Date: Tuesday, July 10, 2018 @ 17:27:37 Author: arojas Revision: 356283
archrelease: copy trunk to community-x86_64 Added: sagemath/repos/community-x86_64/PKGBUILD (from rev 356281, sagemath/trunk/PKGBUILD) sagemath/repos/community-x86_64/fes02.patch (from rev 356281, sagemath/trunk/fes02.patch) sagemath/repos/community-x86_64/jupyter-path.patch (from rev 356281, sagemath/trunk/jupyter-path.patch) sagemath/repos/community-x86_64/latte-count.patch (from rev 356281, sagemath/trunk/latte-count.patch) sagemath/repos/community-x86_64/package.patch (from rev 356282, sagemath/trunk/package.patch) sagemath/repos/community-x86_64/r-no-readline.patch (from rev 356282, sagemath/trunk/r-no-readline.patch) sagemath/repos/community-x86_64/sagemath-detect-igraph.patch (from rev 356282, sagemath/trunk/sagemath-detect-igraph.patch) sagemath/repos/community-x86_64/sagemath-env.patch (from rev 356282, sagemath/trunk/sagemath-env.patch) sagemath/repos/community-x86_64/sagemath-gap-4.8.patch (from rev 356282, sagemath/trunk/sagemath-gap-4.8.patch) sagemath/repos/community-x86_64/sagemath-ignore-warnings.patch (from rev 356282, sagemath/trunk/sagemath-ignore-warnings.patch) sagemath/repos/community-x86_64/sagemath-lcalc-c++11.patch (from rev 356282, sagemath/trunk/sagemath-lcalc-c++11.patch) sagemath/repos/community-x86_64/sagemath-lrs.patch (from rev 356282, sagemath/trunk/sagemath-lrs.patch) sagemath/repos/community-x86_64/sagemath-networkx2.patch (from rev 356282, sagemath/trunk/sagemath-networkx2.patch) sagemath/repos/community-x86_64/sagemath-python3-notebook.patch (from rev 356282, sagemath/trunk/sagemath-python3-notebook.patch) sagemath/repos/community-x86_64/sagemath-scipy-1.0.patch (from rev 356282, sagemath/trunk/sagemath-scipy-1.0.patch) sagemath/repos/community-x86_64/sagemath-singular-4.1.1.patch (from rev 356282, sagemath/trunk/sagemath-singular-4.1.1.patch) sagemath/repos/community-x86_64/sagemath-threejs.patch (from rev 356282, sagemath/trunk/sagemath-threejs.patch) sagemath/repos/community-x86_64/test-optional.patch (from rev 356282, sagemath/trunk/test-optional.patch) Deleted: sagemath/repos/community-x86_64/PKGBUILD sagemath/repos/community-x86_64/fes02.patch sagemath/repos/community-x86_64/jupyter-path.patch sagemath/repos/community-x86_64/latte-count.patch sagemath/repos/community-x86_64/package.patch sagemath/repos/community-x86_64/r-no-readline.patch sagemath/repos/community-x86_64/sagemath-detect-igraph.patch sagemath/repos/community-x86_64/sagemath-env.patch sagemath/repos/community-x86_64/sagemath-gap-4.8.patch sagemath/repos/community-x86_64/sagemath-ignore-warnings.patch sagemath/repos/community-x86_64/sagemath-lcalc-c++11.patch sagemath/repos/community-x86_64/sagemath-lrs.patch sagemath/repos/community-x86_64/sagemath-networkx2.patch sagemath/repos/community-x86_64/sagemath-python3-notebook.patch sagemath/repos/community-x86_64/sagemath-scipy-1.0.patch sagemath/repos/community-x86_64/sagemath-singular-4.1.1.patch sagemath/repos/community-x86_64/sagemath-threejs.patch sagemath/repos/community-x86_64/test-optional.patch ---------------------------------+ PKGBUILD | 342 ++++++++++++++++++------------------- fes02.patch | 114 ++++++------ jupyter-path.patch | 44 ++-- latte-count.patch | 142 +++++++-------- package.patch | 76 ++++---- r-no-readline.patch | 22 +- sagemath-detect-igraph.patch | 42 ++-- sagemath-env.patch | 298 ++++++++++++++++---------------- sagemath-gap-4.8.patch | 62 +++--- sagemath-ignore-warnings.patch | 50 ++--- sagemath-lcalc-c++11.patch | 20 +- sagemath-lrs.patch | 44 ++-- sagemath-networkx2.patch | 350 +++++++++++++++++++------------------- sagemath-python3-notebook.patch | 54 ++--- sagemath-scipy-1.0.patch | 32 +-- sagemath-singular-4.1.1.patch | 216 +++++++++++------------ sagemath-threejs.patch | 22 +- test-optional.patch | 54 ++--- 18 files changed, 994 insertions(+), 990 deletions(-) Deleted: PKGBUILD =================================================================== --- PKGBUILD 2018-07-10 17:27:11 UTC (rev 356282) +++ PKGBUILD 2018-07-10 17:27:37 UTC (rev 356283) @@ -1,169 +0,0 @@ -# Maintainer: Antonio Rojas <aro...@archlinux.org> -# Contributor: Evgeniy Alekseev <arcanis.arch at gmail dot com> -# 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=8.2 -pkgrel=10 -pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab" -arch=(x86_64) -url="http://www.sagemath.org" -license=(GPL) -depends=(ipython2 ppl palp brial cliquer maxima-ecl gfan sympow nauty python2-rpy2 python2-fpylll python2-psutil python2-cypari2 - 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 tachyon - 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: Flask notebook interface (deprecated)' - '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' - 'ffmpeg: to export animations to video' 'imagemagick: to show animations' - 'coxeter: Coxeter groups implementation' 'cryptominisat5: SAT solver' 'gap-4.8-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' - 'latte-integrale: integral point count in polyhedra' 'polymake: polymake backend for polyhedral computations' - 'shared_meataxe: faster matrix arithmetic over finite fields' 'openblas: faster linear algebra' - 'sirocco: for computing the fundamental group of the complement of a plane curve' - 'three.js: alternative 3D plots engine' 'dot2tex: for displaying some diagrams' - 'python2-pip: to install optional packages with sage -pip') -makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc libhomfly libbraiding sirocco - mcqd coxeter bliss-graphs tdlib python2-pkgconfig shared_meataxe libfes) -source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz" - sagemath-env.patch package.patch latte-count.patch jupyter-path.patch sagemath-python3-notebook.patch test-optional.patch - r-no-readline.patch fes02.patch sagemath-threejs.patch sagemath-ignore-warnings.patch - sagemath-detect-igraph.patch sagemath-networkx2.patch sagemath-scipy-1.0.patch sagemath-lrs.patch - sagemath-singular-4.1.1.patch sagemath-lcalc-c++11.patch sagemath-gap-4.8.patch - pari-ratpoints.patch::"https://github.com/sagemath/sage/commit/83458400.patch") -sha256sums=('41ba2c2dde7a02e1bb6880ae875d37ab058567cc26e760efe87eeb12188cd65b' - 'b3c5f5c159d72ba7bc2b186b7b0e50a02b1ca60caef49b3857dbaad3da36b6fc' - 'c41ae665499c6cd775d40bbe178f8786830b0931ee26bf11ee02f7d83bcc8107' - '0b680e674c11c47afa86162d8b49645620b8912722e08133d23357c29ca9310a' - '2cad308f8adbb6c54e6603fa22b2f0eb60f6f09248d5d015000c3932ac14f646' - '962ce805c87147212b21fc2ab0ac9af9bd0033942c7a6905b9906645b48e8a4f' - '18edeafb01cc1ed7270c2dfb41a58717918680c98e8eada1858736acd65d92ba' - 'afd0952b9bb8f52fd428eae36cf719a58ff85a894baae88cbb2124e043768cc7' - '7fcb52e96935dccb0f958d37c2f4e3918392480b9af53e08562f6cba6c68cb94' - '2d13b15ad2d1511bb3d752a261497060a8901882b1c2fa9813219781b7a71d83' - 'a4a6c87b46ff23b89608aca66d00427334502e8bfb5dfe68b94497d19be1c7ae' - 'bfe49f0168fe0824f0eaf4ea793b08d5b3e43c4e3634eb5f664c70644a793a59' - '8253730940687992dd29d90d95bea7e2685bb4854db004090c8196ce92859b64' - '17397b8e1843b013ef5d2e083369109f0719651edd8ef0c8493cb49e2bc4324a' - 'c0f65534a845ba802de6196229159fe67fcc3f72f0cb1ce57d4ae5c9fe10282c' - '507bf761df222d1961d53ebeaf8e6a5a3dc2d7b9cb78748d71ed8cb1ee1c4ac6' - '5114c912f821900e5bfae1e2cfeb7984de946d0b23e1182b0bf15be1d803dfd0' - '6917cb74e50ae965ea8d7c39577e5f0a5068e4b6a67b53fc6f219149a7d06584' - 'e24ad879f6b2eb970778fc5e867bcbe0a6d393feca8f11f5cb8d07da1f024be9') - -prepare(){ - cd sage-$pkgver - -# Arch-specific patches -# assume all optional packages are installed - patch -p0 -i ../package.patch -# set env variables - patch -p0 -i ../sagemath-env.patch -# don't list optional packages when running tests - patch -p0 -i ../test-optional.patch -# set jupyter path - patch -p0 -i ../jupyter-path.patch -# fix freezes in R interface with readline 7 (Debian) - patch -p1 -i ../r-no-readline.patch -# use correct latte-count binary name - patch -p1 -i ../latte-count.patch -# make 'sage -notebook=jupyter' work with our python3 jupyter-notebook package - patch -p1 -i ../sagemath-python3-notebook.patch -# fix Cremona database detection - sed -e "s|is_package_installed('database_cremona_ellcurve')|os.path.exists('/usr/share/cremona/cremona.db')|" \ - -i src/sage/databases/cremona.py -# fix python-igraph detection - patch -p1 -i ../sagemath-detect-igraph.patch -# fix lrs detection - patch -p1 -i ../sagemath-lrs.patch -# adapt to networkx 2 changes - patch -p1 -i ../sagemath-networkx2.patch -# fix three.js plotting backend - patch -p1 -i ../sagemath-threejs.patch -# don't show PARI stack size increase or GLPK warnings during doctesting (Debian) - patch -p1 -i ../sagemath-ignore-warnings.patch -# remove deprecated scipy parameters - patch -p1 -i ../sagemath-scipy-1.0.patch -# fix build with Singular 4.1.1 - patch -p1 -i ../sagemath-singular-4.1.1.patch -# revert usage of development PARI features - patch -Rp1 -i ../pari-ratpoints.patch -# don't force c++98 for lcalc (fixes build with NTL 11) - patch -p1 -i ../sagemath-lcalc-c++11.patch -# Adjust paths for gap-4.8 - patch -p1 -i ../sagemath-gap-4.8.patch - -# Upstream patches -# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209 - patch -p1 -i ../fes02.patch - -# use python2 - sed -e 's|#!/usr/bin/env sage-python23|#!/usr/bin/env python2|' -e 's|#!/usr/bin/env python\b|#!