[arch-commits] Commit in sagemath/repos (58 files)
Antonio Rojas
arojas at archlinux.org
Sun Jan 29 11:19:59 UTC 2017
Date: Sunday, January 29, 2017 @ 11:19:59
Author: arojas
Revision: 209348
archrelease: copy trunk to community-i686, community-x86_64
Added:
sagemath/repos/community-i686/PKGBUILD
(from rev 209347, sagemath/trunk/PKGBUILD)
sagemath/repos/community-i686/cython-sys-path.patch
(from rev 209347, sagemath/trunk/cython-sys-path.patch)
sagemath/repos/community-i686/ecm-7.patch
(from rev 209347, sagemath/trunk/ecm-7.patch)
sagemath/repos/community-i686/env.patch
(from rev 209347, sagemath/trunk/env.patch)
sagemath/repos/community-i686/fes02.patch
(from rev 209347, sagemath/trunk/fes02.patch)
sagemath/repos/community-i686/increase-rtol.patch
(from rev 209347, sagemath/trunk/increase-rtol.patch)
sagemath/repos/community-i686/is-package-installed.patch
(from rev 209347, sagemath/trunk/is-package-installed.patch)
sagemath/repos/community-i686/jupyter-path.patch
(from rev 209347, sagemath/trunk/jupyter-path.patch)
sagemath/repos/community-i686/package.patch
(from rev 209347, sagemath/trunk/package.patch)
sagemath/repos/community-i686/r-no-readline.patch
(from rev 209347, sagemath/trunk/r-no-readline.patch)
sagemath/repos/community-i686/sagemath-gslcblas.patch
(from rev 209347, sagemath/trunk/sagemath-gslcblas.patch)
sagemath/repos/community-i686/sagemath-no-anal.h.patch
(from rev 209347, sagemath/trunk/sagemath-no-anal.h.patch)
sagemath/repos/community-i686/sagemath-planarity3.patch
(from rev 209347, sagemath/trunk/sagemath-planarity3.patch)
sagemath/repos/community-i686/skip-check.patch
(from rev 209347, sagemath/trunk/skip-check.patch)
sagemath/repos/community-i686/test-optional.patch
(from rev 209347, sagemath/trunk/test-optional.patch)
sagemath/repos/community-x86_64/PKGBUILD
(from rev 209347, sagemath/trunk/PKGBUILD)
sagemath/repos/community-x86_64/cython-sys-path.patch
(from rev 209347, sagemath/trunk/cython-sys-path.patch)
sagemath/repos/community-x86_64/ecm-7.patch
(from rev 209347, sagemath/trunk/ecm-7.patch)
sagemath/repos/community-x86_64/env.patch
(from rev 209347, sagemath/trunk/env.patch)
sagemath/repos/community-x86_64/fes02.patch
(from rev 209347, sagemath/trunk/fes02.patch)
sagemath/repos/community-x86_64/increase-rtol.patch
(from rev 209347, sagemath/trunk/increase-rtol.patch)
sagemath/repos/community-x86_64/is-package-installed.patch
(from rev 209347, sagemath/trunk/is-package-installed.patch)
sagemath/repos/community-x86_64/jupyter-path.patch
(from rev 209347, sagemath/trunk/jupyter-path.patch)
sagemath/repos/community-x86_64/package.patch
(from rev 209347, sagemath/trunk/package.patch)
sagemath/repos/community-x86_64/r-no-readline.patch
(from rev 209347, sagemath/trunk/r-no-readline.patch)
sagemath/repos/community-x86_64/sagemath-gslcblas.patch
(from rev 209347, sagemath/trunk/sagemath-gslcblas.patch)
sagemath/repos/community-x86_64/sagemath-no-anal.h.patch
(from rev 209347, sagemath/trunk/sagemath-no-anal.h.patch)
sagemath/repos/community-x86_64/sagemath-planarity3.patch
(from rev 209347, sagemath/trunk/sagemath-planarity3.patch)
sagemath/repos/community-x86_64/skip-check.patch
(from rev 209347, sagemath/trunk/skip-check.patch)
sagemath/repos/community-x86_64/test-optional.patch
(from rev 209347, sagemath/trunk/test-optional.patch)
Deleted:
sagemath/repos/community-i686/PKGBUILD
sagemath/repos/community-i686/cython-sys-path.patch
sagemath/repos/community-i686/disable-fes.patch
sagemath/repos/community-i686/ecm-7.patch
sagemath/repos/community-i686/env.patch
sagemath/repos/community-i686/increase-rtol.patch
sagemath/repos/community-i686/is-package-installed.patch
sagemath/repos/community-i686/jupyter-path.patch
sagemath/repos/community-i686/package.patch
sagemath/repos/community-i686/r-no-readline.patch
sagemath/repos/community-i686/sagemath-gslcblas.patch
sagemath/repos/community-i686/sagemath-no-anal.h.patch
sagemath/repos/community-i686/skip-check.patch
sagemath/repos/community-i686/test-optional.patch
sagemath/repos/community-x86_64/PKGBUILD
sagemath/repos/community-x86_64/cython-sys-path.patch
sagemath/repos/community-x86_64/disable-fes.patch
sagemath/repos/community-x86_64/ecm-7.patch
sagemath/repos/community-x86_64/env.patch
sagemath/repos/community-x86_64/increase-rtol.patch
sagemath/repos/community-x86_64/is-package-installed.patch
sagemath/repos/community-x86_64/jupyter-path.patch
sagemath/repos/community-x86_64/package.patch
sagemath/repos/community-x86_64/r-no-readline.patch
sagemath/repos/community-x86_64/sagemath-gslcblas.patch
sagemath/repos/community-x86_64/sagemath-no-anal.h.patch
sagemath/repos/community-x86_64/skip-check.patch
sagemath/repos/community-x86_64/test-optional.patch
---------------------------------------------+
/PKGBUILD | 320 ++++++++++++
/cython-sys-path.patch | 20
/ecm-7.patch | 158 ++++++
/env.patch | 188 +++++++
/increase-rtol.patch | 74 ++
/is-package-installed.patch | 656 ++++++++++++++++++++++++++
/jupyter-path.patch | 44 +
/package.patch | 76 +++
/r-no-readline.patch | 22
/sagemath-gslcblas.patch | 26 +
/sagemath-no-anal.h.patch | 24
/skip-check.patch | 44 +
/test-optional.patch | 50 +
community-i686/PKGBUILD | 158 ------
community-i686/cython-sys-path.patch | 10
community-i686/disable-fes.patch | 19
community-i686/ecm-7.patch | 79 ---
community-i686/env.patch | 94 ---
community-i686/fes02.patch | 57 ++
community-i686/increase-rtol.patch | 37 -
community-i686/is-package-installed.patch | 328 -------------
community-i686/jupyter-path.patch | 22
community-i686/package.patch | 38 -
community-i686/r-no-readline.patch | 11
community-i686/sagemath-gslcblas.patch | 13
community-i686/sagemath-no-anal.h.patch | 12
community-i686/sagemath-planarity3.patch | 113 ++++
community-i686/skip-check.patch | 22
community-i686/test-optional.patch | 25
community-x86_64/PKGBUILD | 158 ------
community-x86_64/cython-sys-path.patch | 10
community-x86_64/disable-fes.patch | 19
community-x86_64/ecm-7.patch | 79 ---
community-x86_64/env.patch | 94 ---
community-x86_64/fes02.patch | 57 ++
community-x86_64/increase-rtol.patch | 37 -
community-x86_64/is-package-installed.patch | 328 -------------
community-x86_64/jupyter-path.patch | 22
community-x86_64/package.patch | 38 -
community-x86_64/r-no-readline.patch | 11
community-x86_64/sagemath-gslcblas.patch | 13
community-x86_64/sagemath-no-anal.h.patch | 12
community-x86_64/sagemath-planarity3.patch | 113 ++++
community-x86_64/skip-check.patch | 22
community-x86_64/test-optional.patch | 25
45 files changed, 2042 insertions(+), 1736 deletions(-)
Deleted: community-i686/PKGBUILD
===================================================================
--- community-i686/PKGBUILD 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-i686/PKGBUILD 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,158 +0,0 @@
-# $Id$
-# 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
-
-pkgbase=sagemath
-pkgname=(sagemath sagemath-jupyter)
-pkgver=7.5.1
-pkgrel=3
-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 ppl palp brial cliquer maxima-ecl gfan sympow tachyon nauty python2-rpy2 python2-fpylll python2-psutil
- python2-matplotlib python2-scipy python2-sympy python2-networkx python2-pillow python2-future 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' 'python2-igraph: igraph backend for graph theory'
- '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' 'cryptominisat2: 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-pynormaliz: Normaliz backend for polyhedral computations')
-makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc libhomfly libbraiding
- mcqd coxeter3 cryptominisat2 modular_decomposition bliss-graphs tdlib python2-pkgconfig meataxe) # libfes
-source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"
- env.patch skip-check.patch cython-sys-path.patch is-package-installed.patch package.patch disable-fes.patch
- jupyter-path.patch test-optional.patch ecm-7.patch increase-rtol.patch sagemath-gslcblas.patch r-no-readline.patch
- sagemath-no-anal.h.patch)
-sha256sums=('3cd9af3e3bfd7f5cc966b7c36168d04b9a1213aa9a7af3286b5d53d40e7653e3'
- '9dba04ff13626a7b6c338a8b18a6c27d343f68a547a218533cf773af3dae6635'
- 'b02b3d2d5620ca20f96adb62b6fef05e4676c0a60983310a1450fdf3d923cb04'
- 'ff7e034d08ab084fdb193484f7fe3a659ebcd8ab33a2b7177237d65b26de7872'
- 'd60fb0fbd27991ce9496ca035a54b03334b5b53f244227a8d6e13f3327ce75d2'
- '4a2297e4d9d28f0b3a1f58e1b463e332affcb109eafde44837b1657e309c8212'
- '7ab53d30b877dabb6835fbe67a208bef65fa0aaf40221b4d0b58e4b7086bc47a'
- '775051aa9076ebf631c8a291af38b6ec4a13c904740dc9da831641d592d8bcd8'
- '81d08c6a760f171f3381455b66a6c84789c9f0eefddbe6ca5794075514ad8c3a'
- '65ad84c83d5f956fde8eab961f2caad56d64044324c4abc0e56bcd9f44061cb6'
- 'be925eefeac3f28e639794ddc20d64e6faafd7181804e29417a510224d19ccc7'
- '973224f53e9a6fcfaa9c6cb842b02430a601d1c7ce0abb41b3591470d128930c'
- 'ef9f401fa84fe1772af9efee6816643534f2896da4c23b809937b19771bdfbbf'
- '8126c92a5fc15738c4f7982aadb5a4033230fc2d5da05af9133a96ad1181419e')
-
-prepare(){
- cd sage-$pkgver
-
-# Arch-specific patches
-# assume all optional packages are installed
- patch -p0 -i ../package.patch
-# set env variables
- patch -p0 -i ../env.patch
-# skip checking build status
- patch -p0 -i ../skip-check.patch
-# don't list optional packages when running tests
- patch -p0 -i ../test-optional.patch
-# set jupyter path
- patch -p0 -i ../jupyter-path.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
-# increase numerical tolerance, needed by scipy 0.18
- patch -p1 -i ../increase-rtol.patch
-# fix cblas linking in gsl modules
- patch -p1 -i ../sagemath-gslcblas.patch
-# fix freezes in R interface with readline 7 (Debian)
- patch -p1 -i ../r-no-readline.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
-# replace is_package_installed usage http://trac.sagemath.org/ticket/20377
- patch -p1 -i ../is-package-installed.patch
-# Allow compiling without pari's anal.h https://trac.sagemath.org/ticket/22195
- patch -p1 -i ../sagemath-no-anal.h.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|g' -i src/bin/sage
- sed -e "s|'cython'|'cython2'|" -i src/bin/sage-cython
- sed -e 's|bin/python|bin/python2|g' -i src/bin/sage-env
-}
-
-
-build() {
- cd sage-$pkgver/src
-
- export SAGE_LOCAL="/usr"
- export SAGE_ROOT="$PWD"
- export SAGE_SRC="$PWD"
- export CC=gcc
-
- python2 setup.py build
-}
-
-package_sagemath() {
- optdepends+=('sagemath-jupyter: Jupyter kernel')
- conflicts=(sage-mathematics)
- replaces=(sage-mathematics)
- provides=(sage-mathematics)
-
- cd sage-$pkgver/src
-
- export SAGE_ROOT="$PWD"
- export SAGE_LOCAL="/usr"
- export JUPYTER_PATH="$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 and help
- mkdir "$pkgdir"/usr/share/sage/source
- ln -s /usr/share/doc/sage "$pkgdir"/usr/share/sage/source/doc
-
-# Remove sage_setup
- rm -r "$pkgdir"/usr/lib/python2.7/site-packages/sage_setup
-
-# Split jupyter kernel
- rm -r "$pkgdir"/usr/share/jupyter
-}
-
-package_sagemath-jupyter() {
- pkgdesc='Jupyter kernel for SageMath'
- depends=(sagemath python2-jupyter_client python2-ipywidgets jupyter-notebook mathjax)
- optdepends=('sage-notebook-exporter: convert flask notebooks to Jupyter')
-
- cd sage-$pkgver/src
-
- export SAGE_ROOT="$PWD"
- export SAGE_LOCAL="/usr"
- export JUPYTER_PATH="$pkgdir"/usr/share/jupyter
