[arch-commits] Commit in sagemath/repos/community-x86_64 (38 files)
Antonio Rojas
arojas at archlinux.org
Thu Jul 12 14:26:45 UTC 2018
Date: Thursday, July 12, 2018 @ 14:26:44
Author: arojas
Revision: 357921
archrelease: copy trunk to community-x86_64
Added:
sagemath/repos/community-x86_64/PKGBUILD
(from rev 357920, sagemath/trunk/PKGBUILD)
sagemath/repos/community-x86_64/fes02.patch
(from rev 357920, sagemath/trunk/fes02.patch)
sagemath/repos/community-x86_64/jupyter-path.patch
(from rev 357920, sagemath/trunk/jupyter-path.patch)
sagemath/repos/community-x86_64/latte-count.patch
(from rev 357920, sagemath/trunk/latte-count.patch)
sagemath/repos/community-x86_64/package.patch
(from rev 357920, sagemath/trunk/package.patch)
sagemath/repos/community-x86_64/r-no-readline.patch
(from rev 357920, sagemath/trunk/r-no-readline.patch)
sagemath/repos/community-x86_64/sagemath-cddlib-094j.patch
(from rev 357920, sagemath/trunk/sagemath-cddlib-094j.patch)
sagemath/repos/community-x86_64/sagemath-detect-igraph.patch
(from rev 357920, sagemath/trunk/sagemath-detect-igraph.patch)
sagemath/repos/community-x86_64/sagemath-eclib-20180710.patch
(from rev 357920, sagemath/trunk/sagemath-eclib-20180710.patch)
sagemath/repos/community-x86_64/sagemath-env.patch
(from rev 357920, sagemath/trunk/sagemath-env.patch)
sagemath/repos/community-x86_64/sagemath-gap-4.8.patch
(from rev 357920, sagemath/trunk/sagemath-gap-4.8.patch)
sagemath/repos/community-x86_64/sagemath-ignore-warnings.patch
(from rev 357920, sagemath/trunk/sagemath-ignore-warnings.patch)
sagemath/repos/community-x86_64/sagemath-lcalc-c++11.patch
(from rev 357920, sagemath/trunk/sagemath-lcalc-c++11.patch)
sagemath/repos/community-x86_64/sagemath-lrs.patch
(from rev 357920, sagemath/trunk/sagemath-lrs.patch)
sagemath/repos/community-x86_64/sagemath-networkx2.patch
(from rev 357920, sagemath/trunk/sagemath-networkx2.patch)
sagemath/repos/community-x86_64/sagemath-python3-notebook.patch
(from rev 357920, sagemath/trunk/sagemath-python3-notebook.patch)
sagemath/repos/community-x86_64/sagemath-scipy-1.0.patch
(from rev 357920, sagemath/trunk/sagemath-scipy-1.0.patch)
sagemath/repos/community-x86_64/sagemath-singular-4.1.1.patch
(from rev 357920, sagemath/trunk/sagemath-singular-4.1.1.patch)
sagemath/repos/community-x86_64/sagemath-threejs.patch
(from rev 357920, sagemath/trunk/sagemath-threejs.patch)
sagemath/repos/community-x86_64/test-optional.patch
(from rev 357920, 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 | 353 ++++++-------
fes02.patch | 114 ++--
jupyter-path.patch | 44 -
latte-count.patch | 142 ++---
package.patch | 76 +-
r-no-readline.patch | 22
sagemath-cddlib-094j.patch | 980 ++++++++++++++++++++++++++++++++++++++
sagemath-detect-igraph.patch | 42 -
sagemath-eclib-20180710.patch | 24
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 +-
20 files changed, 2005 insertions(+), 994 deletions(-)
Deleted: PKGBUILD
===================================================================
--- PKGBUILD 2018-07-12 14:25:43 UTC (rev 357920)
+++ PKGBUILD 2018-07-12 14:26:44 UTC (rev 357921)
@@ -1,173 +0,0 @@
-# Maintainer: Antonio Rojas <arojas at 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()"
-}
Copied: sagemath/repos/community-x86_64/PKGBUILD (from rev 357920, sagemath/trunk/PKGBUILD)
===================================================================
--- PKGBUILD (rev 0)
