal.h (from rev 185158, sagemath/trunk/anal.h)
===================================================================
--- community-staging-i686/anal.h (rev 0)
+++ community-staging-i686/anal.h 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,65 @@
+/* Copyright (C) 2000 The PARI group.
+
+This file is part of the PARI/GP package.
+
+PARI/GP is free software; you can redistribute it and/or modify it under the
+terms of the GNU General Public License as published by the Free Software
+Foundation. It is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY WHATSOEVER.
+
+Check the License for details. You should have received a copy of it, along
+with the package; see the file 'COPYING'. If not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. */
+
+/*************************************************************************/
+/* */
+/* Declarations specific to the analyzer */
+/* */
+/*************************************************************************/
+BEGINEXTERN
+/* GP control structures */
+#define EXPR_WRAP(code, call) \
+{ GEN z; GEN __E = code; \
+ push_lex(gen_0, __E); z = call; pop_lex(1); return z; }
+#define EXPR_ARG __E, &gp_eval
+#define EXPR_ARGUPTO __E, &gp_evalupto
+#define EXPR_ARGBOOL __E, &gp_evalbool
+
+/* functions */
+void changevalue(entree *ep, GEN val);
+void freeep(entree *ep);
+void pari_fill_hashtable(entree **table, entree *ep);
+
+void compile_err(const char *msg, const char *str);
+void compile_varerr(const char *str);
+
+#ifdef STACK_CHECK
+extern THREAD void *PARI_stack_limit;
+#endif
+
+extern entree **varentries;
+
+struct node_loc
+{
+ const char *start,*end;
+};
+
+union token_value { long val; };
+
+int pari_lex(union token_value *yylval, struct node_loc *yylloc, char **lex);
+int pari_parse(char **lex);
+entree* fetch_entry(const char *s, long len);
+entree* fetch_member(const char *s, long len);
+void pari_close_parser(void);
+void pari_close_compiler(void);
+void pari_close_evaluator(void);
+void pari_init_parser(void);
+void pari_init_compiler(void);
+void pari_init_evaluator(void);
+void optimizenode(long n);
+void push_frame(GEN C, long lpc, long flag);
+const char * closure_func_err(void);
+GEN gp_closure(long n);
+long eval_mnemonic(GEN str, const char *tmplate);
+
+ENDEXTERN
Copied: sagemath/repos/community-staging-i686/clean.patch (from rev 185158, sagemath/trunk/clean.patch)
===================================================================
--- community-staging-i686/clean.patch (rev 0)
+++ community-staging-i686/clean.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,24 @@
+--- src/setup.py.orig 2014-11-16 10:34:05.521441703 +0100
++++ src/setup.py 2014-11-16 10:34:16.054812569 +0100
+@@ -620,21 +620,6 @@
+
+
+ #########################################################
+-### Clean
+-#########################################################
+-
+-print('Cleaning up stale installed files....')
+-t = time.time()
+-from sage_setup.clean import clean_install_dir
+-output_dirs = SITE_PACKAGES + glob.glob(os.path.join(SAGE_SRC, 'build', 'lib*'))
+-for output_dir in output_dirs:
+- print('- cleaning {0}'.format(output_dir))
+- clean_install_dir(output_dir, python_packages, python_modules,
+- ext_modules, python_data_files)
+-print('Finished cleaning, time: %.2f seconds.' % (time.time() - t))
+-
+-
+-#########################################################
+ ### Install also Jupyter kernel spec
+ #########################################################
+
Copied: sagemath/repos/community-staging-i686/cython-sys-path.patch (from rev 185158, sagemath/trunk/cython-sys-path.patch)
===================================================================
--- community-staging-i686/cython-sys-path.patch (rev 0)
+++ community-staging-i686/cython-sys-path.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,10 @@
+--- sage-7.1/src/setup.py.orig 2016-04-08 16:59:24.691349473 +0000
++++ sage-7.1/src/setup.py 2016-04-08 17:03:03.847153796 +0000
+@@ -591,6 +591,7 @@
+ build_dir=SAGE_CYTHONIZED,
+ force=force,
+ aliases=aliases,
++ include_path=sys.path,
+ compiler_directives={
+ 'embedsignature': True,
+ 'profile': profile,
Copied: sagemath/repos/community-staging-i686/disable-fes.patch (from rev 185158, sagemath/trunk/disable-fes.patch)
===================================================================
--- community-staging-i686/disable-fes.patch (rev 0)
+++ community-staging-i686/disable-fes.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,19 @@
+--- src/module_list.py.orig 2015-06-07 11:29:30.710612146 +0200
++++ src/module_list.py 2015-06-07 11:30:21.877506106 +0200
+@@ -564,11 +564,11 @@
+ sources = ["sage/libs/ecl.pyx"],
+ libraries = ["ecl"]),
+
+- OptionalExtension("sage.libs.fes",
+- ["sage/libs/fes.pyx"],
+- language = "c",
+- libraries = ['fes'],
+- package = 'fes'),
++# OptionalExtension("sage.libs.fes",
++# ["sage/libs/fes.pyx"],
++# language = "c",
++# libraries = ['fes'],
++# package = 'fes'),
+
+ Extension('sage.libs.flint.flint',
+ sources = ["sage/libs/flint/flint.pyx"],
Copied: sagemath/repos/community-staging-i686/ecm-7.patch (from rev 185158, sagemath/trunk/ecm-7.patch)
===================================================================
--- community-staging-i686/ecm-7.patch (rev 0)
+++ community-staging-i686/ecm-7.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,79 @@
+--- a/src/sage/interfaces/ecm.py.orig 2016-05-16 22:18:03.894827738 +0200
++++ b/src/sage/interfaces/ecm.py 2016-05-16 22:19:14.674904932 +0200
+@@ -140,9 +140,6 @@
+ - ``ve`` -- integer `n`. Verbosely show short (`< n`
+ character) expressions on each loop
+
+- - ``cofdec`` -- boolean. Force cofactor output in decimal
+- (even if expressions are used )
+-
+ - ``B2scale`` -- integer. Multiplies the default B2 value
+
+ - ``go`` -- integer. Preload with group order val, which can
+@@ -395,15 +392,15 @@
+ if m is not None:
+ factor = m.group('factor')
+ primality = m.group('primality')
+- assert primality in ['probable prime', 'composite']
+- result += [(ZZ(factor), primality == 'probable prime')]
++ assert primality in ['prime', 'composite']
++ result += [(ZZ(factor), primality == 'prime')]
+ continue # cofactor on the next line
+ m = self._found_cofactor_re.match(line)
+ if m is not None:
+ cofactor = m.group('cofactor')
+ primality = m.group('primality')
+- assert primality in ['Probable prime', 'Composite']
+- result += [(ZZ(cofactor), primality == 'Probable prime')]
++ assert primality in ['Prime', 'Composite']
++ result += [(ZZ(cofactor), primality == 'Prime')]
+ # assert len(result) == 2
+ return result
+ raise ValueError('failed to parse ECM output')
+@@ -501,7 +498,6 @@
+ if factor_digits is not None:
+ B1 = self.recommended_B1(factor_digits)
+ kwds['one'] = True
+- kwds['cofdec'] = True
+ cmd = self._make_cmd(B1, None, kwds)
+ out = self._run_ecm(cmd, n)
+ return self._parse_output(n, out)
+@@ -828,8 +828,8 @@
+ Step 1 took 12ms
+ Step 2 took 17ms
+ ********** Factor found in step 2: 79792266297612017
+-Found probable prime factor of 17 digits: 79792266297612017
+-Probable prime cofactor 6366805760909027985741435139224233 has 34 digits
++Found prime factor of 17 digits: 79792266297612017
++Prime cofactor 6366805760909027985741435139224233 has 34 digits
+ """
+
+ TEST_ECM_OUTPUT_2 = """
+@@ -839,8 +839,8 @@
+ Step 1 took 2ms
+ Step 2 took 3ms
+ ********** Factor found in step 2: 179424673
+-Found probable prime factor of 9 digits: 179424673
+-Probable prime cofactor 179424673 has 9 digits
++Found prime factor of 9 digits: 179424673
++Prime cofactor 179424673 has 9 digits
+ """
+
+ TEST_ECM_OUTPUT_3 = """
+@@ -858,7 +858,7 @@
+ Step 1 took 5ms
+ Step 2 took 4ms
+ ********** Factor found in step 2: 197002597249
+-Found probable prime factor of 12 digits: 197002597249
++Found prime factor of 12 digits: 197002597249
+ Composite cofactor 339872432034468861533158743041639097889948066859 has 48 digits
+ """
+
+@@ -870,5 +870,5 @@
+ Step 2 took 2ms
+ ********** Factor found in step 2: 265748496095531068869578877937
+ Found composite factor of 30 digits: 265748496095531068869578877937
+-Probable prime cofactor 251951573867253012259144010843 has 30 digits
++Prime cofactor 251951573867253012259144010843 has 30 digits
+ """
+
Copied: sagemath/repos/community-staging-i686/env.patch (from rev 185158, sagemath/trunk/env.patch)
===================================================================
--- community-staging-i686/env.patch (rev 0)
+++ community-staging-i686/env.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,150 @@
+--- src/bin/sage-env.orig 2015-01-06 10:46:04.469687605 +0100
++++ src/bin/sage-env 2015-01-06 10:49:59.547762019 +0100
+@@ -110,41 +110,7 @@
+ }
+
+
+-# New value for SAGE_ROOT: either SAGE_ROOT (if given)
+-# or a guessed value based on pwd.
+-if [ -n "$SAGE_ROOT" ]; then
+- NEW_SAGE_ROOT="$SAGE_ROOT"
+-elif [ -f sage -a -d build ]; then
+- NEW_SAGE_ROOT="."
+-elif [ -f ../../sage -a -d ../../build ]; then
+- NEW_SAGE_ROOT="../.."
+-else
+- # No idea what SAGE_ROOT should be...
+- echo >&2 "Error: You must set the SAGE_ROOT environment variable or run this"
+- echo >&2 "script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory."
+- return 1
+-fi
+-
+-# Make NEW_SAGE_ROOT absolute
+-NEW_SAGE_ROOT=`cd "$NEW_SAGE_ROOT" && pwd -P`
+-
+-# Sanity check NEW_SAGE_ROOT
+-if [ -f "$NEW_SAGE_ROOT/sage" -a -d "$NEW_SAGE_ROOT/build" ]; then
+- :
+-else
+- echo >&2 "Error: SAGE_ROOT is set to a bad value:"
+- echo >&2 "SAGE_ROOT=$SAGE_ROOT"
+- echo >&2 "You must correct it or erase it and run this script from the SAGE_ROOT"
+- echo >&2 "or SAGE_ROOT/local/bin/ directory."
+- return 1
+-fi
+-
+-# Warn if NEW_SAGE_ROOT does not equal the old SAGE_ROOT
+-if [ "$SAGE_ROOT" != "$NEW_SAGE_ROOT" -a -n "$SAGE_ROOT" ]; then
+- echo >&2 "Warning: overwriting SAGE_ROOT environment variable:"
+- echo >&2 "Old SAGE_ROOT=$SAGE_ROOT"
+- echo >&2 "New SAGE_ROOT=$NEW_SAGE_ROOT"
+-fi
++NEW_SAGE_ROOT="/usr"
+
+ # Don't execute the commands more than once for the same version of
+ # sage-env. Check this after checking the validity of SAGE_ROOT, but
+@@ -245,21 +211,13 @@
+ fi
+
+ # Setting Sage-related location environment variables.
+-export SAGE_LOCAL="$SAGE_ROOT/local"
+-export SAGE_ETC="$SAGE_LOCAL/etc"
+-export SAGE_SHARE="$SAGE_LOCAL/share"
+-export SAGE_EXTCODE="$SAGE_SHARE/sage/ext"
+-export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed"
+-export SAGE_LOGS="$SAGE_ROOT/logs/pkgs"
+-export SAGE_SRC="$SAGE_ROOT/src"
+-export SAGE_DOC_SRC="$SAGE_SRC/doc"
+-export SAGE_DOC="$SAGE_SHARE/doc/sage"
+-
+-if [ -z "${SAGE_ORIG_PATH_SET}" ]; then
+- SAGE_ORIG_PATH=$PATH && export SAGE_ORIG_PATH
+- SAGE_ORIG_PATH_SET=True && export SAGE_ORIG_PATH_SET
+-fi
+-export PATH="$SAGE_ROOT/build/bin:$SAGE_SRC/bin:$SAGE_LOCAL/bin:$PATH"
++export SAGE_LOCAL="$SAGE_ROOT"
++export SAGE_ETC="/etc/sage"
++export SAGE_SHARE="$SAGE_LOCAL/share/sage"
++export SAGE_EXTCODE="$SAGE_SHARE/ext"
++export SAGE_SRC="$SAGE_SHARE/source"
++export SAGE_DOC_SRC="/usr/share/doc/sage"
++export SAGE_DOC="/usr/share/doc/sage"
+
+ # We offer a toolchain option, so if $SAGE_LOCAL/toolchain/toolchain-env exists source it.
+ # Since the user might do something crazy we do not do any checks, but hope for the best.
+@@ -309,9 +267,6 @@
+ GIT_TEMPLATE_DIR="$SAGE_LOCAL"/share/git-core/templates && export GIT_TEMPLATE_DIR
+ GIT_EXEC_PATH="$SAGE_LOCAL"/libexec/git-core && export GIT_EXEC_PATH
+
+-SINGULARPATH="$SAGE_LOCAL/share/singular" && export SINGULARPATH
+-SINGULAR_EXECUTABLE="$SAGE_LOCAL/bin/Singular" && export SINGULAR_EXECUTABLE
+-
+ if [ -z "$SAGE_REPO_ANONYMOUS" ]; then
+ SAGE_REPO_ANONYMOUS="git://trac.sagemath.org/sage.git"
+ export SAGE_REPO_ANONYMOUS
+@@ -363,38 +318,33 @@
+ export SAGE_STARTUP_FILE
+ fi
+
++export LIBMTX="$DOT_SAGE/meataxe"
++[[ -d $LIBMTX ]] || mkdir $LIBMTX # Create meataxe data dir
++
+-IPYTHONDIR=`find "$SAGE_SPKG_INST" -name "ipython*"`
+-if [ -n "$IPYTHONDIR" ]; then
+- export IPYTHONDIR="$DOT_SAGE/${IPYTHONDIR##*/}"
+-fi
++export IPYTHONDIR="$DOT_SAGE/ipython"
+
+ if [ "$PYTHON_EGG_CACHE" = "" ]; then
+ PYTHON_EGG_CACHE="$DOT_SAGE/.python-eggs"
+ export PYTHON_EGG_CACHE
+ fi
+
+ # Set PYTHONUSERBASE to avoid picking up non-Sage versions of
+ # Matplotlib, numpy, etc. See http://trac.sagemath.org/ticket/19612.
+ #
+ # For more history (it used to be PYTHONNOUSERSITE=yes which killed
+ # the ability to do "sage -pip install PACKAGE --user"), see
+ # http://trac.sagemath.org/ticket/14243 and
+ # http://trac.sagemath.org/ticket/18955.
+
+ if [ "$PYTHONUSERBASE" = "" ]; then
+ PYTHONUSERBASE="$DOT_SAGE/local"
+ export PYTHONUSERBASE
+ fi
+
+-if [ -d "$SAGE_LOCAL/lib/python" ]; then
+- PYTHONPATH="$SAGE_LOCAL/lib/python:$SAGE_LOCAL/lib/python/site_packages"
+- if [ -n "$SAGE_PATH" ]; then
+- PYTHONPATH="$SAGE_PATH:$PYTHONPATH"
+- fi
+- PYTHONHOME="$SAGE_LOCAL"
+- export PYTHONPATH
+- export PYTHONHOME
+-fi
++PYTHONPATH="/usr/lib/sage/site-packages:$PYTHONPATH"
++PYTHONHOME="$SAGE_ROOT"
++export PYTHONPATH
++export PYTHONHOME
+
+ if [ -z "${SAGE_ORIG_LD_LIBRARY_PATH_SET}" ]; then
+ SAGE_ORIG_LD_LIBRARY_PATH=$LD_LIBRARY_PATH && export SAGE_ORIG_LD_LIBRARY_PATH
+@@ -431,8 +378,6 @@
+ fi
+ fi
+ fi
+-MAXIMA_PREFIX="$SAGE_ROOT/local" && export MAXIMA_PREFIX
+-
+ PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB
+
+ ############ architecture flags
+@@ -602,9 +547,6 @@
+ LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH
+ fi
+
+-# See trac 7186 -- this is needed if ecl is moved
+-ECLDIR="$SAGE_LOCAL/lib/ecl/" && export ECLDIR
+-
+ # Handle parallel building/testing/...