-
- python2 -c "from sage.repl.ipython_kernel.install import SageKernelSpec; SageKernelSpec.update()"
-}
Copied: sagemath/repos/community-i686/PKGBUILD (from rev 209347, sagemath/trunk/PKGBUILD)
===================================================================
--- community-i686/PKGBUILD (rev 0)
+++ community-i686/PKGBUILD 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,160 @@
+# $Id$
+# 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
+
+pkgbase=sagemath
+pkgname=(sagemath sagemath-jupyter)
+pkgver=7.5.1
+pkgrel=4
+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 ppl palp brial cliquer maxima-ecl gfan sympow tachyon nauty python2-rpy2 python2-fpylll python2-psutil
+ python2-matplotlib python2-scipy python2-sympy python2-networkx python2-pillow python2-future 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' 'python2-igraph: igraph backend for graph theory'
+ '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' 'cryptominisat2: 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'
+ 'libfes: exhaustive search of solutions for boolean equations' 'python2-pynormaliz: Normaliz backend for polyhedral computations')
+makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc libhomfly libbraiding
+ mcqd coxeter3 cryptominisat2 modular_decomposition bliss-graphs tdlib python2-pkgconfig meataxe libfes)
+source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"
+ env.patch skip-check.patch cython-sys-path.patch is-package-installed.patch package.patch disable-fes.patch
+ jupyter-path.patch test-optional.patch ecm-7.patch increase-rtol.patch sagemath-gslcblas.patch r-no-readline.patch
+ sagemath-no-anal.h.patch sagemath-planarity3.patch fes02.patch)
+sha256sums=('3cd9af3e3bfd7f5cc966b7c36168d04b9a1213aa9a7af3286b5d53d40e7653e3'
+ '9dba04ff13626a7b6c338a8b18a6c27d343f68a547a218533cf773af3dae6635'
+ 'b02b3d2d5620ca20f96adb62b6fef05e4676c0a60983310a1450fdf3d923cb04'
+ 'ff7e034d08ab084fdb193484f7fe3a659ebcd8ab33a2b7177237d65b26de7872'
+ 'd60fb0fbd27991ce9496ca035a54b03334b5b53f244227a8d6e13f3327ce75d2'
+ '4a2297e4d9d28f0b3a1f58e1b463e332affcb109eafde44837b1657e309c8212'
+ '7ab53d30b877dabb6835fbe67a208bef65fa0aaf40221b4d0b58e4b7086bc47a'
+ '775051aa9076ebf631c8a291af38b6ec4a13c904740dc9da831641d592d8bcd8'
+ '81d08c6a760f171f3381455b66a6c84789c9f0eefddbe6ca5794075514ad8c3a'
+ '65ad84c83d5f956fde8eab961f2caad56d64044324c4abc0e56bcd9f44061cb6'
+ 'be925eefeac3f28e639794ddc20d64e6faafd7181804e29417a510224d19ccc7'
+ '973224f53e9a6fcfaa9c6cb842b02430a601d1c7ce0abb41b3591470d128930c'
+ 'ef9f401fa84fe1772af9efee6816643534f2896da4c23b809937b19771bdfbbf'
+ '8126c92a5fc15738c4f7982aadb5a4033230fc2d5da05af9133a96ad1181419e'
+ 'a1c562ebe4538d672404ca3ac2e954a3c955afeb7463f7b4fe6eaa6fa74fe5c7'
+ 'a39da083c038ada797ffc5bedc9ba47455a3f77057d42f86484ae877ef9172ea')
+
+prepare(){
+ cd sage-$pkgver
+
+# Arch-specific patches
+# assume all optional packages are installed
+ patch -p0 -i ../package.patch
+# set env variables
+ patch -p0 -i ../env.patch
+# skip checking build status
+ patch -p0 -i ../skip-check.patch
+# don't list optional packages when running tests
+ patch -p0 -i ../test-optional.patch
+# set jupyter path
+ patch -p0 -i ../jupyter-path.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
+# increase numerical tolerance, needed by scipy 0.18
+ patch -p1 -i ../increase-rtol.patch
+# fix cblas linking in gsl modules
+ patch -p1 -i ../sagemath-gslcblas.patch
+# fix freezes in R interface with readline 7 (Debian)
+ patch -p1 -i ../r-no-readline.patch
+# fix build with planarity 3 (Debian)
+ patch -p2 -i ../sagemath-planarity3.patch
+
+# Upstream patches
+# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209
+ patch -p1 -i ../fes02.patch
+# replace is_package_installed usage http://trac.sagemath.org/ticket/20377
+ patch -p1 -i ../is-package-installed.patch
+# Allow compiling without pari's anal.h https://trac.sagemath.org/ticket/22195
+ patch -p1 -i ../sagemath-no-anal.h.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|g' -i src/bin/sage
+ sed -e "s|'cython'|'cython2'|" -i src/bin/sage-cython
+ sed -e 's|bin/python|bin/python2|g' -i src/bin/sage-env
+}
+
+
+build() {
+ cd sage-$pkgver/src
+
+ export SAGE_LOCAL="/usr"
+ export SAGE_ROOT="$PWD"
+ export SAGE_SRC="$PWD"
+ export CC=gcc
+
+ python2 setup.py build
+}
+
+package_sagemath() {
+ optdepends+=('sagemath-jupyter: Jupyter kernel')
+ conflicts=(sage-mathematics)
+ replaces=(sage-mathematics)
+ provides=(sage-mathematics)
+
+ cd sage-$pkgver/src
+
+ export SAGE_ROOT="$PWD"
+ export SAGE_LOCAL="/usr"
+ export JUPYTER_PATH="$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 and help
+ mkdir "$pkgdir"/usr/share/sage/source
+ ln -s /usr/share/doc/sage "$pkgdir"/usr/share/sage/source/doc
+
+# Remove sage_setup
+ rm -r "$pkgdir"/usr/lib/python2.7/site-packages/sage_setup
+
+# Split jupyter kernel
+ rm -r "$pkgdir"/usr/share/jupyter
+}
+
+package_sagemath-jupyter() {
+ pkgdesc='Jupyter kernel for SageMath'
+ depends=(sagemath python2-jupyter_client python2-ipywidgets jupyter-notebook mathjax)
+ optdepends=('sage-notebook-exporter: convert flask notebooks to Jupyter')
+
+ cd sage-$pkgver/src
+
+ export SAGE_ROOT="$PWD"
+ export SAGE_LOCAL="/usr"
+ export JUPYTER_PATH="$pkgdir"/usr/share/jupyter
+
+ python2 -c "from sage.repl.ipython_kernel.install import SageKernelSpec; SageKernelSpec.update()"
+}
Deleted: community-i686/cython-sys-path.patch
===================================================================
--- community-i686/cython-sys-path.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-i686/cython-sys-path.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,10 +0,0 @@
---- 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
-@@ -414,6 +414,7 @@
- build_dir=SAGE_CYTHONIZED,
- force=force,
- aliases=aliases,
-+ include_path=sys.path,
- compiler_directives={
- 'autotestdict': False,
- 'cdivision': True,
Copied: sagemath/repos/community-i686/cython-sys-path.patch (from rev 209347, sagemath/trunk/cython-sys-path.patch)
===================================================================
--- community-i686/cython-sys-path.patch (rev 0)
+++ community-i686/cython-sys-path.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -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
+@@ -414,6 +414,7 @@
+ build_dir=SAGE_CYTHONIZED,
+ force=force,
+ aliases=aliases,
++ include_path=sys.path,
+ compiler_directives={
+ 'autotestdict': False,
+ 'cdivision': True,
Deleted: community-i686/disable-fes.patch
===================================================================
--- community-i686/disable-fes.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-i686/disable-fes.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,19 +0,0 @@
---- 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"],
Deleted: community-i686/ecm-7.patch
===================================================================
--- community-i686/ecm-7.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-i686/ecm-7.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,79 +0,0 @@
---- 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-i686/ecm-7.patch (from rev 209347, sagemath/trunk/ecm-7.patch)
===================================================================
--- community-i686/ecm-7.patch (rev 0)
+++ community-i686/ecm-7.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -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
+ """
+
Deleted: community-i686/env.patch
===================================================================
--- community-i686/env.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-i686/env.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,94 +0,0 @@
---- 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"
-
- # Display the Sage startup banner, used in src/bin/sage
- sage_banner() {
-@@ -187,7 +187,7 @@
-
- # SAGE_LOCAL is the installation prefix and can be customized
- if [ -z "$SAGE_LOCAL" ]; then
-- export SAGE_LOCAL="$SAGE_ROOT/local"
-+ export SAGE_LOCAL="/usr"
- fi
-
- # sage-env must know where the Sage's script files are
-@@ -233,8 +233,9 @@
- 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="$SAGE_SRC/doc"
-+export GAP_ROOT_DIR="/usr/lib/gap"
-+export SAGE_SRC="$SAGE_SHARE/sage/source"
-+export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage"
- export SAGE_DOC="$SAGE_SHARE/doc/sage"
-
- if [ -z "${SAGE_ORIG_PATH_SET}" ]; then
-@@ -374,6 +337,9 @@
- export SAGE_STARTUP_FILE
- fi
-
-+export LIBMTX="$DOT_SAGE/meataxe"
-+[[ -d $LIBMTX ]] || mkdir $LIBMTX # Create meataxe data dir
-+
- if [ -z "$IPYTHONDIR" ]; then
- # We hardcode a version number in the directory name. The idea is
- # that we keep using the same version number as long as that is
-@@ -468,7 +400,6 @@
- fi
- fi
- fi
--export MAXIMA_PREFIX="$SAGE_LOCAL"
-
- PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB
-
-@@ -629,9 +608,6 @@
- LD_LIBRARY_PATH="$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-i686/env.patch (from rev 209347, sagemath/trunk/env.patch)
===================================================================
--- community-i686/env.patch (rev 0)
+++ community-i686/env.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,94 @@
+--- 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=$NEW_SAGE_ROOT"
+-fi
++NEW_SAGE_ROOT="/usr"
+
+ # Display the Sage startup banner, used in src/bin/sage
+ sage_banner() {
+@@ -187,7 +187,7 @@
+
+ # SAGE_LOCAL is the installation prefix and can be customized
+ if [ -z "$SAGE_LOCAL" ]; then
+- export SAGE_LOCAL="$SAGE_ROOT/local"
++ export SAGE_LOCAL="/usr"
+ fi
+
+ # sage-env must know where the Sage's script files are
+@@ -233,8 +233,9 @@
+ export SAGE_EXTCODE="$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 GAP_ROOT_DIR="/usr/lib/gap"
++export SAGE_SRC="$SAGE_SHARE/sage/source"
++export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage"
+ export SAGE_DOC="$SAGE_SHARE/doc/sage"
+
+ if [ -z "${SAGE_ORIG_PATH_SET}" ]; then
+@@ -374,6 +337,9 @@
+ export SAGE_STARTUP_FILE
+ fi
+
++export LIBMTX="$DOT_SAGE/meataxe"
++[[ -d $LIBMTX ]] || mkdir $LIBMTX # Create meataxe data dir
++
+ if [ -z "$IPYTHONDIR" ]; then
+ # We hardcode a version number in the directory name. The idea is
+ # that we keep using the same version number as long as that is
+@@ -468,7 +400,6 @@
+ fi
+ fi
+ fi
+-export MAXIMA_PREFIX="$SAGE_LOCAL"
+
+ PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB
+
+@@ -629,9 +608,6 @@
+ LD_LIBRARY_PATH="$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-i686/fes02.patch (from rev 209347, sagemath/trunk/fes02.patch)
===================================================================
--- community-i686/fes02.patch (rev 0)
+++ community-i686/fes02.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,57 @@
+From b1f5e3ecc789db674fe17552812f2d0e2ab84be0 Mon Sep 17 00:00:00 2001
+From: Charles Bouillaguet <charles.bouillaguet at lifl.fr>
+Date: Thu, 19 Sep 2013 10:31:11 +0200
+Subject: updating the libFES binding to match a change in the interface
+
+---
+ src/sage/libs/fes.pyx | 12 +++++++-----
+ 1 file changed, 7 insertions(+), 5 deletions(-)
+
+diff --git a/src/sage/libs/fes.pyx b/src/sage/libs/fes.pyx
+index 40b9c23..d188cf0 100644
+--- a/src/sage/libs/fes.pyx
++++ b/src/sage/libs/fes.pyx
+@@ -1,17 +1,19 @@
+ """
+-Binding for the FES library.