+++ PKGBUILD 2018-07-12 14:26:44 UTC (rev 357921)
@@ -0,0 +1,180 @@
+# Maintainer: Antonio Rojas <arojas at 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=12
+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"
+ sagemath-cddlib-094j.patch sagemath-eclib-20180710.patch)
+sha256sums=('41ba2c2dde7a02e1bb6880ae875d37ab058567cc26e760efe87eeb12188cd65b'
+ 'b3c5f5c159d72ba7bc2b186b7b0e50a02b1ca60caef49b3857dbaad3da36b6fc'
+ 'c41ae665499c6cd775d40bbe178f8786830b0931ee26bf11ee02f7d83bcc8107'
+ '0b680e674c11c47afa86162d8b49645620b8912722e08133d23357c29ca9310a'
+ '2cad308f8adbb6c54e6603fa22b2f0eb60f6f09248d5d015000c3932ac14f646'
+ '962ce805c87147212b21fc2ab0ac9af9bd0033942c7a6905b9906645b48e8a4f'
+ '18edeafb01cc1ed7270c2dfb41a58717918680c98e8eada1858736acd65d92ba'
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+ 'bfe49f0168fe0824f0eaf4ea793b08d5b3e43c4e3634eb5f664c70644a793a59'
+ '8253730940687992dd29d90d95bea7e2685bb4854db004090c8196ce92859b64'
+ '17397b8e1843b013ef5d2e083369109f0719651edd8ef0c8493cb49e2bc4324a'
+ 'c0f65534a845ba802de6196229159fe67fcc3f72f0cb1ce57d4ae5c9fe10282c'
+ '507bf761df222d1961d53ebeaf8e6a5a3dc2d7b9cb78748d71ed8cb1ee1c4ac6'
+ '5114c912f821900e5bfae1e2cfeb7984de946d0b23e1182b0bf15be1d803dfd0'
+ '6917cb74e50ae965ea8d7c39577e5f0a5068e4b6a67b53fc6f219149a7d06584'
+ 'e24ad879f6b2eb970778fc5e867bcbe0a6d393feca8f11f5cb8d07da1f024be9'
+ '94847fc033fd36bc59217c8484d4cf48d0640ff35bb5ca5ffba88a8158c6dd44'
+ '092a928b77c8bb1e23399f22be39f67797a0065954128b690ead6a09f9ce1e44'
+ '182b0765d58494978bf27628bada8b42c95ef7eb2671b91ddf9c67608560c662')
+
+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
+# Fix build with eclib 20180710
+ patch -p1 -i ../sagemath-eclib-20180710.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
+# port to cddlib 0.94j https://trac.sagemath.org/ticket/25344
+ patch -p1 -i ../sagemath-cddlib-094j.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 2018-07-12 14:25:43 UTC (rev 357920)
+++ fes02.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -1,57 +0,0 @@
-From b1f5e3ecc789db674fe17552812f2d0e2ab84be0 Mon Sep 17 00:00:00 2001
-From: Charles Bouillaguet <charles.bouillaguet at lifl.fr>
-Date: Thu, 19 Sep 2013 10:31:11 +0200
-Subject: updating the libFES binding to match a change in the interface
-
----
- src/sage/libs/fes.pyx | 12 +++++++-----
- 1 file changed, 7 insertions(+), 5 deletions(-)
-
-diff --git a/src/sage/libs/fes.pyx b/src/sage/libs/fes.pyx
-index 40b9c23..d188cf0 100644
---- a/src/sage/libs/fes.pyx
-+++ b/src/sage/libs/fes.pyx
-@@ -1,17 +1,19 @@
- """
--Binding for the FES library.
-+Binding for the libFES library.
-
- Finding solutions of systems of boolean equations by exhaustive
- search, via the fes library. This is usually (much) faster than
- computing a Groebner basis, except in special cases where the latter
- is particularly easy.
-
--The FES library is presently only able to deal with polynomials in 64
-+More information is available at [http://www.lifl.fr/~bouillag/fes].
-+
-+The libFES library is presently only able to deal with polynomials in 64
- variables. Performing a full exhaustive search over 64 variables will
- take a **long** time. The number of variables can be artificially
- reduced to 64 by specializing some of them.
-
--Note that the FES library **requires** at least of the equations to be
-+Note that the libFES library **requires** at least of the equations to be
- non-linear.