+ # See Trac Ticket #12016
+ # First, figure out the right values for SAGE_NUM_THREADS (default
Copied: sagemath/repos/community-staging-i686/is-package-installed.patch (from rev 185158, sagemath/trunk/is-package-installed.patch)
===================================================================
--- community-staging-i686/is-package-installed.patch (rev 0)
+++ community-staging-i686/is-package-installed.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,387 @@
+diff --git a/src/sage/databases/cremona.py b/src/sage/databases/cremona.py
+index 0a5f794..2969d92 100644
+--- a/src/sage/databases/cremona.py
++++ b/src/sage/databases/cremona.py
+@@ -53,7 +53,6 @@ from sage.misc.prandom import randint
+
+ import sage.schemes.elliptic_curves.constructor as elliptic
+ from .sql_db import SQLDatabase, verify_column
+-from sage.misc.package import is_package_installed
+ from sage.env import SAGE_SHARE
+ from sage.misc.all import walltime
+
+@@ -828,7 +827,7 @@ class MiniCremonaDatabase(SQLDatabase):
+ if N < self.largest_conductor():
+ message = "There is no elliptic curve with label " + label \
+ + " in the database"
+- elif is_package_installed('database_cremona_ellcurve'):
++ elif os.path.isfile(os.path.join(SAGE_SHARE, "cremona", "cremona.db")):
+ message = "There is no elliptic curve with label " + label \
+ + " in the currently available databases"
+ else:
+@@ -1677,7 +1676,7 @@ def CremonaDatabase(name=None,mini=None,set_global=None):
+ if name is None and not set_global:
+ return _db
+ if set_global and name is None:
+- if is_package_installed('database_cremona_ellcurve'):
++ if os.path.isfile(os.path.join(SAGE_SHARE, "cremona", "cremona.db")):
+ name = 'cremona'
+ else:
+ name = 'cremona mini'
+diff --git a/src/sage/game_theory/normal_form_game.py b/src/sage/game_theory/normal_form_game.py
+index b917d2a..80fb20c 100644
+--- a/src/sage/game_theory/normal_form_game.py
++++ b/src/sage/game_theory/normal_form_game.py
+@@ -614,8 +614,9 @@ from sage.rings.all import QQ
+ from sage.structure.sage_object import SageObject
+ from sage.matrix.constructor import matrix
+ from sage.matrix.constructor import vector
+-from sage.misc.package import is_package_installed
+ from sage.misc.temporary_file import tmp_filename
++import os
++from sage.env import SAGE_LOCAL
+
+ try:
+ from gambit import Game
+@@ -1317,13 +1318,13 @@ class NormalFormGame(SageObject, MutableMapping):
+ raise ValueError("utilities have not been populated")
+
+ if not algorithm:
+- if is_package_installed('lrslib'):
++ if os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'lrs')):
+ algorithm = "lrs"
+ else:
+ algorithm = "enumeration"
+
+ if algorithm == "lrs":
+- if not is_package_installed('lrslib'):
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'lrs')):
+ raise NotImplementedError("lrslib is not installed")
+
+ return self._solve_lrs(maximization)
+diff --git a/src/sage/geometry/polyhedron/base.py b/src/sage/geometry/polyhedron/base.py
+index 2f58d8b..eb519a2 100644
+--- a/src/sage/geometry/polyhedron/base.py
++++ b/src/sage/geometry/polyhedron/base.py
+@@ -21,7 +21,6 @@ import six
+ from sage.structure.element import Element, coerce_binop, is_Vector
+
+ from sage.misc.all import cached_method, prod
+-from sage.misc.package import is_package_installed
+
+ from sage.rings.all import QQ, ZZ
+ from sage.rings.real_double import RDF
+@@ -3691,7 +3690,9 @@ class Polyhedron_base(Element):
+
+ David Avis's lrs program.
+ """
+- if not is_package_installed('lrslib'):
++ import os
++ from sage.env import SAGE_LOCAL
++ if os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'lrs')) != True:
+ raise NotImplementedError('You must install the optional lrslib package '
+ 'for this function to work')
+
+diff --git a/src/sage/graphs/generators/classical_geometries.py b/src/sage/graphs/generators/classical_geometries.py
+index e80f2a5..04cd9ce 100644
+--- a/src/sage/graphs/generators/classical_geometries.py
++++ b/src/sage/graphs/generators/classical_geometries.py
+@@ -1287,10 +1287,9 @@ def CossidentePenttilaGraph(q):
+ raise ValueError('q(={}) must be an odd prime power'.format(q))
+
+ from sage.libs.gap.libgap import libgap
+- from sage.misc.package import is_package_installed, PackageNotFoundError
++ from sage.interfaces.gap import gap
+
+- if not is_package_installed('gap_packages'):
+- raise PackageNotFoundError('gap_packages')
++ gap.load_package("grape")
+
+ adj_list=libgap.function_factory("""function(q)
+ local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x;
+diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
+index 252984f..ce19682 100644
+--- a/src/sage/graphs/generic_graph.py
++++ b/src/sage/graphs/generic_graph.py
+@@ -7856,7 +7856,6 @@ class GenericGraph(GenericGraph_pyx):
+ sage: abs(flow_ff-flow_igraph) < 0.00001 # optional python_igraph
+ True
+ """
+- from sage.misc.package import is_package_installed
+ self._scream_if_not_simple(allow_loops=True)
+ if vertex_bound and algorithm in ["FF", "igraph"]:
+ raise ValueError("This method does not support both " +
+@@ -7874,10 +7873,12 @@ class GenericGraph(GenericGraph_pyx):
+ if algorithm is None:
+ if vertex_bound:
+ algorithm = "LP"
+- elif is_package_installed("python_igraph"):
+- algorithm = "igraph"
+ else:
+- algorithm = "FF"
++ algorithm = "igraph"
++ try:
++ import igraph
++ except ImportError:
++ algorithm = "FF"
+
+ if (algorithm == "FF"):
+ return self._ford_fulkerson(x,y, value_only=value_only, integer=integer, use_edge_labels=use_edge_labels)
+@@ -20251,17 +20252,22 @@ class GenericGraph(GenericGraph_pyx):
+ Subgroup of (Permutation Group with generators [(0,7)(1,4)(2,3)(6,8)]) generated by [(0,7)(1,4)(2,3)(6,8)]]
+
+ """
+- from sage.misc.package import is_package_installed
++ has_bliss=True
++ try:
++ from sage.graphs.bliss import automorphism_group
++ except ImportError:
++ has_bliss=False
++
+ if (algorithm == 'bliss' or # explicit choice from the user; or
+ (algorithm is None and # by default
+ not edge_labels and
+- is_package_installed('bliss'))):
++ has_bliss)):
++
++ if (not has_bliss):
++ raise NotImplementedError("you need to install bliss or set algorithm=sage to use this command")
++
+ if edge_labels:
+ raise ValueError("bliss cannot be used when edge_labels is True")
+- try:
+- from sage.graphs.bliss import automorphism_group
+- except ImportError:
+- raise ImportError("You must install the 'bliss' package to run this command.")
+
+ A = automorphism_group(self, partition)
+
+@@ -20903,17 +20909,22 @@ class GenericGraph(GenericGraph_pyx):
+ True
+
+ """
+- from sage.misc.package import is_package_installed
++ has_bliss=True
++ try:
++ from sage.graphs.bliss import canonical_form
++ except ImportError:
++ has_bliss=False
++
+ if (algorithm == 'bliss' or # explicit request; or
+ (algorithm is None and # default choice
+- is_package_installed('bliss') and
++ has_bliss and
+ not edge_labels)):
++
++ if (not has_bliss):
++ raise NotImplementedError("you need to install bliss or set algorithm=sage to use this command")
++
+ if edge_labels:
+ raise ValueError("bliss cannot be used when edge_labels is True")
+- try:
+- from sage.graphs.bliss import canonical_form
+- except ImportError:
+- raise ImportError("You must install the 'bliss' package to run this command.")
+ return canonical_form(self, partition, return_graph, certify)
+
+ if (algorithm is not None and
+diff --git a/src/sage/graphs/graph_generators.py b/src/sage/graphs/graph_generators.py
+index 5919ab3..1766796 100644
+--- a/src/sage/graphs/graph_generators.py
++++ b/src/sage/graphs/graph_generators.py
+@@ -1195,8 +1195,9 @@ class GraphGenerators():
+ .. [buckygen] \G. Brinkmann, J. Goedgebeur and B.D. McKay, Generation of Fullerenes,
+ Journal of Chemical Information and Modeling, 52(11):2910-2918, 2012.
+ """
+- from sage.misc.package import is_package_installed
+- if not is_package_installed("buckygen"):
++ import os
++ from sage.env import SAGE_LOCAL
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'buckygen')):
+ raise TypeError("the optional buckygen package is not installed")
+
+ # number of vertices should be positive
+@@ -1280,8 +1281,9 @@ class GraphGenerators():
+ .. [benzene] \G. Brinkmann, G. Caporossi and P. Hansen, A Constructive Enumeration of Fusenes and Benzenoids,
+ Journal of Algorithms, 45:155-166, 2002.
+ """
+- from sage.misc.package import is_package_installed
+- if not is_package_installed("benzene"):
++ import os
++ from sage.env import SAGE_LOCAL
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'benzene')):
+ raise TypeError("the optional benzene package is not installed")
+
+ # number of hexagons should be positive
+@@ -1433,8 +1435,9 @@ class GraphGenerators():
+ .. [plantri] \G. Brinkmann and B.D. McKay, Fast generation of planar graphs,
+ MATCH-Communications in Mathematical and in Computer Chemistry, 58(2):323-357, 2007.
+ """
+- from sage.misc.package import is_package_installed
+- if not is_package_installed("plantri"):
++ import os
++ from sage.env import SAGE_LOCAL
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'plantri')):
+ raise TypeError("the optional plantri package is not installed")
+
+ # number of vertices should be positive
+@@ -1632,8 +1635,9 @@ class GraphGenerators():
+ sage: [g.size() for g in graphs.triangulations(6, minimum_connectivity=3)] # optional plantri
+ [12, 12]
+ """
+- from sage.misc.package import is_package_installed
+- if not is_package_installed("plantri"):
++ import os
++ from sage.env import SAGE_LOCAL
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'plantri')):
+ raise TypeError("the optional plantri package is not installed")
+
+ # number of vertices should be positive
+@@ -1786,8 +1790,9 @@ class GraphGenerators():
+ sage: [len(g) for g in graphs.quadrangulations(12, no_nonfacial_quadrangles=True, dual=True)] # optional plantri
+ [10, 10]
+ """
+- from sage.misc.package import is_package_installed
+- if not is_package_installed("plantri"):
++ import os
++ from sage.env import SAGE_LOCAL
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'plantri')):
+ raise TypeError("the optional plantri package is not installed")
+
+ # number of vertices should be positive
+diff --git a/src/sage/graphs/lovasz_theta.py b/src/sage/graphs/lovasz_theta.py
+index 0d345c9..60948d2 100644
+--- a/src/sage/graphs/lovasz_theta.py
++++ b/src/sage/graphs/lovasz_theta.py
+@@ -65,10 +65,9 @@ def lovasz_theta(graph):
+ from sage.misc.temporary_file import tmp_filename
+ import os, subprocess
+ from sage.env import SAGE_LOCAL
+- from sage.misc.package import is_package_installed, PackageNotFoundError
+
+- if not is_package_installed('csdp'):
+- raise PackageNotFoundError("csdp")
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'theta')):
++ raise NotImplementedError("You must install csdp before using this function")
+
+ g = graph.relabel(inplace=False, perm=range(1,n+1)).networkx_graph()
+ tf_name = tmp_filename()
+diff --git a/src/sage/groups/generic.py b/src/sage/groups/generic.py
+index c801636..f43e6d9 100644
+--- a/src/sage/groups/generic.py
++++ b/src/sage/groups/generic.py
+@@ -1396,15 +1396,15 @@ def structure_description(G, latex=False):
+ sage: groups.matrix.GL(4,2).structure_description() # optional - database_gap
+ 'A8'
+ """
+- import re
+- from sage.misc.package import is_package_installed
++ import re, os
++ from sage.env import SAGE_LOCAL
+ def correct_dihedral_degree(match):
+ return "%sD%d" % (match.group(1), int(match.group(2))/2)
+
+ try:
+ description = str(G._gap_().StructureDescription())
+ except RuntimeError:
+- if not is_package_installed('database_gap'):
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, "gap", "latest", "small", "readsml.g")):
+ raise RuntimeError("You must install the optional database_gap package first.")
+ raise
+
+diff --git a/src/sage/groups/perm_gps/permgroup.py b/src/sage/groups/perm_gps/permgroup.py
+index e42db61..d4d5684 100644
+--- a/src/sage/groups/perm_gps/permgroup.py
++++ b/src/sage/groups/perm_gps/permgroup.py
+@@ -145,7 +145,6 @@ from sage.groups.perm_gps.permgroup_element import PermutationGroupElement, stan
+ from sage.groups.abelian_gps.abelian_group import AbelianGroup
+ from sage.misc.cachefunc import cached_method
+ from sage.groups.class_function import ClassFunction
+-from sage.misc.package import is_package_installed
+ from sage.sets.finite_enumerated_set import FiniteEnumeratedSet
+ from sage.categories.all import FiniteEnumeratedSets
+ from sage.groups.conjugacy_classes import ConjugacyClassGAP
+@@ -190,8 +189,6 @@ def hap_decorator(f):
+ """
+ @wraps(f)
+ def wrapped(self, n, p=0):
+- if not is_package_installed('gap_packages'):
+- raise RuntimeError("You must install the optional gap_packages package.")
+ load_hap()
+ from sage.arith.all import is_prime
+ if not (p == 0 or is_prime(p)):
+@@ -1683,9 +1680,7 @@ class PermutationGroup_generic(group.FiniteGroup):
+ try:
+ return [Integer(n) for n in self._gap_().IdGroup()]
+ except RuntimeError:
+- if not is_package_installed('database_gap'):
+- raise RuntimeError("You must install the optional database_gap package first.")
+- raise
++ raise RuntimeError("You must install the optional gap_packages package.")
+
+ def id(self):
+ """
+@@ -1736,9 +1731,7 @@ class PermutationGroup_generic(group.FiniteGroup):
+ try:
+ return Integer(self._gap_().PrimitiveIdentification())
+ except RuntimeError:
+- if not is_package_installed('database_gap'):
+- raise RuntimeError("You must install the optional database_gap package first.")
+- raise
++ raise RuntimeError("You must install the optional gap_packages package.")
+
+ def center(self):
+ """
+@@ -4114,8 +4107,6 @@ class PermutationGroup_generic(group.FiniteGroup):
+ - David Joyner and Graham Ellis
+
+ """
+- if not is_package_installed('gap_packages'):
+- raise RuntimeError("You must install the optional gap_packages package.")
+ load_hap()
+ from sage.arith.all import is_prime
+ if not (p == 0 or is_prime(p)):
+diff --git a/src/sage/misc/all.py b/src/sage/misc/all.py
+index 90e6985..21daeb0 100644
+--- a/src/sage/misc/all.py
++++ b/src/sage/misc/all.py
+@@ -53,11 +53,6 @@ from fpickle import pickle_function, unpickle_function
+
+ from .dist import install_scripts
+
+-from .package import (install_package,
+- installed_packages, is_package_installed,
+- standard_packages, optional_packages, experimental_packages,
+- upgrade, package_versions)
+-
+ from .pager import pager
+
+ lazy_import('sage.misc.sagedoc', ['browse_sage_doc',
+diff --git a/src/sage/rings/polynomial/multi_polynomial_sequence.py b/src/sage/rings/polynomial/multi_polynomial_sequence.py
+index da41cb0..49cae0b 100644
+--- a/src/sage/rings/polynomial/multi_polynomial_sequence.py
++++ b/src/sage/rings/polynomial/multi_polynomial_sequence.py
+@@ -159,7 +159,6 @@ from sage.misc.cachefunc import cached_method
+
+ from types import GeneratorType
+ from sage.misc.converting_dict import KeyConvertingDict
+-from sage.misc.package import is_package_installed
+
+ from sage.structure.sequence import Sequence, Sequence_generic
+
+@@ -1429,10 +1428,11 @@ class PolynomialSequence_gf2(PolynomialSequence_generic):
+
+ if S != []:
+ if algorithm == "exhaustive_search":
+- if not is_package_installed('fes'):
+- from sage.misc.package import PackageNotFoundError
+- raise PackageNotFoundError("fes")
+- from sage.libs.fes import exhaustive_search
++ try:
++ from sage.libs.fes import exhaustive_search
++ except ImportError:
++ raise RuntimeError("You must install the optional fes package.")
++
+ solutions = exhaustive_search(S, max_sols=n, verbose=verbose, **kwds)
+
+ elif algorithm == "polybori":
Copied: sagemath/repos/community-staging-i686/jupyter-path.patch (from rev 185158, sagemath/trunk/jupyter-path.patch)
===================================================================
--- community-staging-i686/jupyter-path.patch (rev 0)
+++ community-staging-i686/jupyter-path.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,31 @@
+--- src/sage/repl/ipython_kernel/install.py.orig 2015-10-23 19:23:39.728456590 +0000
++++ src/sage/repl/ipython_kernel/install.py 2015-10-23 19:24:00.965018978 +0000
+@@ -13,8 +13,7 @@
+ SAGE_ROOT, SAGE_DOC, SAGE_LOCAL, SAGE_EXTCODE,
+ SAGE_VERSION
+ )
+-from jupyter_core.paths import ENV_JUPYTER_PATH
+-JUPYTER_PATH = ENV_JUPYTER_PATH[0]
++JUPYTER_PATH = os.environ.get('JUPYTER_PATH')
+
+ class SageKernelSpec(object):
+
+@@ -151,7 +151,7 @@
+ '{connection_file}']
+ """
+ return [
+- os.path.join(SAGE_ROOT, 'sage'),
++ os.path.join(SAGE_ROOT, 'bin', 'sage'),
+ '--python',
+ '-m', 'sage.repl.ipython_kernel',
+ '-f', '{connection_file}',
+@@ -208,7 +208,7 @@
+ sage: spec._symlink_resources() # not tested
+ """
+ path = os.path.join(SAGE_EXTCODE, 'notebook-ipython')
+- for filename in os.listdir(path):
++ for filename in os.listdir('ext/notebook-ipython'):
+ self.symlink(
+ os.path.join(path, filename),
+ os.path.join(self.kernel_dir, filename)
+
Copied: sagemath/repos/community-staging-i686/linbox-1.4.patch (from rev 185158, sagemath/trunk/linbox-1.4.patch)
===================================================================
--- community-staging-i686/linbox-1.4.patch (rev 0)
+++ community-staging-i686/linbox-1.4.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,470 @@
+diff --git a/src/module_list.py b/src/module_list.py
+index a49ed36..7798cb8 100644
+--- a/src/module_list.py
++++ b/src/module_list.py
+@@ -27,6 +27,18 @@ lapack_libs = list(lapack_pc['libraries'])
+ lapack_library_dirs = list(lapack_pc['library_dirs'])
+ lapack_include_dirs = list(lapack_pc['include_dirs'])
+
++# FFLAS-FFPACK
++fflas_ffpack_pc = pkgconfig.parse('fflas-ffpack')
++fflas_ffpack_libs = list(fflas_ffpack_pc['libraries'])
++fflas_ffpack_library_dirs = list(fflas_ffpack_pc['library_dirs'])
++fflas_ffpack_cflags = pkgconfig.cflags('fflas-ffpack').split()
++
++# Givaro
++givaro_pc = pkgconfig.parse('givaro')
++givaro_libs = list(givaro_pc['libraries'])
++givaro_library_dirs = list(givaro_pc['library_dirs'])
++givaro_cflags = pkgconfig.cflags('givaro').split()
++
+ # GNU Scientific Library
+ # Note we replace the built-in gslcblas with the above cblas
+ gsl_pc = pkgconfig.parse('gsl')
+@@ -40,6 +52,12 @@ gd_libs = list(gd_pc['libraries'])
+ gd_library_dirs = list(gd_pc['library_dirs'])
+ gd_include_dirs = list(gd_pc['include_dirs'])
+
++# LinBox
++linbox_pc = pkgconfig.parse('linbox')
++linbox_libs = list(linbox_pc['libraries'])
++linbox_library_dirs = list(linbox_pc['library_dirs'])
++linbox_cflags = pkgconfig.cflags('linbox').split()
++
+ # PNG image library
+ png_pc = pkgconfig.parse('libpng')
+ png_libs = list(png_pc['libraries'])
+@@ -58,9 +76,18 @@ zlib_include_dirs = list(zlib_pc['include_dirs'])
+ #########################################################
+
+ aliases = dict(
++ FFLASFFPACK_CFLAGS=fflas_ffpack_cflags,
++ FFLASFFPACK_LIBRARIES=fflas_ffpack_libs,
++ FFLASFFPACK_LIBDIR=fflas_ffpack_library_dirs,
++ GIVARO_CFLAGS=givaro_cflags,
++ GIVARO_LIBRARIES=givaro_libs,
++ GIVARO_LIBDIR=givaro_library_dirs,
+ GSL_LIBRARIES=gsl_libs,
+ GSL_LIBDIR=gsl_library_dirs,
+ GSL_INCDIR=gsl_include_dirs,
++ LINBOX_CFLAGS=linbox_cflags,
++ LINBOX_LIBRARIES=linbox_libs,
++ LINBOX_LIBDIR=linbox_library_dirs,
+ )
+
+ #########################################################
+@@ -91,12 +118,6 @@ except ValueError:
+ singular_libs = ['singular', 'flint', 'ntl', 'gmpxx', 'gmp', 'readline', 'm']
+
+ #########################################################
+-### Givaro flags
+-#########################################################
+-
+-givaro_extra_compile_args =['-D__STDC_LIMIT_MACROS']
+-
+-#########################################################
+ ### Library order
+ #########################################################
+
+@@ -111,8 +132,7 @@ givaro_extra_compile_args =['-D__STDC_LIMIT_MACROS']
+ # at the very end of the list.