++Binding for the libFES library.
+
+ Finding solutions of systems of boolean equations by exhaustive
+ search, via the fes library. This is usually (much) faster than
+ computing a Groebner basis, except in special cases where the latter
+ is particularly easy.
+
+-The FES library is presently only able to deal with polynomials in 64
++More information is available at [http://www.lifl.fr/~bouillag/fes].
++
++The libFES library is presently only able to deal with polynomials in 64
+ variables. Performing a full exhaustive search over 64 variables will
+ take a **long** time. The number of variables can be artificially
+ reduced to 64 by specializing some of them.
+
+-Note that the FES library **requires** at least of the equations to be
++Note that the libFES library **requires** at least of the equations to be
+ non-linear.
+
+ AUTHORS:
+@@ -71,7 +73,7 @@ from libc.stdint cimport uint64_t
+ cdef extern from "fes_interface.h":
+ ctypedef int (*solution_callback_t)(void *, uint64_t)
+
+- void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose)
++ void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose, int T)
+
+
+ include 'sage/ext/interrupt.pxi' #sig_on(), sig_off()
+@@ -219,7 +221,7 @@ def exhaustive_search(eqs, max_sols=Infinity, verbose=False):
+
+ # ------- runs the library
+ sig_on()
+- exhaustive_search_wrapper(n, len(eqs), degree, coeffs, report_solution, <void *> internal_state, verbose)
++ exhaustive_search_wrapper(n, len(eqs), degree, coeffs, report_solution, <void *> internal_state, verbose, 0)
+ sig_off()
+
+ # ------- frees memory occupied by the dense representation of the equations
+--
+cgit v1.0-1-gd88e
+
Deleted: community-i686/increase-rtol.patch
===================================================================
--- community-i686/increase-rtol.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-i686/increase-rtol.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,37 +0,0 @@
-diff -ru sage-7.3.orig/src/sage/coding/code_bounds.py sage-7.3/src/sage/coding/code_bounds.py
---- sage-7.3.orig/src/sage/coding/code_bounds.py 2016-08-05 20:26:10.033204091 +0200
-+++ sage-7.3/src/sage/coding/code_bounds.py 2016-08-05 20:32:27.276579565 +0200
-@@ -554,7 +554,7 @@
- if q < 2: # Here we check that q is actually at least 2
- raise ValueError("The value q must be an integer greater than 1")
-
-- eps = 4.5e-16 # find_root has about this as the default xtol
-+ eps = 4.5e-15 # find_root has about this as the default xtol
- ymax = 1 - 1/q
- if x <= eps:
- return 0
-diff -ru sage-7.3.orig/src/sage/numerical/optimize.py sage-7.3/src/sage/numerical/optimize.py
---- sage-7.3.orig/src/sage/numerical/optimize.py 2016-08-05 20:26:10.816536625 +0200
-+++ sage-7.3/src/sage/numerical/optimize.py 2016-08-05 20:32:21.449907130 +0200
-@@ -15,7 +15,7 @@
- from sage.rings.real_double import RDF
-
-
--def find_root(f, a, b, xtol=10e-13, rtol=4.5e-16, maxiter=100, full_output=False):
-+def find_root(f, a, b, xtol=10e-13, rtol=4.5e-15, maxiter=100, full_output=False):
- """
- Numerically find a root of ``f`` on the closed interval `[a,b]`
- (or `[b,a]`) if possible, where ``f`` is a function in the one variable.
-diff -ru sage-7.3.orig/src/sage/symbolic/expression.pyx sage-7.3/src/sage/symbolic/expression.pyx
---- sage-7.3.orig/src/sage/symbolic/expression.pyx 2016-08-05 20:26:11.333202767 +0200
-+++ sage-7.3/src/sage/symbolic/expression.pyx 2016-08-05 20:32:14.236566826 +0200
-@@ -10884,7 +10884,7 @@
- ret = ret[0]
- return ret
-
-- def find_root(self, a, b, var=None, xtol=10e-13, rtol=4.5e-16, maxiter=100, full_output=False):
-+ def find_root(self, a, b, var=None, xtol=10e-13, rtol=4.5e-15, maxiter=100, full_output=False):
- """
- Numerically find a root of self on the closed interval [a,b] (or
- [b,a]) if possible, where self is a function in the one variable.
-
Copied: sagemath/repos/community-i686/increase-rtol.patch (from rev 209347, sagemath/trunk/increase-rtol.patch)
===================================================================
--- community-i686/increase-rtol.patch (rev 0)
+++ community-i686/increase-rtol.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,37 @@
+diff -ru sage-7.3.orig/src/sage/coding/code_bounds.py sage-7.3/src/sage/coding/code_bounds.py
+--- sage-7.3.orig/src/sage/coding/code_bounds.py 2016-08-05 20:26:10.033204091 +0200
++++ sage-7.3/src/sage/coding/code_bounds.py 2016-08-05 20:32:27.276579565 +0200
+@@ -554,7 +554,7 @@
+ if q < 2: # Here we check that q is actually at least 2
+ raise ValueError("The value q must be an integer greater than 1")
+
+- eps = 4.5e-16 # find_root has about this as the default xtol
++ eps = 4.5e-15 # find_root has about this as the default xtol
+ ymax = 1 - 1/q
+ if x <= eps:
+ return 0
+diff -ru sage-7.3.orig/src/sage/numerical/optimize.py sage-7.3/src/sage/numerical/optimize.py
+--- sage-7.3.orig/src/sage/numerical/optimize.py 2016-08-05 20:26:10.816536625 +0200
++++ sage-7.3/src/sage/numerical/optimize.py 2016-08-05 20:32:21.449907130 +0200
+@@ -15,7 +15,7 @@
+ from sage.rings.real_double import RDF
+
+
+-def find_root(f, a, b, xtol=10e-13, rtol=4.5e-16, maxiter=100, full_output=False):
++def find_root(f, a, b, xtol=10e-13, rtol=4.5e-15, maxiter=100, full_output=False):
+ """
+ Numerically find a root of ``f`` on the closed interval `[a,b]`
+ (or `[b,a]`) if possible, where ``f`` is a function in the one variable.
+diff -ru sage-7.3.orig/src/sage/symbolic/expression.pyx sage-7.3/src/sage/symbolic/expression.pyx
+--- sage-7.3.orig/src/sage/symbolic/expression.pyx 2016-08-05 20:26:11.333202767 +0200
++++ sage-7.3/src/sage/symbolic/expression.pyx 2016-08-05 20:32:14.236566826 +0200
+@@ -10884,7 +10884,7 @@
+ ret = ret[0]
+ return ret
+
+- def find_root(self, a, b, var=None, xtol=10e-13, rtol=4.5e-16, maxiter=100, full_output=False):
++ def find_root(self, a, b, var=None, xtol=10e-13, rtol=4.5e-15, maxiter=100, full_output=False):
+ """
+ Numerically find a root of self on the closed interval [a,b] (or
+ [b,a]) if possible, where self is a function in the one variable.