-
- AUTHORS:
-@@ -71,7 +73,7 @@ from libc.stdint cimport uint64_t
- cdef extern from "fes_interface.h":
- ctypedef int (*solution_callback_t)(void *, uint64_t)
-
-- void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose)
-+ void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose, int T)
-
-
- 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 357920, sagemath/trunk/fes02.patch)
===================================================================
--- fes02.patch (rev 0)
+++ fes02.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -0,0 +1,57 @@
+From b1f5e3ecc789db674fe17552812f2d0e2ab84be0 Mon Sep 17 00:00:00 2001
+From: Charles Bouillaguet <charles.bouillaguet at lifl.fr>
+Date: Thu, 19 Sep 2013 10:31:11 +0200
+Subject: updating the libFES binding to match a change in the interface
+
+---
+ src/sage/libs/fes.pyx | 12 +++++++-----
+ 1 file changed, 7 insertions(+), 5 deletions(-)
+
+diff --git a/src/sage/libs/fes.pyx b/src/sage/libs/fes.pyx
+index 40b9c23..d188cf0 100644
+--- a/src/sage/libs/fes.pyx
++++ b/src/sage/libs/fes.pyx
+@@ -1,17 +1,19 @@
+ """
+-Binding for the FES library.
++Binding for the libFES library.
+
+ Finding solutions of systems of boolean equations by exhaustive
+ search, via the fes library. This is usually (much) faster than
+ computing a Groebner basis, except in special cases where the latter
+ is particularly easy.
+
+-The FES library is presently only able to deal with polynomials in 64
++More information is available at [http://www.lifl.fr/~bouillag/fes].
++
++The libFES library is presently only able to deal with polynomials in 64
+ variables. Performing a full exhaustive search over 64 variables will
+ take a **long** time. The number of variables can be artificially
+ reduced to 64 by specializing some of them.
+
+-Note that the FES library **requires** at least of the equations to be
++Note that the libFES library **requires** at least of the equations to be
+ non-linear.
+
+ AUTHORS:
+@@ -71,7 +73,7 @@ from libc.stdint cimport uint64_t
+ cdef extern from "fes_interface.h":
+ ctypedef int (*solution_callback_t)(void *, uint64_t)
+
+- void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose)
++ void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose, int T)
+
+
+ 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 2018-07-12 14:25:43 UTC (rev 357920)
+++ jupyter-path.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 357920, sagemath/trunk/jupyter-path.patch)
===================================================================
--- jupyter-path.patch (rev 0)
+++ jupyter-path.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 2018-07-12 14:25:43 UTC (rev 357920)
+++ latte-count.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 357920, sagemath/trunk/latte-count.patch)
===================================================================
--- latte-count.patch (rev 0)
+++ latte-count.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 2018-07-12 14:25:43 UTC (rev 357920)
+++ package.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 357920, sagemath/trunk/package.patch)
===================================================================
--- package.patch (rev 0)
+++ package.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 2018-07-12 14:25:43 UTC (rev 357920)
+++ r-no-readline.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 357920, sagemath/trunk/r-no-readline.patch)
===================================================================
--- r-no-readline.patch (rev 0)
+++ r-no-readline.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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,
Copied: sagemath/repos/community-x86_64/sagemath-cddlib-094j.patch (from rev 357920, sagemath/trunk/sagemath-cddlib-094j.patch)
===================================================================
--- sagemath-cddlib-094j.patch (rev 0)
+++ sagemath-cddlib-094j.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -0,0 +1,980 @@
+diff --git a/src/sage/geometry/polyhedron/backend_cdd.py b/src/sage/geometry/polyhedron/backend_cdd.py
+index 9e0ca53ba7b..8497741b0c4 100644
+--- a/src/sage/geometry/polyhedron/backend_cdd.py
++++ b/src/sage/geometry/polyhedron/backend_cdd.py
+@@ -154,7 +154,9 @@ def _init_from_cdd_input(self, cdd_input_string, cmdline_arg='--all', verbose=Fa
+ ....: [0.62, -1.38, 0.38],[0.144, -1.04, 0.04],
+ ....: [0.1309090909, -1.0290909091, 0.04]]
+ sage: Polyhedron(point_list)
+- A 3-dimensional polyhedron in RDF^3 defined as the convex hull of 14 vertices
++ Traceback (most recent call last):
++ ...
++ ValueError: *Error: Numerical inconsistency is found. Use the GMP exact arithmetic.