+ library_order_list = [
+ "singular", "ec", "ecm",
+- "linboxsage", "ntl", "iml", "linbox", "givaro",
+-] + gsl_libs + [
++] + linbox_libs + gsl_libs + [
+ "pari", "flint", "ratpoints", "ecl", "glpk", "ppl",
+ "arb", "fplll", "mpfi", "mpfr", "mpc", "gmp", "gmpxx",
+ "brial",
+@@ -611,13 +631,10 @@ ext_modules = [
+
+ Extension('sage.libs.linbox.linbox',
+ sources = ['sage/libs/linbox/linbox.pyx'],
+- libraries = ['linboxsage', 'ntl', 'iml', 'linbox',
+- 'givaro', 'mpfr', 'gmp', 'gmpxx'] + cblas_libs,
++ libraries = linbox_libs,
+ language = 'c++',
+ library_dirs = cblas_library_dirs,
+- include_dirs = cblas_include_dirs,
+- extra_compile_args = givaro_extra_compile_args,
+- depends = [os.path.join(SAGE_INC, 'givaro', 'givconfig.h')]),
++ include_dirs = cblas_include_dirs),
+
+ Extension('sage.libs.lcalc.lcalc_Lfunction',
+ sources = ['sage/libs/lcalc/lcalc_Lfunction.pyx'],
+@@ -665,9 +682,8 @@ ext_modules = [
+
+ Extension('sage.libs.singular.singular',
+ sources = ['sage/libs/singular/singular.pyx'],
+- libraries = ['givaro'] + singular_libs,
+- language="c++",
+- extra_compile_args = givaro_extra_compile_args),
++ libraries = singular_libs,
++ language="c++"),
+
+ Extension('sage.libs.singular.polynomial',
+ sources = ['sage/libs/singular/polynomial.pyx'],
+@@ -687,8 +703,7 @@ ext_modules = [
+ Extension('sage.libs.singular.function',
+ sources = ['sage/libs/singular/function.pyx'],
+ libraries = singular_libs,
+- language="c++",
+- extra_compile_args = givaro_extra_compile_args),
++ language="c++"),
+
+ Extension('sage.libs.singular.option',
+ sources = ['sage/libs/singular/option.pyx'],
+@@ -944,19 +959,17 @@ ext_modules = [
+ Extension('sage.matrix.matrix_modn_dense_float',
+ sources = ['sage/matrix/matrix_modn_dense_float.pyx'],
+ language="c++",
+- libraries = ['ntl', 'linbox', 'givaro', 'mpfr', 'gmpxx', 'gmp'] + cblas_libs,
++ libraries = linbox_libs + cblas_libs,
+ library_dirs = cblas_library_dirs,
+- include_dirs = cblas_include_dirs,
+- extra_compile_args = nocxx11_args + ['-DDISABLE_COMMENTATOR'] + givaro_extra_compile_args),
++ include_dirs = cblas_include_dirs),
+
+ Extension('sage.matrix.matrix_modn_dense_double',
+ sources = ['sage/matrix/matrix_modn_dense_double.pyx'],
+ language="c++",
+- libraries = ['ntl', 'linbox', 'givaro', 'mpfr', 'gmpxx', 'gmp'] + cblas_libs,
++ libraries = linbox_libs + cblas_libs,
+ library_dirs = cblas_library_dirs,
+ include_dirs = cblas_include_dirs,
+- extra_compile_args = nocxx11_args + ["-D_XPG6", "-DDISABLE_COMMENTATOR"]
+- + m4ri_extra_compile_args + givaro_extra_compile_args),
++ extra_compile_args = ["-D_XPG6"]),
+
+ Extension('sage.matrix.matrix_modn_sparse',
+ sources = ['sage/matrix/matrix_modn_sparse.pyx']),
+@@ -1400,8 +1413,7 @@ ext_modules = [
+ Extension('sage.rings.finite_rings.element_givaro',
+ sources = ["sage/rings/finite_rings/element_givaro.pyx"],
+ libraries = ['givaro', 'ntl', 'gmpxx', 'gmp', 'm'],
+- language='c++',
+- extra_compile_args = givaro_extra_compile_args),
++ language='c++'),
+
+ Extension('sage.rings.finite_rings.element_ntl_gf2e',
+ sources = ['sage/rings/finite_rings/element_ntl_gf2e.pyx'],
+@@ -1421,8 +1433,7 @@ ext_modules = [
+ sources = ["sage/rings/finite_rings/hom_finite_field_givaro.pyx"],
+ # this order is needed to compile under windows.
+ libraries = ['givaro', 'ntl', 'gmpxx', 'gmp', 'm'],
+- language='c++',
+- extra_compile_args = givaro_extra_compile_args),
++ language='c++'),
+
+ ################################
+ ##
+@@ -1574,8 +1585,7 @@ ext_modules = [
+ Extension('sage.rings.polynomial.plural',
+ sources = ['sage/rings/polynomial/plural.pyx'],
+ libraries = ['m', 'readline', 'singular', 'givaro', 'gmpxx', 'gmp'],
+- language="c++",
+- extra_compile_args = givaro_extra_compile_args),
++ language="c++"),
+
+ Extension('sage.rings.polynomial.multi_polynomial_libsingular',
+ sources = ['sage/rings/polynomial/multi_polynomial_libsingular.pyx'],
+diff --git a/src/sage/libs/linbox/echelonform.pxd b/src/sage/libs/linbox/echelonform.pxd
+index 3097c8b..cf4902d 100644
+--- a/src/sage/libs/linbox/echelonform.pxd
++++ b/src/sage/libs/linbox/echelonform.pxd
+@@ -1,23 +1,27 @@
++# distutils: extra_compile_args = LINBOX_CFLAGS
++# distutils: libraries = LINBOX_LIBRARIES
++# distutils: library_dirs = LINBOX_LIBDIR
++
+ from sage.libs.linbox.modular cimport ModDoubleField, ModDoubleFieldElement, ModFloatField, ModFloatFieldElement
+ from libc.stdint cimport uint64_t
+
+-cdef extern from "linbox/matrix/blas-matrix.h" namespace "LinBox":
+- cdef cppclass BlasMatrixDouble "LinBox::BlasMatrix<LinBox::Modular<double> >":
++cdef extern from "linbox/matrix/dense-matrix.h" namespace "LinBox":
++ cdef cppclass BlasMatrixDouble "LinBox::DenseMatrix<Givaro::Modular<double> >":
+ BlasMatrixDouble(ModDoubleField F, uint64_t nrows, uint64_t ncols)
+ void setEntry(size_t i, size_t j, ModDoubleFieldElement t)
+ ModDoubleFieldElement &getEntry(size_t i, size_t j)
+
+- cdef cppclass BlasMatrixFloat "LinBox::BlasMatrix<LinBox::Modular<float> >":
++ cdef cppclass BlasMatrixFloat "LinBox::DenseMatrix<Givaro::Modular<float> >":
+ BlasMatrixFloat(ModFloatField F, uint64_t nrows, uint64_t ncols)
+ void setEntry(size_t i, size_t j, ModFloatFieldElement t)
+ ModFloatFieldElement &getEntry(size_t i, size_t j)
+
+ cdef extern from "linbox/algorithms/echelon-form.h":
+- cdef cppclass EchelonFormDomainDouble "LinBox::EchelonFormDomain<LinBox::Modular<double> >":
++ cdef cppclass EchelonFormDomainDouble "LinBox::EchelonFormDomain<Givaro::Modular<double> >":
+ EchelonFormDomainDouble(ModDoubleField)
+ int rowReducedEchelon(BlasMatrixDouble, BlasMatrixDouble)
+
+- cdef cppclass EchelonFormDomainFloat "LinBox::EchelonFormDomain<LinBox::Modular<float> >":
++ cdef cppclass EchelonFormDomainFloat "LinBox::EchelonFormDomain<Givaro::Modular<float> >":
+ EchelonFormDomainFloat(ModFloatField)
+ int rowReducedEchelon(BlasMatrixFloat, BlasMatrixFloat)
+
+diff --git a/src/sage/libs/linbox/fflas.pxd b/src/sage/libs/linbox/fflas.pxd
+index e102004..01ab1b1 100644
+--- a/src/sage/libs/linbox/fflas.pxd
++++ b/src/sage/libs/linbox/fflas.pxd
+@@ -1,3 +1,7 @@
++# distutils: extra_compile_args = FFLASFFPACK_CFLAGS
++# distutils: libraries = FFLASFFPACK_LIBRARIES
++# distutils: library_dirs = FFLASFFPACK_LIBDIR
++
+ from .modular cimport ModDoubleField, ModFloatField, ModDoubleFieldElement, ModFloatFieldElement
+
+ cdef extern from "fflas-ffpack/fflas-ffpack.h" namespace "std":
+diff --git a/src/sage/libs/linbox/linbox.pyx b/src/sage/libs/linbox/linbox.pyx
+index e932347..a9bd6d1 100644
+--- a/src/sage/libs/linbox/linbox.pyx
++++ b/src/sage/libs/linbox/linbox.pyx
+@@ -1,3 +1,7 @@
++# distutils: extra_compile_args = LINBOX_CFLAGS
++# distutils: libraries = LINBOX_LIBRARIES
++# distutils: library_dirs = LINBOX_LIBDIR
++
+ r"""
+ Linbox interface
+ """
+diff --git a/src/sage/libs/linbox/modular.pxd b/src/sage/libs/linbox/modular.pxd
+index 7ef204c..ea5fb29 100644
+--- a/src/sage/libs/linbox/modular.pxd
++++ b/src/sage/libs/linbox/modular.pxd
+@@ -1,10 +1,10 @@
+-cdef extern from "linbox/field/modular.h":
++cdef extern from "givaro/modular.h":
+ # double
+
+- cdef cppclass ModDoubleFieldElement "LinBox::Modular<double>::Element":
++ cdef cppclass ModDoubleFieldElement "Givaro::Modular<double>::Element":
+ pass
+
+- cdef cppclass ModDoubleField "LinBox::Modular<double>":
++ cdef cppclass ModDoubleField "Givaro::Modular<double>":
+ ModDoubleField(int modulus)
+ ModDoubleFieldElement init(ModDoubleFieldElement res, int v)
+ ModDoubleFieldElement init(ModDoubleFieldElement res, double v)
+@@ -20,10 +20,10 @@ cdef extern from "linbox/field/modular.h":
+
+
+ # float
+- cdef cppclass ModFloatFieldElement "LinBox::Modular<float>::Element":
++ cdef cppclass ModFloatFieldElement "Givaro::Modular<float>::Element":
+ pass
+
+- cdef cppclass ModFloatField "LinBox::Modular<float>":
++ cdef cppclass ModFloatField "Givaro::Modular<float>":
+ ModFloatField(int modulus)
+ ModFloatFieldElement init(ModFloatFieldElement res, int v)
+ ModFloatFieldElement init(ModFloatFieldElement res, double v)
+diff --git a/src/sage/libs/singular/singular.pyx b/src/sage/libs/singular/singular.pyx
+index 33d7f7ec..77f6e0a 100644
+--- a/src/sage/libs/singular/singular.pyx
++++ b/src/sage/libs/singular/singular.pyx
+@@ -23,6 +23,7 @@ cdef extern from "limits.h":
+
+ import os
+
++from libc.stdint cimport int64_t
+ from sage.libs.singular.decl cimport intvec
+ from sage.libs.singular.decl cimport SR_HDL, SR_INT, SR_TO_INT
+ from sage.libs.singular.decl cimport singular_options, singular_verbose_options
+@@ -156,7 +157,7 @@ cdef FFgivE si2sa_GFqGivaro(number *n, ring *_ring, Cache_givaro cache):
+ order = cache.objectptr.cardinality() - 1
+
+ while z:
+- c = cache.objectptr.initi(c, <long>napGetCoeff(z))
++ c = cache.objectptr.initi(c, <int64_t>napGetCoeff(z))
+ e = napGetExpFrom(z,1, _ring)
+ if e == 0:
+ ret = cache.objectptr.add(ret, c, ret)
+diff --git a/src/sage/rings/finite_rings/element_givaro.pxd b/src/sage/rings/finite_rings/element_givaro.pxd
+index 68def46..91c4ed7 100644
+--- a/src/sage/rings/finite_rings/element_givaro.pxd
++++ b/src/sage/rings/finite_rings/element_givaro.pxd
+@@ -1,9 +1,15 @@
+-from sage.structure.element cimport Element, RingElement, ModuleElement
+-from sage.rings.finite_rings.element_base cimport FinitePolyExtElement
++# distutils: extra_compile_args = GIVARO_CFLAGS
++
++from libcpp.vector cimport vector
++ctypedef vector[int] intvec
++
++from libc.stdint cimport int64_t
+
+-from sage.structure.parent cimport Parent
++from sage.rings.finite_rings.element_base cimport FinitePolyExtElement
++from sage.structure.parent cimport Parent
+ from sage.structure.sage_object cimport SageObject
+
++
+ cdef extern from "givaro/givconfig.h":
+ pass
+
+@@ -13,16 +19,7 @@ cdef extern from "givaro/givrandom.h":
+
+ GivRandom GivRandomSeeded "Givaro::GivRandom"(unsigned long seed)
+
+-cdef extern from "givaro/givgfq.h":
+- ctypedef struct intvec "std::vector<unsigned int>":
+- void (* push_back)(int elem)
+-
+- ctypedef struct constintvec "const std::vector<unsigned int>"
+-
+- intvec intvec_factory "std::vector<unsigned int>"(int len)
+-
+-cdef extern from "givaro/givgfq.h":
+-
++cdef extern from "givaro/gfq.h":
+ ctypedef struct GivaroGfq "Givaro::GFqDom<int>":
+ #attributes
+ unsigned int one
+@@ -40,10 +37,10 @@ cdef extern from "givaro/givgfq.h":
+ unsigned int (* cardinality)()
+ int (* exponent)()
+ int (* random)(GivRandom gen, int res)
+- int (* initi "init")(int res, int e)
++ int (* initi "init")(int res, int64_t e)
+ int (* initd "init")(int res, double e)
+ int (* indeterminate)()
+- int (* convert)(int r, int p)
++ int (* convert)(int64_t r, int p)
+ int (* read)(int r, int p)
+ int (* axpyin)(int r, int a, int x)
+ int (* axpy)(int r, int a, int b, int c)
+@@ -60,7 +57,12 @@ cdef extern from "givaro/givgfq.h":
+ void delete "delete "(void *o)
+ int gfq_element_factory "Givaro::GFqDom<int>::Element"()
+
+-cdef class FiniteField_givaroElement(FinitePolyExtElement) #forward declaration
++
++cdef class FiniteField_givaroElement(FinitePolyExtElement):
++ cdef int element
++ cdef Cache_givaro _cache
++ cdef object _multiplicative_order
++ cdef FiniteField_givaroElement _new_c(self, int value)
+
+ cdef class Cache_givaro(SageObject):
+ cdef GivaroGfq *objectptr # C++ object
+@@ -85,11 +87,4 @@ cdef class FiniteField_givaro_iterator:
+ cdef int iterator
+ cdef Cache_givaro _cache
+
+-cdef class FiniteField_givaroElement(FinitePolyExtElement):
+- cdef int element
+- cdef Cache_givaro _cache
+- cdef object _multiplicative_order
+- cdef FiniteField_givaroElement _new_c(self, int value)
+-
+-
+ cdef inline FiniteField_givaroElement make_FiniteField_givaroElement(Cache_givaro cache, int x)
+diff --git a/src/sage/rings/finite_rings/element_givaro.pyx b/src/sage/rings/finite_rings/element_givaro.pyx
+index d32b5cf..f2afa44 100644
+--- a/src/sage/rings/finite_rings/element_givaro.pyx
++++ b/src/sage/rings/finite_rings/element_givaro.pyx
+@@ -59,8 +59,9 @@ from sage.misc.randstate cimport randstate, current_randstate
+ from sage.rings.finite_rings.finite_field_base cimport FiniteField
+ from sage.rings.ring cimport Ring
+ from element_ext_pari import FiniteField_ext_pariElement
+-from element_pari_ffelt import FiniteFieldElement_pari_ffelt
++from element_pari_ffelt cimport FiniteFieldElement_pari_ffelt
+ from sage.structure.sage_object cimport SageObject
++from sage.structure.element cimport Element, ModuleElement, RingElement
+ import operator
+ import sage.arith.all
+ import finite_field_constructor as finite_field
+@@ -374,18 +375,16 @@ cdef class Cache_givaro(SageObject):
+ elif isinstance(e, int) or \
+ isinstance(e, Integer) or \
+ isinstance(e, long) or is_IntegerMod(e):
+- try:
+- e_int = e
+- except OverflowError:
+- e_int = e % self.characteristic()
++ e_int = e % self.characteristic()
+ res = self.objectptr.initi(res, e_int)
+
+ elif e is None:
+ e_int = 0
+- res = self.objectptr.initi(res,e_int)
++ res = self.objectptr.initi(res, e_int)
+
+ elif isinstance(e, float):
+- res = self.objectptr.initd(res,e)
++ e_int = int(e) % self.characteristic()
++ res = self.objectptr.initd(res, e_int)
+
+ elif isinstance(e, str):
+ return self.parent(eval(e.replace("^","**"),self.parent.gens_dict()))
+@@ -395,8 +394,8 @@ cdef class Cache_givaro(SageObject):
+ raise TypeError("e.parent must match self.vector_space")
+ ret = self._zero_element
+ for i in range(len(e)):
+- e_entry = e[i] % self.characteristic()
+- res = self.objectptr.initi(res, int(e_entry))
++ e_int = e[i] % self.characteristic()
++ res = self.objectptr.initi(res, e_int)
+ to_add = make_FiniteField_givaroElement(self, res)
+ ret = ret + to_add*self.parent.gen()**i
+ return ret
+@@ -435,8 +434,8 @@ cdef class Cache_givaro(SageObject):
+ raise ValueError("list is too long")
+ ret = self._zero_element
+ for i in range(len(e)):
+- e_entry = e[i] % self.characteristic()
+- res = self.objectptr.initi(res, int(e_entry))
++ e_int = e[i] % self.characteristic()
++ res = self.objectptr.initi(res, e_int)
+ to_add = make_FiniteField_givaroElement(self, res)
+ ret = ret + to_add*self.parent.gen()**i
+ return ret
+@@ -573,19 +572,17 @@ cdef class Cache_givaro(SageObject):
+ cdef int ret = k.zero
+ cdef int a = k.indeterminate()
+ cdef int at = k.one
+- cdef unsigned int ch = k.characteristic()
+- cdef int _n, t, i
++ cdef int ch = k.characteristic()
++ cdef int t, i
+
+ if n<0 or n>k.cardinality():
+ raise TypeError("n must be between 0 and self.order()")
+
+- _n = n
+-
+ for i from 0 <= i < k.exponent():
+- t = k.initi(t, _n%ch)
++ t = k.initi(t, n % ch)
+ ret = k.axpy(ret, t, at, ret)
+ at = k.mul(at,at,a)
+- _n = _n/ch
++ n //= ch
+ return make_FiniteField_givaroElement(self, ret)
+
+ def _element_repr(self, FiniteField_givaroElement e):
+diff --git a/src/sage/rings/finite_rings/finite_field_givaro.py b/src/sage/rings/finite_rings/finite_field_givaro.py
+index adbaab3..c431f6d 100644
+--- a/src/sage/rings/finite_rings/finite_field_givaro.py
++++ b/src/sage/rings/finite_rings/finite_field_givaro.py
+@@ -270,7 +270,8 @@ class FiniteField_givaro(FiniteField):
+ sage: k(2) # indirect doctest
+ 0
+
+- Floats coerce in:
++ Floats are converted like integers::
++
+ sage: k(float(2.0))
+ 0
+
+@@ -344,7 +345,7 @@ class FiniteField_givaro(FiniteField):
+ sage: k(pari('Mod(1,2)'))
+ 1
+ sage: k(pari('Mod(2,3)'))
+- 0
++ a
+ sage: k(pari('Mod(1,3)*a^20'))
+ a^7 + a^5 + a^4 + a^2
+
Copied: sagemath/repos/community-staging-i686/package.patch (from rev 185158, sagemath/trunk/package.patch)
===================================================================
--- community-staging-i686/package.patch (rev 0)
+++ community-staging-i686/package.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,11 @@
+--- src/sage/misc/package.py.orig 2014-11-23 15:58:13.000000000 +0100
++++ src/sage/misc/package.py 2015-01-22 20:32:25.651383902 +0100
+@@ -204,7 +204,7 @@
+ Otherwise, installing "pillow" will cause this function to think
+ that "pil" is installed, for example.