+
Deleted: community-i686/is-package-installed.patch
===================================================================
--- community-i686/is-package-installed.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-i686/is-package-installed.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,328 +0,0 @@
-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
-
-@@ -824,7 +823,7 @@ 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:
-@@ -1673,7 +1672,7 @@ 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
-@@ -7858,7 +7858,6 @@ 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 " +
-@@ -7876,10 +7875,12 @@ 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)
-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
-@@ -1400,15 +1400,15 @@ 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, "lib", "gap", "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)):
-@@ -1682,9 +1679,7 @@ 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):
- """
-@@ -1735,9 +1730,7 @@ 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):
- """
-@@ -4113,8 +4106,6 @@ 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
-@@ -53,10 +53,6 @@ from fpickle import pickle_function, unpickle_function
-
- from .dist import install_scripts
-
--from .package import (installed_packages, is_package_installed,
-- standard_packages, optional_packages, experimental_packages,
-- 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
-@@ -163,7 +163,6 @@ 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
-
-@@ -1433,10 +1432,11 @@ 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-i686/is-package-installed.patch (from rev 209347, sagemath/trunk/is-package-installed.patch)
===================================================================
--- community-i686/is-package-installed.patch (rev 0)
+++ community-i686/is-package-installed.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,328 @@
+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
+
+@@ -824,7 +823,7 @@ 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:
+@@ -1673,7 +1672,7 @@ 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
+@@ -7858,7 +7858,6 @@ 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 " +
+@@ -7876,10 +7875,12 @@ 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)
+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
+@@ -1400,15 +1400,15 @@ 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, "lib", "gap", "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)):
+@@ -1682,9 +1679,7 @@ 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):
+ """
+@@ -1735,9 +1730,7 @@ 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):
+ """
+@@ -4113,8 +4106,6 @@ 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
+@@ -53,10 +53,6 @@ from fpickle import pickle_function, unpickle_function
+
+ from .dist import install_scripts
+
+-from .package import (installed_packages, is_package_installed,
+- standard_packages, optional_packages, experimental_packages,
+- 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
+@@ -163,7 +163,6 @@ 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
+
+@@ -1433,10 +1432,11 @@ 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":
Deleted: community-i686/jupyter-path.patch
===================================================================
--- community-i686/jupyter-path.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-i686/jupyter-path.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,22 +0,0 @@
---- 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):
-
-@@ -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-i686/jupyter-path.patch (from rev 209347, sagemath/trunk/jupyter-path.patch)
===================================================================
--- community-i686/jupyter-path.patch (rev 0)
+++ community-i686/jupyter-path.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,22 @@
+--- 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):
+
+@@ -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)
+
Deleted: community-i686/package.patch
===================================================================
--- community-i686/package.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-i686/package.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,38 +0,0 @@
---- 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
-@@ -343,7 +343,7 @@
- sage: for pkg in list_packages('pip', local=True):
- ....: assert not is_package_installed(pkg)
- """
-- return any(p.split('-')[0] == package for p in installed_packages(exclude_pip))
-+ return True
-
- def package_versions(package_type, local=False):
- r"""
---- src/sage_setup/optional_extension.py.orig 2016-10-19 18:35:10.092577510 +0000
-+++ src/sage_setup/optional_extension.py 2016-10-19 18:38:13.514765366 +0000
-@@ -21,8 +21,6 @@
- from distutils.extension import Extension
- from sage.misc.package import is_package_installed, list_packages
-
--all_packages = list_packages(local=True)
--
-
- class CythonizeExtension(Extension):
- """
-@@ -76,14 +74,7 @@
- condition = kwds.pop("condition")
- except KeyError:
- pkg = kwds.pop("package")
-- try:
-- pkginfo = all_packages[pkg]
-- except KeyError:
-- # Might be an installed old-style package
-- condition = is_package_installed(pkg)
-- else:
-- condition = (pkginfo["installed_version"] == pkginfo["remote_version"])
--
-+ condition = True
- if condition:
- return Extension(*args, **kwds)
- else:
Copied: sagemath/repos/community-i686/package.patch (from rev 209347, sagemath/trunk/package.patch)
===================================================================
--- community-i686/package.patch (rev 0)
+++ community-i686/package.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,38 @@
+--- 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
+@@ -343,7 +343,7 @@
+ sage: for pkg in list_packages('pip', local=True):
+ ....: assert not is_package_installed(pkg)
+ """
+- return any(p.split('-')[0] == package for p in installed_packages(exclude_pip))
++ return True
+
+ def package_versions(package_type, local=False):
+ r"""
+--- src/sage_setup/optional_extension.py.orig 2016-10-19 18:35:10.092577510 +0000
++++ src/sage_setup/optional_extension.py 2016-10-19 18:38:13.514765366 +0000
+@@ -21,8 +21,6 @@
+ from distutils.extension import Extension
+ from sage.misc.package import is_package_installed, list_packages
+
+-all_packages = list_packages(local=True)
+-
+
+ class CythonizeExtension(Extension):
+ """
+@@ -76,14 +74,7 @@
+ condition = kwds.pop("condition")
+ except KeyError:
+ pkg = kwds.pop("package")
+- try:
+- pkginfo = all_packages[pkg]
+- except KeyError:
+- # Might be an installed old-style package
+- condition = is_package_installed(pkg)
+- else:
+- condition = (pkginfo["installed_version"] == pkginfo["remote_version"])
+-
++ condition = True
+ if condition:
+ return Extension(*args, **kwds)
+ else:
Deleted: community-i686/r-no-readline.patch
===================================================================
--- community-i686/r-no-readline.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-i686/r-no-readline.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,11 +0,0 @@
---- a/src/sage/interfaces/r.py
-+++ b/src/sage/interfaces/r.py
-@@ -331,7 +331,7 @@
- prompt = '> ', #default, later comes the change
-
- # This is the command that starts up your program
-- command = "R --vanilla --quiet",
-+ command = "R --no-readline --vanilla --quiet",
-
- server=server,
- server_tmpdir=server_tmpdir,
Copied: sagemath/repos/community-i686/r-no-readline.patch (from rev 209347, sagemath/trunk/r-no-readline.patch)
===================================================================
--- community-i686/r-no-readline.patch (rev 0)
+++ community-i686/r-no-readline.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,11 @@
+--- a/src/sage/interfaces/r.py
++++ b/src/sage/interfaces/r.py
+@@ -331,7 +331,7 @@
+ prompt = '> ', #default, later comes the change
+
+ # This is the command that starts up your program
+- command = "R --vanilla --quiet",
++ command = "R --no-readline --vanilla --quiet",
+
+ server=server,
+ server_tmpdir=server_tmpdir,
Deleted: community-i686/sagemath-gslcblas.patch
===================================================================
--- community-i686/sagemath-gslcblas.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-i686/sagemath-gslcblas.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,13 +0,0 @@
-diff --git a/src/module_list.py b/src/module_list.py
-index 96e8081..4728e9a 100644
---- a/src/module_list.py
-+++ b/src/module_list.py
-@@ -45,6 +45,7 @@ givaro_library_dirs = givaro_pc['library_dirs']
- gsl_pc = pkgconfig.parse('gsl')
- gsl_libs = gsl_pc['libraries']
- gsl_libs.remove('gslcblas')
-+gsl_libs.extend(cblas_libs)
- gsl_library_dirs = gsl_pc['library_dirs']
- gsl_include_dirs = gsl_pc['include_dirs']
-
-
Copied: sagemath/repos/community-i686/sagemath-gslcblas.patch (from rev 209347, sagemath/trunk/sagemath-gslcblas.patch)
===================================================================
--- community-i686/sagemath-gslcblas.patch (rev 0)
+++ community-i686/sagemath-gslcblas.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,13 @@
+diff --git a/src/module_list.py b/src/module_list.py
+index 96e8081..4728e9a 100644
+--- a/src/module_list.py
++++ b/src/module_list.py
+@@ -45,6 +45,7 @@ givaro_library_dirs = givaro_pc['library_dirs']
+ gsl_pc = pkgconfig.parse('gsl')
+ gsl_libs = gsl_pc['libraries']
+ gsl_libs.remove('gslcblas')
++gsl_libs.extend(cblas_libs)
+ gsl_library_dirs = gsl_pc['library_dirs']
+ gsl_include_dirs = gsl_pc['include_dirs']
+
+
Deleted: community-i686/sagemath-no-anal.h.patch
===================================================================
--- community-i686/sagemath-no-anal.h.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-i686/sagemath-no-anal.h.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,12 +0,0 @@
-diff --git a/src/sage/libs/cypari2/paripriv.pxd b/src/sage/libs/cypari2/paripriv.pxd
-index b6ea381..921599d 100644
---- a/src/sage/libs/cypari2/paripriv.pxd
-+++ b/src/sage/libs/cypari2/paripriv.pxd
-@@ -26,5 +26,5 @@ cdef extern from "pari/paripriv.h":
-
- extern gp_data* GP_DATA
-
--cdef extern from "pari/anal.h":
-- char* closure_func_err()
-+cdef extern: # Declared in private PARI header file "anal.h"
-+ const char* closure_func_err()
Copied: sagemath/repos/community-i686/sagemath-no-anal.h.patch (from rev 209347, sagemath/trunk/sagemath-no-anal.h.patch)
===================================================================
--- community-i686/sagemath-no-anal.h.patch (rev 0)
+++ community-i686/sagemath-no-anal.h.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,12 @@
+diff --git a/src/sage/libs/cypari2/paripriv.pxd b/src/sage/libs/cypari2/paripriv.pxd
+index b6ea381..921599d 100644
+--- a/src/sage/libs/cypari2/paripriv.pxd
++++ b/src/sage/libs/cypari2/paripriv.pxd
+@@ -26,5 +26,5 @@ cdef extern from "pari/paripriv.h":
+
+ extern gp_data* GP_DATA
+
+-cdef extern from "pari/anal.h":
+- char* closure_func_err()
++cdef extern: # Declared in private PARI header file "anal.h"
++ const char* closure_func_err()
Copied: sagemath/repos/community-i686/sagemath-planarity3.patch (from rev 209347, sagemath/trunk/sagemath-planarity3.patch)
===================================================================
--- community-i686/sagemath-planarity3.patch (rev 0)
+++ community-i686/sagemath-planarity3.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,113 @@
+Author: Ximin Luo <infinity0 at debian.org>
+Bug: https://trac.sagemath.org/ticket/21774
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- a/sage/src/sage/graphs/planarity.pyx
++++ b/sage/src/sage/graphs/planarity.pyx
+@@ -3,13 +3,19 @@
+ """
+
+ cdef extern from "planarity/graph.h":
+- ctypedef struct graphNode:
+- int v
++ ctypedef struct vertexRec:
+ int link[2]
+- ctypedef graphNode * graphNodeP
++ int index
++ ctypedef vertexRec * vertexRecP
++
++ ctypedef struct edgeRec:
++ int link[2]
++ int neighbor
++ ctypedef edgeRec * edgeRecP
+
+ ctypedef struct BM_graph:
+- graphNodeP G
++ vertexRecP V
++ edgeRecP E
+ int N
+ ctypedef BM_graph * graphP
+
+@@ -93,15 +99,16 @@
+ g._pos = { u: [0,0], v: [0,1] }
+ return (True, None) if kuratowski else True
+
+- # create to and from mappings to relabel vertices to the set {0,...,n-1}
++ # create to and from mappings to relabel vertices to the set {1,...,n}
++ # (planarity 3 uses 1-based array indexing, with 0 representing NIL)
+ cdef int i
+ listto = g.vertices()
+ ffrom = {}
+ for vvv in listto:
+- ffrom[vvv] = listto.index(vvv)
++ ffrom[vvv] = listto.index(vvv) + 1
+ to = {}
+ for i from 0 <= i < len(listto):
+- to[i] = listto[i]
++ to[i + 1] = listto[i]
+ g.relabel(ffrom)
+
+ cdef graphP theGraph
+@@ -125,7 +132,7 @@
+ status = gp_Embed(theGraph, EMBEDFLAGS_PLANAR)
+ gp_SortVertices(theGraph)
+
+- # use to and from mappings to relabel vertices back from the set {0,...,n-1}
++ # use to and from mappings to relabel vertices back from the set {1,...,n}
+ g.relabel(to)
+
+ if status == NOTOK:
+@@ -134,12 +141,12 @@
+ # Kuratowski subgraph isolator
+ g_dict = {}
+ from sage.graphs.graph import Graph
+- for i from 0 <= i < theGraph.N:
++ for i from 0 < i <= theGraph.N:
+ linked_list = []
+- j = theGraph.G[i].link[1]
+- while j >= theGraph.N:
+- linked_list.append(to[theGraph.G[j].v])
+- j = theGraph.G[j].link[1]
++ j = theGraph.V[i].link[1]
++ while j:
++ linked_list.append(to[theGraph.E[j].neighbor])
++ j = theGraph.E[j].link[1]
+ if len(linked_list) > 0:
+ g_dict[to[i]] = linked_list
+ G = Graph(g_dict)
+@@ -153,12 +160,12 @@
+ if set_embedding:
+ emb_dict = {}
+ #for i in range(theGraph.N):
+- for i from 0 <= i < theGraph.N:
++ for i from 0 < i <= theGraph.N:
+ linked_list = []
+- j = theGraph.G[i].link[1]
+- while j >= theGraph.N:
+- linked_list.append(to[theGraph.G[j].v])
+- j = theGraph.G[j].link[1]
++ j = theGraph.V[i].link[1]
++ while j:
++ linked_list.append(to[theGraph.E[j].neighbor])
++ j = theGraph.E[j].link[1]
+ emb_dict[to[i]] = linked_list
+ g._embedding = emb_dict
+ if set_pos:
+@@ -174,12 +181,12 @@
+
+ emb_dict = {}
+ #for i in range(theGraph.N):
+- for i from 0 <= i < theGraph.N:
++ for i from 0 < i <= theGraph.N:
+ linked_list = []
+- j = theGraph.G[i].link[0]
+- while j >= theGraph.N:
+- linked_list.append(to[theGraph.G[j].v])
+- j = theGraph.G[j].link[0]
++ j = theGraph.V[i].link[0]
++ while j:
++ linked_list.append(to[theGraph.E[j].neighbor])
++ j = theGraph.E[j].link[0]
+ emb_dict[to[i]] = linked_list
+ g._embedding = emb_dict
+ gp_Free(&theGraph)
Deleted: community-i686/skip-check.patch
===================================================================
--- community-i686/skip-check.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-i686/skip-check.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,22 +0,0 @@
---- 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-i686/skip-check.patch (from rev 209347, sagemath/trunk/skip-check.patch)
===================================================================
--- community-i686/skip-check.patch (rev 0)
+++ community-i686/skip-check.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -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
+
Deleted: community-i686/test-optional.patch
===================================================================
--- community-i686/test-optional.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-i686/test-optional.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,25 +0,0 @@
---- src/sage/doctest/control.py.orig 2016-10-20 19:39:53.714618246 +0200
-+++ src/sage/doctest/control.py 2016-10-20 19:40:15.158049920 +0200
-@@ -307,22 +307,6 @@
- if "all" in options.optional:
- # Special case to run all optional tests
- options.optional = True
-- else:
-- # We replace the 'optional' tag by all optional
-- # packages for which the installed version matches the
-- # latest available version (this implies in particular
-- # that the package is actually installed).