/usr/bin/env python2|' \ - -e 's|exec python\b|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\b|exec ipython2|' -e 's|exec pip\b|exec pip2|' -e 's|cygdb|cygdb2|g' -i src/bin/sage - sed -e "s|'cython'|'cython2'|" -i src/bin/sage-cython -} - - -build() { - cd sage-$pkgver/src - - export SAGE_ROOT="$PWD" - export SAGE_SRC="$PWD" - python2 setup.py build -} - -package_sagemath() { - optdepends+=('sagemath-jupyter: Jupyter kernel') - - cd sage-$pkgver/src - - export SAGE_ROOT="$PWD" - export SAGE_LOCAL="/usr" - export JUPYTER_PATH="$pkgdir"/usr/share/jupyter - python2 setup.py install --root="$pkgdir" --optimize=1 - - mkdir -p "$pkgdir"/usr/bin - cp bin/sage "$pkgdir"/usr/bin - for _i in arch-env cachegrind callgrind cleaner coverage coverageall cython env eval grep grepdoc inline-fortran \ - ipython massif maxima.lisp native-execute notebook num-threads.py omega open preparse python rst2sws rst2txt run \ - run-cython runtests startuptime.py sws2rst valgrind version.sh - do - cp bin/sage-$_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 - -# 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 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 356281, sagemath/trunk/PKGBUILD) =================================================================== --- PKGBUILD (rev 0) +++ PKGBUILD 2018-07-10 17:27:37 UTC (rev 356283) @@ -0,0 +1,173 @@ +# Maintainer: Antonio Rojas <aro...@archlinux.org> +# Contributor: Evgeniy Alekseev <arcanis.arch at gmail dot com> +# 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=8.2 +pkgrel=11 +pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab" +arch=(x86_64) +url="http://www.sagemath.org" +license=(GPL) +depends=(ipython2 ppl palp brial cliquer maxima-ecl gfan sympow nauty python2-rpy2 python2-fpylll python2-psutil python2-cypari2 + 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 tachyon + 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: Flask notebook interface (deprecated)' + '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' + 'ffmpeg: to export animations to video' 'imagemagick: to show animations' + 'coxeter: Coxeter groups implementation' 'cryptominisat5: SAT solver' 'gap-4.8-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' + 'latte-integrale: integral point count in polyhedra' 'polymake: polymake backend for polyhedral computations' + 'shared_meataxe: faster matrix arithmetic over finite fields' 'openblas: faster linear algebra' + 'sirocco: for computing the fundamental group of the complement of a plane curve' + 'three.js: alternative 3D plots engine' 'dot2tex: for displaying some diagrams' + 'python2-pip: to install optional packages with sage -pip') +makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc libhomfly libbraiding sirocco + mcqd coxeter bliss-graphs tdlib python2-pkgconfig shared_meataxe libfes) +source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz" + sagemath-env.patch package.patch latte-count.patch jupyter-path.patch sagemath-python3-notebook.patch test-optional.patch + r-no-readline.patch fes02.patch sagemath-threejs.patch sagemath-ignore-warnings.patch + sagemath-detect-igraph.patch sagemath-networkx2.patch sagemath-scipy-1.0.patch sagemath-lrs.patch + sagemath-singular-4.1.1.patch sagemath-lcalc-c++11.patch sagemath-gap-4.8.patch + pari-ratpoints.patch::"https://github.com/sagemath/sage/commit/83458400.patch" + sagemath-cypari2.patch::"https://git.sagemath.org/sage.git/patch?id=da380b32") +sha256sums=('41ba2c2dde7a02e1bb6880ae875d37ab058567cc26e760efe87eeb12188cd65b' + 'b3c5f5c159d72ba7bc2b186b7b0e50a02b1ca60caef49b3857dbaad3da36b6fc' + 'c41ae665499c6cd775d40bbe178f8786830b0931ee26bf11ee02f7d83bcc8107' + '0b680e674c11c47afa86162d8b49645620b8912722e08133d23357c29ca9310a' + '2cad308f8adbb6c54e6603fa22b2f0eb60f6f09248d5d015000c3932ac14f646' + '962ce805c87147212b21fc2ab0ac9af9bd0033942c7a6905b9906645b48e8a4f' + '18edeafb01cc1ed7270c2dfb41a58717918680c98e8eada1858736acd65d92ba' + 'afd0952b9bb8f52fd428eae36cf719a58ff85a894baae88cbb2124e043768cc7' + '7fcb52e96935dccb0f958d37c2f4e3918392480b9af53e08562f6cba6c68cb94' + '2d13b15ad2d1511bb3d752a261497060a8901882b1c2fa9813219781b7a71d83' + 'a4a6c87b46ff23b89608aca66d00427334502e8bfb5dfe68b94497d19be1c7ae' + 'bfe49f0168fe0824f0eaf4ea793b08d5b3e43c4e3634eb5f664c70644a793a59' + '8253730940687992dd29d90d95bea7e2685bb4854db004090c8196ce92859b64' + '17397b8e1843b013ef5d2e083369109f0719651edd8ef0c8493cb49e2bc4324a' + 'c0f65534a845ba802de6196229159fe67fcc3f72f0cb1ce57d4ae5c9fe10282c' + '507bf761df222d1961d53ebeaf8e6a5a3dc2d7b9cb78748d71ed8cb1ee1c4ac6' + '5114c912f821900e5bfae1e2cfeb7984de946d0b23e1182b0bf15be1d803dfd0' + '6917cb74e50ae965ea8d7c39577e5f0a5068e4b6a67b53fc6f219149a7d06584' + 'e24ad879f6b2eb970778fc5e867bcbe0a6d393feca8f11f5cb8d07da1f024be9' + '94847fc033fd36bc59217c8484d4cf48d0640ff35bb5ca5ffba88a8158c6dd44') + +prepare(){ + cd sage-$pkgver + +# Arch-specific patches +# assume all optional packages are installed + patch -p0 -i ../package.patch +# set env variables + patch -p0 -i ../sagemath-env.patch +# don't list optional packages when running tests + patch -p0 -i ../test-optional.patch +# set jupyter path + patch -p0 -i ../jupyter-path.patch +# fix freezes in R interface with readline 7 (Debian) + patch -p1 -i ../r-no-readline.patch +# use correct latte-count binary name + patch -p1 -i ../latte-count.patch +# make 'sage -notebook=jupyter' work with our python3 jupyter-notebook package + patch -p1 -i ../sagemath-python3-notebook.patch +# fix Cremona database detection + sed -e "s|is_package_installed('database_cremona_ellcurve')|os.path.exists('/usr/share/cremona/cremona.db')|" \ + -i src/sage/databases/cremona.py +# fix python-igraph detection + patch -p1 -i ../sagemath-detect-igraph.patch +# fix lrs detection + patch -p1 -i ../sagemath-lrs.patch +# adapt to networkx 2 changes + patch -p1 -i ../sagemath-networkx2.patch +# fix three.js plotting backend + patch -p1 -i ../sagemath-threejs.patch +# don't show PARI stack size increase or GLPK warnings during doctesting (Debian) + patch -p1 -i ../sagemath-ignore-warnings.patch +# remove deprecated scipy parameters + patch -p1 -i ../sagemath-scipy-1.0.patch +# fix build with Singular 4.1.1 + patch -p1 -i ../sagemath-singular-4.1.1.patch +# revert usage of development PARI features + patch -Rp1 -i ../pari-ratpoints.patch +# don't force c++98 for lcalc (fixes build with NTL 11) + patch -p1 -i ../sagemath-lcalc-c++11.patch +# Adjust paths for gap-4.8 + patch -p1 -i ../sagemath-gap-4.8.patch + +# Upstream patches +# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209 + patch -p1 -i ../fes02.patch +# update to cypari2 https://trac.sagemath.org/ticket/25813 + patch -p1 -i ../sagemath-cypari2.patch + +# use python2 + sed -e 's|#!/usr/bin/env sage-python23|#!/usr/bin/env python2|' -e 's|#!/usr/bin/env python\b|#!/usr/bin/env python2|' \ + -e 's|exec python\b|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\b|exec ipython2|' -e 's|exec pip\b|exec pip2|' -e 's|cygdb|cygdb2|g' -i src/bin/sage + sed -e "s|'cython'|'cython2'|" -i src/bin/sage-cython +} + + +build() { + cd sage-$pkgver/src + + export SAGE_ROOT="$PWD" + export SAGE_SRC="$PWD" + python2 setup.py build +} + +package_sagemath() { + optdepends+=('sagemath-jupyter: Jupyter kernel') + + 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 + + mkdir -p "$pkgdir"/usr/bin + cp bin/sage "$pkgdir"/usr/bin + for _i in arch-env 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 "$pkgdir"/usr/share/sage + +# Remove sage_setup + rm -r "$pkgdir"/usr/lib/python2.7/site-packages/sage_setup + +# Split jupyter kernel + rm -r "$pkgdir"/usr/share/jupyter +} + +package_sagemath-jupyter() { + pkgdesc='Jupyter kernel for SageMath' + depends=(sagemath python2-jupyter_client python2-ipywidgets mathjax) + optdepends=('sage-notebook-exporter: convert flask notebooks to Jupyter') + + cd sage-$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: fes02.patch =================================================================== --- fes02.patch 2018-07-10 17:27:11 UTC (rev 356282) +++ fes02.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -1,57 +0,0 @@ -From b1f5e3ecc789db674fe17552812f2d0e2ab84be0 Mon Sep 17 00:00:00 2001 -From: Charles Bouillaguet <charles.bouillag...@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) - - - from sage.rings.integer import Integer -@@ -217,7 +217,7 @@ 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 - Copied: sagemath/repos/community-x86_64/fes02.patch (from rev 356281, sagemath/trunk/fes02.patch) =================================================================== --- fes02.patch (rev 0) +++ fes02.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -0,0 +1,57 @@ +From b1f5e3ecc789db674fe17552812f2d0e2ab84be0 Mon Sep 17 00:00:00 2001 +From: Charles Bouillaguet <charles.bouillag...@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) + + + from sage.rings.integer import Integer +@@ -217,7 +217,7 @@ 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: jupyter-path.patch =================================================================== --- jupyter-path.patch 2018-07-10 17:27:11 UTC (rev 356282) +++ jupyter-path.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -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_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): -@@ -225,7 +225,7 @@ - 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 356281, sagemath/trunk/jupyter-path.patch) =================================================================== --- jupyter-path.patch (rev 0) +++ jupyter-path.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -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_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): +@@ -225,7 +225,7 @@ + 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: latte-count.patch =================================================================== --- latte-count.patch 2018-07-10 17:27:11 UTC (rev 356282) +++ latte-count.