+ """
+- return any(p.split('-')[0] == package for p in installed_packages())
++ return True
+
+ def package_versions(package_type, local=False):
+ r"""
Copied: sagemath/repos/community-staging-i686/paths.patch (from rev 185158, sagemath/trunk/paths.patch)
===================================================================
--- community-staging-i686/paths.patch (rev 0)
+++ community-staging-i686/paths.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,32 @@
+--- src/sage/env.py.orig 2014-06-25 10:47:25.827203554 +1200
++++ src/sage/env.py 2014-06-25 10:49:07.667402821 +1200
+@@ -90,10 +90,10 @@
+
+ # bunch of sage directories and files
+ _add_variable_or_fallback('SAGE_ROOT', None)
+-_add_variable_or_fallback('SAGE_LOCAL', opj('$SAGE_ROOT', 'local'))
+-_add_variable_or_fallback('SAGE_ETC', opj('$SAGE_LOCAL', 'etc'))
++_add_variable_or_fallback('SAGE_LOCAL', '/usr')
++_add_variable_or_fallback('SAGE_ETC', '/etc/sage')
+ _add_variable_or_fallback('SAGE_INC', opj('$SAGE_LOCAL', 'include'))
+-_add_variable_or_fallback('SAGE_SHARE', opj('$SAGE_LOCAL', 'share'))
++_add_variable_or_fallback('SAGE_SHARE', opj('$SAGE_LOCAL', 'share', 'sage'))
+
+ _add_variable_or_fallback('SAGE_SRC', opj('$SAGE_ROOT', 'src'))
+
+@@ -102,13 +102,13 @@
+ except AttributeError: # in case of use inside virtualenv
+ sitepackages_dirs = [os.path.join(os.path.dirname(site.__file__),
+ 'site-packages')]
+-_add_variable_or_fallback('SITE_PACKAGES', sitepackages_dirs)
++_add_variable_or_fallback('SITE_PACKAGES', sitepackages_dirs + ['/usr/lib/sage/site-packages'])
+
+ _add_variable_or_fallback('SAGE_LIB', SITE_PACKAGES[0])
+
+ _add_variable_or_fallback('SAGE_CYTHONIZED', opj('$SAGE_SRC', 'build', 'cythonized'))
+
+-_add_variable_or_fallback('SAGE_EXTCODE', opj('$SAGE_SHARE', 'sage', 'ext'))
++_add_variable_or_fallback('SAGE_EXTCODE', opj('$SAGE_SHARE', 'ext'))
+ _add_variable_or_fallback('SAGE_LOGS', opj('$SAGE_ROOT', 'logs', 'pkgs'))
+ _add_variable_or_fallback('SAGE_SPKG_INST', opj('$SAGE_LOCAL', 'var', 'lib', 'sage', 'installed'))
+ _add_variable_or_fallback('SAGE_DOC_SRC', opj('$SAGE_SRC', 'doc'))
Copied: sagemath/repos/community-staging-i686/python-2.7.11.patch (from rev 185158, sagemath/trunk/python-2.7.11.patch)
===================================================================
--- community-staging-i686/python-2.7.11.patch (rev 0)
+++ community-staging-i686/python-2.7.11.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,11 @@
+--- src/sage/misc/sage_timeit.py.orig 2015-12-19 11:09:42.836938821 +0100
++++ src/sage/misc/sage_timeit.py 2015-12-19 11:10:27.090217304 +0100
+@@ -217,7 +217,7 @@
+ # but is there a better way to achieve that the code stmt has access
+ # to the shell namespace?
+
+- src = timeit_.template % {'stmt': timeit_.reindent(stmt, 8),
++ src = timeit_.template % {'init': "", 'stmt': timeit_.reindent(stmt, 8),
+ 'setup': "pass"}
+ code = compile(src, "<magic-timeit>", "exec")
+ ns = {}
Copied: sagemath/repos/community-staging-i686/sagemath-ipython5.patch (from rev 185158, sagemath/trunk/sagemath-ipython5.patch)
===================================================================
--- community-staging-i686/sagemath-ipython5.patch (rev 0)
+++ community-staging-i686/sagemath-ipython5.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,120 @@
+diff --git a/src/sage/repl/interpreter.py b/src/sage/repl/interpreter.py
+index ef8724d..6896985 100644
+--- a/src/sage/repl/interpreter.py
++++ b/src/sage/repl/interpreter.py
+@@ -107,6 +107,7 @@ import os
+ import re
+ import sys
+ from sage.repl.preparse import preparse
++from sage.repl.prompts import SagePrompts, InterfacePrompts
+
+ from traitlets.config.loader import Config
+ from traitlets import Bool, Type
+@@ -375,11 +376,6 @@ class SageTestShell(SageShellOverride, TerminalInteractiveShell):
+ ###################################################################
+
+ DEFAULT_SAGE_CONFIG = Config(
+- PromptManager = Config(
+- in_template = 'sage: ',
+- in2_template = '....: ',
+- justify = False,
+- out_template = ''),
+ TerminalIPythonApp = Config(
+ display_banner = False,
+ verbose_crash = True,
+@@ -387,6 +383,7 @@ DEFAULT_SAGE_CONFIG = Config(
+ shell_class = SageTerminalInteractiveShell,
+ ),
+ InteractiveShell = Config(
++ prompts_class = SagePrompts,
+ ast_node_interactivity = 'all',
+ colors = 'LightBG' if sys.stdout.isatty() else 'NoColor',
+ confirm_exit = False,
+@@ -620,13 +617,11 @@ def interface_shell_embed(interface):
+ cfg = copy.deepcopy(get_ipython().config)
+ except NameError:
+ cfg = copy.deepcopy(DEFAULT_SAGE_CONFIG)
+- cfg.PromptManager['in_template'] = interface.name() + ': '
+- cfg.PromptManager['in2_template'] = len(interface.name())*'.' + ': '
+-
+ ipshell = InteractiveShellEmbed(config=cfg,
+ banner1='\n --> Switching to %s <--\n\n'%interface,
+ exit_msg = '\n --> Exiting back to Sage <--\n')
+ ipshell.interface = interface
++ ipshell.prompts = InterfacePrompts(interface.name())
+
+ while ipshell.prefilter_manager.transformers:
+ ipshell.prefilter_manager.transformers.pop()
+diff --git a/src/sage/repl/prompts.py b/src/sage/repl/prompts.py
+new file mode 100644
+index 0000000..69f8cdd
+--- /dev/null
++++ b/src/sage/repl/prompts.py
+@@ -0,0 +1,67 @@
++r"""
++Sage Commandline Prompts
++"""
++
++#*****************************************************************************
++# Copyright (C) 2016 Volker Braun <vbraun.name at gmail.com>
++#
++# This program is free software: you can redistribute it and/or modify
++# it under the terms of the GNU General Public License as published by
++# the Free Software Foundation, either version 2 of the License, or
++# (at your option) any later version.
++# http://www.gnu.org/licenses/
++#*****************************************************************************
++
++from pygments.token import Token
++from IPython.terminal.prompts import Prompts
++
++
++class SagePrompts(Prompts):
++
++ def in_prompt_tokens(self, cli=None):
++ return [
++ (Token.Prompt, 'sage: '),
++ ]
++
++ def continuation_prompt_tokens(self, cli=None, width=None):
++ return [
++ (Token.Prompt, '....: '),
++ ]
++
++ def rewrite_prompt_tokens(self):
++ return [
++ (Token.Prompt, '----> '),
++ ]
++
++ def out_prompt_tokens(self):
++ return [
++ (Token.OutPrompt, ''),
++ ]
++
++
++class InterfacePrompts(Prompts):
++
++ def __init__(self, interface_name):
++ self.__name = interface_name
++ self.__width = len(interface_name)
++
++ def in_prompt_tokens(self, cli=None):
++ return [
++ (Token.Prompt, self.__name + ': '),
++ ]
++
++ def continuation_prompt_tokens(self, cli=None, width=None):
++ return [
++ (Token.Prompt, '.' * self.__width + ': '),
++ ]
++
++ def rewrite_prompt_tokens(self):
++ return [
++ (Token.Prompt, '-' * self.__width + '> '),
++ ]
++
++ def out_prompt_tokens(self):
++ return [
++ (Token.OutPrompt, ''),
++ ]
++
Copied: sagemath/repos/community-staging-i686/skip-check.patch (from rev 185158, sagemath/trunk/skip-check.patch)
===================================================================
--- community-staging-i686/skip-check.patch (rev 0)
+++ community-staging-i686/skip-check.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,22 @@
+--- src/bin/sage.orig 2014-12-18 09:47:27.354829070 +0100
++++ src/bin/sage 2014-12-18 09:48:00.041563401 +0100
+@@ -352,18 +352,6 @@
+
+ # 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).
+- 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'
+- echo >&2 'tarball, but you have not compiled it yet (or maybe the build has not'
+- echo >&2 'finished). You should run `make` in the Sage root directory first.'
+- echo >&2 'If you did not intend to build Sage from source, you should download'
+- echo >&2 'a binary tarball instead. Read README.txt for more information.'
+- echo >&2 '************************************************************************'
+- exit 1
+- fi
+-
+ # Display the startup banner (unless SAGE_BANNER is explictly "no")
+ if [ "$SAGE_BANNER" != "no" ]; then
+ # can be 'bare', or 'yes', or unspecified
+
Copied: sagemath/repos/community-staging-i686/test-optional.patch (from rev 185158, sagemath/trunk/test-optional.patch)
===================================================================
--- community-staging-i686/test-optional.patch (rev 0)
+++ community-staging-i686/test-optional.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,11 @@
+--- src/sage/doctest/control.py.orig 2015-10-31 09:40:55.173671531 +0100
++++ src/sage/doctest/control.py 2015-10-31 09:40:05.370125436 +0100
+@@ -253,7 +253,7 @@
+ if 'optional' in options.optional:
+ options.optional.discard('optional')
+ from sage.misc.package import package_versions
+- optional_pkgs = package_versions("optional", local=True)
++ optional_pkgs = {}
+ for pkg, versions in optional_pkgs.items():
+ if versions[0] == versions[1]:
+ options.optional.add(pkg)
Copied: sagemath/repos/community-staging-x86_64/PKGBUILD (from rev 185158, sagemath/trunk/PKGBUILD)
===================================================================
--- community-staging-x86_64/PKGBUILD (rev 0)
+++ community-staging-x86_64/PKGBUILD 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,157 @@
+# $Id$
+# Maintainer: Evgeniy Alekseev <arcanis.arch at gmail dot com>
+# Maintainer: Antonio Rojas <arojas at archlinux.org>
+# Contributor: Daniel Wallace <danielwallace at gtmanfred dot com>
+# Contributor: Thomas Dziedzic <gostrc at gmail dot com>
+# Contributor: Osman Ugus <ugus11 at yahoo dot com>
+# Contributor: Stefan Husmann <stefan-husmann at t-online dot de>
+# Special thanks to Nareto for moving the compile from the .install to the PKGBUILD
+
+pkgname=sagemath
+pkgver=7.3
+pkgrel=1
+pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab"
+arch=(i686 x86_64)
+url="http://www.sagemath.org"
+license=(GPL)
+depends=(ipython2 cysignals ppl palp brial singular cliquer maxima-ecl gfan sympow tachyon python2-rpy2 nauty
+ python2-matplotlib python2-scipy python2-sympy python2-networkx python2-pillow libgap flintqs lcalc lrcalc arb
+ eclib gmp-ecm zn_poly gd python2-cvxopt pynac linbox rubiks pari-galdata pari-seadata-small planarity rankwidth
+ sage-data-combinatorial_designs sage-data-elliptic_curves sage-data-graphs sage-data-polytopes_db sage-data-conway_polynomials)
+optdepends=('cython2: to compile cython code' 'python2-pkgconfig: to compile cython code'
+ 'jmol: 3D plots' 'sage-notebook: Browser-based (flask) notebook interface'
+ 'sagemath-doc: Documentation and inline help' 'ipython2-notebook: Jupyter notebook interface' 'mathjax: Jupyter notebook interface'
+ 'coin-or-cbc: COIN backend for numerical computations' 'coin-or-csdp: for computing Lovász theta-function of graphs'
+ 'buckygen: for generating fullerene graphs' 'plantri: for generating some classes of graphs' 'benzene: for generating fusenes and benzenoids'
+ 'modular_decomposition: modular decomposition of graphs' 'ffmpeg: to export animations to video' 'imagemagick: to show animations'
+ 'coxeter3: Coxeter groups implementation' 'cryptominisat: SAT solver' 'gap-data: for computing Galois groups'
+ 'lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes'
+ 'libhomfly: for computing the homfly polynomial of links' 'libbraiding: for computing in braid groups'
+ 'python2-igraph: igraph backend for graph theory' 'sage-notebook-export: convert flask notebooks to jupyter'
+ 'jupyter-notebook: Jupyter notebook interface')
+makedepends=(cython2 boost ratpoints symmetrica fflas-ffpack python2-jinja coin-or-cbc libhomfly libbraiding
+ mcqd coxeter3 cryptominisat modular_decomposition bliss-graphs tdlib python2-pkgconfig meataxe) # libfes
+conflicts=(sage-mathematics)
+replaces=(sage-mathematics)
+provides=(sage-mathematics)
+source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"
+ anal.h env.patch paths.patch clean.patch skip-check.patch cython-sys-path.patch is-package-installed.patch package.patch
+ disable-fes.patch jupyter-path.patch test-optional.patch python-2.7.11.patch linbox-1.4.patch ecm-7.patch sagemath-ipython5.patch)
+md5sums=('cb2aed3d24de7b2228a9b34e81a27870'
+ 'a906a180d198186a39820b0a2f9a9c63'
+ '4c8ddf07861abe703816e045e9e22de0'
+ '6f4dd6ec97affa2ce9a00ddf7e35db4c'
+ '6d9ae0978ce6a05a0da2cafdfb178a09'
+ '6cafcb381437d4751fd55b25d5090987'
+ 'a1bcdd3fe620dbae60ed8b0e98b2ece7'
+ 'b3ecf7c93a90e0afccbc686af9fdc85f'
+ '9ba81f717ffd4e20b8b2f2a318307488'
+ '06a67e611d10aa2381efe1f08ea4ffd9'
+ '16b529194c6105c3364127bd8f1efa83'
+ 'cdcabd475b80afe0534a5621e972736e'
+ 'ef927896f2071b442b1d07d7e69f5f3a'
+ 'a276f0fbbff6eade409d0569ebd728d4'
+ '0c9a57d35de80c2cd418ebec912efbbb'
+ 'abf4a70811d4f19191348202a923fe4b')
+
+prepare(){
+ cd sage-$pkgver
+
+# Arch-specific patches
+# assume all optional packages are installed
+ patch -p0 -i ../package.patch
+# find L.h header
+ sed -e 's|libLfunction|Lfunction|' -i src/sage/libs/lcalc/lcalc_sage.h
+# don't try to link against libpng 1.2
+ sed -e 's|png12|png|' -i src/module_list.py
+# set env variables
+ patch -p0 -i ../env.patch
+# fix paths in python imports
+ patch -p0 -i ../paths.patch
+# don't try to remove installed files
+ patch -p0 -i ../clean.patch
+# skip checking build status
+ patch -p0 -i ../skip-check.patch
+# supress warning about GAP install dir
+ sed -e "s|gapdir = os.path.join(SAGE_LOCAL, 'gap', 'latest')|gapdir = '/usr/lib/gap'|" -i src/sage/libs/gap/util.pyx
+# find bliss headers
+ sed -e 's|graph.hh|bliss/graph.hh|' -i src/sage/graphs/bliss.pyx
+# don't list optional packages when running tests
+ patch -p0 -i ../test-optional.patch
+# set jupyter path
+ patch -p0 -i ../jupyter-path.patch
+# fix timeit with Python 2.7.11
+ patch -p0 -i ../python-2.7.11.patch
+# search system paths for cython includes
+ patch -p1 -i ../cython-sys-path.patch
+# fix regressions with ECM 7
+ patch -p1 -i ../ecm-7.patch
+
+# Upstream patches
+# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209
+# patch -p0 -i ../fes02.patch
+# disable fes module, fails to compile
+ patch -p0 -i ../disable-fes.patch
+# port to new givaro/fflas-ffpack/linbox http://trac.sagemath.org/ticket/17635
+ patch -p1 -i ../linbox-1.4.patch
+# port to ipython 5.0 https://trac.sagemath.org/ticket/21006
+ patch -p1 -i ../sagemath-ipython5.patch
+# replace is_package_installed usage http://trac.sagemath.org/ticket/20377
+ patch -p1 -i ../is-package-installed.patch
+
+# use python2
+ sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' -e 's|exec python|exec python2|' -i src/bin/*
+ sed -e 's|cython {OPT}|cython2 {OPT}|' -e 's|python setup.py|python2 setup.py|' -i src/sage/misc/cython.py
+ sed -e 's|exec ipython|exec ipython2|' -e 's|cygdb|cygdb2|' -i src/bin/sage
+ sed -e "s|'cython'|'cython2'|" -i src/bin/sage-cython
+ sed -e 's|python -c|python2 -c|' -i src/Makefile
+
+# copy required private PARI header
+ mkdir -p src/pari
+ cp "$srcdir"/anal.h src/pari/anal.h
+}
+
+
+build() {
+ cd sage-$pkgver/src
+
+ export SAGE_LOCAL="/usr"
+ export SAGE_SRC="$PWD"
+ export CC=gcc
+
+ make sage/libs/pari/auto_gen.pxi
+ make sage/ext/interpreters/__init__.py
+
+ python2 setup.py build
+}
+
+package() {
+ cd sage-$pkgver/src
+
+ export SAGE_ROOT="/usr"
+ export SAGE_LOCAL="$SAGE_ROOT"
+ export SAGE_SRC="$PWD"
+ export CC=gcc
+ export JUPYTER_PATH="$pkgdir"/usr/share/jupyter
+
+ python2 setup.py install --root="$pkgdir" --optimize=1 --skip-build
+
+ mkdir -p "$pkgdir"/usr/bin
+ cp bin/sage "$pkgdir"/usr/bin
+ for _i in arch-env banner cachegrind callgrind cleaner coverage coverageall cython env eval grep grepdoc inline-fortran ipython \
+ massif maxima.lisp native-execute notebook num-threads.py omega open preparse python rst2sws rst2txt run run-cython runtests startuptime.py \
+ sws2rst valgrind version.sh
+ do
+ cp bin/sage-$_i "$pkgdir"/usr/bin
+ done
+ cp bin/math-readline "$pkgdir"/usr/bin
+
+ mkdir -p "$pkgdir"/usr/share/sage
+ cp -r ext "$pkgdir"/usr/share/sage
+
+# Create SAGE_SRC, needed for the notebook
+ mkdir "$pkgdir"/usr/share/sage/source
+
+# Remove sage_setup
+ rm -r "$pkgdir"/usr/lib/python2.7/site-packages/sage_setup
+}
Copied: sagemath/repos/community-staging-x86_64/anal.h (from rev 185158, sagemath/trunk/anal.h)
===================================================================
--- community-staging-x86_64/anal.h (rev 0)
+++ community-staging-x86_64/anal.h 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,65 @@
+/* Copyright (C) 2000 The PARI group.