-- if 'optional' in options.optional:
-- options.optional.discard('optional')
-- from sage.misc.package import list_packages
-- for pkg in list_packages('optional', local=True).values():
-- if pkg['installed_version'] == pkg['remote_version']:
-- options.optional.add(pkg['name'])
--
-- # Check that all tags are valid
-- for o in options.optional:
-- if not optionaltag_regex.search(o):
-- raise ValueError('invalid optional tag {!r}'.format(o))
-
- self.options = options
- self.files = args
Copied: sagemath/repos/community-i686/test-optional.patch (from rev 209347, sagemath/trunk/test-optional.patch)
===================================================================
--- community-i686/test-optional.patch (rev 0)
+++ community-i686/test-optional.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,25 @@
+--- src/sage/doctest/control.py.orig 2016-10-20 19:39:53.714618246 +0200
++++ src/sage/doctest/control.py 2016-10-20 19:40:15.158049920 +0200
+@@ -307,22 +307,6 @@
+ if "all" in options.optional:
+ # Special case to run all optional tests
+ options.optional = True
+- else:
+- # We replace the 'optional' tag by all optional
+- # packages for which the installed version matches the
+- # latest available version (this implies in particular
+- # that the package is actually installed).
+- if 'optional' in options.optional:
+- options.optional.discard('optional')
+- from sage.misc.package import list_packages
+- for pkg in list_packages('optional', local=True).values():
+- if pkg['installed_version'] == pkg['remote_version']:
+- options.optional.add(pkg['name'])
+-
+- # Check that all tags are valid
+- for o in options.optional:
+- if not optionaltag_regex.search(o):
+- raise ValueError('invalid optional tag {!r}'.format(o))
+
+ self.options = options
+ self.files = args
Deleted: community-x86_64/PKGBUILD
===================================================================
--- community-x86_64/PKGBUILD 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-x86_64/PKGBUILD 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,158 +0,0 @@
-# $Id$
-# 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
-
-pkgbase=sagemath
-pkgname=(sagemath sagemath-jupyter)
-pkgver=7.5.1
-pkgrel=3
-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 ppl palp brial cliquer maxima-ecl gfan sympow tachyon nauty python2-rpy2 python2-fpylll python2-psutil
- python2-matplotlib python2-scipy python2-sympy python2-networkx python2-pillow python2-future 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' 'python2-igraph: igraph backend for graph theory'
- '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' 'cryptominisat2: 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-pynormaliz: Normaliz backend for polyhedral computations')
-makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc libhomfly libbraiding
- mcqd coxeter3 cryptominisat2 modular_decomposition bliss-graphs tdlib python2-pkgconfig meataxe) # libfes
-source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"
- env.patch skip-check.patch cython-sys-path.patch is-package-installed.patch package.patch disable-fes.patch
- jupyter-path.patch test-optional.patch ecm-7.patch increase-rtol.patch sagemath-gslcblas.patch r-no-readline.patch
- sagemath-no-anal.h.patch)
-sha256sums=('3cd9af3e3bfd7f5cc966b7c36168d04b9a1213aa9a7af3286b5d53d40e7653e3'
- '9dba04ff13626a7b6c338a8b18a6c27d343f68a547a218533cf773af3dae6635'
- 'b02b3d2d5620ca20f96adb62b6fef05e4676c0a60983310a1450fdf3d923cb04'
- 'ff7e034d08ab084fdb193484f7fe3a659ebcd8ab33a2b7177237d65b26de7872'
- 'd60fb0fbd27991ce9496ca035a54b03334b5b53f244227a8d6e13f3327ce75d2'
- '4a2297e4d9d28f0b3a1f58e1b463e332affcb109eafde44837b1657e309c8212'
- '7ab53d30b877dabb6835fbe67a208bef65fa0aaf40221b4d0b58e4b7086bc47a'
- '775051aa9076ebf631c8a291af38b6ec4a13c904740dc9da831641d592d8bcd8'
- '81d08c6a760f171f3381455b66a6c84789c9f0eefddbe6ca5794075514ad8c3a'
- '65ad84c83d5f956fde8eab961f2caad56d64044324c4abc0e56bcd9f44061cb6'
- 'be925eefeac3f28e639794ddc20d64e6faafd7181804e29417a510224d19ccc7'
- '973224f53e9a6fcfaa9c6cb842b02430a601d1c7ce0abb41b3591470d128930c'
- 'ef9f401fa84fe1772af9efee6816643534f2896da4c23b809937b19771bdfbbf'
- '8126c92a5fc15738c4f7982aadb5a4033230fc2d5da05af9133a96ad1181419e')
-
-prepare(){
- cd sage-$pkgver
-
-# Arch-specific patches
-# assume all optional packages are installed
- patch -p0 -i ../package.patch
-# set env variables
- patch -p0 -i ../env.patch
-# skip checking build status
- patch -p0 -i ../skip-check.patch
-# don't list optional packages when running tests
- patch -p0 -i ../test-optional.patch
-# set jupyter path
- patch -p0 -i ../jupyter-path.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
-# increase numerical tolerance, needed by scipy 0.18
- patch -p1 -i ../increase-rtol.patch
-# fix cblas linking in gsl modules
- patch -p1 -i ../sagemath-gslcblas.patch
-# fix freezes in R interface with readline 7 (Debian)
- patch -p1 -i ../r-no-readline.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
-# replace is_package_installed usage http://trac.sagemath.org/ticket/20377
- patch -p1 -i ../is-package-installed.patch
-# Allow compiling without pari's anal.h https://trac.sagemath.org/ticket/22195
- patch -p1 -i ../sagemath-no-anal.h.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|g' -i src/bin/sage
- sed -e "s|'cython'|'cython2'|" -i src/bin/sage-cython
- sed -e 's|bin/python|bin/python2|g' -i src/bin/sage-env
-}
-
-
-build() {
- cd sage-$pkgver/src
-
- export SAGE_LOCAL="/usr"
- export SAGE_ROOT="$PWD"
- export SAGE_SRC="$PWD"
- export CC=gcc
-
- python2 setup.py build
-}
-
-package_sagemath() {
- optdepends+=('sagemath-jupyter: Jupyter kernel')
- conflicts=(sage-mathematics)
- replaces=(sage-mathematics)
- provides=(sage-mathematics)
-
- cd sage-$pkgver/src
-
- export SAGE_ROOT="$PWD"
- export SAGE_LOCAL="/usr"
- export JUPYTER_PATH="$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 and help
- mkdir "$pkgdir"/usr/share/sage/source
- ln -s /usr/share/doc/sage "$pkgdir"/usr/share/sage/source/doc
-
-# Remove sage_setup
- rm -r "$pkgdir"/usr/lib/python2.7/site-packages/sage_setup
-
-# Split jupyter kernel
- rm -r "$pkgdir"/usr/share/jupyter
-}
-
-package_sagemath-jupyter() {
- pkgdesc='Jupyter kernel for SageMath'
- depends=(sagemath python2-jupyter_client python2-ipywidgets jupyter-notebook mathjax)
- optdepends=('sage-notebook-exporter: convert flask notebooks to Jupyter')
-
- cd sage-$pkgver/src
-
- export SAGE_ROOT="$PWD"
- export SAGE_LOCAL="/usr"
- export JUPYTER_PATH="$pkgdir"/usr/share/jupyter
-
- python2 -c "from sage.repl.ipython_kernel.install import SageKernelSpec; SageKernelSpec.update()"
-}
Copied: sagemath/repos/community-x86_64/PKGBUILD (from rev 209347, sagemath/trunk/PKGBUILD)
===================================================================
--- community-x86_64/PKGBUILD (rev 0)
+++ community-x86_64/PKGBUILD 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,160 @@
+# $Id$
+# 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
+
+pkgbase=sagemath
+pkgname=(sagemath sagemath-jupyter)
+pkgver=7.5.1
+pkgrel=4
+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 ppl palp brial cliquer maxima-ecl gfan sympow tachyon nauty python2-rpy2 python2-fpylll python2-psutil
+ python2-matplotlib python2-scipy python2-sympy python2-networkx python2-pillow python2-future 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' 'python2-igraph: igraph backend for graph theory'
+ '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' 'cryptominisat2: 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'
+ 'libfes: exhaustive search of solutions for boolean equations' 'python2-pynormaliz: Normaliz backend for polyhedral computations')
+makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc libhomfly libbraiding
+ mcqd coxeter3 cryptominisat2 modular_decomposition bliss-graphs tdlib python2-pkgconfig meataxe libfes)
+source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"
+ env.patch skip-check.patch cython-sys-path.patch is-package-installed.patch package.patch disable-fes.patch
+ jupyter-path.patch test-optional.patch ecm-7.patch increase-rtol.patch sagemath-gslcblas.patch r-no-readline.patch
+ sagemath-no-anal.h.patch sagemath-planarity3.patch fes02.patch)
+sha256sums=('3cd9af3e3bfd7f5cc966b7c36168d04b9a1213aa9a7af3286b5d53d40e7653e3'
+ '9dba04ff13626a7b6c338a8b18a6c27d343f68a547a218533cf773af3dae6635'
+ 'b02b3d2d5620ca20f96adb62b6fef05e4676c0a60983310a1450fdf3d923cb04'
+ 'ff7e034d08ab084fdb193484f7fe3a659ebcd8ab33a2b7177237d65b26de7872'
+ 'd60fb0fbd27991ce9496ca035a54b03334b5b53f244227a8d6e13f3327ce75d2'
+ '4a2297e4d9d28f0b3a1f58e1b463e332affcb109eafde44837b1657e309c8212'
+ '7ab53d30b877dabb6835fbe67a208bef65fa0aaf40221b4d0b58e4b7086bc47a'
+ '775051aa9076ebf631c8a291af38b6ec4a13c904740dc9da831641d592d8bcd8'
+ '81d08c6a760f171f3381455b66a6c84789c9f0eefddbe6ca5794075514ad8c3a'
+ '65ad84c83d5f956fde8eab961f2caad56d64044324c4abc0e56bcd9f44061cb6'
+ 'be925eefeac3f28e639794ddc20d64e6faafd7181804e29417a510224d19ccc7'
+ '973224f53e9a6fcfaa9c6cb842b02430a601d1c7ce0abb41b3591470d128930c'
+ 'ef9f401fa84fe1772af9efee6816643534f2896da4c23b809937b19771bdfbbf'
+ '8126c92a5fc15738c4f7982aadb5a4033230fc2d5da05af9133a96ad1181419e'
+ 'a1c562ebe4538d672404ca3ac2e954a3c955afeb7463f7b4fe6eaa6fa74fe5c7'
+ 'a39da083c038ada797ffc5bedc9ba47455a3f77057d42f86484ae877ef9172ea')
+