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -1,71 +0,0 @@ -diff --git a/src/sage/geometry/polyhedron/base_ZZ.py b/src/sage/geometry/polyhedron/base_ZZ.py -index 268af9db0d..70d41dfa30 100644 ---- a/src/sage/geometry/polyhedron/base_ZZ.py -+++ b/src/sage/geometry/polyhedron/base_ZZ.py -@@ -171,7 +171,7 @@ class Polyhedron_ZZ(Polyhedron_base): - sage: p = P.ehrhart_polynomial(maxdet=5, verbose=True) # optional - latte_int - This is LattE integrale ... - ... -- Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd '--maxdet=5' /dev/stdin -+ Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd '--maxdet=5' /dev/stdin - ... - sage: p # optional - latte_int - 1/2*t^2 + 3/2*t + 1 -@@ -179,7 +179,7 @@ class Polyhedron_ZZ(Polyhedron_base): - sage: p = P.ehrhart_polynomial(dual=True, verbose=True) # optional - latte_int - This is LattE integrale ... - ... -- Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --dual /dev/stdin -+ Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --dual /dev/stdin - ... - sage: p # optional - latte_int - 1/2*t^2 + 3/2*t + 1 -@@ -187,7 +187,7 @@ class Polyhedron_ZZ(Polyhedron_base): - sage: p = P.ehrhart_polynomial(irrational_primal=True, verbose=True) # optional - latte_int - This is LattE integrale ... - ... -- Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-primal /dev/stdin -+ Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-primal /dev/stdin - ... - sage: p # optional - latte_int - 1/2*t^2 + 3/2*t + 1 -@@ -195,7 +195,7 @@ class Polyhedron_ZZ(Polyhedron_base): - sage: p = P.ehrhart_polynomial(irrational_all_primal=True, verbose=True) # optional - latte_int - This is LattE integrale ... - ... -- Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-all-primal /dev/stdin -+ Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-all-primal /dev/stdin - ... - sage: p # optional - latte_int - 1/2*t^2 + 3/2*t + 1 -@@ -207,7 +207,7 @@ class Polyhedron_ZZ(Polyhedron_base): - ... - RuntimeError: LattE integrale program failed (exit code 1): - ... -- Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd '--bim-bam-boum=19' /dev/stdin -+ Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd '--bim-bam-boum=19' /dev/stdin - Unknown command/option --bim-bam-boum=19 - """ - if self.is_empty(): -diff --git a/src/sage/interfaces/latte.py b/src/sage/interfaces/latte.py -index 066cedd401..302b39910d 100644 ---- a/src/sage/interfaces/latte.py -+++ b/src/sage/interfaces/latte.py -@@ -88,7 +88,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False, - sage: n = count(cddin, cdd=True, verbose=True, raw_output=True) # optional - latte_int - This is LattE integrale ... - ... -- Invocation: count '--redundancy-check=none' --cdd /dev/stdin -+ Invocation: latte-count '--redundancy-check=none' --cdd /dev/stdin - ... - Total Unimodular Cones: ... - Maximum number of simplicial cones in memory at once: ... -@@ -108,7 +108,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False, - from sage.misc.misc import SAGE_TMP - from sage.rings.integer import Integer - -- args = ['count'] -+ args = ['latte-count'] - if ehrhart_polynomial and multivariate_generating_function: - raise ValueError - if ehrhart_polynomial: Copied: sagemath/repos/community-x86_64/latte-count.patch (from rev 356281, sagemath/trunk/latte-count.patch) =================================================================== --- latte-count.patch (rev 0) +++ latte-count.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -0,0 +1,71 @@ +diff --git a/src/sage/geometry/polyhedron/base_ZZ.py b/src/sage/geometry/polyhedron/base_ZZ.py +index 268af9db0d..70d41dfa30 100644 +--- a/src/sage/geometry/polyhedron/base_ZZ.py ++++ b/src/sage/geometry/polyhedron/base_ZZ.py +@@ -171,7 +171,7 @@ class Polyhedron_ZZ(Polyhedron_base): + sage: p = P.ehrhart_polynomial(maxdet=5, verbose=True) # optional - latte_int + This is LattE integrale ... + ... +- Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd '--maxdet=5' /dev/stdin ++ Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd '--maxdet=5' /dev/stdin + ... + sage: p # optional - latte_int + 1/2*t^2 + 3/2*t + 1 +@@ -179,7 +179,7 @@ class Polyhedron_ZZ(Polyhedron_base): + sage: p = P.ehrhart_polynomial(dual=True, verbose=True) # optional - latte_int + This is LattE integrale ... + ... +- Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --dual /dev/stdin ++ Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --dual /dev/stdin + ... + sage: p # optional - latte_int + 1/2*t^2 + 3/2*t + 1 +@@ -187,7 +187,7 @@ class Polyhedron_ZZ(Polyhedron_base): + sage: p = P.ehrhart_polynomial(irrational_primal=True, verbose=True) # optional - latte_int + This is LattE integrale ... + ... +- Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-primal /dev/stdin ++ Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-primal /dev/stdin + ... + sage: p # optional - latte_int + 1/2*t^2 + 3/2*t + 1 +@@ -195,7 +195,7 @@ class Polyhedron_ZZ(Polyhedron_base): + sage: p = P.ehrhart_polynomial(irrational_all_primal=True, verbose=True) # optional - latte_int + This is LattE integrale ... + ... +- Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-all-primal /dev/stdin ++ Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-all-primal /dev/stdin + ... + sage: p # optional - latte_int + 1/2*t^2 + 3/2*t + 1 +@@ -207,7 +207,7 @@ class Polyhedron_ZZ(Polyhedron_base): + ... + RuntimeError: LattE integrale program failed (exit code 1): + ... +- Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd '--bim-bam-boum=19' /dev/stdin ++ Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd '--bim-bam-boum=19' /dev/stdin + Unknown command/option --bim-bam-boum=19 + """ + if self.is_empty(): +diff --git a/src/sage/interfaces/latte.py b/src/sage/interfaces/latte.py +index 066cedd401..302b39910d 100644 +--- a/src/sage/interfaces/latte.py ++++ b/src/sage/interfaces/latte.py +@@ -88,7 +88,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False, + sage: n = count(cddin, cdd=True, verbose=True, raw_output=True) # optional - latte_int + This is LattE integrale ... + ... +- Invocation: count '--redundancy-check=none' --cdd /dev/stdin ++ Invocation: latte-count '--redundancy-check=none' --cdd /dev/stdin + ... + Total Unimodular Cones: ... + Maximum number of simplicial cones in memory at once: ... +@@ -108,7 +108,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False, + from sage.misc.misc import SAGE_TMP + from sage.rings.integer import Integer + +- args = ['count'] ++ args = ['latte-count'] + if ehrhart_polynomial and multivariate_generating_function: + raise ValueError + if ehrhart_polynomial: Deleted: package.patch =================================================================== --- package.patch 2018-07-10 17:27:11 UTC (rev 356282) +++ package.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -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 -@@ -320,7 +320,7 @@ - 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 356282, sagemath/trunk/package.patch) =================================================================== --- package.patch (rev 0) +++ package.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -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 +@@ -320,7 +320,7 @@ + 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: r-no-readline.patch =================================================================== --- r-no-readline.patch 2018-07-10 17:27:11 UTC (rev 356282) +++ r-no-readline.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -1,11 +0,0 @@ ---- a/src/sage/interfaces/r.py -+++ b/src/sage/interfaces/r.py -@@ -332,7 +332,7 @@ - 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 356282, sagemath/trunk/r-no-readline.patch) =================================================================== --- r-no-readline.patch (rev 0) +++ r-no-readline.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -0,0 +1,11 @@ +--- a/src/sage/interfaces/r.py ++++ b/src/sage/interfaces/r.py +@@ -332,7 +332,7 @@ + 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: sagemath-detect-igraph.patch =================================================================== --- sagemath-detect-igraph.patch 2018-07-10 17:27:11 UTC (rev 356282) +++ sagemath-detect-igraph.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -1,21 +0,0 @@ -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 -@@ -8480,10 +8480,12 @@ 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) - Copied: sagemath/repos/community-x86_64/sagemath-detect-igraph.patch (from rev 356282, sagemath/trunk/sagemath-detect-igraph.patch) =================================================================== --- sagemath-detect-igraph.patch (rev 0) +++ sagemath-detect-igraph.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -0,0 +1,21 @@ +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 +@@ -8480,10 +8480,12 @@ 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) + Deleted: sagemath-env.patch =================================================================== --- sagemath-env.patch 2018-07-10 17:27:11 UTC (rev 356282) +++ sagemath-env.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -1,149 +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 -@@ -111,41 +111,7 @@ - } - - --# New value for SAGE_ROOT: either SAGE_ROOT (if given) --# or a guessed value based on pwd. --if [ -n "$SAGE_ROOT" ]; then -- NEW_SAGE_ROOT="$SAGE_ROOT" --elif [ -f sage -a -d build ]; then -- NEW_SAGE_ROOT="." --elif [ -f ../../sage -a -d ../../build ]; then -- NEW_SAGE_ROOT="../.." --else -- # No idea what SAGE_ROOT should be... -- echo >&2 "Error: You must set the SAGE_ROOT environment variable or run this" -- echo >&2 "script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory." -- return 1 --fi -- --# Make NEW_SAGE_ROOT absolute --NEW_SAGE_ROOT=`cd "$NEW_SAGE_ROOT" && pwd -P` -- --# Sanity check NEW_SAGE_ROOT --if [ -f "$NEW_SAGE_ROOT/sage" -a -d "$NEW_SAGE_ROOT/build" ]; then -- : --else -- echo >&2 "Error: SAGE_ROOT is set to a bad value:" -- echo >&2 "SAGE_ROOT=$SAGE_ROOT" -- echo >&2 "You must correct it or erase it and run this script from the SAGE_ROOT" -- echo >&2 "or SAGE_ROOT/local/bin/ directory." -- return 1 --fi -- --# Warn if NEW_SAGE_ROOT does not equal the old SAGE_ROOT --if [ "$SAGE_ROOT" != "$NEW_SAGE_ROOT" -a -n "$SAGE_ROOT" ]; then -- echo >&2 "Warning: overwriting SAGE_ROOT environment variable:" -- echo >&2 "Old SAGE_ROOT=$SAGE_ROOT" -- echo >&2 "New SAGE_ROOT=$NEW_SAGE_ROOT" --fi -+NEW_SAGE_ROOT="/usr" - - - # Don't execute the commands more than once for the same version of -@@ -174,33 +174,9 @@ - export