+
+This file is part of the PARI/GP package.
+
+PARI/GP is free software; you can redistribute it and/or modify it under the
+terms of the GNU General Public License as published by the Free Software
+Foundation. It is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY WHATSOEVER.
+
+Check the License for details. You should have received a copy of it, along
+with the package; see the file 'COPYING'. If not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. */
+
+/*************************************************************************/
+/* */
+/* Declarations specific to the analyzer */
+/* */
+/*************************************************************************/
+BEGINEXTERN
+/* GP control structures */
+#define EXPR_WRAP(code, call) \
+{ GEN z; GEN __E = code; \
+ push_lex(gen_0, __E); z = call; pop_lex(1); return z; }
+#define EXPR_ARG __E, &gp_eval
+#define EXPR_ARGUPTO __E, &gp_evalupto
+#define EXPR_ARGBOOL __E, &gp_evalbool
+
+/* functions */
+void changevalue(entree *ep, GEN val);
+void freeep(entree *ep);
+void pari_fill_hashtable(entree **table, entree *ep);
+
+void compile_err(const char *msg, const char *str);
+void compile_varerr(const char *str);
+
+#ifdef STACK_CHECK
+extern THREAD void *PARI_stack_limit;
+#endif
+
+extern entree **varentries;
+
+struct node_loc
+{
+ const char *start,*end;
+};
+
+union token_value { long val; };
+
+int pari_lex(union token_value *yylval, struct node_loc *yylloc, char **lex);
+int pari_parse(char **lex);
+entree* fetch_entry(const char *s, long len);
+entree* fetch_member(const char *s, long len);
+void pari_close_parser(void);
+void pari_close_compiler(void);
+void pari_close_evaluator(void);
+void pari_init_parser(void);
+void pari_init_compiler(void);
+void pari_init_evaluator(void);
+void optimizenode(long n);
+void push_frame(GEN C, long lpc, long flag);
+const char * closure_func_err(void);
+GEN gp_closure(long n);
+long eval_mnemonic(GEN str, const char *tmplate);
+
+ENDEXTERN
Copied: sagemath/repos/community-staging-x86_64/clean.patch (from rev 185158, sagemath/trunk/clean.patch)
===================================================================
--- community-staging-x86_64/clean.patch (rev 0)
+++ community-staging-x86_64/clean.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,24 @@
+--- src/setup.py.orig 2014-11-16 10:34:05.521441703 +0100
++++ src/setup.py 2014-11-16 10:34:16.054812569 +0100
+@@ -620,21 +620,6 @@
+
+
+ #########################################################
+-### Clean
+-#########################################################
+-
+-print('Cleaning up stale installed files....')
+-t = time.time()
+-from sage_setup.clean import clean_install_dir
+-output_dirs = SITE_PACKAGES + glob.glob(os.path.join(SAGE_SRC, 'build', 'lib*'))
+-for output_dir in output_dirs:
+- print('- cleaning {0}'.format(output_dir))
+- clean_install_dir(output_dir, python_packages, python_modules,
+- ext_modules, python_data_files)
+-print('Finished cleaning, time: %.2f seconds.' % (time.time() - t))
+-
+-
+-#########################################################
+ ### Install also Jupyter kernel spec
+ #########################################################
+
Copied: sagemath/repos/community-staging-x86_64/cython-sys-path.patch (from rev 185158, sagemath/trunk/cython-sys-path.patch)
===================================================================
--- community-staging-x86_64/cython-sys-path.patch (rev 0)
+++ community-staging-x86_64/cython-sys-path.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,10 @@
+--- sage-7.1/src/setup.py.orig 2016-04-08 16:59:24.691349473 +0000
++++ sage-7.1/src/setup.py 2016-04-08 17:03:03.847153796 +0000
+@@ -591,6 +591,7 @@
+ build_dir=SAGE_CYTHONIZED,
+ force=force,
+ aliases=aliases,
++ include_path=sys.path,
+ compiler_directives={
+ 'embedsignature': True,
+ 'profile': profile,
Copied: sagemath/repos/community-staging-x86_64/disable-fes.patch (from rev 185158, sagemath/trunk/disable-fes.patch)
===================================================================
--- community-staging-x86_64/disable-fes.patch (rev 0)
+++ community-staging-x86_64/disable-fes.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,19 @@
+--- src/module_list.py.orig 2015-06-07 11:29:30.710612146 +0200
++++ src/module_list.py 2015-06-07 11:30:21.877506106 +0200
+@@ -564,11 +564,11 @@
+ sources = ["sage/libs/ecl.pyx"],
+ libraries = ["ecl"]),
+
+- OptionalExtension("sage.libs.fes",
+- ["sage/libs/fes.pyx"],
+- language = "c",
+- libraries = ['fes'],
+- package = 'fes'),
++# OptionalExtension("sage.libs.fes",
++# ["sage/libs/fes.pyx"],
++# language = "c",
++# libraries = ['fes'],
++# package = 'fes'),
+
+ Extension('sage.libs.flint.flint',
+ sources = ["sage/libs/flint/flint.pyx"],
Copied: sagemath/repos/community-staging-x86_64/ecm-7.patch (from rev 185158, sagemath/trunk/ecm-7.patch)
===================================================================
--- community-staging-x86_64/ecm-7.patch (rev 0)
+++ community-staging-x86_64/ecm-7.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,79 @@
+--- a/src/sage/interfaces/ecm.py.orig 2016-05-16 22:18:03.894827738 +0200
++++ b/src/sage/interfaces/ecm.py 2016-05-16 22:19:14.674904932 +0200
+@@ -140,9 +140,6 @@
+ - ``ve`` -- integer `n`. Verbosely show short (`< n`
+ character) expressions on each loop
+
+- - ``cofdec`` -- boolean. Force cofactor output in decimal
+- (even if expressions are used )
+-
+ - ``B2scale`` -- integer. Multiplies the default B2 value
+
+ - ``go`` -- integer. Preload with group order val, which can
+@@ -395,15 +392,15 @@
+ if m is not None:
+ factor = m.group('factor')
+ primality = m.group('primality')
+- assert primality in ['probable prime', 'composite']
+- result += [(ZZ(factor), primality == 'probable prime')]
++ assert primality in ['prime', 'composite']
++ result += [(ZZ(factor), primality == 'prime')]
+ continue # cofactor on the next line
+ m = self._found_cofactor_re.match(line)
+ if m is not None:
+ cofactor = m.group('cofactor')
+ primality = m.group('primality')
+- assert primality in ['Probable prime', 'Composite']
+- result += [(ZZ(cofactor), primality == 'Probable prime')]
++ assert primality in ['Prime', 'Composite']
++ result += [(ZZ(cofactor), primality == 'Prime')]
+ # assert len(result) == 2
+ return result
+ raise ValueError('failed to parse ECM output')
+@@ -501,7 +498,6 @@
+ if factor_digits is not None:
+ B1 = self.recommended_B1(factor_digits)
+ kwds['one'] = True
+- kwds['cofdec'] = True
+ cmd = self._make_cmd(B1, None, kwds)
+ out = self._run_ecm(cmd, n)
+ return self._parse_output(n, out)
+@@ -828,8 +828,8 @@
+ Step 1 took 12ms
+ Step 2 took 17ms
+ ********** Factor found in step 2: 79792266297612017
+-Found probable prime factor of 17 digits: 79792266297612017
+-Probable prime cofactor 6366805760909027985741435139224233 has 34 digits
++Found prime factor of 17 digits: 79792266297612017
++Prime cofactor 6366805760909027985741435139224233 has 34 digits
+ """
+
+ TEST_ECM_OUTPUT_2 = """
+@@ -839,8 +839,8 @@
+ Step 1 took 2ms
+ Step 2 took 3ms
+ ********** Factor found in step 2: 179424673
+-Found probable prime factor of 9 digits: 179424673
+-Probable prime cofactor 179424673 has 9 digits
++Found prime factor of 9 digits: 179424673
++Prime cofactor 179424673 has 9 digits
+ """
+
+ TEST_ECM_OUTPUT_3 = """
+@@ -858,7 +858,7 @@
+ Step 1 took 5ms
+ Step 2 took 4ms
+ ********** Factor found in step 2: 197002597249
+-Found probable prime factor of 12 digits: 197002597249
++Found prime factor of 12 digits: 197002597249
+ Composite cofactor 339872432034468861533158743041639097889948066859 has 48 digits
+ """
+
+@@ -870,5 +870,5 @@
+ Step 2 took 2ms
+ ********** Factor found in step 2: 265748496095531068869578877937
+ Found composite factor of 30 digits: 265748496095531068869578877937
+-Probable prime cofactor 251951573867253012259144010843 has 30 digits
++Prime cofactor 251951573867253012259144010843 has 30 digits
+ """
+
Copied: sagemath/repos/community-staging-x86_64/env.patch (from rev 185158, sagemath/trunk/env.patch)
===================================================================
--- community-staging-x86_64/env.patch (rev 0)
+++ community-staging-x86_64/env.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,150 @@
+--- src/bin/sage-env.orig 2015-01-06 10:46:04.469687605 +0100
++++ src/bin/sage-env 2015-01-06 10:49:59.547762019 +0100
+@@ -110,41 +110,7 @@
+ }
+
+
+-# New value for SAGE_ROOT: either SAGE_ROOT (if given)
+-# or a guessed value based on pwd.
+-if [ -n "$SAGE_ROOT" ]; then
+- NEW_SAGE_ROOT="$SAGE_ROOT"
+-elif [ -f sage -a -d build ]; then
+- NEW_SAGE_ROOT="."
+-elif [ -f ../../sage -a -d ../../build ]; then
+- NEW_SAGE_ROOT="../.."
+-else
+- # No idea what SAGE_ROOT should be...
+- echo >&2 "Error: You must set the SAGE_ROOT environment variable or run this"
+- echo >&2 "script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory."
+- return 1
+-fi
+-
+-# Make NEW_SAGE_ROOT absolute
+-NEW_SAGE_ROOT=`cd "$NEW_SAGE_ROOT" && pwd -P`
+-
+-# Sanity check NEW_SAGE_ROOT
+-if [ -f "$NEW_SAGE_ROOT/sage" -a -d "$NEW_SAGE_ROOT/build" ]; then
+- :
+-else
+- echo >&2 "Error: SAGE_ROOT is set to a bad value:"
+- echo >&2 "SAGE_ROOT=$SAGE_ROOT"
+- echo >&2 "You must correct it or erase it and run this script from the SAGE_ROOT"
+- echo >&2 "or SAGE_ROOT/local/bin/ directory."
+- return 1
+-fi
+-
+-# Warn if NEW_SAGE_ROOT does not equal the old SAGE_ROOT
+-if [ "$SAGE_ROOT" != "$NEW_SAGE_ROOT" -a -n "$SAGE_ROOT" ]; then
+- echo >&2 "Warning: overwriting SAGE_ROOT environment variable:"
+- echo >&2 "Old SAGE_ROOT=$SAGE_ROOT"
+- echo >&2 "New SAGE_ROOT=$NEW_SAGE_ROOT"
+-fi
++NEW_SAGE_ROOT="/usr"
+
+ # Don't execute the commands more than once for the same version of
+ # sage-env. Check this after checking the validity of SAGE_ROOT, but
+@@ -245,21 +211,13 @@
+ fi
+
+ # Setting Sage-related location environment variables.
+-export SAGE_LOCAL="$SAGE_ROOT/local"
+-export SAGE_ETC="$SAGE_LOCAL/etc"
+-export SAGE_SHARE="$SAGE_LOCAL/share"
+-export SAGE_EXTCODE="$SAGE_SHARE/sage/ext"
+-export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed"
+-export SAGE_LOGS="$SAGE_ROOT/logs/pkgs"
+-export SAGE_SRC="$SAGE_ROOT/src"
+-export SAGE_DOC_SRC="$SAGE_SRC/doc"
+-export SAGE_DOC="$SAGE_SHARE/doc/sage"
+-
+-if [ -z "${SAGE_ORIG_PATH_SET}" ]; then
+- SAGE_ORIG_PATH=$PATH && export SAGE_ORIG_PATH
+- SAGE_ORIG_PATH_SET=True && export SAGE_ORIG_PATH_SET
+-fi
+-export PATH="$SAGE_ROOT/build/bin:$SAGE_SRC/bin:$SAGE_LOCAL/bin:$PATH"
++export SAGE_LOCAL="$SAGE_ROOT"
++export SAGE_ETC="/etc/sage"
++export SAGE_SHARE="$SAGE_LOCAL/share/sage"
++export SAGE_EXTCODE="$SAGE_SHARE/ext"
++export SAGE_SRC="$SAGE_SHARE/source"
++export SAGE_DOC_SRC="/usr/share/doc/sage"
++export SAGE_DOC="/usr/share/doc/sage"
+
+ # We offer a toolchain option, so if $SAGE_LOCAL/toolchain/toolchain-env exists source it.
+ # Since the user might do something crazy we do not do any checks, but hope for the best.
+@@ -309,9 +267,6 @@
+ GIT_TEMPLATE_DIR="$SAGE_LOCAL"/share/git-core/templates && export GIT_TEMPLATE_DIR
+ GIT_EXEC_PATH="$SAGE_LOCAL"/libexec/git-core && export GIT_EXEC_PATH
+
+-SINGULARPATH="$SAGE_LOCAL/share/singular" && export SINGULARPATH
+-SINGULAR_EXECUTABLE="$SAGE_LOCAL/bin/Singular" && export SINGULAR_EXECUTABLE
+-
+ if [ -z "$SAGE_REPO_ANONYMOUS" ]; then
+ SAGE_REPO_ANONYMOUS="git://trac.sagemath.org/sage.git"
+ export SAGE_REPO_ANONYMOUS
+@@ -363,38 +318,33 @@
+ export SAGE_STARTUP_FILE
+ fi
+
++export LIBMTX="$DOT_SAGE/meataxe"
++[[ -d $LIBMTX ]] || mkdir $LIBMTX # Create meataxe data dir
++
+-IPYTHONDIR=`find "$SAGE_SPKG_INST" -name "ipython*"`
+-if [ -n "$IPYTHONDIR" ]; then
+- export IPYTHONDIR="$DOT_SAGE/${IPYTHONDIR##*/}"
+-fi
++export IPYTHONDIR="$DOT_SAGE/ipython"
+
+ if [ "$PYTHON_EGG_CACHE" = "" ]; then
+ PYTHON_EGG_CACHE="$DOT_SAGE/.python-eggs"
+ export PYTHON_EGG_CACHE
+ fi
+
+ # Set PYTHONUSERBASE to avoid picking up non-Sage versions of
+ # Matplotlib, numpy, etc. See http://trac.sagemath.org/ticket/19612.