+ sage: Polyhedron(point_list, base_ring=QQ)
+ A 3-dimensional polyhedron in QQ^3 defined as the convex hull of 14 vertices
+ """
+@@ -286,7 +288,9 @@ def cdd_adjacencies():
+ else:
+ n_cdd=n;
+ self._V_adjacency_matrix = matrix(ZZ, n, n, 0)
+- expect_in_cddout('begin')
++ if not find_in_cddout('begin'):
++ raise ValueError('Error while parsing cdd output: could not '
++ 'find "begin" after "Vertex graph"')
+ l = cddout.pop(0).split()
+ assert int(l[0]) == n_cdd, "Not enough V-adjacencies in cdd output?"
+ for i in range(n_cdd):
+@@ -309,7 +313,9 @@ def cdd_adjacencies():
+ if find_in_cddout('Facet graph'):
+ n = len(self._Hrepresentation);
+ self._H_adjacency_matrix = matrix(ZZ, n, n, 0)
+- expect_in_cddout('begin')
++ if not find_in_cddout('begin'):
++ raise ValueError('Error while parsing cdd output: could not '
++ 'find "begin" after "Facet graph"')
+ l = cddout.pop(0).split()
+ assert int(l[0]) == n, "Not enough H-adjacencies in cdd output?"
+ for i in range(n):
+---
+diff --git a/src/sage/geometry/hasse_diagram.py b/src/sage/geometry/hasse_diagram.py
+index 9d336ce..c5bff21 100644
+--- a/src/sage/geometry/hasse_diagram.py
++++ b/src/sage/geometry/hasse_diagram.py
+@@ -44,7 +44,7 @@ def Hasse_diagram_from_incidences(atom_to_coatoms, coatom_to_atoms,
+ implementation will just return these two tuples as a tuple;
+
+ - ``required_atoms`` -- list of atoms (default:None). Each
+- non-empty "face" requires at least on of the specified atoms
++ non-empty "face" requires at least one of the specified atoms
+ present. Used to ensure that each face has a vertex.
+
+ - ``key`` -- any hashable value (default: None). It is passed down
+diff --git a/src/sage/geometry/polyhedron/backend_cdd.py b/src/sage/geometry/polyhedron/backend_cdd.py
+index 8497741..85f6632 100644
+--- a/src/sage/geometry/polyhedron/backend_cdd.py
++++ b/src/sage/geometry/polyhedron/backend_cdd.py
+@@ -1,6 +1,19 @@
+-"""
++# -*- coding: utf-8 -*-
++r"""
+ The cdd backend for polyhedral computations
+ """
++# ****************************************************************************
++# Copyright (C) 2011-2014 Volker Braun <vbraun.name at gmail.com>
++# 2018 Timo Kaufmann <timokau at zoho.com>
++# 2018 Julian Rüth <julian.rueth at fsfe.org>
++#
++# This program is free software: you can redistribute it and/or modify
++# it under the terms of the GNU General Public License as published by
++# the Free Software Foundation, either version 2 of the License, or
++# (at your option) any later version.
++# https://www.gnu.org/licenses/
++# ****************************************************************************
++
+ from __future__ import print_function
+ from __future__ import absolute_import
+
+@@ -13,12 +26,10 @@ from .base import Polyhedron_base
+ from .base_QQ import Polyhedron_QQ
+ from .base_RDF import Polyhedron_RDF
+
+-#########################################################################
+ class Polyhedron_cdd(Polyhedron_base):
+- """
++ r"""
+ Base class for the cdd backend.
+ """
+-
+ def _init_from_Vrepresentation(self, vertices, rays, lines, verbose=False):
+ """
+ Construct polyhedron from V-representation data.
+@@ -49,8 +60,30 @@ class Polyhedron_cdd(Polyhedron_base):
+ """
+ from .cdd_file_format import cdd_Vrepresentation
+ s = cdd_Vrepresentation(self._cdd_type, vertices, rays, lines)
+- self._init_from_cdd_input(s, '--reps', verbose)
+-
++ s = self._run_cdd(s, '--redcheck', verbose=verbose)
++ s = self._run_cdd(s, '--repall', verbose=verbose)
++ self._init_from_cdd_output(s)
++ if not self.base_ring().is_exact():
++ # cdd's parser can not handle the full output of --repall, so we
++ # need to extract the first block before we feed it back into cdd
++ s = s.splitlines()
++ s = s[:s.index('end')+1]
++ s = '\n'.join(s)
++ t = self._run_cdd(s, '--rep', verbose=verbose)
++
++ def parse(intro, data):
++ count = int(data[0][0])
++ if count != len(self._cdd_V_to_sage_V):
++ # Upstream claims that nothing can be done about these
++ # cases/that they are features not bugs. Imho, cddlib is
++ # not really suitable for automatic parsing of its output,
++ # the implementation backed by doubles has not really been
++ # optimized for numerical stability, and makes some
++ # somewhat random numerical choices. (But I am not an
++ # expert in that field by any means.) See also
++ # https://github.com/cddlib/cddlib/pull/7.