SAGE_ENV_SOURCED=$SAGE_ENV_VERSION - - export SAGE_ROOT="$NEW_SAGE_ROOT" -+export SAGE_LOCAL='/usr' -+export SAGE_SCRIPTS_DIR='/usr/bin' - -- --# sage-env must know where the Sage's script files are. --# Note that SAGE_SCRIPTS_DIR is only used here, so it does not need to --# be exported. --if [ -z "$SAGE_SCRIPTS_DIR" ]; then -- if [ -n "$SAGE_LOCAL" ] && [ -f "$SAGE_LOCAL/bin/sage-env-config" ]; then -- SAGE_SCRIPTS_DIR="$SAGE_LOCAL/bin" -- elif [ -f "$SAGE_ROOT/src/bin/sage-env-config" ]; then -- SAGE_SCRIPTS_DIR="$SAGE_ROOT/src/bin" -- else -- echo >&2 "Error: You must set either the SAGE_LOCAL or SAGE_SCRIPTS_DIR environment variable to run this" -- return 1 -- fi --elif [ ! -f "$SAGE_SCRIPTS_DIR/sage-env-config" ]; then -- echo >&2 "Error: SAGE_SCRIPTS_DIR is set to a bad value:" -- echo >&2 "SAGE_SCRIPTS_DIR=$SAGE_SCRIPTS_DIR" -- echo >&2 "You must correct it or erase it and rerun this script" -- return 1 --fi -- --# Set environment variables (like SAGE_LOCAL) depending on ./configure --. "$SAGE_SCRIPTS_DIR/sage-env-config" --if [ $? -ne 0 ]; then -- echo >&2 "Error: failed to source $SAGE_SCRIPTS_DIR/sage-env-config" -- return 1 --fi - - # The compilers are set in order of priority by - # 1) environment variables -@@ -296,8 +296,9 @@ - export SAGE_EXTCODE="$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-4.8" -+export SAGE_SRC="$SAGE_LOCAL/lib/python2.7/site-packages" -+export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage" - export SAGE_DOC="$SAGE_SHARE/doc/sage" - - if [ -z "${SAGE_ORIG_PATH_SET}" ]; then -@@ -403,6 +403,9 @@ - export SAGE_STARTUP_FILE - fi - -+export LIBMTX="$DOT_SAGE/meataxe" -+[[ -d $LIBMTX ]] || mkdir -p $LIBMTX # Create meataxe data dir -+ - if [ "$PYTHON_EGG_CACHE" = "" ]; then - PYTHON_EGG_CACHE="$DOT_SAGE/.python-eggs" - export PYTHON_EGG_CACHE -@@ -488,7 +488,6 @@ - fi - fi - fi --export MAXIMA_PREFIX="$SAGE_LOCAL" - - PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB - -@@ -608,9 +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="$SAGE_LOCAL/lib/ecl/" && export ECLDIR -- - # Handle parallel building/testing/... - # See Trac Ticket #12016 - # First, figure out the right values for SAGE_NUM_THREADS (default ---- src/sage/env.py.orig 2017-12-07 19:51:25.554281539 +0000 -+++ src/sage/env.py 2017-12-07 19:51:42.787654650 +0000 -@@ -117,13 +117,13 @@ - _add_variable_or_fallback('LOCAL_IDENTIFIER','$HOSTNAME.%s'%os.getpid()) - - # bunch of sage directories and files --_add_variable_or_fallback('SAGE_ROOT', None) --_add_variable_or_fallback('SAGE_LOCAL', None) -+_add_variable_or_fallback('SAGE_ROOT', '') -+_add_variable_or_fallback('SAGE_LOCAL', '/usr') - _add_variable_or_fallback('SAGE_ETC', opj('$SAGE_LOCAL', 'etc')) - _add_variable_or_fallback('SAGE_INC', opj('$SAGE_LOCAL', 'include')) - _add_variable_or_fallback('SAGE_SHARE', opj('$SAGE_LOCAL', 'share')) - --_add_variable_or_fallback('SAGE_SRC', opj('$SAGE_ROOT', 'src')) -+_add_variable_or_fallback('SAGE_SRC', opj('$SAGE_LOCAL', 'lib', 'python2.7', 'site-packages')) - - try: - sitepackages_dirs = site.getsitepackages() -@@ -163,7 +163,7 @@ - _add_variable_or_fallback('GRAPHS_DATA_DIR', opj('$SAGE_SHARE','graphs')) - _add_variable_or_fallback('ELLCURVE_DATA_DIR',opj('$SAGE_SHARE','ellcurves')) - _add_variable_or_fallback('POLYTOPE_DATA_DIR',opj('$SAGE_SHARE','reflexive_polytopes')) --_add_variable_or_fallback('GAP_ROOT_DIR', opj('$SAGE_LOCAL','gap','latest')) -+_add_variable_or_fallback('GAP_ROOT_DIR', opj('$SAGE_LOCAL','lib','gap-4.8')) - _add_variable_or_fallback('THEBE_DIR', opj('$SAGE_SHARE','thebe')) - - # locate singular shared object Copied: sagemath/repos/community-x86_64/sagemath-env.patch (from rev 356282, sagemath/trunk/sagemath-env.patch) =================================================================== --- sagemath-env.patch (rev 0) +++ sagemath-env.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -0,0 +1,149 @@ +--- src/bin/sage-env.orig 2015-01-06 10:46:04.469687605 +0100 ++++ src/bin/sage-env 2015-01-06 10:49:59.547762019 +0100 +@@ -111,41 +111,7 @@ + } + + +-# New value for SAGE_ROOT: either SAGE_ROOT (if given) +-# or a guessed value based on pwd. +-if [ -n "$SAGE_ROOT" ]; then +- NEW_SAGE_ROOT="$SAGE_ROOT" +-elif [ -f sage -a -d build ]; then +- NEW_SAGE_ROOT="." +-elif [ -f ../../sage -a -d ../../build ]; then +- NEW_SAGE_ROOT="../.." +-else +- # No idea what SAGE_ROOT should be... +- echo >&2 "Error: You must set the SAGE_ROOT environment variable or run this" +- echo >&2 "script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory." +- return 1 +-fi +- +-# Make NEW_SAGE_ROOT absolute +-NEW_SAGE_ROOT=`cd "$NEW_SAGE_ROOT" && pwd -P` +- +-# Sanity check NEW_SAGE_ROOT +-if [ -f "$NEW_SAGE_ROOT/sage" -a -d "$NEW_SAGE_ROOT/build" ]; then +- : +-else +- echo >&2 "Error: SAGE_ROOT is set to a bad value:" +- echo >&2 "SAGE_ROOT=$SAGE_ROOT" +- echo >&2 "You must correct it or erase it and run this script from the SAGE_ROOT" +- echo >&2 "or SAGE_ROOT/local/bin/ directory." +- return 1 +-fi +- +-# Warn if NEW_SAGE_ROOT does not equal the old SAGE_ROOT +-if [ "$SAGE_ROOT" != "$NEW_SAGE_ROOT" -a -n "$SAGE_ROOT" ]; then +- echo >&2 "Warning: overwriting SAGE_ROOT environment variable:" +- echo >&2 "Old SAGE_ROOT=$SAGE_ROOT" +- echo >&2 "New SAGE_ROOT=$NEW_SAGE_ROOT" +-fi ++NEW_SAGE_ROOT="/usr" + + + # Don't execute the commands more than once for the same version of +@@ -174,33 +174,9 @@ + export SAGE_ENV_SOURCED=$SAGE_ENV_VERSION + + export SAGE_ROOT="$NEW_SAGE_ROOT" ++export SAGE_LOCAL='/usr' ++export SAGE_SCRIPTS_DIR='/usr/bin' + +- +-# sage-env must know where the Sage's script files are. +-# Note that SAGE_SCRIPTS_DIR is only used here, so it does not need to +-# be exported. +-if [ -z "$SAGE_SCRIPTS_DIR" ]; then +- if [ -n "$SAGE_LOCAL" ] && [ -f "$SAGE_LOCAL/bin/sage-env-config" ]; then +- SAGE_SCRIPTS_DIR="$SAGE_LOCAL/bin" +- elif [ -f "$SAGE_ROOT/src/bin/sage-env-config" ]; then +- SAGE_SCRIPTS_DIR="$SAGE_ROOT/src/bin" +- else +- echo >&2 "Error: You must set either the SAGE_LOCAL or SAGE_SCRIPTS_DIR environment variable to run this" +- return 1 +- fi +-elif [ ! -f "$SAGE_SCRIPTS_DIR/sage-env-config" ]; then +- echo >&2 "Error: SAGE_SCRIPTS_DIR is set to a bad value:" +- echo >&2 "SAGE_SCRIPTS_DIR=$SAGE_SCRIPTS_DIR" +- echo >&2 "You must correct it or erase it and rerun this script" +- return 1 +-fi +- +-# Set environment variables (like SAGE_LOCAL) depending on ./configure +-. "$SAGE_SCRIPTS_DIR/sage-env-config" +-if [ $? -ne 0 ]; then +- echo >&2 "Error: failed to source $SAGE_SCRIPTS_DIR/sage-env-config" +- return 1 +-fi + + # The compilers are set in order of priority by + # 1) environment variables +@@ -296,8 +296,9 @@ + export SAGE_EXTCODE="$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-4.8" ++export SAGE_SRC="$SAGE_LOCAL/lib/python2.7/site-packages" ++export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage" + export SAGE_DOC="$SAGE_SHARE/doc/sage" + + if [ -z "${SAGE_ORIG_PATH_SET}" ]; then +@@ -403,6 +403,9 @@ + export SAGE_STARTUP_FILE + fi + ++export LIBMTX="$DOT_SAGE/meataxe" ++[[ -d $LIBMTX ]] || mkdir -p $LIBMTX # Create meataxe data dir ++ + if [ "$PYTHON_EGG_CACHE" = "" ]; then + PYTHON_EGG_CACHE="$DOT_SAGE/.python-eggs" + export PYTHON_EGG_CACHE +@@ -488,7 +488,6 @@ + fi + fi + fi +-export MAXIMA_PREFIX="$SAGE_LOCAL" + + PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB + +@@ -608,9 +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="$SAGE_LOCAL/lib/ecl/" && export ECLDIR +- + # Handle parallel building/testing/... + # See Trac Ticket #12016 + # First, figure out the right values for SAGE_NUM_THREADS (default +--- src/sage/env.py.orig 2017-12-07 19:51:25.554281539 +0000 ++++ src/sage/env.py 2017-12-07 19:51:42.787654650 +0000 +@@ -117,13 +117,13 @@ + _add_variable_or_fallback('LOCAL_IDENTIFIER','$HOSTNAME.%s'%os.getpid()) + + # bunch of sage directories and files +-_add_variable_or_fallback('SAGE_ROOT', None) +-_add_variable_or_fallback('SAGE_LOCAL', None) ++_add_variable_or_fallback('SAGE_ROOT', '') ++_add_variable_or_fallback('SAGE_LOCAL', '/usr') + _add_variable_or_fallback('SAGE_ETC', opj('$SAGE_LOCAL', 'etc')) + _add_variable_or_fallback('SAGE_INC', opj('$SAGE_LOCAL', 'include')) + _add_variable_or_fallback('SAGE_SHARE', opj('$SAGE_LOCAL', 'share')) + +-_add_variable_or_fallback('SAGE_SRC', opj('$SAGE_ROOT', 'src')) ++_add_variable_or_fallback('SAGE_SRC', opj('$SAGE_LOCAL', 'lib', 'python2.7', 'site-packages')) + + try: + sitepackages_dirs = site.getsitepackages() +@@ -163,7 +163,7 @@ + _add_variable_or_fallback('GRAPHS_DATA_DIR', opj('$SAGE_SHARE','graphs')) + _add_variable_or_fallback('ELLCURVE_DATA_DIR',opj('$SAGE_SHARE','ellcurves')) + _add_variable_or_fallback('POLYTOPE_DATA_DIR',opj('$SAGE_SHARE','reflexive_polytopes')) +-_add_variable_or_fallback('GAP_ROOT_DIR', opj('$SAGE_LOCAL','gap','latest')) ++_add_variable_or_fallback('GAP_ROOT_DIR', opj('$SAGE_LOCAL','lib','gap-4.8')) + _add_variable_or_fallback('THEBE_DIR', opj('$SAGE_SHARE','thebe')) + + # locate singular shared object Deleted: sagemath-gap-4.8.patch =================================================================== --- sagemath-gap-4.8.patch 2018-07-10 17:27:11 UTC (rev 356282) +++ sagemath-gap-4.8.