+prepare(){
+ cd sage-$pkgver
+
+# Arch-specific patches
+# assume all optional packages are installed
+ patch -p0 -i ../package.patch
+# set env variables
+ patch -p0 -i ../env.patch
+# skip checking build status
+ patch -p0 -i ../skip-check.patch
+# don't list optional packages when running tests
+ patch -p0 -i ../test-optional.patch
+# set jupyter path
+ patch -p0 -i ../jupyter-path.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
+# increase numerical tolerance, needed by scipy 0.18
+ patch -p1 -i ../increase-rtol.patch
+# fix cblas linking in gsl modules
+ patch -p1 -i ../sagemath-gslcblas.patch
+# fix freezes in R interface with readline 7 (Debian)
+ patch -p1 -i ../r-no-readline.patch
+# fix build with planarity 3 (Debian)
+ patch -p2 -i ../sagemath-planarity3.patch
+
+# Upstream patches
+# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209
+ patch -p1 -i ../fes02.patch
+# replace is_package_installed usage http://trac.sagemath.org/ticket/20377
+ patch -p1 -i ../is-package-installed.patch
+# Allow compiling without pari's anal.h https://trac.sagemath.org/ticket/22195
+ patch -p1 -i ../sagemath-no-anal.h.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|g' -i src/bin/sage
+ sed -e "s|'cython'|'cython2'|" -i src/bin/sage-cython
+ sed -e 's|bin/python|bin/python2|g' -i src/bin/sage-env
+}
+
+
+build() {
+ cd sage-$pkgver/src
+
+ export SAGE_LOCAL="/usr"
+ export SAGE_ROOT="$PWD"
+ export SAGE_SRC="$PWD"
+ export CC=gcc
+
+ python2 setup.py build
+}
+
+package_sagemath() {
+ optdepends+=('sagemath-jupyter: Jupyter kernel')
+ conflicts=(sage-mathematics)
+ replaces=(sage-mathematics)
+ provides=(sage-mathematics)
+
+ cd sage-$pkgver/src
+
+ export SAGE_ROOT="$PWD"
+ export SAGE_LOCAL="/usr"
+ export JUPYTER_PATH="$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 and help
+ mkdir "$pkgdir"/usr/share/sage/source
+ ln -s /usr/share/doc/sage "$pkgdir"/usr/share/sage/source/doc
+
+# Remove sage_setup
+ rm -r "$pkgdir"/usr/lib/python2.7/site-packages/sage_setup
+
+# Split jupyter kernel
+ rm -r "$pkgdir"/usr/share/jupyter
+}
+
+package_sagemath-jupyter() {
+ pkgdesc='Jupyter kernel for SageMath'
+ depends=(sagemath python2-jupyter_client python2-ipywidgets jupyter-notebook mathjax)
+ optdepends=('sage-notebook-exporter: convert flask notebooks to Jupyter')
+
+ cd sage-$pkgver/src
+
+ export SAGE_ROOT="$PWD"
+ export SAGE_LOCAL="/usr"
+ export JUPYTER_PATH="$pkgdir"/usr/share/jupyter
+
+ python2 -c "from sage.repl.ipython_kernel.install import SageKernelSpec; SageKernelSpec.update()"
+}
Deleted: community-x86_64/cython-sys-path.patch
===================================================================
--- community-x86_64/cython-sys-path.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-x86_64/cython-sys-path.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,10 +0,0 @@
---- 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
-@@ -414,6 +414,7 @@
- build_dir=SAGE_CYTHONIZED,
- force=force,
- aliases=aliases,
-+ include_path=sys.path,
- compiler_directives={
- 'autotestdict': False,
- 'cdivision': True,
Copied: sagemath/repos/community-x86_64/cython-sys-path.patch (from rev 209347, sagemath/trunk/cython-sys-path.patch)
===================================================================
--- community-x86_64/cython-sys-path.patch (rev 0)
+++ community-x86_64/cython-sys-path.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -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
+@@ -414,6 +414,7 @@
+ build_dir=SAGE_CYTHONIZED,
+ force=force,
+ aliases=aliases,
++ include_path=sys.path,
+ compiler_directives={
+ 'autotestdict': False,
+ 'cdivision': True,
Deleted: community-x86_64/disable-fes.patch
===================================================================
--- community-x86_64/disable-fes.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-x86_64/disable-fes.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,19 +0,0 @@
---- 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"],
Deleted: community-x86_64/ecm-7.patch
===================================================================
--- community-x86_64/ecm-7.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-x86_64/ecm-7.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,79 +0,0 @@
---- 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-x86_64/ecm-7.patch (from rev 209347, sagemath/trunk/ecm-7.patch)
===================================================================
--- community-x86_64/ecm-7.patch (rev 0)
+++ community-x86_64/ecm-7.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -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
+ """
+
Deleted: community-x86_64/env.patch
===================================================================
--- community-x86_64/env.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-x86_64/env.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,94 +0,0 @@
---- 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"
-
- # Display the Sage startup banner, used in src/bin/sage
- sage_banner() {
-@@ -187,7 +187,7 @@
-
- # SAGE_LOCAL is the installation prefix and can be customized
- if [ -z "$SAGE_LOCAL" ]; then
-- export SAGE_LOCAL="$SAGE_ROOT/local"
-+ export SAGE_LOCAL="/usr"
- fi
-
- # sage-env must know where the Sage's script files are
-@@ -233,8 +233,9 @@
- 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="$SAGE_SRC/doc"
-+export GAP_ROOT_DIR="/usr/lib/gap"
-+export SAGE_SRC="$SAGE_SHARE/sage/source"
-+export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage"
- export SAGE_DOC="$SAGE_SHARE/doc/sage"
-
- if [ -z "${SAGE_ORIG_PATH_SET}" ]; then
-@@ -374,6 +337,9 @@
- export SAGE_STARTUP_FILE
- fi
-
-+export LIBMTX="$DOT_SAGE/meataxe"
-+[[ -d $LIBMTX ]] || mkdir $LIBMTX # Create meataxe data dir
-+
- if [ -z "$IPYTHONDIR" ]; then
- # We hardcode a version number in the directory name. The idea is
- # that we keep using the same version number as long as that is
-@@ -468,7 +400,6 @@
- fi
- fi
- fi
--export MAXIMA_PREFIX="$SAGE_LOCAL"
-
- PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB
-
-@@ -629,9 +608,6 @@
- LD_LIBRARY_PATH="$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-x86_64/env.patch (from rev 209347, sagemath/trunk/env.patch)
===================================================================
--- community-x86_64/env.patch (rev 0)
+++ community-x86_64/env.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,94 @@
+--- 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=$NEW_SAGE_ROOT"
+-fi
++NEW_SAGE_ROOT="/usr"
+
+ # Display the Sage startup banner, used in src/bin/sage
+ sage_banner() {
+@@ -187,7 +187,7 @@
+
+ # SAGE_LOCAL is the installation prefix and can be customized
+ if [ -z "$SAGE_LOCAL" ]; then
+- export SAGE_LOCAL="$SAGE_ROOT/local"
++ export SAGE_LOCAL="/usr"
+ fi
+
+ # sage-env must know where the Sage's script files are
+@@ -233,8 +233,9 @@
+ export SAGE_EXTCODE="$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 GAP_ROOT_DIR="/usr/lib/gap"
++export SAGE_SRC="$SAGE_SHARE/sage/source"
++export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage"
+ export SAGE_DOC="$SAGE_SHARE/doc/sage"
+
+ if [ -z "${SAGE_ORIG_PATH_SET}" ]; then
+@@ -374,6 +337,9 @@
+ export SAGE_STARTUP_FILE
+ fi
+
++export LIBMTX="$DOT_SAGE/meataxe"
++[[ -d $LIBMTX ]] || mkdir $LIBMTX # Create meataxe data dir
++
+ if [ -z "$IPYTHONDIR" ]; then
+ # We hardcode a version number in the directory name. The idea is
+ # that we keep using the same version number as long as that is
+@@ -468,7 +400,6 @@
+ fi
+ fi
+ fi
+-export MAXIMA_PREFIX="$SAGE_LOCAL"
+
+ PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB
+
+@@ -629,9 +608,6 @@
+ LD_LIBRARY_PATH="$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-x86_64/fes02.patch (from rev 209347, sagemath/trunk/fes02.patch)
===================================================================
--- community-x86_64/fes02.patch (rev 0)
+++ community-x86_64/fes02.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,57 @@
+From b1f5e3ecc789db674fe17552812f2d0e2ab84be0 Mon Sep 17 00:00:00 2001
+From: Charles Bouillaguet <charles.bouillaguet at lifl.fr>
+Date: Thu, 19 Sep 2013 10:31:11 +0200
+Subject: updating the libFES binding to match a change in the interface
+
+---
+ src/sage/libs/fes.pyx | 12 +++++++-----
+ 1 file changed, 7 insertions(+), 5 deletions(-)
+
+diff --git a/src/sage/libs/fes.pyx b/src/sage/libs/fes.pyx
+index 40b9c23..d188cf0 100644
+--- a/src/sage/libs/fes.pyx
++++ b/src/sage/libs/fes.pyx
+@@ -1,17 +1,19 @@
+ """
+-Binding for the FES library.
++Binding for the libFES library.
+
+ Finding solutions of systems of boolean equations by exhaustive
+ search, via the fes library. This is usually (much) faster than
+ computing a Groebner basis, except in special cases where the latter
+ is particularly easy.
+
+-The FES library is presently only able to deal with polynomials in 64
++More information is available at [http://www.lifl.fr/~bouillag/fes].
++
++The libFES library is presently only able to deal with polynomials in 64
+ variables. Performing a full exhaustive search over 64 variables will
+ take a **long** time. The number of variables can be artificially
+ reduced to 64 by specializing some of them.
+
+-Note that the FES library **requires** at least of the equations to be
++Note that the libFES library **requires** at least of the equations to be
+ non-linear.