++ raise ValueError("polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data")
++ Polyhedron_cdd._parse_block(t.splitlines(), 'V-representation', parse)
+
+ def _init_from_Hrepresentation(self, ieqs, eqns, verbose=False):
+ """
+@@ -78,88 +111,32 @@ class Polyhedron_cdd(Polyhedron_base):
+ """
+ from .cdd_file_format import cdd_Hrepresentation
+ s = cdd_Hrepresentation(self._cdd_type, ieqs, eqns)
+- self._init_from_cdd_input(s, '--reps', verbose)
+-
+-
+- def _init_facet_adjacency_matrix(self, verbose=False):
+- """
+- Compute the facet adjacency matrix in case it has not been
+- computed during initialization.
+-
+- INPUT:
+-
+- - ``verbose`` -- boolean (default: ``False``). Whether to print
+- verbose output for debugging purposes.
+-
+- EXAMPLES::
+-
+- sage: p = Polyhedron(vertices=[(0,0),(1,0),(0,1)], backend='cdd', base_ring=QQ)
+- sage: '_H_adjacency_matrix' in p.__dict__
+- False
+- sage: p._init_facet_adjacency_matrix()
+- sage: p._H_adjacency_matrix
+- [0 1 1]
+- [1 0 1]
+- [1 1 0]
+- """
+- self._init_from_cdd_input(self.cdd_Hrepresentation(),
+- '--adjacency', verbose)
+-
+-
+- def _init_vertex_adjacency_matrix(self, verbose=False):
+- """
+- Compute the vertex adjacency matrix in case it has not been
+- computed during initialization.
+-
+- INPUT:
+-
+- - ``verbose`` -- boolean (default: ``False``). Whether to print
+- verbose output for debugging purposes.
+-
+- EXAMPLES::
+-
+- sage: p = Polyhedron(vertices=[(0,0),(1,0),(0,1)], backend='cdd', base_ring=QQ)
+- sage: '_V_adjacency_matrix' in p.__dict__
+- False
+- sage: p._init_vertex_adjacency_matrix()
+- sage: p._V_adjacency_matrix
+- [0 1 1]
+- [1 0 1]
+- [1 1 0]
+- """
+- self._init_from_cdd_input(self.cdd_Vrepresentation(),
+- '--adjacency', verbose)
+-
+-
+- def _init_from_cdd_input(self, cdd_input_string, cmdline_arg='--all', verbose=False):
+- """
+- Internal method: run cdd on a cdd H- or V-representation
+- and initialize ourselves with the output.
+-
+- TESTS::
+-
+- sage: p = Polyhedron(vertices=[[0,0,0],[1,0,0],[0,1,0],[0,0,1]],
+- ....: backend='cdd', base_ring=QQ)
+- sage: from sage.geometry.polyhedron.cdd_file_format import cdd_Vrepresentation
+- sage: s = cdd_Vrepresentation('rational', [[0,0,1],[0,1,0],[1,0,0]], [], [])
+- sage: p._init_from_cdd_input(s)
+- sage: p.dim()
+- 2
+-
+- sage: point_list = [[0.132, -1.028, 0.028],[0.5, 0.5, -1.5],
+- ....: [-0.5, 1.5, -0.5],[0.5, 0.5, 0.5],[1.5, -0.5, -0.5],
+- ....: [-0.332, -0.332, -0.668],[-1.332, 0.668, 0.332],
+- ....: [-0.932, 0.068, 0.932],[-0.38, -0.38, 1.38],
+- ....: [-0.744, -0.12, 1.12],[-0.7781818182, -0.12, 0.9490909091],
+- ....: [0.62, -1.38, 0.38],[0.144, -1.04, 0.04],
+- ....: [0.1309090909, -1.0290909091, 0.04]]
+- sage: Polyhedron(point_list)
+- Traceback (most recent call last):
+- ...
+- ValueError: *Error: Numerical inconsistency is found. Use the GMP exact arithmetic.