+ #
+ # For more history (it used to be PYTHONNOUSERSITE=yes which killed
+ # the ability to do "sage -pip install PACKAGE --user"), see
+ # http://trac.sagemath.org/ticket/14243 and
+ # http://trac.sagemath.org/ticket/18955.
+
+ if [ "$PYTHONUSERBASE" = "" ]; then
+ PYTHONUSERBASE="$DOT_SAGE/local"
+ export PYTHONUSERBASE
+ fi
+
+-if [ -d "$SAGE_LOCAL/lib/python" ]; then
+- PYTHONPATH="$SAGE_LOCAL/lib/python:$SAGE_LOCAL/lib/python/site_packages"
+- if [ -n "$SAGE_PATH" ]; then
+- PYTHONPATH="$SAGE_PATH:$PYTHONPATH"
+- fi
+- PYTHONHOME="$SAGE_LOCAL"
+- export PYTHONPATH
+- export PYTHONHOME
+-fi
++PYTHONPATH="/usr/lib/sage/site-packages:$PYTHONPATH"
++PYTHONHOME="$SAGE_ROOT"
++export PYTHONPATH
++export PYTHONHOME
+
+ if [ -z "${SAGE_ORIG_LD_LIBRARY_PATH_SET}" ]; then
+ SAGE_ORIG_LD_LIBRARY_PATH=$LD_LIBRARY_PATH && export SAGE_ORIG_LD_LIBRARY_PATH
+@@ -431,8 +378,6 @@
+ fi
+ fi
+ fi
+-MAXIMA_PREFIX="$SAGE_ROOT/local" && export MAXIMA_PREFIX
+-
+ PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB
+
+ ############ architecture flags
+@@ -602,9 +547,6 @@
+ LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH
+ fi
+
+-# See trac 7186 -- this is needed if ecl is moved
+-ECLDIR="$SAGE_LOCAL/lib/ecl/" && export ECLDIR
+-
+ # Handle parallel building/testing/...
+ # See Trac Ticket #12016
+ # First, figure out the right values for SAGE_NUM_THREADS (default
Copied: sagemath/repos/community-staging-x86_64/is-package-installed.patch (from rev 185158, sagemath/trunk/is-package-installed.patch)
===================================================================
--- community-staging-x86_64/is-package-installed.patch (rev 0)
+++ community-staging-x86_64/is-package-installed.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,387 @@
+diff --git a/src/sage/databases/cremona.py b/src/sage/databases/cremona.py
+index 0a5f794..2969d92 100644
+--- a/src/sage/databases/cremona.py
++++ b/src/sage/databases/cremona.py
+@@ -53,7 +53,6 @@ from sage.misc.prandom import randint
+
+ import sage.schemes.elliptic_curves.constructor as elliptic
+ from .sql_db import SQLDatabase, verify_column
+-from sage.misc.package import is_package_installed
+ from sage.env import SAGE_SHARE
+ from sage.misc.all import walltime
+
+@@ -828,7 +827,7 @@ class MiniCremonaDatabase(SQLDatabase):
+ if N < self.largest_conductor():
+ message = "There is no elliptic curve with label " + label \
+ + " in the database"
+- elif is_package_installed('database_cremona_ellcurve'):
++ elif os.path.isfile(os.path.join(SAGE_SHARE, "cremona", "cremona.db")):
+ message = "There is no elliptic curve with label " + label \
+ + " in the currently available databases"
+ else:
+@@ -1677,7 +1676,7 @@ def CremonaDatabase(name=None,mini=None,set_global=None):
+ if name is None and not set_global:
+ return _db
+ if set_global and name is None:
+- if is_package_installed('database_cremona_ellcurve'):
++ if os.path.isfile(os.path.join(SAGE_SHARE, "cremona", "cremona.db")):
+ name = 'cremona'
+ else:
+ name = 'cremona mini'
+diff --git a/src/sage/game_theory/normal_form_game.py b/src/sage/game_theory/normal_form_game.py
+index b917d2a..80fb20c 100644
+--- a/src/sage/game_theory/normal_form_game.py
++++ b/src/sage/game_theory/normal_form_game.py
+@@ -614,8 +614,9 @@ from sage.rings.all import QQ
+ from sage.structure.sage_object import SageObject
+ from sage.matrix.constructor import matrix
+ from sage.matrix.constructor import vector
+-from sage.misc.package import is_package_installed
+ from sage.misc.temporary_file import tmp_filename
++import os
++from sage.env import SAGE_LOCAL
+
+ try:
+ from gambit import Game
+@@ -1317,13 +1318,13 @@ class NormalFormGame(SageObject, MutableMapping):
+ raise ValueError("utilities have not been populated")
+
+ if not algorithm:
+- if is_package_installed('lrslib'):
++ if os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'lrs')):
+ algorithm = "lrs"
+ else:
+ algorithm = "enumeration"
+
+ if algorithm == "lrs":
+- if not is_package_installed('lrslib'):
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'lrs')):
+ raise NotImplementedError("lrslib is not installed")
+
+ return self._solve_lrs(maximization)
+diff --git a/src/sage/geometry/polyhedron/base.py b/src/sage/geometry/polyhedron/base.py
+index 2f58d8b..eb519a2 100644
+--- a/src/sage/geometry/polyhedron/base.py
++++ b/src/sage/geometry/polyhedron/base.py
+@@ -21,7 +21,6 @@ import six
+ from sage.structure.element import Element, coerce_binop, is_Vector
+
+ from sage.misc.all import cached_method, prod
+-from sage.misc.package import is_package_installed
+
+ from sage.rings.all import QQ, ZZ
+ from sage.rings.real_double import RDF
+@@ -3691,7 +3690,9 @@ class Polyhedron_base(Element):
+
+ David Avis's lrs program.
+ """
+- if not is_package_installed('lrslib'):
++ import os
++ from sage.env import SAGE_LOCAL
++ if os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'lrs')) != True:
+ raise NotImplementedError('You must install the optional lrslib package '
+ 'for this function to work')
+
+diff --git a/src/sage/graphs/generators/classical_geometries.py b/src/sage/graphs/generators/classical_geometries.py
+index e80f2a5..04cd9ce 100644
+--- a/src/sage/graphs/generators/classical_geometries.py
++++ b/src/sage/graphs/generators/classical_geometries.py
+@@ -1287,10 +1287,9 @@ def CossidentePenttilaGraph(q):
+ raise ValueError('q(={}) must be an odd prime power'.format(q))
+
+ from sage.libs.gap.libgap import libgap
+- from sage.misc.package import is_package_installed, PackageNotFoundError
++ from sage.interfaces.gap import gap
+
+- if not is_package_installed('gap_packages'):
+- raise PackageNotFoundError('gap_packages')
++ gap.load_package("grape")
+
+ adj_list=libgap.function_factory("""function(q)
+ local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x;
+diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
+index 252984f..ce19682 100644
+--- a/src/sage/graphs/generic_graph.py
++++ b/src/sage/graphs/generic_graph.py
+@@ -7856,7 +7856,6 @@ class GenericGraph(GenericGraph_pyx):
+ sage: abs(flow_ff-flow_igraph) < 0.00001 # optional python_igraph
+ True
+ """
+- from sage.misc.package import is_package_installed
+ self._scream_if_not_simple(allow_loops=True)
+ if vertex_bound and algorithm in ["FF", "igraph"]:
+ raise ValueError("This method does not support both " +
+@@ -7874,10 +7873,12 @@ class GenericGraph(GenericGraph_pyx):
+ if algorithm is None:
+ if vertex_bound:
+ algorithm = "LP"
+- elif is_package_installed("python_igraph"):
+- algorithm = "igraph"
+ else:
+- algorithm = "FF"
++ algorithm = "igraph"
++ try:
++ import igraph
++ except ImportError:
++ algorithm = "FF"
+
+ if (algorithm == "FF"):
+ return self._ford_fulkerson(x,y, value_only=value_only, integer=integer, use_edge_labels=use_edge_labels)
+@@ -20251,17 +20252,22 @@ class GenericGraph(GenericGraph_pyx):
+ Subgroup of (Permutation Group with generators [(0,7)(1,4)(2,3)(6,8)]) generated by [(0,7)(1,4)(2,3)(6,8)]]
+
+ """
+- from sage.misc.package import is_package_installed
++ has_bliss=True
++ try:
++ from sage.graphs.bliss import automorphism_group
++ except ImportError:
++ has_bliss=False
++
+ if (algorithm == 'bliss' or # explicit choice from the user; or
+ (algorithm is None and # by default
+ not edge_labels and
+- is_package_installed('bliss'))):
++ has_bliss)):
++
++ if (not has_bliss):
++ raise NotImplementedError("you need to install bliss or set algorithm=sage to use this command")
++
+ if edge_labels:
+ raise ValueError("bliss cannot be used when edge_labels is True")
+- try:
+- from sage.graphs.bliss import automorphism_group
+- except ImportError:
+- raise ImportError("You must install the 'bliss' package to run this command.")
+
+ A = automorphism_group(self, partition)
+
+@@ -20903,17 +20909,22 @@ class GenericGraph(GenericGraph_pyx):
+ True
+
+ """
+- from sage.misc.package import is_package_installed
++ has_bliss=True
++ try:
++ from sage.graphs.bliss import canonical_form
++ except ImportError:
++ has_bliss=False
++
+ if (algorithm == 'bliss' or # explicit request; or
+ (algorithm is None and # default choice
+- is_package_installed('bliss') and
++ has_bliss and
+ not edge_labels)):
++
++ if (not has_bliss):
++ raise NotImplementedError("you need to install bliss or set algorithm=sage to use this command")
++
+ if edge_labels:
+ raise ValueError("bliss cannot be used when edge_labels is True")
+- try:
+- from sage.graphs.bliss import canonical_form
+- except ImportError:
+- raise ImportError("You must install the 'bliss' package to run this command.")
+ return canonical_form(self, partition, return_graph, certify)
+
+ if (algorithm is not None and
+diff --git a/src/sage/graphs/graph_generators.py b/src/sage/graphs/graph_generators.py
+index 5919ab3..1766796 100644
+--- a/src/sage/graphs/graph_generators.py
++++ b/src/sage/graphs/graph_generators.py
+@@ -1195,8 +1195,9 @@ class GraphGenerators():
+ .. [buckygen] \G. Brinkmann, J. Goedgebeur and B.D. McKay, Generation of Fullerenes,
+ Journal of Chemical Information and Modeling, 52(11):2910-2918, 2012.
+ """
+- from sage.misc.package import is_package_installed
+- if not is_package_installed("buckygen"):
++ import os
++ from sage.env import SAGE_LOCAL
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'buckygen')):
+ raise TypeError("the optional buckygen package is not installed")
+
+ # number of vertices should be positive
+@@ -1280,8 +1281,9 @@ class GraphGenerators():
+ .. [benzene] \G. Brinkmann, G. Caporossi and P. Hansen, A Constructive Enumeration of Fusenes and Benzenoids,
+ Journal of Algorithms, 45:155-166, 2002.
+ """
+- from sage.misc.package import is_package_installed
+- if not is_package_installed("benzene"):
++ import os
++ from sage.env import SAGE_LOCAL
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'benzene')):
+ raise TypeError("the optional benzene package is not installed")
+
+ # number of hexagons should be positive
+@@ -1433,8 +1435,9 @@ class GraphGenerators():
+ .. [plantri] \G. Brinkmann and B.D. McKay, Fast generation of planar graphs,
+ MATCH-Communications in Mathematical and in Computer Chemistry, 58(2):323-357, 2007.
+ """
+- from sage.misc.package import is_package_installed
+- if not is_package_installed("plantri"):
++ import os
++ from sage.env import SAGE_LOCAL
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'plantri')):
+ raise TypeError("the optional plantri package is not installed")
+
+ # number of vertices should be positive
+@@ -1632,8 +1635,9 @@ class GraphGenerators():
+ sage: [g.size() for g in graphs.triangulations(6, minimum_connectivity=3)] # optional plantri
+ [12, 12]
+ """
+- from sage.misc.package import is_package_installed
+- if not is_package_installed("plantri"):
++ import os
++ from sage.env import SAGE_LOCAL
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'plantri')):
+ raise TypeError("the optional plantri package is not installed")
+
+ # number of vertices should be positive
+@@ -1786,8 +1790,9 @@ class GraphGenerators():
+ sage: [len(g) for g in graphs.quadrangulations(12, no_nonfacial_quadrangles=True, dual=True)] # optional plantri
+ [10, 10]
+ """
+- from sage.misc.package import is_package_installed
+- if not is_package_installed("plantri"):
++ import os
++ from sage.env import SAGE_LOCAL
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'plantri')):
+ raise TypeError("the optional plantri package is not installed")
+
+ # number of vertices should be positive
+diff --git a/src/sage/graphs/lovasz_theta.py b/src/sage/graphs/lovasz_theta.py
+index 0d345c9..60948d2 100644
+--- a/src/sage/graphs/lovasz_theta.py
++++ b/src/sage/graphs/lovasz_theta.py
+@@ -65,10 +65,9 @@ def lovasz_theta(graph):
+ from sage.misc.temporary_file import tmp_filename
+ import os, subprocess
+ from sage.env import SAGE_LOCAL
+- from sage.misc.package import is_package_installed, PackageNotFoundError
+
+- if not is_package_installed('csdp'):
+- raise PackageNotFoundError("csdp")
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'theta')):
++ raise NotImplementedError("You must install csdp before using this function")
+
+ g = graph.relabel(inplace=False, perm=range(1,n+1)).networkx_graph()
+ tf_name = tmp_filename()
+diff --git a/src/sage/groups/generic.py b/src/sage/groups/generic.py
+index c801636..f43e6d9 100644
+--- a/src/sage/groups/generic.py
++++ b/src/sage/groups/generic.py
+@@ -1396,15 +1396,15 @@ def structure_description(G, latex=False):
+ sage: groups.matrix.GL(4,2).structure_description() # optional - database_gap
+ 'A8'
+ """
+- import re
+- from sage.misc.package import is_package_installed
++ import re, os
++ from sage.env import SAGE_LOCAL
+ def correct_dihedral_degree(match):
+ return "%sD%d" % (match.group(1), int(match.group(2))/2)
+
+ try:
+ description = str(G._gap_().StructureDescription())
+ except RuntimeError:
+- if not is_package_installed('database_gap'):
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, "gap", "latest", "small", "readsml.g")):
+ raise RuntimeError("You must install the optional database_gap package first.")
+ raise
+
+diff --git a/src/sage/groups/perm_gps/permgroup.py b/src/sage/groups/perm_gps/permgroup.py
+index e42db61..d4d5684 100644
+--- a/src/sage/groups/perm_gps/permgroup.py
++++ b/src/sage/groups/perm_gps/permgroup.py
+@@ -145,7 +145,6 @@ from sage.groups.perm_gps.permgroup_element import PermutationGroupElement, stan
+ from sage.groups.abelian_gps.abelian_group import AbelianGroup
+ from sage.misc.cachefunc import cached_method
+ from sage.groups.class_function import ClassFunction
+-from sage.misc.package import is_package_installed
+ from sage.sets.finite_enumerated_set import FiniteEnumeratedSet
+ from sage.categories.all import FiniteEnumeratedSets
+ from sage.groups.conjugacy_classes import ConjugacyClassGAP
+@@ -190,8 +189,6 @@ def hap_decorator(f):
+ """
+ @wraps(f)
+ def wrapped(self, n, p=0):
+- if not is_package_installed('gap_packages'):
+- raise RuntimeError("You must install the optional gap_packages package.")
+ load_hap()
+ from sage.arith.all import is_prime
+ if not (p == 0 or is_prime(p)):
+@@ -1683,9 +1680,7 @@ class PermutationGroup_generic(group.FiniteGroup):
+ try:
+ return [Integer(n) for n in self._gap_().IdGroup()]
+ except RuntimeError:
+- if not is_package_installed('database_gap'):
+- raise RuntimeError("You must install the optional database_gap package first.")
+- raise
++ raise RuntimeError("You must install the optional gap_packages package.")
+
+ def id(self):
+ """
+@@ -1736,9 +1731,7 @@ class PermutationGroup_generic(group.FiniteGroup):
+ try:
+ return Integer(self._gap_().PrimitiveIdentification())
+ except RuntimeError:
+- if not is_package_installed('database_gap'):
+- raise RuntimeError("You must install the optional database_gap package first.")
+- raise
++ raise RuntimeError("You must install the optional gap_packages package.")
+
+ def center(self):
+ """
+@@ -4114,8 +4107,6 @@ class PermutationGroup_generic(group.FiniteGroup):
+ - David Joyner and Graham Ellis
+
+ """
+- if not is_package_installed('gap_packages'):
+- raise RuntimeError("You must install the optional gap_packages package.")
+ load_hap()
+ from sage.arith.all import is_prime
+ if not (p == 0 or is_prime(p)):
+diff --git a/src/sage/misc/all.py b/src/sage/misc/all.py
+index 90e6985..21daeb0 100644
+--- a/src/sage/misc/all.py
++++ b/src/sage/misc/all.py
+@@ -53,11 +53,6 @@ from fpickle import pickle_function, unpickle_function
+
+ from .dist import install_scripts
+
+-from .package import (install_package,
+- installed_packages, is_package_installed,
+- standard_packages, optional_packages, experimental_packages,
+- upgrade, package_versions)
+-
+ from .pager import pager
+
+ lazy_import('sage.misc.sagedoc', ['browse_sage_doc',
+diff --git a/src/sage/rings/polynomial/multi_polynomial_sequence.py b/src/sage/rings/polynomial/multi_polynomial_sequence.py
+index da41cb0..49cae0b 100644
+--- a/src/sage/rings/polynomial/multi_polynomial_sequence.py
++++ b/src/sage/rings/polynomial/multi_polynomial_sequence.py
+@@ -159,7 +159,6 @@ from sage.misc.cachefunc import cached_method
+
+ from types import GeneratorType
+ from sage.misc.converting_dict import KeyConvertingDict
+-from sage.misc.package import is_package_installed
+
+ from sage.structure.sequence import Sequence, Sequence_generic
+
+@@ -1429,10 +1428,11 @@ class PolynomialSequence_gf2(PolynomialSequence_generic):
+
+ if S != []:
+ if algorithm == "exhaustive_search":
+- if not is_package_installed('fes'):
+- from sage.misc.package import PackageNotFoundError
+- raise PackageNotFoundError("fes")
+- from sage.libs.fes import exhaustive_search
++ try:
++ from sage.libs.fes import exhaustive_search
++ except ImportError:
++ raise RuntimeError("You must install the optional fes package.")