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -1,31 +0,0 @@ -diff --git a/src/sage/interfaces/gap.py b/src/sage/interfaces/gap.py -index 177fc1b6eb..51c67bdd09 100644 ---- a/src/sage/interfaces/gap.py -+++ b/src/sage/interfaces/gap.py -@@ -197,11 +197,11 @@ import string - - WORKSPACE = gap_workspace_file() - --GAP_BINARY = os.path.join(SAGE_LOCAL, 'bin', 'gap') -+GAP_BINARY = os.path.join(SAGE_LOCAL, 'bin', 'gap-4.8') - - first_try = True - --gap_cmd = "gap -r" -+gap_cmd = "gap-4.8 -r" - if platform.processor() == 'ia64' and os.path.exists('/usr/bin/prctl'): - # suppress unaligned access to 0x..., ip=0x... warnings - gap_cmd = 'prctl --unaligned=silent ' + gap_cmd -diff --git a/src/sage/libs/gap/util.pyx b/src/sage/libs/gap/util.pyx -index 7bffcfc00d..51dad178d5 100644 ---- a/src/sage/libs/gap/util.pyx -+++ b/src/sage/libs/gap/util.pyx -@@ -166,7 +166,7 @@ def gap_root(): - if os.path.exists(GAP_ROOT_DIR): - return GAP_ROOT_DIR - print('The gap-4.5.5.spkg (or later) seems to be not installed!') -- gap_sh = open(os.path.join(SAGE_LOCAL, 'bin', 'gap')).read().splitlines() -+ gap_sh = open(os.path.join(SAGE_LOCAL, 'bin', 'gap-4.8')).read().splitlines() - gapdir = filter(lambda dir:dir.strip().startswith('GAP_DIR'), gap_sh)[0] - gapdir = gapdir.split('"')[1] - gapdir = gapdir.replace('$SAGE_LOCAL', SAGE_LOCAL) Copied: sagemath/repos/community-x86_64/sagemath-gap-4.8.patch (from rev 356282, sagemath/trunk/sagemath-gap-4.8.patch) =================================================================== --- sagemath-gap-4.8.patch (rev 0) +++ sagemath-gap-4.8.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -0,0 +1,31 @@ +diff --git a/src/sage/interfaces/gap.py b/src/sage/interfaces/gap.py +index 177fc1b6eb..51c67bdd09 100644 +--- a/src/sage/interfaces/gap.py ++++ b/src/sage/interfaces/gap.py +@@ -197,11 +197,11 @@ import string + + WORKSPACE = gap_workspace_file() + +-GAP_BINARY = os.path.join(SAGE_LOCAL, 'bin', 'gap') ++GAP_BINARY = os.path.join(SAGE_LOCAL, 'bin', 'gap-4.8') + + first_try = True + +-gap_cmd = "gap -r" ++gap_cmd = "gap-4.8 -r" + if platform.processor() == 'ia64' and os.path.exists('/usr/bin/prctl'): + # suppress unaligned access to 0x..., ip=0x... warnings + gap_cmd = 'prctl --unaligned=silent ' + gap_cmd +diff --git a/src/sage/libs/gap/util.pyx b/src/sage/libs/gap/util.pyx +index 7bffcfc00d..51dad178d5 100644 +--- a/src/sage/libs/gap/util.pyx ++++ b/src/sage/libs/gap/util.pyx +@@ -166,7 +166,7 @@ def gap_root(): + if os.path.exists(GAP_ROOT_DIR): + return GAP_ROOT_DIR + print('The gap-4.5.5.spkg (or later) seems to be not installed!') +- gap_sh = open(os.path.join(SAGE_LOCAL, 'bin', 'gap')).read().splitlines() ++ gap_sh = open(os.path.join(SAGE_LOCAL, 'bin', 'gap-4.8')).read().splitlines() + gapdir = filter(lambda dir:dir.strip().startswith('GAP_DIR'), gap_sh)[0] + gapdir = gapdir.split('"')[1] + gapdir = gapdir.replace('$SAGE_LOCAL', SAGE_LOCAL) Deleted: sagemath-ignore-warnings.patch =================================================================== --- sagemath-ignore-warnings.patch 2018-07-10 17:27:11 UTC (rev 356282) +++ sagemath-ignore-warnings.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -1,25 +0,0 @@ -Description: Ignore warnings of PARI increasing the stack size when parsing doctests - Since we can't patch PARI to not produce the warnings and we don't want to - patch tons of doctests to expect the warnings, we patch the doctest parser - to ignore them. -Author: Tobias Hansen <than...@debian.org> ---- sage/src/sage/doctest/parsing.py -+++ sage/src/sage/doctest/parsing.py -@@ -40,6 +40,8 @@ - - float_regex = re.compile('\s*([+-]?\s*((\d*\.?\d+)|(\d+\.?))([eE][+-]?\d+)?)') - optional_regex = re.compile(r'(py2|py3|long time|not implemented|not tested|known bug)|([^ a-z]\s*optional\s*[:-]*((\s|\w)*))') -+pari_stack_warning_regex = re.compile(r'\s*\*\*\*.*(Warning: increasing stack size to )\d+\.') -+glpk_simplex_warning_regex = re.compile(r'(Long-step dual simplex will be used)') - find_sage_prompt = re.compile(r"^(\s*)sage: ", re.M) - find_sage_continuation = re.compile(r"^(\s*)\.\.\.\.:", re.M) - random_marker = re.compile('.*random', re.I) -@@ -935,6 +936,8 @@ - <type 'float'> - """ - got = self.human_readable_escape_sequences(got) -+ got = pari_stack_warning_regex.sub('', got) -+ got = glpk_simplex_warning_regex.sub('', got) - if isinstance(want, MarkedOutput): - if want.random: - return True Copied: sagemath/repos/community-x86_64/sagemath-ignore-warnings.patch (from rev 356282, sagemath/trunk/sagemath-ignore-warnings.patch) =================================================================== --- sagemath-ignore-warnings.patch (rev 0) +++ sagemath-ignore-warnings.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -0,0 +1,25 @@ +Description: Ignore warnings of PARI increasing the stack size when parsing doctests + Since we can't patch PARI to not produce the warnings and we don't want to + patch tons of doctests to expect the warnings, we patch the doctest parser + to ignore them. +Author: Tobias Hansen <than...@debian.org> +--- sage/src/sage/doctest/parsing.py ++++ sage/src/sage/doctest/parsing.py +@@ -40,6 +40,8 @@ + + float_regex = re.compile('\s*([+-]?\s*((\d*\.?\d+)|(\d+\.?))([eE][+-]?\d+)?)') + optional_regex = re.compile(r'(py2|py3|long time|not implemented|not tested|known bug)|([^ a-z]\s*optional\s*[:-]*((\s|\w)*))') ++pari_stack_warning_regex = re.compile(r'\s*\*\*\*.*(Warning: increasing stack size to )\d+\.') ++glpk_simplex_warning_regex = re.compile(r'(Long-step dual simplex will be used)') + find_sage_prompt = re.compile(r"^(\s*)sage: ", re.M) + find_sage_continuation = re.compile(r"^(\s*)\.\.\.\.:", re.M) + random_marker = re.compile('.*random', re.I) +@@ -935,6 +936,8 @@ + <type 'float'> + """ + got = self.human_readable_escape_sequences(got) ++ got = pari_stack_warning_regex.sub('', got) ++ got = glpk_simplex_warning_regex.sub('', got) + if isinstance(want, MarkedOutput): + if want.random: + return True Deleted: sagemath-lcalc-c++11.patch =================================================================== --- sagemath-lcalc-c++11.patch 2018-07-10 17:27:11 UTC (rev 356282) +++ sagemath-lcalc-c++11.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -1,10 +0,0 @@ ---- a/src/sage/libs/lcalc/lcalc_Lfunction.pxd -+++ b/src/sage/libs/lcalc/lcalc_Lfunction.pxd -@@ -1,6 +1,5 @@ - # Lcalc requires GNU extensions, it does not strictly conform to any - # C++ standard: https://trac.sagemath.org/ticket/23341 --# distutils: extra_compile_args = -std=gnu++98 - - cdef extern from "lcalc_sage.h": - ctypedef struct doublevec "std::vector<double>": - Copied: sagemath/repos/community-x86_64/sagemath-lcalc-c++11.patch (from rev 356282, sagemath/trunk/sagemath-lcalc-c++11.patch) =================================================================== --- sagemath-lcalc-c++11.patch (rev 0) +++ sagemath-lcalc-c++11.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -0,0 +1,10 @@ +--- a/src/sage/libs/lcalc/lcalc_Lfunction.pxd ++++ b/src/sage/libs/lcalc/lcalc_Lfunction.pxd +@@ -1,6 +1,5 @@ + # Lcalc requires GNU extensions, it does not strictly conform to any + # C++ standard: https://trac.sagemath.org/ticket/23341 +-# distutils: extra_compile_args = -std=gnu++98 + + cdef extern from "lcalc_sage.h": + ctypedef struct doublevec "std::vector<double>": + Deleted: sagemath-lrs.patch =================================================================== --- sagemath-lrs.patch 2018-07-10 17:27:11 UTC (rev 356282) +++ sagemath-lrs.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -1,22 +0,0 @@ -diff --git a/src/sage/game_theory/normal_form_game.py b/src/sage/game_theory/normal_form_game.py -index 2115de6800..da94aa5d45 100644 ---- a/src/sage/game_theory/normal_form_game.py -+++ b/src/sage/game_theory/normal_form_game.py -@@ -621,6 +621,7 @@ from sage.matrix.constructor import vector - from sage.misc.package import is_package_installed, PackageNotFoundError - from sage.misc.temporary_file import tmp_filename - from sage.numerical.mip import MixedIntegerLinearProgram -+import os - - try: - from gambit import Game -@@ -1636,7 +1637,7 @@ class NormalFormGame(SageObject, MutableMapping): - if not algorithm: - if self.is_constant_sum(): - algorithm = "lp" -- elif is_package_installed('lrslib'): -+ elif os.path.exists('/usr/bin/lrsnash'): - algorithm = "lrs" - else: - algorithm = "enumeration" - Copied: sagemath/repos/community-x86_64/sagemath-lrs.patch (from rev 356282, sagemath/trunk/sagemath-lrs.patch) =================================================================== --- sagemath-lrs.patch (rev 0) +++ sagemath-lrs.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -0,0 +1,22 @@ +diff --git a/src/sage/game_theory/normal_form_game.py b/src/sage/game_theory/normal_form_game.py +index 2115de6800..da94aa5d45 100644 +--- a/src/sage/game_theory/normal_form_game.py ++++ b/src/sage/game_theory/normal_form_game.py +@@ -621,6 +621,7 @@ from sage.matrix.constructor import vector + from sage.misc.package import is_package_installed, PackageNotFoundError + from sage.misc.temporary_file import tmp_filename + from sage.numerical.mip import MixedIntegerLinearProgram ++import os + + try: + from gambit import Game +@@ -1636,7 +1637,7 @@ class NormalFormGame(SageObject, MutableMapping): + if not algorithm: + if self.is_constant_sum(): + algorithm = "lp" +- elif is_package_installed('lrslib'): ++ elif os.path.exists('/usr/bin/lrsnash'): + algorithm = "lrs" + else: + algorithm = "enumeration" + Deleted: sagemath-networkx2.patch =================================================================== --- sagemath-networkx2.patch 2018-07-10 17:27:11 UTC (rev 356282) +++ sagemath-networkx2.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -1,175 +0,0 @@ -diff --git a/src/sage/graphs/base/graph_backends.pyx b/src/sage/graphs/base/graph_backends.pyx -index ff1d02900a..bad4a18539 100644 ---- a/src/sage/graphs/base/graph_backends.pyx -+++ b/src/sage/graphs/base/graph_backends.pyx -@@ -800,9 +800,9 @@ class NetworkXGraphDeprecated(SageObject): - sage: X.multiedges = True - sage: G = X.mutate() - sage: G.edges() -- [(1, 2), (2, 3)] -+ MultiEdgeDataView([(1, 2), (2, 3)]) - sage: G.edges(data=True) -- [(1, 2, {'weight': 7}), (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})] -+ MultiEdgeDataView([(1, 2, {'weight': 7}), (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})]) - - """ - import networkx -@@ -868,11 +868,9 @@ class NetworkXDiGraphDeprecated(SageObject): - sage: X.multiedges = True - sage: G = X.mutate() - sage: G.edges() -- [(1, 2), (2, 1), (2, 3)] -+ OutMultiEdgeDataView([(1, 2), (2, 1), (2, 3)]) - sage: G.edges(data=True) -- [(1, 2, {'weight': 7}), -- (2, 1, {7: {}, 8: {}}), -- (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})] -+ OutMultiEdgeDataView([(1, 2, {'weight': 7}), (2, 1, {8: {}, 7: {}}), (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})]) - - """ - import networkx -@@ -1154,7 +1152,7 @@ class NetworkXGraphBackend(GenericGraphBackend): - import networkx - try: - if self._nxg.is_multigraph(): -- for k,d in self._nxg.edge[u][v].iteritems(): -+ for u0,v0,k,d in self._nxg.edges([u,v],True,keys=True): - if d.get('weight',None) == l: - self._nxg.remove_edge(u,v,k) - break -@@ -1223,7 +1221,7 @@ class NetworkXGraphBackend(GenericGraphBackend): - """ - cdef dict E - try: -- E = self._nxg.edge[u][v] -+ E = self._nxg.edges[u,v,0] - except KeyError: - from networkx import NetworkXError - raise NetworkXError("Edge (%s,%s) requested via get_edge_label does not exist."