+- sage: Polyhedron(point_list, base_ring=QQ)
+- A 3-dimensional polyhedron in QQ^3 defined as the convex hull of 14 vertices
+- """
++ s = self._run_cdd(s, '--redcheck', verbose=verbose)
++ s = self._run_cdd(s, '--repall', verbose=verbose)
++ self._init_from_cdd_output(s)
++ if not self.base_ring().is_exact():
++ # cdd's parser can not handle the full output of --repall, so we
++ # need to extract the first block before we feed it back into cdd
++ s = s.splitlines()
++ s = s[:s.index('end')+1]
++ s = '\n'.join(s)
++ t = self._run_cdd(s, '--rep', verbose=verbose)
++
++ def parse(intro, data):
++ count = int(data[0][0])
++ infinite_count = len([d for d in data[1:] if d[0] == '1' and all(c == '0' for c in d[1:])])
++ if count - infinite_count != len(self._Hrepresentation):
++ # Upstream claims that nothing can be done about these
++ # cases/that they are features not bugs. Imho, cddlib is
++ # not really suitable for automatic parsing of its output,
++ # the implementation backed by doubles has not really been
++ # optimized for numerical stability, and makes some
++ # somewhat random numerical choices. (But I am not an
++ # expert in that field by any means.)
++ raise ValueError("polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data")
++ Polyhedron_cdd._parse_block(t.splitlines(), 'H-representation', parse)
++
++ def _run_cdd(self, cdd_input_string, cmdline_arg, verbose=False):
+ if verbose:
+ print('---- CDD input -----')
+ print(cdd_input_string)
+@@ -175,157 +152,189 @@ class Polyhedron_cdd(Polyhedron_base):
+ if 'Error:' in ans + err:
+ # cdd reports errors on stdout and misc information on stderr
+ raise ValueError(ans.strip())
+- self._init_from_cdd_output(ans)
++ return ans
++
++ @classmethod
++ def _parse_block(cls, cddout, header, parser):
++ r"""
++ Parse a block of cdd data identified by ``header`` by invoking
++ ``parser`` on it.
++
++ EXAMPLES::
+
++ sage: cddout = r'''
++ ....: unrelated
++ ....: HEADER
++ ....: intro 0 1 2
++ ....: begin
++ ....: data 0 1 2
++ ....: data 3 4 5
++ ....: end
++ ....: unrelated
++ ....: '''.splitlines()
++ sage: from sage.geometry.polyhedron.backend_cdd import Polyhedron_cdd
++ sage: def parser(intro, data):
++ ....: print("INTRO:", intro)
++ ....: print("DATA:", data)
++ sage: Polyhedron_cdd._parse_block(cddout, 'HEADER', parser)
++ INTRO: [['intro', '0', '1', '2']]
++ DATA: [['data', '0', '1', '2'], ['data', '3', '4', '5']]
+
+- def _init_from_cdd_output(self, cdd_output_string):
++ """
++ try:
++ block = cddout[cddout.index(header)+1:]
++ except ValueError:
++ # section is missing in the cdd output
++ return
++
++ intro = block[:block.index('begin')]
++ intro = [i.strip().split() for i in intro]
++ data = block[block.index('begin')+1:block.index('end')]
++ data = [d.strip().split() for d in data]
++ parser(intro, data)
++
++ def _init_from_cdd_output(self, cddout):
+ """
+ Initialize ourselves with the output from cdd.
+
+ TESTS::
+
+- sage: from sage.geometry.polyhedron.cdd_file_format import cdd_Vrepresentation
+- sage: s = cdd_Vrepresentation('rational',[[0,0],[1,0],[0,1],[1,1]], [], [])
+- sage: from subprocess import Popen, PIPE
+- sage: cdd_proc = Popen(['cdd_both_reps_gmp', '--all'], stdin=PIPE, stdout=PIPE, stderr=PIPE)
+- sage: ans, err = cdd_proc.communicate(input=s)
+- sage: p = Polyhedron(vertices = [[0,0],[1,0],[0,1],[1,1]], backend='cdd', base_ring=QQ)
+- sage: p._init_from_cdd_output(ans)
++ sage: p = Polyhedron(vertices = [[0,0],[1,0],[0,1],[1,1]], backend='cdd', base_ring=QQ) # indirect doctest
+ sage: p.vertices()
+ (A vertex at (0, 0), A vertex at (1, 0), A vertex at (0, 1), A vertex at (1, 1))
+ """
+- cddout=cdd_output_string.splitlines()
+- suppressed_vertex = False # whether cdd suppressed the vertex in output
+- parent = self.parent()
+-
+- # nested function
+- def expect_in_cddout(expected_string):
+- l = cddout.pop(0).strip()
+- if l!=expected_string:
+- raise ValueError('Error while parsing cdd output: expected "'
+- +expected_string+'" but got "'+l+'".\n')
+- # nested function
+- def cdd_linearities():
+- l = cddout[0].split()
+- if l[0] != "linearity":
+- return []
+- cddout.pop(0)
+- assert len(l) == int(l[1])+2, "Not enough linearities given"
+- return [int(i)-1 for i in l[2:]] # make indices pythonic
+-
+- # nested function
+- def cdd_convert(string, base_ring=self.base_ring()):
+- """
+- Converts the cdd output string to a numerical value.