++
+ solutions = exhaustive_search(S, max_sols=n, verbose=verbose, **kwds)
+
+ elif algorithm == "polybori":
Copied: sagemath/repos/community-staging-x86_64/jupyter-path.patch (from rev 185158, sagemath/trunk/jupyter-path.patch)
===================================================================
--- community-staging-x86_64/jupyter-path.patch (rev 0)
+++ community-staging-x86_64/jupyter-path.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,31 @@
+--- src/sage/repl/ipython_kernel/install.py.orig 2015-10-23 19:23:39.728456590 +0000
++++ src/sage/repl/ipython_kernel/install.py 2015-10-23 19:24:00.965018978 +0000
+@@ -13,8 +13,7 @@
+ SAGE_ROOT, SAGE_DOC, SAGE_LOCAL, SAGE_EXTCODE,
+ SAGE_VERSION
+ )
+-from jupyter_core.paths import ENV_JUPYTER_PATH
+-JUPYTER_PATH = ENV_JUPYTER_PATH[0]
++JUPYTER_PATH = os.environ.get('JUPYTER_PATH')
+
+ class SageKernelSpec(object):
+
+@@ -151,7 +151,7 @@
+ '{connection_file}']
+ """
+ return [
+- os.path.join(SAGE_ROOT, 'sage'),
++ os.path.join(SAGE_ROOT, 'bin', 'sage'),
+ '--python',
+ '-m', 'sage.repl.ipython_kernel',
+ '-f', '{connection_file}',
+@@ -208,7 +208,7 @@
+ sage: spec._symlink_resources() # not tested
+ """
+ path = os.path.join(SAGE_EXTCODE, 'notebook-ipython')
+- for filename in os.listdir(path):
++ for filename in os.listdir('ext/notebook-ipython'):
+ self.symlink(
+ os.path.join(path, filename),
+ os.path.join(self.kernel_dir, filename)
+
Copied: sagemath/repos/community-staging-x86_64/linbox-1.4.patch (from rev 185158, sagemath/trunk/linbox-1.4.patch)
===================================================================
--- community-staging-x86_64/linbox-1.4.patch (rev 0)
+++ community-staging-x86_64/linbox-1.4.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,470 @@
+diff --git a/src/module_list.py b/src/module_list.py
+index a49ed36..7798cb8 100644
+--- a/src/module_list.py
++++ b/src/module_list.py
+@@ -27,6 +27,18 @@ lapack_libs = list(lapack_pc['libraries'])
+ lapack_library_dirs = list(lapack_pc['library_dirs'])
+ lapack_include_dirs = list(lapack_pc['include_dirs'])
+
++# FFLAS-FFPACK
++fflas_ffpack_pc = pkgconfig.parse('fflas-ffpack')
++fflas_ffpack_libs = list(fflas_ffpack_pc['libraries'])
++fflas_ffpack_library_dirs = list(fflas_ffpack_pc['library_dirs'])
++fflas_ffpack_cflags = pkgconfig.cflags('fflas-ffpack').split()
++
++# Givaro
++givaro_pc = pkgconfig.parse('givaro')
++givaro_libs = list(givaro_pc['libraries'])
++givaro_library_dirs = list(givaro_pc['library_dirs'])
++givaro_cflags = pkgconfig.cflags('givaro').split()
++
+ # GNU Scientific Library
+ # Note we replace the built-in gslcblas with the above cblas
+ gsl_pc = pkgconfig.parse('gsl')
+@@ -40,6 +52,12 @@ gd_libs = list(gd_pc['libraries'])
+ gd_library_dirs = list(gd_pc['library_dirs'])
+ gd_include_dirs = list(gd_pc['include_dirs'])
+
++# LinBox
++linbox_pc = pkgconfig.parse('linbox')
++linbox_libs = list(linbox_pc['libraries'])
++linbox_library_dirs = list(linbox_pc['library_dirs'])
++linbox_cflags = pkgconfig.cflags('linbox').split()
++
+ # PNG image library
+ png_pc = pkgconfig.parse('libpng')
+ png_libs = list(png_pc['libraries'])
+@@ -58,9 +76,18 @@ zlib_include_dirs = list(zlib_pc['include_dirs'])
+ #########################################################
+
+ aliases = dict(
++ FFLASFFPACK_CFLAGS=fflas_ffpack_cflags,
++ FFLASFFPACK_LIBRARIES=fflas_ffpack_libs,
++ FFLASFFPACK_LIBDIR=fflas_ffpack_library_dirs,
++ GIVARO_CFLAGS=givaro_cflags,
++ GIVARO_LIBRARIES=givaro_libs,
++ GIVARO_LIBDIR=givaro_library_dirs,
+ GSL_LIBRARIES=gsl_libs,
+ GSL_LIBDIR=gsl_library_dirs,
+ GSL_INCDIR=gsl_include_dirs,
++ LINBOX_CFLAGS=linbox_cflags,
++ LINBOX_LIBRARIES=linbox_libs,
++ LINBOX_LIBDIR=linbox_library_dirs,
+ )
+
+ #########################################################
+@@ -91,12 +118,6 @@ except ValueError:
+ singular_libs = ['singular', 'flint', 'ntl', 'gmpxx', 'gmp', 'readline', 'm']
+
+ #########################################################
+-### Givaro flags
+-#########################################################
+-
+-givaro_extra_compile_args =['-D__STDC_LIMIT_MACROS']
+-
+-#########################################################
+ ### Library order
+ #########################################################
+
+@@ -111,8 +132,7 @@ givaro_extra_compile_args =['-D__STDC_LIMIT_MACROS']
+ # at the very end of the list.
+ library_order_list = [
+ "singular", "ec", "ecm",
+- "linboxsage", "ntl", "iml", "linbox", "givaro",
+-] + gsl_libs + [
++] + linbox_libs + gsl_libs + [
+ "pari", "flint", "ratpoints", "ecl", "glpk", "ppl",
+ "arb", "fplll", "mpfi", "mpfr", "mpc", "gmp", "gmpxx",
+ "brial",
+@@ -611,13 +631,10 @@ ext_modules = [
+
+ Extension('sage.libs.linbox.linbox',
+ sources = ['sage/libs/linbox/linbox.pyx'],
+- libraries = ['linboxsage', 'ntl', 'iml', 'linbox',
+- 'givaro', 'mpfr', 'gmp', 'gmpxx'] + cblas_libs,
++ libraries = linbox_libs,
+ language = 'c++',
+ library_dirs = cblas_library_dirs,
+- include_dirs = cblas_include_dirs,
+- extra_compile_args = givaro_extra_compile_args,
+- depends = [os.path.join(SAGE_INC, 'givaro', 'givconfig.h')]),
++ include_dirs = cblas_include_dirs),
+
+ Extension('sage.libs.lcalc.lcalc_Lfunction',
+ sources = ['sage/libs/lcalc/lcalc_Lfunction.pyx'],
+@@ -665,9 +682,8 @@ ext_modules = [
+
+ Extension('sage.libs.singular.singular',
+ sources = ['sage/libs/singular/singular.pyx'],
+- libraries = ['givaro'] + singular_libs,
+- language="c++",
+- extra_compile_args = givaro_extra_compile_args),
++ libraries = singular_libs,
++ language="c++"),
+
+ Extension('sage.libs.singular.polynomial',
+ sources = ['sage/libs/singular/polynomial.pyx'],
+@@ -687,8 +703,7 @@ ext_modules = [
+ Extension('sage.libs.singular.function',
+ sources = ['sage/libs/singular/function.pyx'],
+ libraries = singular_libs,
+- language="c++",
+- extra_compile_args = givaro_extra_compile_args),
++ language="c++"),
+
+ Extension('sage.libs.singular.option',
+ sources = ['sage/libs/singular/option.pyx'],
+@@ -944,19 +959,17 @@ ext_modules = [
+ Extension('sage.matrix.matrix_modn_dense_float',
+ sources = ['sage/matrix/matrix_modn_dense_float.pyx'],
+ language="c++",
+- libraries = ['ntl', 'linbox', 'givaro', 'mpfr', 'gmpxx', 'gmp'] + cblas_libs,
++ libraries = linbox_libs + cblas_libs,
+ library_dirs = cblas_library_dirs,
+- include_dirs = cblas_include_dirs,
+- extra_compile_args = nocxx11_args + ['-DDISABLE_COMMENTATOR'] + givaro_extra_compile_args),
++ include_dirs = cblas_include_dirs),
+
+ Extension('sage.matrix.matrix_modn_dense_double',
+ sources = ['sage/matrix/matrix_modn_dense_double.pyx'],
+ language="c++",
+- libraries = ['ntl', 'linbox', 'givaro', 'mpfr', 'gmpxx', 'gmp'] + cblas_libs,
++ libraries = linbox_libs + cblas_libs,
+ library_dirs = cblas_library_dirs,
+ include_dirs = cblas_include_dirs,
+- extra_compile_args = nocxx11_args + ["-D_XPG6", "-DDISABLE_COMMENTATOR"]
+- + m4ri_extra_compile_args + givaro_extra_compile_args),
++ extra_compile_args = ["-D_XPG6"]),
+
+ Extension('sage.matrix.matrix_modn_sparse',
+ sources = ['sage/matrix/matrix_modn_sparse.pyx']),
+@@ -1400,8 +1413,7 @@ ext_modules = [
+ Extension('sage.rings.finite_rings.element_givaro',
+ sources = ["sage/rings/finite_rings/element_givaro.pyx"],
+ libraries = ['givaro', 'ntl', 'gmpxx', 'gmp', 'm'],
+- language='c++',
+- extra_compile_args = givaro_extra_compile_args),
++ language='c++'),
+
+ Extension('sage.rings.finite_rings.element_ntl_gf2e',
+ sources = ['sage/rings/finite_rings/element_ntl_gf2e.pyx'],
+@@ -1421,8 +1433,7 @@ ext_modules = [
+ sources = ["sage/rings/finite_rings/hom_finite_field_givaro.pyx"],
+ # this order is needed to compile under windows.
+ libraries = ['givaro', 'ntl', 'gmpxx', 'gmp', 'm'],
+- language='c++',
+- extra_compile_args = givaro_extra_compile_args),
++ language='c++'),
+
+ ################################
+ ##
+@@ -1574,8 +1585,7 @@ ext_modules = [
+ Extension('sage.rings.polynomial.plural',
+ sources = ['sage/rings/polynomial/plural.pyx'],
+ libraries = ['m', 'readline', 'singular', 'givaro', 'gmpxx', 'gmp'],
+- language="c++",
+- extra_compile_args = givaro_extra_compile_args),
++ language="c++"),
+
+ Extension('sage.rings.polynomial.multi_polynomial_libsingular',
+ sources = ['sage/rings/polynomial/multi_polynomial_libsingular.pyx'],
+diff --git a/src/sage/libs/linbox/echelonform.pxd b/src/sage/libs/linbox/echelonform.pxd
+index 3097c8b..cf4902d 100644
+--- a/src/sage/libs/linbox/echelonform.pxd
++++ b/src/sage/libs/linbox/echelonform.pxd
+@@ -1,23 +1,27 @@
++# distutils: extra_compile_args = LINBOX_CFLAGS
++# distutils: libraries = LINBOX_LIBRARIES
++# distutils: library_dirs = LINBOX_LIBDIR
++
+ from sage.libs.linbox.modular cimport ModDoubleField, ModDoubleFieldElement, ModFloatField, ModFloatFieldElement
+ from libc.stdint cimport uint64_t
+
+-cdef extern from "linbox/matrix/blas-matrix.h" namespace "LinBox":
+- cdef cppclass BlasMatrixDouble "LinBox::BlasMatrix<LinBox::Modular<double> >":
++cdef extern from "linbox/matrix/dense-matrix.h" namespace "LinBox":
++ cdef cppclass BlasMatrixDouble "LinBox::DenseMatrix<Givaro::Modular<double> >":
+ BlasMatrixDouble(ModDoubleField F, uint64_t nrows, uint64_t ncols)
+ void setEntry(size_t i, size_t j, ModDoubleFieldElement t)
+ ModDoubleFieldElement &getEntry(size_t i, size_t j)
+
+- cdef cppclass BlasMatrixFloat "LinBox::BlasMatrix<LinBox::Modular<float> >":
++ cdef cppclass BlasMatrixFloat "LinBox::DenseMatrix<Givaro::Modular<float> >":
+ BlasMatrixFloat(ModFloatField F, uint64_t nrows, uint64_t ncols)
+ void setEntry(size_t i, size_t j, ModFloatFieldElement t)
+ ModFloatFieldElement &getEntry(size_t i, size_t j)
+
+ cdef extern from "linbox/algorithms/echelon-form.h":
+- cdef cppclass EchelonFormDomainDouble "LinBox::EchelonFormDomain<LinBox::Modular<double> >":
++ cdef cppclass EchelonFormDomainDouble "LinBox::EchelonFormDomain<Givaro::Modular<double> >":
+ EchelonFormDomainDouble(ModDoubleField)
+ int rowReducedEchelon(BlasMatrixDouble, BlasMatrixDouble)
+
+- cdef cppclass EchelonFormDomainFloat "LinBox::EchelonFormDomain<LinBox::Modular<float> >":
++ cdef cppclass EchelonFormDomainFloat "LinBox::EchelonFormDomain<Givaro::Modular<float> >":
+ EchelonFormDomainFloat(ModFloatField)
+ int rowReducedEchelon(BlasMatrixFloat, BlasMatrixFloat)
+
+diff --git a/src/sage/libs/linbox/fflas.pxd b/src/sage/libs/linbox/fflas.pxd
+index e102004..01ab1b1 100644
+--- a/src/sage/libs/linbox/fflas.pxd
++++ b/src/sage/libs/linbox/fflas.pxd
+@@ -1,3 +1,7 @@
++# distutils: extra_compile_args = FFLASFFPACK_CFLAGS
++# distutils: libraries = FFLASFFPACK_LIBRARIES
++# distutils: library_dirs = FFLASFFPACK_LIBDIR
++
+ from .modular cimport ModDoubleField, ModFloatField, ModDoubleFieldElement, ModFloatFieldElement
+
+ cdef extern from "fflas-ffpack/fflas-ffpack.h" namespace "std":
+diff --git a/src/sage/libs/linbox/linbox.pyx b/src/sage/libs/linbox/linbox.pyx
+index e932347..a9bd6d1 100644
+--- a/src/sage/libs/linbox/linbox.pyx
++++ b/src/sage/libs/linbox/linbox.pyx
+@@ -1,3 +1,7 @@
++# distutils: extra_compile_args = LINBOX_CFLAGS
++# distutils: libraries = LINBOX_LIBRARIES
++# distutils: library_dirs = LINBOX_LIBDIR
++
+ r"""
+ Linbox interface
+ """
+diff --git a/src/sage/libs/linbox/modular.pxd b/src/sage/libs/linbox/modular.pxd
+index 7ef204c..ea5fb29 100644
+--- a/src/sage/libs/linbox/modular.pxd
++++ b/src/sage/libs/linbox/modular.pxd
+@@ -1,10 +1,10 @@
+-cdef extern from "linbox/field/modular.h":
++cdef extern from "givaro/modular.h":
+ # double
+
+- cdef cppclass ModDoubleFieldElement "LinBox::Modular<double>::Element":
++ cdef cppclass ModDoubleFieldElement "Givaro::Modular<double>::Element":
+ pass
+
+- cdef cppclass ModDoubleField "LinBox::Modular<double>":
++ cdef cppclass ModDoubleField "Givaro::Modular<double>":
+ ModDoubleField(int modulus)
+ ModDoubleFieldElement init(ModDoubleFieldElement res, int v)
+ ModDoubleFieldElement init(ModDoubleFieldElement res, double v)
+@@ -20,10 +20,10 @@ cdef extern from "linbox/field/modular.h":
+
+
+ # float
+- cdef cppclass ModFloatFieldElement "LinBox::Modular<float>::Element":
++ cdef cppclass ModFloatFieldElement "Givaro::Modular<float>::Element":
+ pass
+
+- cdef cppclass ModFloatField "LinBox::Modular<float>":
++ cdef cppclass ModFloatField "Givaro::Modular<float>":
+ ModFloatField(int modulus)
+ ModFloatFieldElement init(ModFloatFieldElement res, int v)
+ ModFloatFieldElement init(ModFloatFieldElement res, double v)
+diff --git a/src/sage/libs/singular/singular.pyx b/src/sage/libs/singular/singular.pyx
+index 33d7f7ec..77f6e0a 100644
+--- a/src/sage/libs/singular/singular.pyx
++++ b/src/sage/libs/singular/singular.pyx
+@@ -23,6 +23,7 @@ cdef extern from "limits.h":
+
+ import os
+
++from libc.stdint cimport int64_t
+ from sage.libs.singular.decl cimport intvec
+ from sage.libs.singular.decl cimport SR_HDL, SR_INT, SR_TO_INT
+ from sage.libs.singular.decl cimport singular_options, singular_verbose_options
+@@ -156,7 +157,7 @@ cdef FFgivE si2sa_GFqGivaro(number *n, ring *_ring, Cache_givaro cache):
+ order = cache.objectptr.cardinality() - 1
+
+ while z:
+- c = cache.objectptr.initi(c, <long>napGetCoeff(z))
++ c = cache.objectptr.initi(c, <int64_t>napGetCoeff(z))
+ e = napGetExpFrom(z,1, _ring)
+ if e == 0:
+ ret = cache.objectptr.add(ret, c, ret)
+diff --git a/src/sage/rings/finite_rings/element_givaro.pxd b/src/sage/rings/finite_rings/element_givaro.pxd
+index 68def46..91c4ed7 100644
+--- a/src/sage/rings/finite_rings/element_givaro.pxd
++++ b/src/sage/rings/finite_rings/element_givaro.pxd
+@@ -1,9 +1,15 @@
+-from sage.structure.element cimport Element, RingElement, ModuleElement
+-from sage.rings.finite_rings.element_base cimport FinitePolyExtElement
++# distutils: extra_compile_args = GIVARO_CFLAGS
++
++from libcpp.vector cimport vector
++ctypedef vector[int] intvec
++
++from libc.stdint cimport int64_t
+
+-from sage.structure.parent cimport Parent
++from sage.rings.finite_rings.element_base cimport FinitePolyExtElement
++from sage.structure.parent cimport Parent
+ from sage.structure.sage_object cimport SageObject
+
++
+ cdef extern from "givaro/givconfig.h":
+ pass
+
+@@ -13,16 +19,7 @@ cdef extern from "givaro/givrandom.h":
+
+ GivRandom GivRandomSeeded "Givaro::GivRandom"(unsigned long seed)
+
+-cdef extern from "givaro/givgfq.h":
+- ctypedef struct intvec "std::vector<unsigned int>":
+- void (* push_back)(int elem)
+-
+- ctypedef struct constintvec "const std::vector<unsigned int>"
+-
+- intvec intvec_factory "std::vector<unsigned int>"(int len)
+-
+-cdef extern from "givaro/givgfq.h":
+-
++cdef extern from "givaro/gfq.h":
+ ctypedef struct GivaroGfq "Givaro::GFqDom<int>":
+ #attributes