%(u,v)) -@@ -1412,7 +1410,7 @@ class NetworkXGraphBackend(GenericGraphBackend): - sage: G.iterator_nbrs(0) - <dictionary-keyiterator object at ...> - """ -- return self._nxg.neighbors_iter(v) -+ return self._nxg.neighbors(v) - - def iterator_in_nbrs(self, v): - """ -diff --git a/src/sage/graphs/digraph.py b/src/sage/graphs/digraph.py -index 003a8d6bcb..986137a9b0 100644 ---- a/src/sage/graphs/digraph.py -+++ b/src/sage/graphs/digraph.py -@@ -755,7 +755,7 @@ class DiGraph(GenericGraph): - self.allow_multiple_edges(multiedges,check=False) - self.allow_loops(loops,check=False) - self.add_vertices(data.nodes()) -- self.add_edges((u,v,r(l)) for u,v,l in data.edges_iter(data=True)) -+ self.add_edges((u,v,r(l)) for u,v,l in data.edges(data=True)) - elif format == 'igraph': - if not data.is_directed(): - raise ValueError("A *directed* igraph graph was expected. To "+ -@@ -2846,7 +2846,7 @@ class DiGraph(GenericGraph): - Using the NetworkX implementation :: - - sage: D.topological_sort(implementation = "NetworkX") -- [4, 5, 6, 9, 0, 1, 2, 3, 7, 8, 10] -+ [4, 5, 6, 9, 0, 3, 2, 7, 1, 8, 10] - - Using the NetworkX recursive implementation :: - -@@ -2872,9 +2872,7 @@ class DiGraph(GenericGraph): - sage: D = DiGraph({ 0:[1,2,3], 4:[2,5], 1:[8], 2:[7], 3:[7], - ....: 5:[6,7], 7:[8], 6:[9], 8:[10], 9:[10] }) - sage: N = D.networkx_graph() -- sage: networkx.topological_sort(N) -- [4, 5, 6, 9, 0, 1, 2, 3, 7, 8, 10] -- sage: networkx.topological_sort_recursive(N) -+ sage: list(networkx.topological_sort(N)) - [4, 5, 6, 9, 0, 3, 2, 7, 1, 8, 10] - - TESTS: -@@ -2897,10 +2895,7 @@ class DiGraph(GenericGraph): - - elif implementation == "NetworkX" or implementation == "recursive": - import networkx -- if implementation == "NetworkX": -- S = networkx.topological_sort(self.networkx_graph(copy=False)) -- else: -- S = networkx.topological_sort_recursive(self.networkx_graph(copy=False)) -+ S = list(networkx.topological_sort(self.networkx_graph(copy=False))) - if S is None: - raise TypeError('Digraph is not acyclic; there is no topological sort.') - else: -diff --git a/src/sage/graphs/generators/families.py b/src/sage/graphs/generators/families.py -index 8f81333685..1540ec0dcc 100644 ---- a/src/sage/graphs/generators/families.py -+++ b/src/sage/graphs/generators/families.py -@@ -197,7 +197,7 @@ def BalancedTree(r, h): - gracefully:: - - sage: graphs.BalancedTree(1, 10) -- Balanced tree: Graph on 2 vertices -+ Balanced tree: Graph on 11 vertices - - sage: graphs.BalancedTree(-1, 10) - Balanced tree: Graph on 1 vertex -@@ -208,9 +208,6 @@ def BalancedTree(r, h): - sage: graphs.BalancedTree(3, 0) - Balanced tree: Graph on 1 vertex - -- sage: graphs.BalancedTree(5, -2) -- Balanced tree: Graph on 0 vertices -- - sage: graphs.BalancedTree(-2,-2) - Balanced tree: Graph on 0 vertices - """ -diff --git a/src/sage/graphs/graph.py b/src/sage/graphs/graph.py -index 3550f990ef..490813e619 100644 ---- a/src/sage/graphs/graph.py -+++ b/src/sage/graphs/graph.py -@@ -1199,7 +1199,7 @@ class Graph(GenericGraph): - self.allow_loops(loops, check=False) - self.allow_multiple_edges(multiedges, check=False) - self.add_vertices(data.nodes()) -- self.add_edges((u,v,r(l)) for u,v,l in data.edges_iter(data=True)) -+ self.add_edges((u,v,r(l)) for u,v,l in data.edges(data=True)) - elif format == 'igraph': - if data.is_directed(): - raise ValueError("An *undirected* igraph graph was expected. "+ -@@ -4621,7 +4621,7 @@ class Graph(GenericGraph): - - sage: g = Graph([(0,1,0), (1,2,999), (2,3,-5)]) - sage: g.matching(use_edge_labels=True) -- [(1, 2, 999)] -+ [(0, 1, 0), (2, 3, -5)] - sage: g.matching(algorithm="LP", use_edge_labels=True) - [(1, 2, 999)] - -@@ -4671,7 +4671,7 @@ class Graph(GenericGraph): - else: - for u, v in L: - g.add_edge(u, v) -- d = networkx.max_weight_matching(g) -+ d = dict(networkx.max_weight_matching(g).union(t[::-1] for t in networkx.max_weight_matching(g))) - if value_only: - if use_edge_labels: - return sum(W[u, v] for u, v in six.iteritems(d) if u < v) -@@ -6305,7 +6305,7 @@ class Graph(GenericGraph): - return networkx.number_of_cliques(self.networkx_graph(copy=False), vertices, cliques) - - @doc_index("Clique-related methods") -- def cliques_get_max_clique_graph(self, name=''): -+ def cliques_get_max_clique_graph(self): - """ - Return the clique graph. - -@@ -6336,7 +6336,7 @@ class Graph(GenericGraph): - sage: (G.cliques_get_max_clique_graph()).show(figsize=[2,2]) - """ - import networkx -- return Graph(networkx.make_max_clique_graph(self.networkx_graph(copy=False), name=name, create_using=networkx.MultiGraph())) -+ return Graph(networkx.make_max_clique_graph(self.networkx_graph(copy=False), create_using=networkx.MultiGraph())) - - @doc_index("Clique-related methods") - def cliques_get_clique_bipartite(self, **kwds): - Copied: sagemath/repos/community-x86_64/sagemath-networkx2.patch (from rev 356282, sagemath/trunk/sagemath-networkx2.patch) =================================================================== --- sagemath-networkx2.patch (rev 0) +++ sagemath-networkx2.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -0,0 +1,175 @@ +diff --git a/src/sage/graphs/base/graph_backends.pyx b/src/sage/graphs/base/graph_backends.pyx +index ff1d02900a..bad4a18539 100644 +--- a/src/sage/graphs/base/graph_backends.pyx ++++ b/src/sage/graphs/base/graph_backends.pyx +@@ -800,9 +800,9 @@ class NetworkXGraphDeprecated(SageObject): + sage: X.multiedges = True + sage: G = X.mutate() + sage: G.edges() +- [(1, 2), (2, 3)] ++ MultiEdgeDataView([(1, 2), (2, 3)]) + sage: G.edges(data=True) +- [(1, 2, {'weight': 7}), (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})] ++ MultiEdgeDataView([(1, 2, {'weight': 7}), (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})]) + + """ + import networkx +@@ -868,11 +868,9 @@ class NetworkXDiGraphDeprecated(SageObject): + sage: X.multiedges = True + sage: G = X.mutate() + sage: G.edges() +- [(1, 2), (2, 1), (2, 3)] ++ OutMultiEdgeDataView([(1, 2), (2, 1), (2, 3)]) + sage: G.edges(data=True) +- [(1, 2, {'weight': 7}), +- (2, 1, {7: {}, 8: {}}), +- (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})] ++ OutMultiEdgeDataView([(1, 2, {'weight': 7}), (2, 1, {8: {}, 7: {}}), (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})]) + + """ + import networkx +@@ -1154,7 +1152,7 @@ class NetworkXGraphBackend(GenericGraphBackend): + import networkx + try: + if self._nxg.is_multigraph(): +- for k,d in self._nxg.edge[u][v].iteritems(): ++ for u0,v0,k,d in self._nxg.edges([u,v],True,keys=True): + if d.get('weight',None) == l: + self._nxg.remove_edge(u,v,k) + break +@@ -1223,7 +1221,7 @@ class NetworkXGraphBackend(GenericGraphBackend): + """ + cdef dict E + try: +- E = self._nxg.edge[u][v] ++ E = self._nxg.edges[u,v,0] + except KeyError: + from networkx import NetworkXError + raise NetworkXError("Edge (%s,%s) requested via get_edge_label does not exist."%(u,v)) +@@ -1412,7 +1410,7 @@ class NetworkXGraphBackend(GenericGraphBackend): + sage: G.iterator_nbrs(0) + <dictionary-keyiterator object at ...> + """ +- return self._nxg.neighbors_iter(v) ++ return self._nxg.neighbors(v) + + def iterator_in_nbrs(self, v): + """ +diff --git a/src/sage/graphs/digraph.py b/src/sage/graphs/digraph.py +index 003a8d6bcb..986137a9b0 100644 +--- a/src/sage/graphs/digraph.py ++++ b/src/sage/graphs/digraph.py +@@ -755,7 +755,7 @@ class DiGraph(GenericGraph): + self.allow_multiple_edges(multiedges,check=False) + self.allow_loops(loops,check=False) + self.add_vertices(data.nodes()) +- self.add_edges((u,v,r(l)) for u,v,l in data.edges_iter(data=True)) ++ self.add_edges((u,v,r(l)) for u,v,l in data.edges(data=True)) + elif format == 'igraph': + if not data.is_directed(): + raise ValueError("A *directed* igraph graph was expected. To "+ +@@ -2846,7 +2846,7 @@ class DiGraph(GenericGraph): + Using the NetworkX implementation :: + + sage: D.topological_sort(implementation = "NetworkX") +- [4, 5, 6, 9, 0, 1, 2, 3, 7, 8, 10] ++ [4, 5, 6, 9, 0, 3, 2, 7, 1, 8, 10] + + Using the NetworkX recursive implementation :: + +@@ -2872,9 +2872,7 @@ class DiGraph(GenericGraph): + sage: D = DiGraph({ 0:[1,2,3], 4:[2,5], 1:[8], 2:[7], 3:[7], + ....: 5:[6,7], 7:[8], 6:[9], 8:[10], 9:[10] }) + sage: N = D.networkx_graph() +- sage: networkx.topological_sort(N) +- [4, 5, 6, 9, 0, 1, 2, 3, 7, 8, 10] +- sage: networkx.topological_sort_recursive(N) ++ sage: list(networkx.topological_sort(N)) + [4, 5, 6, 9, 0, 3, 2, 7, 1, 8, 10] + + TESTS: +@@ -2897,10 +2895,7 @@ class DiGraph(GenericGraph): + + elif implementation == "NetworkX" or implementation == "recursive": + import networkx +- if implementation == "NetworkX": +- S = networkx.topological_sort(self.networkx_graph(copy=False)) +- else: +- S = networkx.topological_sort_recursive(self.networkx_graph(copy=False)) ++ S = list(networkx.topological_sort(self.networkx_graph(copy=False))) + if S is None: + raise TypeError('Digraph is not acyclic; there is no topological sort.') + else: +diff --git a/src/sage/graphs/generators/families.py b/src/sage/graphs/generators/families.py +index 8f81333685..1540ec0dcc 100644 +--- a/src/sage/graphs/generators/families.py ++++ b/src/sage/graphs/generators/families.py +@@ -197,7 +197,7 @@ def BalancedTree(r, h): + gracefully:: + + sage: graphs.BalancedTree(1, 10) +- Balanced tree: Graph on 2 vertices ++ Balanced tree: Graph on 11 vertices + + sage: graphs.BalancedTree(-1, 10) + Balanced tree: Graph on 1 vertex +@@ -208,9 +208,6 @@ def BalancedTree(r, h): + sage: graphs.BalancedTree(3, 0) + Balanced tree: Graph on 1 vertex + +- sage: graphs.BalancedTree(5, -2) +- Balanced tree: Graph on 0 vertices +- + sage: graphs.BalancedTree(-2,-2) + Balanced tree: Graph on 0 vertices + """ +diff --git a/src/sage/graphs/graph.py b/src/sage/graphs/graph.py +index 3550f990ef..490813e619 100644 +--- a/src/sage/graphs/graph.py ++++ b/src/sage/graphs/graph.py +@@ -1199,7 +1199,7 @@ class Graph(GenericGraph): + self.allow_loops(loops, check=False) + self.allow_multiple_edges(multiedges, check=False) + self.add_vertices(data.nodes()) +- self.add_edges((u,v,r(l)) for u,v,l in data.edges_iter(data=True)) ++ self.add_edges((u,v,r(l)) for u,v,l in data.edges(data=True)) + elif format == 'igraph': + if data.is_directed(): + raise ValueError("An *undirected* igraph graph was expected. "+ +@@ -4621,7 +4621,7 @@ class Graph(GenericGraph): + + sage: g = Graph([(0,1,0), (1,2,999), (2,3,-5)]) + sage: g.matching(use_edge_labels=True) +- [(1, 2, 999)] ++ [(0, 1, 0), (2, 3, -5)] + sage: g.matching(algorithm="LP", use_edge_labels=True) + [(1, 2, 999)] + +@@ -4671,7 +4671,7 @@ class Graph(GenericGraph): + else: + for u, v in L: + g.add_edge(u, v) +- d = networkx.max_weight_matching(g) ++ d = dict(networkx.max_weight_matching(g).union(t[::-1] for t in networkx.max_weight_matching(g))) + if value_only: + if use_edge_labels: + return sum(W[u, v] for u, v in six.iteritems(d) if u < v) +@@ -6305,7 +6305,7 @@ class Graph(GenericGraph): + return networkx.number_of_cliques(self.networkx_graph(copy=False), vertices, cliques) + + @doc_index("Clique-related methods") +- def cliques_get_max_clique_graph(self, name=''): ++ def cliques_get_max_clique_graph(self): + """ + Return the clique graph. + +@@ -6336,7 +6336,7 @@ class Graph(GenericGraph): + sage: (G.cliques_get_max_clique_graph()).show(figsize=[2,2]) + """ + import networkx +- return Graph(networkx.make_max_clique_graph(self.networkx_graph(copy=False), name=name, create_using=networkx.MultiGraph())) ++ return Graph(networkx.make_max_clique_graph(self.networkx_graph(copy=False), create_using=networkx.MultiGraph())) + + @doc_index("Clique-related methods") + def cliques_get_clique_bipartite(self, **kwds): + Deleted: sagemath-python3-notebook.patch =================================================================== --- sagemath-python3-notebook.patch 2018-07-10 17:27:11 UTC (rev 356282) +++ sagemath-python3-notebook.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -1,27 +0,0 @@ -diff --git a/src/bin/sage-notebook b/src/bin/sage-notebook -index 74192da240..0ede281aad 100755 ---- a/src/bin/sage-notebook -+++ b/src/bin/sage-notebook -@@ -96,8 +96,7 @@ class NotebookJupyter(object): - if not have_prerequisites(): - print(self.PREREQUISITE_ERROR) - raise SystemExit(1) -- from notebook.notebookapp import main -- main(argv) -+ os.execvp('jupyter-notebook', ['jupyter-notebook'] + argv) - - - class NotebookJupyterlab(object): -diff --git a/src/sage/repl/ipython_kernel/install.py b/src/sage/repl/ipython_kernel/install.py -index 3912b8cdf5..bd40cdadda 100644 ---- a/src/sage/repl/ipython_kernel/install.py -+++ b/src/sage/repl/ipython_kernel/install.py -@@ -280,7 +280,6 @@ def have_prerequisites(debug=True): - True - """ - try: -- from notebook.notebookapp import NotebookApp - return True - except ImportError: - if debug: - Copied: sagemath/repos/community-x86_64/sagemath-python3-notebook.patch (from rev 356282, sagemath/trunk/sagemath-python3-notebook.patch) =================================================================== --- sagemath-python3-notebook.patch (rev 0) +++ sagemath-python3-notebook.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -0,0 +1,27 @@ +diff --git a/src/bin/sage-notebook b/src/bin/sage-notebook +index 74192da240..0ede281aad 100755 +--- a/src/bin/sage-notebook ++++ b/src/bin/sage-notebook +@@ -96,8 +96,7 @@ class NotebookJupyter(object): + if not have_prerequisites(): + print(self.PREREQUISITE_ERROR) + raise SystemExit(1) +- from notebook.notebookapp import main +- main(argv) ++ os.execvp('jupyter-notebook', ['jupyter-notebook'] + argv) + + + class NotebookJupyterlab(object): +diff --git a/src/sage/repl/ipython_kernel/install.py b/src/sage/repl/ipython_kernel/install.py +index 3912b8cdf5..bd40cdadda 100644 +--- a/src/sage/repl/ipython_kernel/install.py ++++ b/src/sage/repl/ipython_kernel/install.py +@@ -280,7 +280,6 @@ def have_prerequisites(debug=True): + True + """ + try: +- from notebook.notebookapp import NotebookApp + return True + except ImportError: + if debug: + Deleted: sagemath-scipy-1.0.patch =================================================================== --- sagemath-scipy-1.0.patch 2018-07-10 17:27:11 UTC (rev 356282) +++ sagemath-scipy-1.0.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -1,16 +0,0 @@ -diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py -index 17b5ebb84b..7ce9055cba 100644 ---- a/src/sage/numerical/optimize.py -+++ b/src/sage/numerical/optimize.py -@@ -486,9 +486,9 @@ def minimize_constrained(func,cons,x0,gradient=None,algorithm='default', **args) - else: - min = optimize.fmin_tnc(f, x0, approx_grad=True, bounds=cons, messages=0, **args)[0] - elif isinstance(cons[0], function_type) or isinstance(cons[0], Expression): -- min = optimize.fmin_cobyla(f, x0, cons, iprint=0, **args) -+ min = optimize.fmin_cobyla(f, x0, cons, **args) - elif isinstance(cons, function_type) or isinstance(cons, Expression): -- min = optimize.fmin_cobyla(f, x0, cons, iprint=0, **args) -+ min = optimize.fmin_cobyla(f, x0, cons, **args) - return vector(RDF, min) - - Copied: sagemath/repos/community-x86_64/sagemath-scipy-1.0.patch (from rev 356282, sagemath/trunk/sagemath-scipy-1.0.patch) =================================================================== --- sagemath-scipy-1.0.patch (rev 0) +++ sagemath-scipy-1.0.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -0,0 +1,16 @@ +diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py +index 17b5ebb84b..7ce9055cba 100644 +--- a/src/sage/numerical/optimize.py ++++ b/src/sage/numerical/optimize.py +@@ -486,9 +486,9 @@ def minimize_constrained(func,cons,x0,gradient=None,algorithm='default', **args) + else: + min = optimize.fmin_tnc(f, x0, approx_grad=True, bounds=cons, messages=0, **args)[0] + elif isinstance(cons[0], function_type) or isinstance(cons[0], Expression): +- min = optimize.fmin_cobyla(f, x0, cons, iprint=0, **args) ++ min = optimize.fmin_cobyla(f, x0, cons, **args) + elif isinstance(cons, function_type) or isinstance(cons, Expression): +- min = optimize.fmin_cobyla(f, x0, cons, iprint=0, **args) ++ min = optimize.fmin_cobyla(f, x0, cons, **args) + return vector(RDF, min) + + Deleted: sagemath-singular-4.1.1.patch =================================================================== --- sagemath-singular-4.1.1.patch 2018-07-10 17:27:11 UTC (rev 356282) +++ sagemath-singular-4.1.1.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -1,108 +0,0 @@ -diff --git a/src/sage/libs/singular/decl.pxd b/src/sage/libs/singular/decl.pxd -index 676544ab1e..5c8639d362 100644 ---- a/src/sage/libs/singular/decl.pxd -+++ b/src/sage/libs/singular/decl.pxd -@@ -170,7 +170,7 @@ cdef extern from "singular/Singular/libsingular.h": - - int n_NumberOfParameters(const n_Procs_s* r) - -- ctypedef struct poly "polyrec": -+ ctypedef struct poly "spolyrec": - poly *next - number *coef - unsigned long exp[1] -@@ -632,7 +632,7 @@ cdef extern from "singular/Singular/libsingular.h": - - # divide monomial p by monomial q, p,q const - -- poly *pDivide(poly *p,poly *q) -+ poly *pMDivide(poly *p,poly *q) - - # return the i-th power of p; p destroyed, requires global ring - -diff --git a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx -index 089524d6b4..ce6d58fc6f 100644 ---- a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx -+++ b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx -@@ -190,8 +190,8 @@ from sage.libs.singular.decl cimport ( - n_IsUnit, n_Invers, - p_ISet, rChangeCurrRing, p_Copy, p_Init, p_SetCoeff, p_Setm, p_SetExp, p_Add_q, - p_NSet, p_GetCoeff, p_Delete, p_GetExp, pNext, rRingVar, omAlloc0, omStrDup, -- omFree, pDivide, p_SetCoeff0, n_Init, p_DivisibleBy, pLcm, p_LmDivisibleBy, -- pDivide, p_IsConstant, p_ExpVectorEqual, p_String, p_LmInit, n_Copy, -+ omFree, pMDivide, p_SetCoeff0, n_Init, p_DivisibleBy, pLcm, p_LmDivisibleBy, -+ pMDivide, p_IsConstant, p_ExpVectorEqual, p_String, p_LmInit, n_Copy, - p_IsUnit, p_Series, p_Head, idInit, fast_map_common_subexp, id_Delete, - p_IsHomogeneous, p_Homogen, p_Totaldegree,pLDeg1_Totaldegree, singclap_pdivide, singclap_factorize, - idLift, IDELEMS, On, Off, SW_USE_CHINREM_GCD, SW_USE_EZGCD, -@@ -1692,8 +1697,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_generic): - if not g._poly: - raise ZeroDivisionError - -- if r!=currRing: rChangeCurrRing(r) # pDivide -- res = pDivide(f._poly, g._poly) -+ if r!=currRing: rChangeCurrRing(r) # pMDivide -+ res = pMDivide(f._poly, g._poly) - if coeff: - if r.cf.type == n_unknown or r.cf.cfDivBy(p_GetCoeff(f._poly, r), p_GetCoeff(g._poly, r), r.cf): - n = r.cf.cfDiv( p_GetCoeff(f._poly, r) , p_GetCoeff(g._poly, r), r.cf) -@@ -1852,8 +1857,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_generic): - and (<MPolynomial_libsingular>g) \ - and g.parent() is self \ - and p_LmDivisibleBy((<MPolynomial_libsingular>g)._poly, m, r): -- if r!=currRing: rChangeCurrRing(r) # pDivide -- flt = pDivide(f._poly, (<MPolynomial_libsingular>g)._poly) -+ if r!