+- """
+- return [base_ring(x) for x in string.split()]
+-
+- # nested function
+- def find_in_cddout(expected_string):
+- """
+- Find the expected string in a list of strings, and
+- truncates ``cddout`` to start at that point. Returns
+- ``False`` if search fails.
+- """
+- for pos in range(0,len(cddout)):
+- l = cddout[pos].strip();
+- if l==expected_string:
+- # must not assign to cddout in nested function
+- for i in range(0,pos+1):
+- cddout.pop(0)
+- return True
+- return False
+-
+- if find_in_cddout('V-representation'):
++ cddout = cddout.splitlines()
++
++ def parse_indices(count, cdd_indices, cdd_indices_to_sage_indices=None):
++ cdd_indices = map(int, cdd_indices)
++ if cdd_indices_to_sage_indices is None:
++ cdd_indices_to_sage_indices = {i:i-1 for i in cdd_indices}
++ if count < 0:
++ assert cdd_indices_to_sage_indices is not None, "Did not expect negative counts here"
++ count = -count
++ cdd_indices = list(set(cdd_indices_to_sage_indices.keys()) - set(cdd_indices))
++ assert count in [len(cdd_indices), len(cdd_indices) -1]
++ assert count == len(cdd_indices)
++ return [cdd_indices_to_sage_indices[i] for i in cdd_indices if cdd_indices_to_sage_indices[i] is not None]
++
++ def parse_linearities(intro):
++ for entries in intro:
++ if entries and entries.pop(0) == 'linearity':
++ return parse_indices(int(entries.pop(0)), entries)
++ return []
++
++ def parse_H_representation(intro, data):
++ if '_Hrepresentation' in self.__dict__:
++ raise NotImplementedError("can not replace internal representation as this breaks caching")
++ self._Hrepresentation = []
++ # we drop some entries in cdd's output and this changes the numbering; this dict keeps track of that
++ self._cdd_H_to_sage_H = {}
++ equations = parse_linearities(intro)
++ data[0].pop(2) # ignore data type, we know the base ring already
++ count, dimension = map(int, data.pop(0))
++ assert self.ambient_dim() == dimension - 1, "Unexpected ambient dimension"
++ assert len(data) == count, "Unexpected number of lines"
++ for i, line in enumerate(data):
++ coefficients = map(self.base_ring(), line)
++ if coefficients[0] != 0 and all([e == 0 for e in coefficients[1:]]):
++ # cddlib sometimes includes an implicit plane at infinity: 1 0 0 ... 0
++ # We do not care about this entry.
++ self._cdd_H_to_sage_H[i+1] = None
++ continue
++
++ self._cdd_H_to_sage_H[i+1] = len(self._Hrepresentation)
++ if i in equations:
++ self.parent()._make_Equation(self, coefficients)
++ else:
++ self.parent()._make_Inequality(self, coefficients)
++
++ self._Hrepresentation = tuple(self._Hrepresentation)
++
++ def parse_V_representation(intro, data):
++ if '_Vrepresentation' in self.__dict__:
++ raise NotImplementedError("can not replace internal representation as this breaks caching")
+ self._Vrepresentation = []
+- lines = cdd_linearities()
+- expect_in_cddout('begin')
+- l = cddout.pop(0).split()
+- assert self.ambient_dim() == int(l[1])-1, "Different ambient dimension?"