+ unsigned int one
+@@ -40,10 +37,10 @@ cdef extern from "givaro/givgfq.h":
+ unsigned int (* cardinality)()
+ int (* exponent)()
+ int (* random)(GivRandom gen, int res)
+- int (* initi "init")(int res, int e)
++ int (* initi "init")(int res, int64_t e)
+ int (* initd "init")(int res, double e)
+ int (* indeterminate)()
+- int (* convert)(int r, int p)
++ int (* convert)(int64_t r, int p)
+ int (* read)(int r, int p)
+ int (* axpyin)(int r, int a, int x)
+ int (* axpy)(int r, int a, int b, int c)
+@@ -60,7 +57,12 @@ cdef extern from "givaro/givgfq.h":
+ void delete "delete "(void *o)
+ int gfq_element_factory "Givaro::GFqDom<int>::Element"()
+
+-cdef class FiniteField_givaroElement(FinitePolyExtElement) #forward declaration
++
++cdef class FiniteField_givaroElement(FinitePolyExtElement):
++ cdef int element
++ cdef Cache_givaro _cache
++ cdef object _multiplicative_order
++ cdef FiniteField_givaroElement _new_c(self, int value)
+
+ cdef class Cache_givaro(SageObject):
+ cdef GivaroGfq *objectptr # C++ object
+@@ -85,11 +87,4 @@ cdef class FiniteField_givaro_iterator:
+ cdef int iterator
+ cdef Cache_givaro _cache
+
+-cdef class FiniteField_givaroElement(FinitePolyExtElement):
+- cdef int element
+- cdef Cache_givaro _cache
+- cdef object _multiplicative_order
+- cdef FiniteField_givaroElement _new_c(self, int value)
+-
+-
+ cdef inline FiniteField_givaroElement make_FiniteField_givaroElement(Cache_givaro cache, int x)
+diff --git a/src/sage/rings/finite_rings/element_givaro.pyx b/src/sage/rings/finite_rings/element_givaro.pyx
+index d32b5cf..f2afa44 100644
+--- a/src/sage/rings/finite_rings/element_givaro.pyx
++++ b/src/sage/rings/finite_rings/element_givaro.pyx
+@@ -59,8 +59,9 @@ from sage.misc.randstate cimport randstate, current_randstate
+ from sage.rings.finite_rings.finite_field_base cimport FiniteField
+ from sage.rings.ring cimport Ring
+ from element_ext_pari import FiniteField_ext_pariElement
+-from element_pari_ffelt import FiniteFieldElement_pari_ffelt
++from element_pari_ffelt cimport FiniteFieldElement_pari_ffelt
+ from sage.structure.sage_object cimport SageObject
++from sage.structure.element cimport Element, ModuleElement, RingElement
+ import operator
+ import sage.arith.all
+ import finite_field_constructor as finite_field
+@@ -374,18 +375,16 @@ cdef class Cache_givaro(SageObject):
+ elif isinstance(e, int) or \
+ isinstance(e, Integer) or \
+ isinstance(e, long) or is_IntegerMod(e):
+- try:
+- e_int = e
+- except OverflowError:
+- e_int = e % self.characteristic()
++ e_int = e % self.characteristic()
+ res = self.objectptr.initi(res, e_int)
+
+ elif e is None:
+ e_int = 0
+- res = self.objectptr.initi(res,e_int)
++ res = self.objectptr.initi(res, e_int)
+
+ elif isinstance(e, float):
+- res = self.objectptr.initd(res,e)
++ e_int = int(e) % self.characteristic()
++ res = self.objectptr.initd(res, e_int)
+
+ elif isinstance(e, str):
+ return self.parent(eval(e.replace("^","**"),self.parent.gens_dict()))
+@@ -395,8 +394,8 @@ cdef class Cache_givaro(SageObject):
+ raise TypeError("e.parent must match self.vector_space")
+ ret = self._zero_element
+ for i in range(len(e)):
+- e_entry = e[i] % self.characteristic()
+- res = self.objectptr.initi(res, int(e_entry))
++ e_int = e[i] % self.characteristic()
++ res = self.objectptr.initi(res, e_int)
+ to_add = make_FiniteField_givaroElement(self, res)
+ ret = ret + to_add*self.parent.gen()**i
+ return ret
+@@ -435,8 +434,8 @@ cdef class Cache_givaro(SageObject):
+ raise ValueError("list is too long")
+ ret = self._zero_element
+ for i in range(len(e)):
+- e_entry = e[i] % self.characteristic()
+- res = self.objectptr.initi(res, int(e_entry))
++ e_int = e[i] % self.characteristic()
++ res = self.objectptr.initi(res, e_int)
+ to_add = make_FiniteField_givaroElement(self, res)
+ ret = ret + to_add*self.parent.gen()**i
+ return ret
+@@ -573,19 +572,17 @@ cdef class Cache_givaro(SageObject):
+ cdef int ret = k.zero
+ cdef int a = k.indeterminate()
+ cdef int at = k.one
+- cdef unsigned int ch = k.characteristic()
+- cdef int _n, t, i
++ cdef int ch = k.characteristic()
++ cdef int t, i
+
+ if n<0 or n>k.cardinality():
+ raise TypeError("n must be between 0 and self.order()")
+
+- _n = n
+-
+ for i from 0 <= i < k.exponent():
+- t = k.initi(t, _n%ch)
++ t = k.initi(t, n % ch)
+ ret = k.axpy(ret, t, at, ret)
+ at = k.mul(at,at,a)
+- _n = _n/ch
++ n //= ch
+ return make_FiniteField_givaroElement(self, ret)
+
+ def _element_repr(self, FiniteField_givaroElement e):
+diff --git a/src/sage/rings/finite_rings/finite_field_givaro.py b/src/sage/rings/finite_rings/finite_field_givaro.py
+index adbaab3..c431f6d 100644
+--- a/src/sage/rings/finite_rings/finite_field_givaro.py
++++ b/src/sage/rings/finite_rings/finite_field_givaro.py
+@@ -270,7 +270,8 @@ class FiniteField_givaro(FiniteField):
+ sage: k(2) # indirect doctest
+ 0
+
+- Floats coerce in:
++ Floats are converted like integers::
++
+ sage: k(float(2.0))
+ 0
+
+@@ -344,7 +345,7 @@ class FiniteField_givaro(FiniteField):
+ sage: k(pari('Mod(1,2)'))
+ 1
+ sage: k(pari('Mod(2,3)'))
+- 0
++ a
+ sage: k(pari('Mod(1,3)*a^20'))
+ a^7 + a^5 + a^4 + a^2
+
Copied: sagemath/repos/community-staging-x86_64/package.patch (from rev 185158, sagemath/trunk/package.patch)
===================================================================
--- community-staging-x86_64/package.patch (rev 0)
+++ community-staging-x86_64/package.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,11 @@
+--- src/sage/misc/package.py.orig 2014-11-23 15:58:13.000000000 +0100
++++ src/sage/misc/package.py 2015-01-22 20:32:25.651383902 +0100
+@@ -204,7 +204,7 @@
+ Otherwise, installing "pillow" will cause this function to think
+ that "pil" is installed, for example.
+ """
+- return any(p.split('-')[0] == package for p in installed_packages())
++ return True
+
+ def package_versions(package_type, local=False):
+ r"""
Copied: sagemath/repos/community-staging-x86_64/paths.patch (from rev 185158, sagemath/trunk/paths.patch)
===================================================================
--- community-staging-x86_64/paths.patch (rev 0)
+++ community-staging-x86_64/paths.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,32 @@
+--- src/sage/env.py.orig 2014-06-25 10:47:25.827203554 +1200
++++ src/sage/env.py 2014-06-25 10:49:07.667402821 +1200
+@@ -90,10 +90,10 @@
+
+ # bunch of sage directories and files
+ _add_variable_or_fallback('SAGE_ROOT', None)
+-_add_variable_or_fallback('SAGE_LOCAL', opj('$SAGE_ROOT', 'local'))
+-_add_variable_or_fallback('SAGE_ETC', opj('$SAGE_LOCAL', 'etc'))
++_add_variable_or_fallback('SAGE_LOCAL', '/usr')
++_add_variable_or_fallback('SAGE_ETC', '/etc/sage')
+ _add_variable_or_fallback('SAGE_INC', opj('$SAGE_LOCAL', 'include'))
+-_add_variable_or_fallback('SAGE_SHARE', opj('$SAGE_LOCAL', 'share'))
++_add_variable_or_fallback('SAGE_SHARE', opj('$SAGE_LOCAL', 'share', 'sage'))
+
+ _add_variable_or_fallback('SAGE_SRC', opj('$SAGE_ROOT', 'src'))
+
+@@ -102,13 +102,13 @@
+ except AttributeError: # in case of use inside virtualenv
+ sitepackages_dirs = [os.path.join(os.path.dirname(site.__file__),
+ 'site-packages')]
+-_add_variable_or_fallback('SITE_PACKAGES', sitepackages_dirs)
++_add_variable_or_fallback('SITE_PACKAGES', sitepackages_dirs + ['/usr/lib/sage/site-packages'])
+
+ _add_variable_or_fallback('SAGE_LIB', SITE_PACKAGES[0])
+
+ _add_variable_or_fallback('SAGE_CYTHONIZED', opj('$SAGE_SRC', 'build', 'cythonized'))
+
+-_add_variable_or_fallback('SAGE_EXTCODE', opj('$SAGE_SHARE', 'sage', 'ext'))
++_add_variable_or_fallback('SAGE_EXTCODE', opj('$SAGE_SHARE', 'ext'))
+ _add_variable_or_fallback('SAGE_LOGS', opj('$SAGE_ROOT', 'logs', 'pkgs'))
+ _add_variable_or_fallback('SAGE_SPKG_INST', opj('$SAGE_LOCAL', 'var', 'lib', 'sage', 'installed'))
+ _add_variable_or_fallback('SAGE_DOC_SRC', opj('$SAGE_SRC', 'doc'))
Copied: sagemath/repos/community-staging-x86_64/python-2.7.11.patch (from rev 185158, sagemath/trunk/python-2.7.11.patch)
===================================================================
--- community-staging-x86_64/python-2.7.11.patch (rev 0)
+++ community-staging-x86_64/python-2.7.11.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,11 @@
+--- src/sage/misc/sage_timeit.py.orig 2015-12-19 11:09:42.836938821 +0100
++++ src/sage/misc/sage_timeit.py 2015-12-19 11:10:27.090217304 +0100
+@@ -217,7 +217,7 @@
+ # but is there a better way to achieve that the code stmt has access
+ # to the shell namespace?
+
+- src = timeit_.template % {'stmt': timeit_.reindent(stmt, 8),
++ src = timeit_.template % {'init': "", 'stmt': timeit_.reindent(stmt, 8),
+ 'setup': "pass"}
+ code = compile(src, "<magic-timeit>", "exec")
+ ns = {}
Copied: sagemath/repos/community-staging-x86_64/sagemath-ipython5.patch (from rev 185158, sagemath/trunk/sagemath-ipython5.patch)
===================================================================
--- community-staging-x86_64/sagemath-ipython5.patch (rev 0)
+++ community-staging-x86_64/sagemath-ipython5.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,120 @@
+diff --git a/src/sage/repl/interpreter.py b/src/sage/repl/interpreter.py
+index ef8724d..6896985 100644
+--- a/src/sage/repl/interpreter.py
++++ b/src/sage/repl/interpreter.py
+@@ -107,6 +107,7 @@ import os
+ import re
+ import sys
+ from sage.repl.preparse import preparse
++from sage.repl.prompts import SagePrompts, InterfacePrompts
+
+ from traitlets.config.loader import Config
+ from traitlets import Bool, Type
+@@ -375,11 +376,6 @@ class SageTestShell(SageShellOverride, TerminalInteractiveShell):
+ ###################################################################
+
+ DEFAULT_SAGE_CONFIG = Config(
+- PromptManager = Config(
+- in_template = 'sage: ',
+- in2_template = '....: ',
+- justify = False,
+- out_template = ''),
+ TerminalIPythonApp = Config(
+ display_banner = False,
+ verbose_crash = True,
+@@ -387,6 +383,7 @@ DEFAULT_SAGE_CONFIG = Config(
+ shell_class = SageTerminalInteractiveShell,
+ ),
+ InteractiveShell = Config(
++ prompts_class = SagePrompts,
+ ast_node_interactivity = 'all',
+ colors = 'LightBG' if sys.stdout.isatty() else 'NoColor',
+ confirm_exit = False,
+@@ -620,13 +617,11 @@ def interface_shell_embed(interface):
+ cfg = copy.deepcopy(get_ipython().config)
+ except NameError:
+ cfg = copy.deepcopy(DEFAULT_SAGE_CONFIG)
+- cfg.PromptManager['in_template'] = interface.name() + ': '
+- cfg.PromptManager['in2_template'] = len(interface.name())*'.' + ': '
+-
+ ipshell = InteractiveShellEmbed(config=cfg,
+ banner1='\n --> Switching to %s <--\n\n'%interface,
+ exit_msg = '\n --> Exiting back to Sage <--\n')
+ ipshell.interface = interface
++ ipshell.prompts = InterfacePrompts(interface.name())
+
+ while ipshell.prefilter_manager.transformers:
+ ipshell.prefilter_manager.transformers.pop()
+diff --git a/src/sage/repl/prompts.py b/src/sage/repl/prompts.py
+new file mode 100644
+index 0000000..69f8cdd
+--- /dev/null
++++ b/src/sage/repl/prompts.py
+@@ -0,0 +1,67 @@
++r"""
++Sage Commandline Prompts
++"""
++
++#*****************************************************************************
++# Copyright (C) 2016 Volker Braun <vbraun.name at gmail.com>
++#
++# This program is free software: you can redistribute it and/or modify
++# it under the terms of the GNU General Public License as published by
++# the Free Software Foundation, either version 2 of the License, or
++# (at your option) any later version.
++# http://www.gnu.org/licenses/
++#*****************************************************************************
++
++from pygments.token import Token
++from IPython.terminal.prompts import Prompts
++
++
++class SagePrompts(Prompts):
++
++ def in_prompt_tokens(self, cli=None):
++ return [
++ (Token.Prompt, 'sage: '),
++ ]
++
++ def continuation_prompt_tokens(self, cli=None, width=None):
++ return [
++ (Token.Prompt, '....: '),
++ ]
++
++ def rewrite_prompt_tokens(self):
++ return [
++ (Token.Prompt, '----> '),
++ ]
++
++ def out_prompt_tokens(self):
++ return [
++ (Token.OutPrompt, ''),
++ ]
++
++
++class InterfacePrompts(Prompts):
++
++ def __init__(self, interface_name):
++ self.__name = interface_name
++ self.__width = len(interface_name)
++
++ def in_prompt_tokens(self, cli=None):
++ return [
++ (Token.Prompt, self.__name + ': '),
++ ]
++
++ def continuation_prompt_tokens(self, cli=None, width=None):
++ return [
++ (Token.Prompt, '.' * self.__width + ': '),
++ ]
++
++ def rewrite_prompt_tokens(self):
++ return [
++ (Token.Prompt, '-' * self.__width + '> '),
++ ]
++
++ def out_prompt_tokens(self):
++ return [
++ (Token.OutPrompt, ''),
++ ]
++
Copied: sagemath/repos/community-staging-x86_64/skip-check.patch (from rev 185158, sagemath/trunk/skip-check.patch)
===================================================================
--- community-staging-x86_64/skip-check.patch (rev 0)
+++ community-staging-x86_64/skip-check.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,22 @@
+--- src/bin/sage.orig 2014-12-18 09:47:27.354829070 +0100
++++ src/bin/sage 2014-12-18 09:48:00.041563401 +0100
+@@ -352,18 +352,6 @@
+
+ # 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).
+- 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'
+- echo >&2 'tarball, but you have not compiled it yet (or maybe the build has not'
+- echo >&2 'finished). You should run `make` in the Sage root directory first.'
+- echo >&2 'If you did not intend to build Sage from source, you should download'
+- echo >&2 'a binary tarball instead. Read README.txt for more information.'
+- echo >&2 '************************************************************************'
+- exit 1
+- fi
+-
+ # Display the startup banner (unless SAGE_BANNER is explictly "no")
+ if [ "$SAGE_BANNER" != "no" ]; then
+ # can be 'bare', or 'yes', or unspecified
+
Copied: sagemath/repos/community-staging-x86_64/test-optional.patch (from rev 185158, sagemath/trunk/test-optional.patch)
===================================================================
--- community-staging-x86_64/test-optional.patch (rev 0)
+++ community-staging-x86_64/test-optional.patch 2016-08-04 23:02:50 UTC (rev 185159)
@@ -0,0 +1,11 @@
+--- src/sage/doctest/control.py.orig 2015-10-31 09:40:55.173671531 +0100
++++ src/sage/doctest/control.py 2015-10-31 09:40:05.370125436 +0100
+@@ -253,7 +253,7 @@
+ if 'optional' in options.optional:
+ options.optional.discard('optional')
+ from sage.misc.package import package_versions
+- optional_pkgs = package_versions("optional", local=True)
++ optional_pkgs = {}
+ for pkg, versions in optional_pkgs.items():
+ if versions[0] == versions[1]:
+ options.optional.add(pkg)
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