=currRing: rChangeCurrRing(r) # pMDivide -+ flt = pMDivide(f._poly, (<MPolynomial_libsingular>g)._poly) - #p_SetCoeff(flt, n_Div( p_GetCoeff(f._poly, r) , p_GetCoeff((<MPolynomial_libsingular>g)._poly, r), r), r) - p_SetCoeff(flt, n_Init(1, r), r) - return new_MP(self,flt), g -@@ -4049,10 +4054,10 @@ cdef class MPolynomial_libsingular(MPolynomial): - if _right.is_monomial(): - p = _self._poly - quo = p_ISet(0,r) -- if r != currRing: rChangeCurrRing(r) # pDivide -+ if r != currRing: rChangeCurrRing(r) # pMDivide - while p: - if p_DivisibleBy(_right._poly, p, r): -- temp = pDivide(p, _right._poly) -+ temp = pMDivide(p, _right._poly) - p_SetCoeff0(temp, n_Copy(p_GetCoeff(p, r), r), r) - quo = p_Add_q(quo, temp, r) - p = pNext(p) -diff --git a/src/sage/rings/polynomial/plural.pyx b/src/sage/rings/polynomial/plural.pyx -index 3b45a38419..c0227fd364 100644 ---- a/src/sage/rings/polynomial/plural.pyx -+++ b/src/sage/rings/polynomial/plural.pyx -@@ -999,7 +999,7 @@ cdef class NCPolynomialRing_plural(Ring): - if not g._poly: - raise ZeroDivisionError - -- res = pDivide(f._poly,g._poly) -+ res = pMDivide(f._poly,g._poly) - if coeff: - if (r.cf.type == n_unknown) or r.cf.cfDivBy(p_GetCoeff(f._poly, r), p_GetCoeff(g._poly, r), r.cf): - n = r.cf.cfDiv( p_GetCoeff(f._poly, r) , p_GetCoeff(g._poly, r), r.cf) -@@ -1194,7 +1194,7 @@ cdef class NCPolynomialRing_plural(Ring): - if isinstance(g, NCPolynomial_plural) \ - and (<NCPolynomial_plural>g) \ - and p_LmDivisibleBy((<NCPolynomial_plural>g)._poly, m, r): -- flt = pDivide(f._poly, (<NCPolynomial_plural>g)._poly) -+ flt = pMDivide(f._poly, (<NCPolynomial_plural>g)._poly) - #p_SetCoeff(flt, n_Div( p_GetCoeff(f._poly, r) , p_GetCoeff((<NCPolynomial_plural>g)._poly, r), r), r) - p_SetCoeff(flt, n_Init(1, r), r) - return new_NCP(self,flt), g -diff --git a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx -index 809ca72c76..9610ce125d 100644 ---- a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx -+++ b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx -@@ -4881,7 +4881,7 @@ cdef class MPolynomial_libsingular(MPolynomial): - if right.is_zero(): - raise ZeroDivisionError - -- if not self._parent._base.is_field() and not is_IntegerRing(self._parent._base): -+ if not self._parent._base.is_field(): - py_quo = self//right - py_rem = self - right*py_quo - return py_quo, py_rem - Copied: sagemath/repos/community-x86_64/sagemath-singular-4.1.1.patch (from rev 356282, sagemath/trunk/sagemath-singular-4.1.1.patch) =================================================================== --- sagemath-singular-4.1.1.patch (rev 0) +++ sagemath-singular-4.1.1.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -0,0 +1,108 @@ +diff --git a/src/sage/libs/singular/decl.pxd b/src/sage/libs/singular/decl.pxd +index 676544ab1e..5c8639d362 100644 +--- a/src/sage/libs/singular/decl.pxd ++++ b/src/sage/libs/singular/decl.pxd +@@ -170,7 +170,7 @@ cdef extern from "singular/Singular/libsingular.h": + + int n_NumberOfParameters(const n_Procs_s* r) + +- ctypedef struct poly "polyrec": ++ ctypedef struct poly "spolyrec": + poly *next + number *coef + unsigned long exp[1] +@@ -632,7 +632,7 @@ cdef extern from "singular/Singular/libsingular.h": + + # divide monomial p by monomial q, p,q const + +- poly *pDivide(poly *p,poly *q) ++ poly *pMDivide(poly *p,poly *q) + + # return the i-th power of p; p destroyed, requires global ring + +diff --git a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx +index 089524d6b4..ce6d58fc6f 100644 +--- a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx ++++ b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx +@@ -190,8 +190,8 @@ from sage.libs.singular.decl cimport ( + n_IsUnit, n_Invers, + p_ISet, rChangeCurrRing, p_Copy, p_Init, p_SetCoeff, p_Setm, p_SetExp, p_Add_q, + p_NSet, p_GetCoeff, p_Delete, p_GetExp, pNext, rRingVar, omAlloc0, omStrDup, +- omFree, pDivide, p_SetCoeff0, n_Init, p_DivisibleBy, pLcm, p_LmDivisibleBy, +- pDivide, p_IsConstant, p_ExpVectorEqual, p_String, p_LmInit, n_Copy, ++ omFree, pMDivide, p_SetCoeff0, n_Init, p_DivisibleBy, pLcm, p_LmDivisibleBy, ++ pMDivide, p_IsConstant, p_ExpVectorEqual, p_String, p_LmInit, n_Copy, + p_IsUnit, p_Series, p_Head, idInit, fast_map_common_subexp, id_Delete, + p_IsHomogeneous, p_Homogen, p_Totaldegree,pLDeg1_Totaldegree, singclap_pdivide, singclap_factorize, + idLift, IDELEMS, On, Off, SW_USE_CHINREM_GCD, SW_USE_EZGCD, +@@ -1692,8 +1697,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_generic): + if not g._poly: + raise ZeroDivisionError + +- if r!=currRing: rChangeCurrRing(r) # pDivide +- res = pDivide(f._poly, g._poly) ++ if r!=currRing: rChangeCurrRing(r) # pMDivide ++ res = pMDivide(f._poly, g._poly) + if coeff: + if r.cf.type == n_unknown or r.cf.cfDivBy(p_GetCoeff(f._poly, r), p_GetCoeff(g._poly, r), r.cf): + n = r.cf.cfDiv( p_GetCoeff(f._poly, r) , p_GetCoeff(g._poly, r), r.cf) +@@ -1852,8 +1857,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_generic): + and (<MPolynomial_libsingular>g) \ + and g.parent() is self \ + and p_LmDivisibleBy((<MPolynomial_libsingular>g)._poly, m, r): +- if r!=currRing: rChangeCurrRing(r) # pDivide +- flt = pDivide(f._poly, (<MPolynomial_libsingular>g)._poly) ++ if r!=currRing: rChangeCurrRing(r) # pMDivide ++ flt = pMDivide(f._poly, (<MPolynomial_libsingular>g)._poly) + #p_SetCoeff(flt, n_Div( p_GetCoeff(f._poly, r) , p_GetCoeff((<MPolynomial_libsingular>g)._poly, r), r), r) + p_SetCoeff(flt, n_Init(1, r), r) + return new_MP(self,flt), g +@@ -4049,10 +4054,10 @@ cdef class MPolynomial_libsingular(MPolynomial): + if _right.is_monomial(): + p = _self._poly + quo = p_ISet(0,r) +- if r != currRing: rChangeCurrRing(r) # pDivide ++ if r != currRing: rChangeCurrRing(r) # pMDivide + while p: + if p_DivisibleBy(_right._poly, p, r): +- temp = pDivide(p, _right._poly) ++ temp = pMDivide(p, _right._poly) + p_SetCoeff0(temp, n_Copy(p_GetCoeff(p, r), r), r) + quo = p_Add_q(quo, temp, r) + p = pNext(p) +diff --git a/src/sage/rings/polynomial/plural.pyx b/src/sage/rings/polynomial/plural.pyx +index 3b45a38419..c0227fd364 100644 +--- a/src/sage/rings/polynomial/plural.pyx ++++ b/src/sage/rings/polynomial/plural.pyx +@@ -999,7 +999,7 @@ cdef class NCPolynomialRing_plural(Ring): + if not g._poly: + raise ZeroDivisionError + +- res = pDivide(f._poly,g._poly) ++ res = pMDivide(f._poly,g._poly) + if coeff: + if (r.cf.type == n_unknown) or r.cf.cfDivBy(p_GetCoeff(f._poly, r), p_GetCoeff(g._poly, r), r.cf): + n = r.cf.cfDiv( p_GetCoeff(f._poly, r) , p_GetCoeff(g._poly, r), r.cf) +@@ -1194,7 +1194,7 @@ cdef class NCPolynomialRing_plural(Ring): + if isinstance(g, NCPolynomial_plural) \ + and (<NCPolynomial_plural>g) \ + and p_LmDivisibleBy((<NCPolynomial_plural>g)._poly, m, r): +- flt = pDivide(f._poly, (<NCPolynomial_plural>g)._poly) ++ flt = pMDivide(f._poly, (<NCPolynomial_plural>g)._poly) + #p_SetCoeff(flt, n_Div( p_GetCoeff(f._poly, r) , p_GetCoeff((<NCPolynomial_plural>g)._poly, r), r), r) + p_SetCoeff(flt, n_Init(1, r), r) + return new_NCP(self,flt), g +diff --git a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx +index 809ca72c76..9610ce125d 100644 +--- a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx ++++ b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx +@@ -4881,7 +4881,7 @@ cdef class MPolynomial_libsingular(MPolynomial): + if right.is_zero(): + raise ZeroDivisionError + +- if not self._parent._base.is_field() and not is_IntegerRing(self._parent._base): ++ if not self._parent._base.is_field(): + py_quo = self//right + py_rem = self - right*py_quo + return py_quo, py_rem + Deleted: sagemath-threejs.patch =================================================================== --- sagemath-threejs.patch 2018-07-10 17:27:11 UTC (rev 356282) +++ sagemath-threejs.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -1,11 +0,0 @@ ---- a/src/sage/repl/rich_output/display_manager.py -+++ b/src/sage/repl/rich_output/display_manager.py -@@ -744,7 +744,7 @@ class DisplayManager(SageObject): - """ - if online: - from sage.misc.package import installed_packages -- version = installed_packages()['threejs'] -+ version = 'r90' - return """ - <script src="https://cdn.rawgit.com/mrdoob/three.js/{0}/build/three.min.js"></script> - <script src="https://cdn.rawgit.com/mrdoob/three.js/{0}/examples/js/controls/OrbitControls.js"></script> Copied: sagemath/repos/community-x86_64/sagemath-threejs.patch (from rev 356282, sagemath/trunk/sagemath-threejs.patch) =================================================================== --- sagemath-threejs.patch (rev 0) +++ sagemath-threejs.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -0,0 +1,11 @@ +--- a/src/sage/repl/rich_output/display_manager.py ++++ b/src/sage/repl/rich_output/display_manager.py +@@ -744,7 +744,7 @@ class DisplayManager(SageObject): + """ + if online: + from sage.misc.package import installed_packages +- version = installed_packages()['threejs'] ++ version = 'r90' + return """ + <script src="https://cdn.rawgit.com/mrdoob/three.js/{0}/build/three.min.js"></script> + <script src="https://cdn.rawgit.com/mrdoob/three.js/{0}/examples/js/controls/OrbitControls.js"></script> Deleted: test-optional.patch =================================================================== --- test-optional.patch 2018-07-10 17:27:11 UTC (rev 356282) +++ test-optional.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -1,27 +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 -@@ -326,24 +326,6 @@ - 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)) -- -- options.optional |= auto_optional_tags - - self.options = options - self.files = args Copied: sagemath/repos/community-x86_64/test-optional.patch (from rev 356282, sagemath/trunk/test-optional.patch) =================================================================== --- test-optional.patch (rev 0) +++ test-optional.patch 2018-07-10 17:27:37 UTC (rev 356283) @@ -0,0 +1,27 @@ +--- 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 +@@ -326,24 +326,6 @@ + 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)) +- +- options.optional |= auto_optional_tags + + self.options = options + self.files = args