+
+ AUTHORS:
+@@ -71,7 +73,7 @@ from libc.stdint cimport uint64_t
+ cdef extern from "fes_interface.h":
+ ctypedef int (*solution_callback_t)(void *, uint64_t)
+
+- void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose)
++ void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose, int T)
+
+
+ include 'sage/ext/interrupt.pxi' #sig_on(), sig_off()
+@@ -219,7 +221,7 @@ def exhaustive_search(eqs, max_sols=Infinity, verbose=False):
+
+ # ------- runs the library
+ sig_on()
+- exhaustive_search_wrapper(n, len(eqs), degree, coeffs, report_solution, <void *> internal_state, verbose)
++ exhaustive_search_wrapper(n, len(eqs), degree, coeffs, report_solution, <void *> internal_state, verbose, 0)
+ sig_off()
+
+ # ------- frees memory occupied by the dense representation of the equations
+--
+cgit v1.0-1-gd88e
+
Deleted: community-x86_64/increase-rtol.patch
===================================================================
--- community-x86_64/increase-rtol.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-x86_64/increase-rtol.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,37 +0,0 @@
-diff -ru sage-7.3.orig/src/sage/coding/code_bounds.py sage-7.3/src/sage/coding/code_bounds.py
---- sage-7.3.orig/src/sage/coding/code_bounds.py 2016-08-05 20:26:10.033204091 +0200
-+++ sage-7.3/src/sage/coding/code_bounds.py 2016-08-05 20:32:27.276579565 +0200
-@@ -554,7 +554,7 @@
- if q < 2: # Here we check that q is actually at least 2
- raise ValueError("The value q must be an integer greater than 1")
-
-- eps = 4.5e-16 # find_root has about this as the default xtol
-+ eps = 4.5e-15 # find_root has about this as the default xtol
- ymax = 1 - 1/q
- if x <= eps:
- return 0
-diff -ru sage-7.3.orig/src/sage/numerical/optimize.py sage-7.3/src/sage/numerical/optimize.py
---- sage-7.3.orig/src/sage/numerical/optimize.py 2016-08-05 20:26:10.816536625 +0200
-+++ sage-7.3/src/sage/numerical/optimize.py 2016-08-05 20:32:21.449907130 +0200
-@@ -15,7 +15,7 @@
- from sage.rings.real_double import RDF
-
-
--def find_root(f, a, b, xtol=10e-13, rtol=4.5e-16, maxiter=100, full_output=False):
-+def find_root(f, a, b, xtol=10e-13, rtol=4.5e-15, maxiter=100, full_output=False):
- """
- Numerically find a root of ``f`` on the closed interval `[a,b]`
- (or `[b,a]`) if possible, where ``f`` is a function in the one variable.
-diff -ru sage-7.3.orig/src/sage/symbolic/expression.pyx sage-7.3/src/sage/symbolic/expression.pyx
---- sage-7.3.orig/src/sage/symbolic/expression.pyx 2016-08-05 20:26:11.333202767 +0200
-+++ sage-7.3/src/sage/symbolic/expression.pyx 2016-08-05 20:32:14.236566826 +0200
-@@ -10884,7 +10884,7 @@
- ret = ret[0]
- return ret
-
-- def find_root(self, a, b, var=None, xtol=10e-13, rtol=4.5e-16, maxiter=100, full_output=False):
-+ def find_root(self, a, b, var=None, xtol=10e-13, rtol=4.5e-15, maxiter=100, full_output=False):
- """
- Numerically find a root of self on the closed interval [a,b] (or
- [b,a]) if possible, where self is a function in the one variable.
-
Copied: sagemath/repos/community-x86_64/increase-rtol.patch (from rev 209347, sagemath/trunk/increase-rtol.patch)
===================================================================
--- community-x86_64/increase-rtol.patch (rev 0)
+++ community-x86_64/increase-rtol.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,37 @@
+diff -ru sage-7.3.orig/src/sage/coding/code_bounds.py sage-7.3/src/sage/coding/code_bounds.py
+--- sage-7.3.orig/src/sage/coding/code_bounds.py 2016-08-05 20:26:10.033204091 +0200
++++ sage-7.3/src/sage/coding/code_bounds.py 2016-08-05 20:32:27.276579565 +0200
+@@ -554,7 +554,7 @@
+ if q < 2: # Here we check that q is actually at least 2
+ raise ValueError("The value q must be an integer greater than 1")
+
+- eps = 4.5e-16 # find_root has about this as the default xtol
++ eps = 4.5e-15 # find_root has about this as the default xtol
+ ymax = 1 - 1/q
+ if x <= eps:
+ return 0
+diff -ru sage-7.3.orig/src/sage/numerical/optimize.py sage-7.3/src/sage/numerical/optimize.py
+--- sage-7.3.orig/src/sage/numerical/optimize.py 2016-08-05 20:26:10.816536625 +0200
++++ sage-7.3/src/sage/numerical/optimize.py 2016-08-05 20:32:21.449907130 +0200
+@@ -15,7 +15,7 @@
+ from sage.rings.real_double import RDF
+
+
+-def find_root(f, a, b, xtol=10e-13, rtol=4.5e-16, maxiter=100, full_output=False):
++def find_root(f, a, b, xtol=10e-13, rtol=4.5e-15, maxiter=100, full_output=False):
+ """
+ Numerically find a root of ``f`` on the closed interval `[a,b]`
+ (or `[b,a]`) if possible, where ``f`` is a function in the one variable.
+diff -ru sage-7.3.orig/src/sage/symbolic/expression.pyx sage-7.3/src/sage/symbolic/expression.pyx
+--- sage-7.3.orig/src/sage/symbolic/expression.pyx 2016-08-05 20:26:11.333202767 +0200
++++ sage-7.3/src/sage/symbolic/expression.pyx 2016-08-05 20:32:14.236566826 +0200
+@@ -10884,7 +10884,7 @@
+ ret = ret[0]
+ return ret
+
+- def find_root(self, a, b, var=None, xtol=10e-13, rtol=4.5e-16, maxiter=100, full_output=False):
++ def find_root(self, a, b, var=None, xtol=10e-13, rtol=4.5e-15, maxiter=100, full_output=False):
+ """
+ Numerically find a root of self on the closed interval [a,b] (or
+ [b,a]) if possible, where self is a function in the one variable.
+
Deleted: community-x86_64/is-package-installed.patch
===================================================================
--- community-x86_64/is-package-installed.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-x86_64/is-package-installed.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,328 +0,0 @@
-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
-
-@@ -824,7 +823,7 @@ 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:
-@@ -1673,7 +1672,7 @@ 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
-@@ -7858,7 +7858,6 @@ 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 " +
-@@ -7876,10 +7875,12 @@ 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)
-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
-@@ -1400,15 +1400,15 @@ 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, "lib", "gap", "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)):
-@@ -1682,9 +1679,7 @@ 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):
- """
-@@ -1735,9 +1730,7 @@ 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):
- """
-@@ -4113,8 +4106,6 @@ 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
-@@ -53,10 +53,6 @@ from fpickle import pickle_function, unpickle_function
-
- from .dist import install_scripts
-
--from .package import (installed_packages, is_package_installed,
-- standard_packages, optional_packages, experimental_packages,
-- 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
-@@ -163,7 +163,6 @@ 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
-
-@@ -1433,10 +1432,11 @@ 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-x86_64/is-package-installed.patch (from rev 209347, sagemath/trunk/is-package-installed.patch)
===================================================================
--- community-x86_64/is-package-installed.patch (rev 0)
+++ community-x86_64/is-package-installed.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,328 @@
+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
+
+@@ -824,7 +823,7 @@ 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:
+@@ -1673,7 +1672,7 @@ 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
+@@ -7858,7 +7858,6 @@ 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 " +
+@@ -7876,10 +7875,12 @@ 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)
+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
+@@ -1400,15 +1400,15 @@ 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, "lib", "gap", "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)):
+@@ -1682,9 +1679,7 @@ 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):
+ """
+@@ -1735,9 +1730,7 @@ 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):
+ """
+@@ -4113,8 +4106,6 @@ 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
+@@ -53,10 +53,6 @@ from fpickle import pickle_function, unpickle_function
+
+ from .dist import install_scripts
+
+-from .package import (installed_packages, is_package_installed,
+- standard_packages, optional_packages, experimental_packages,
+- 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
+@@ -163,7 +163,6 @@ 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
+
+@@ -1433,10 +1432,11 @@ 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":
Deleted: community-x86_64/jupyter-path.patch
===================================================================
--- community-x86_64/jupyter-path.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-x86_64/jupyter-path.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,22 +0,0 @@
---- 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):
-
-@@ -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-x86_64/jupyter-path.patch (from rev 209347, sagemath/trunk/jupyter-path.patch)
===================================================================
--- community-x86_64/jupyter-path.patch (rev 0)
+++ community-x86_64/jupyter-path.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,22 @@
+--- 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):
+
+@@ -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)
+
Deleted: community-x86_64/package.patch
===================================================================
--- community-x86_64/package.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-x86_64/package.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,38 +0,0 @@
---- 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
-@@ -343,7 +343,7 @@
- sage: for pkg in list_packages('pip', local=True):
- ....: assert not is_package_installed(pkg)
- """
-- return any(p.split('-')[0] == package for p in installed_packages(exclude_pip))
-+ return True
-
- def package_versions(package_type, local=False):
- r"""
---- src/sage_setup/optional_extension.py.orig 2016-10-19 18:35:10.092577510 +0000
-+++ src/sage_setup/optional_extension.py 2016-10-19 18:38:13.514765366 +0000
-@@ -21,8 +21,6 @@
- from distutils.extension import Extension
- from sage.misc.package import is_package_installed, list_packages
-
--all_packages = list_packages(local=True)
--
-
- class CythonizeExtension(Extension):
- """
-@@ -76,14 +74,7 @@
- condition = kwds.pop("condition")
- except KeyError:
- pkg = kwds.pop("package")
-- try:
-- pkginfo = all_packages[pkg]
-- except KeyError:
-- # Might be an installed old-style package
-- condition = is_package_installed(pkg)
-- else:
-- condition = (pkginfo["installed_version"] == pkginfo["remote_version"])
--
-+ condition = True
- if condition:
- return Extension(*args, **kwds)
- else:
Copied: sagemath/repos/community-x86_64/package.patch (from rev 209347, sagemath/trunk/package.patch)
===================================================================
--- community-x86_64/package.patch (rev 0)
+++ community-x86_64/package.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,38 @@
+--- 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
+@@ -343,7 +343,7 @@
+ sage: for pkg in list_packages('pip', local=True):
+ ....: assert not is_package_installed(pkg)
+ """
+- return any(p.split('-')[0] == package for p in installed_packages(exclude_pip))
++ return True
+
+ def package_versions(package_type, local=False):
+ r"""
+--- src/sage_setup/optional_extension.py.orig 2016-10-19 18:35:10.092577510 +0000
++++ src/sage_setup/optional_extension.py 2016-10-19 18:38:13.514765366 +0000
+@@ -21,8 +21,6 @@
+ from distutils.extension import Extension
+ from sage.misc.package import is_package_installed, list_packages
+
+-all_packages = list_packages(local=True)
+-
+
+ class CythonizeExtension(Extension):
+ """
+@@ -76,14 +74,7 @@
+ condition = kwds.pop("condition")
+ except KeyError:
+ pkg = kwds.pop("package")
+- try:
+- pkginfo = all_packages[pkg]
+- except KeyError:
+- # Might be an installed old-style package
+- condition = is_package_installed(pkg)
+- else:
+- condition = (pkginfo["installed_version"] == pkginfo["remote_version"])
+-
++ condition = True
+ if condition:
+ return Extension(*args, **kwds)
+ else:
Deleted: community-x86_64/r-no-readline.patch
===================================================================
--- community-x86_64/r-no-readline.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-x86_64/r-no-readline.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,11 +0,0 @@
---- a/src/sage/interfaces/r.py
-+++ b/src/sage/interfaces/r.py
-@@ -331,7 +331,7 @@
- prompt = '> ', #default, later comes the change
-
- # This is the command that starts up your program
-- command = "R --vanilla --quiet",
-+ command = "R --no-readline --vanilla --quiet",
-
- server=server,
- server_tmpdir=server_tmpdir,
Copied: sagemath/repos/community-x86_64/r-no-readline.patch (from rev 209347, sagemath/trunk/r-no-readline.patch)
===================================================================
--- community-x86_64/r-no-readline.patch (rev 0)
+++ community-x86_64/r-no-readline.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,11 @@
+--- a/src/sage/interfaces/r.py
++++ b/src/sage/interfaces/r.py
+@@ -331,7 +331,7 @@
+ prompt = '> ', #default, later comes the change
+
+ # This is the command that starts up your program
+- command = "R --vanilla --quiet",
++ command = "R --no-readline --vanilla --quiet",
+
+ server=server,
+ server_tmpdir=server_tmpdir,
Deleted: community-x86_64/sagemath-gslcblas.patch
===================================================================
--- community-x86_64/sagemath-gslcblas.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-x86_64/sagemath-gslcblas.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,13 +0,0 @@
-diff --git a/src/module_list.py b/src/module_list.py
-index 96e8081..4728e9a 100644
---- a/src/module_list.py
-+++ b/src/module_list.py
-@@ -45,6 +45,7 @@ givaro_library_dirs = givaro_pc['library_dirs']
- gsl_pc = pkgconfig.parse('gsl')
- gsl_libs = gsl_pc['libraries']
- gsl_libs.remove('gslcblas')
-+gsl_libs.extend(cblas_libs)
- gsl_library_dirs = gsl_pc['library_dirs']
- gsl_include_dirs = gsl_pc['include_dirs']
-
-
Copied: sagemath/repos/community-x86_64/sagemath-gslcblas.patch (from rev 209347, sagemath/trunk/sagemath-gslcblas.patch)
===================================================================
--- community-x86_64/sagemath-gslcblas.patch (rev 0)
+++ community-x86_64/sagemath-gslcblas.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,13 @@
+diff --git a/src/module_list.py b/src/module_list.py
+index 96e8081..4728e9a 100644
+--- a/src/module_list.py
++++ b/src/module_list.py
+@@ -45,6 +45,7 @@ givaro_library_dirs = givaro_pc['library_dirs']
+ gsl_pc = pkgconfig.parse('gsl')
+ gsl_libs = gsl_pc['libraries']
+ gsl_libs.remove('gslcblas')
++gsl_libs.extend(cblas_libs)
+ gsl_library_dirs = gsl_pc['library_dirs']
+ gsl_include_dirs = gsl_pc['include_dirs']
+
+
Deleted: community-x86_64/sagemath-no-anal.h.patch
===================================================================
--- community-x86_64/sagemath-no-anal.h.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-x86_64/sagemath-no-anal.h.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,12 +0,0 @@
-diff --git a/src/sage/libs/cypari2/paripriv.pxd b/src/sage/libs/cypari2/paripriv.pxd
-index b6ea381..921599d 100644
---- a/src/sage/libs/cypari2/paripriv.pxd
-+++ b/src/sage/libs/cypari2/paripriv.pxd
-@@ -26,5 +26,5 @@ cdef extern from "pari/paripriv.h":
-
- extern gp_data* GP_DATA
-
--cdef extern from "pari/anal.h":
-- char* closure_func_err()
-+cdef extern: # Declared in private PARI header file "anal.h"
-+ const char* closure_func_err()
Copied: sagemath/repos/community-x86_64/sagemath-no-anal.h.patch (from rev 209347, sagemath/trunk/sagemath-no-anal.h.patch)
===================================================================
--- community-x86_64/sagemath-no-anal.h.patch (rev 0)
+++ community-x86_64/sagemath-no-anal.h.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,12 @@
+diff --git a/src/sage/libs/cypari2/paripriv.pxd b/src/sage/libs/cypari2/paripriv.pxd
+index b6ea381..921599d 100644
+--- a/src/sage/libs/cypari2/paripriv.pxd
++++ b/src/sage/libs/cypari2/paripriv.pxd
+@@ -26,5 +26,5 @@ cdef extern from "pari/paripriv.h":
+
+ extern gp_data* GP_DATA
+
+-cdef extern from "pari/anal.h":
+- char* closure_func_err()
++cdef extern: # Declared in private PARI header file "anal.h"
++ const char* closure_func_err()
Copied: sagemath/repos/community-x86_64/sagemath-planarity3.patch (from rev 209347, sagemath/trunk/sagemath-planarity3.patch)
===================================================================
--- community-x86_64/sagemath-planarity3.patch (rev 0)
+++ community-x86_64/sagemath-planarity3.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,113 @@
+Author: Ximin Luo <infinity0 at debian.org>
+Bug: https://trac.sagemath.org/ticket/21774
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- a/sage/src/sage/graphs/planarity.pyx
++++ b/sage/src/sage/graphs/planarity.pyx
+@@ -3,13 +3,19 @@
+ """
+
+ cdef extern from "planarity/graph.h":
+- ctypedef struct graphNode:
+- int v
++ ctypedef struct vertexRec:
+ int link[2]
+- ctypedef graphNode * graphNodeP
++ int index
++ ctypedef vertexRec * vertexRecP
++
++ ctypedef struct edgeRec:
++ int link[2]
++ int neighbor
++ ctypedef edgeRec * edgeRecP
+
+ ctypedef struct BM_graph:
+- graphNodeP G
++ vertexRecP V
++ edgeRecP E
+ int N
+ ctypedef BM_graph * graphP
+
+@@ -93,15 +99,16 @@
+ g._pos = { u: [0,0], v: [0,1] }
+ return (True, None) if kuratowski else True
+
+- # create to and from mappings to relabel vertices to the set {0,...,n-1}
++ # create to and from mappings to relabel vertices to the set {1,...,n}
++ # (planarity 3 uses 1-based array indexing, with 0 representing NIL)
+ cdef int i
+ listto = g.vertices()
+ ffrom = {}
+ for vvv in listto:
+- ffrom[vvv] = listto.index(vvv)
++ ffrom[vvv] = listto.index(vvv) + 1
+ to = {}
+ for i from 0 <= i < len(listto):
+- to[i] = listto[i]
++ to[i + 1] = listto[i]
+ g.relabel(ffrom)
+
+ cdef graphP theGraph
+@@ -125,7 +132,7 @@
+ status = gp_Embed(theGraph, EMBEDFLAGS_PLANAR)
+ gp_SortVertices(theGraph)
+
+- # use to and from mappings to relabel vertices back from the set {0,...,n-1}
++ # use to and from mappings to relabel vertices back from the set {1,...,n}
+ g.relabel(to)
+
+ if status == NOTOK:
+@@ -134,12 +141,12 @@
+ # Kuratowski subgraph isolator
+ g_dict = {}
+ from sage.graphs.graph import Graph
+- for i from 0 <= i < theGraph.N:
++ for i from 0 < i <= theGraph.N:
+ linked_list = []
+- j = theGraph.G[i].link[1]
+- while j >= theGraph.N:
+- linked_list.append(to[theGraph.G[j].v])
+- j = theGraph.G[j].link[1]
++ j = theGraph.V[i].link[1]
++ while j:
++ linked_list.append(to[theGraph.E[j].neighbor])
++ j = theGraph.E[j].link[1]
+ if len(linked_list) > 0:
+ g_dict[to[i]] = linked_list
+ G = Graph(g_dict)
+@@ -153,12 +160,12 @@
+ if set_embedding:
+ emb_dict = {}
+ #for i in range(theGraph.N):
+- for i from 0 <= i < theGraph.N:
++ for i from 0 < i <= theGraph.N:
+ linked_list = []
+- j = theGraph.G[i].link[1]
+- while j >= theGraph.N:
+- linked_list.append(to[theGraph.G[j].v])
+- j = theGraph.G[j].link[1]
++ j = theGraph.V[i].link[1]
++ while j:
++ linked_list.append(to[theGraph.E[j].neighbor])
++ j = theGraph.E[j].link[1]
+ emb_dict[to[i]] = linked_list
+ g._embedding = emb_dict
+ if set_pos:
+@@ -174,12 +181,12 @@
+
+ emb_dict = {}
+ #for i in range(theGraph.N):
+- for i from 0 <= i < theGraph.N:
++ for i from 0 < i <= theGraph.N:
+ linked_list = []
+- j = theGraph.G[i].link[0]
+- while j >= theGraph.N:
+- linked_list.append(to[theGraph.G[j].v])
+- j = theGraph.G[j].link[0]
++ j = theGraph.V[i].link[0]
++ while j:
++ linked_list.append(to[theGraph.E[j].neighbor])
++ j = theGraph.E[j].link[0]
+ emb_dict[to[i]] = linked_list
+ g._embedding = emb_dict
+ gp_Free(&theGraph)
Deleted: community-x86_64/skip-check.patch
===================================================================
--- community-x86_64/skip-check.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-x86_64/skip-check.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,22 +0,0 @@
---- 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-x86_64/skip-check.patch (from rev 209347, sagemath/trunk/skip-check.patch)
===================================================================
--- community-x86_64/skip-check.patch (rev 0)
+++ community-x86_64/skip-check.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -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
+
Deleted: community-x86_64/test-optional.patch
===================================================================
--- community-x86_64/test-optional.patch 2017-01-29 11:18:40 UTC (rev 209347)
+++ community-x86_64/test-optional.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -1,25 +0,0 @@
---- src/sage/doctest/control.py.orig 2016-10-20 19:39:53.714618246 +0200
-+++ src/sage/doctest/control.py 2016-10-20 19:40:15.158049920 +0200
-@@ -307,22 +307,6 @@
- if "all" in options.optional:
- # Special case to run all optional tests
- options.optional = True
-- else:
-- # We replace the 'optional' tag by all optional
-- # packages for which the installed version matches the
-- # latest available version (this implies in particular
-- # that the package is actually installed).
-- if 'optional' in options.optional:
-- options.optional.discard('optional')
-- from sage.misc.package import list_packages
-- for pkg in list_packages('optional', local=True).values():
-- if pkg['installed_version'] == pkg['remote_version']:
-- options.optional.add(pkg['name'])
--
-- # Check that all tags are valid
-- for o in options.optional:
-- if not optionaltag_regex.search(o):
-- raise ValueError('invalid optional tag {!r}'.format(o))
-
- self.options = options
- self.files = args
Copied: sagemath/repos/community-x86_64/test-optional.patch (from rev 209347, sagemath/trunk/test-optional.patch)
===================================================================
--- community-x86_64/test-optional.patch (rev 0)
+++ community-x86_64/test-optional.patch 2017-01-29 11:19:59 UTC (rev 209348)
@@ -0,0 +1,25 @@
+--- src/sage/doctest/control.py.orig 2016-10-20 19:39:53.714618246 +0200
++++ src/sage/doctest/control.py 2016-10-20 19:40:15.158049920 +0200
+@@ -307,22 +307,6 @@
+ if "all" in options.optional:
+ # Special case to run all optional tests
+ options.optional = True
+- else:
+- # We replace the 'optional' tag by all optional
+- # packages for which the installed version matches the
+- # latest available version (this implies in particular
+- # that the package is actually installed).
+- if 'optional' in options.optional:
+- options.optional.discard('optional')
+- from sage.misc.package import list_packages
+- for pkg in list_packages('optional', local=True).values():
+- if pkg['installed_version'] == pkg['remote_version']:
+- options.optional.add(pkg['name'])
+-
+- # Check that all tags are valid
+- for o in options.optional:
+- if not optionaltag_regex.search(o):
+- raise ValueError('invalid optional tag {!r}'.format(o))
+
+ self.options = options
+ self.files = args
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