+- suppressed_vertex = True
+- for i in range(int(l[0])):
+- l = cddout.pop(0).strip()
+- l_type = l[0]
+- l = l[1:]
++ # we drop some entries in cdd's output and this changes the numbering; this dict keeps track of that
++ self._cdd_V_to_sage_V = {}
++ lines = parse_linearities(intro)
++ data[0].pop(2) # ignore data type, we know the base ring already
++ count, dimension = map(int, data.pop(0))
++ assert self.ambient_dim() == dimension - 1, "Unexpected ambient dimension"
++ assert len(data) == count, "Unexpected number of lines"
++ has_vertex = False
++ for i, line in enumerate(data):
++ kind = line.pop(0)
++ coefficients = map(self.base_ring(), line)
++ self._cdd_V_to_sage_V[i+1] = len(self._Vrepresentation)
+ if i in lines:
+- parent._make_Line(self, cdd_convert(l));
+- elif l_type == '0':
+- parent._make_Ray(self, cdd_convert(l));
++ self.parent()._make_Line(self, coefficients);
++ elif kind == '0':
++ self.parent()._make_Ray(self, coefficients);
+ else:
+- parent._make_Vertex(self, cdd_convert(l));
+- suppressed_vertex = False
+- if suppressed_vertex and self.n_Vrepresentation()>0:
+- # cdd does not output the vertex if it is only the origin
+- parent._make_Vertex(self, [0] * self.ambient_dim())
++ self.parent()._make_Vertex(self, coefficients)
++ has_vertex = True
++ if len(self._Vrepresentation) and not has_vertex:
++ # when the Polyhedron consists only of lines/rays from the
++ # origin, cddlib does not output the single vertex at the
++ # origin so we have to add it here as the Polyhedron class
++ # expects it to be there.
++ self.parent()._make_Vertex(self, [self.base_ring().zero()] * self.ambient_dim())
+ self._Vrepresentation = tuple(self._Vrepresentation)
+- expect_in_cddout('end')
+
+- if find_in_cddout('H-representation'):
+- self._Hrepresentation = []
+- equations = cdd_linearities()
+- expect_in_cddout('begin')
+- l = cddout.pop(0).split()
+- assert self.ambient_dim() == int(l[1])-1, "Different ambient dimension?"
+- for i in range(int(l[0])):
+- l = cddout.pop(0)
+- if i in equations:
+- parent._make_Equation(self, cdd_convert(l));
+- else:
+- parent._make_Inequality(self, cdd_convert(l));
+- self._Hrepresentation = tuple(self._Hrepresentation)
+- expect_in_cddout('end')
+-
+- # nested function
+- def cdd_adjacencies():
+- l = cddout.pop(0).split()
+- assert l[2] == ':', "Not a line of the adjacency data?"
+- return [int(i)-1 for i in l[3:]]
+-
+- if find_in_cddout('Vertex graph'):
+- n = len(self._Vrepresentation);
+- if suppressed_vertex:
+- n_cdd=n-1;
+- else:
+- n_cdd=n;
+- self._V_adjacency_matrix = matrix(ZZ, n, n, 0)
+- if not find_in_cddout('begin'):
+- raise ValueError('Error while parsing cdd output: could not '
+- 'find "begin" after "Vertex graph"')
+- l = cddout.pop(0).split()
+- assert int(l[0]) == n_cdd, "Not enough V-adjacencies in cdd output?"
+- for i in range(n_cdd):
+- for a in cdd_adjacencies():
+- self._V_adjacency_matrix[i,a] = 1
++ def parse_adjacency(intro, data, N, cdd_indices_to_sage_indices):
++ ret = matrix(ZZ, N, N, 0)
++ cdd_vertex_count = int(data.pop(0)[0])
++ data.reverse()
++ for adjacencies in data:
++ assert adjacencies[2] == ':', "Not a line of adjacency data"
++ cdd_vertex = int(adjacencies[0])
++ count = int(adjacencies[1])
++
++ # cdd sometimes prints implicit adjacencies for the plane at
++ # infinity at the end of the output (even though it's not part
++ # of the V/H representation) so we ignore indices that we do
++ # not know about.
++ if cdd_vertex not in cdd_indices_to_sage_indices:
++ cdd_indices_to_sage_indices[cdd_vertex] = None
++ v = cdd_indices_to_sage_indices[cdd_vertex]
++ if v is None:
++ continue
++ for w in parse_indices(count, adjacencies[3:], cdd_indices_to_sage_indices):
++ if w is None:
++ continue
++ ret[v, w] = 1
++ return ret
++
++ def parse_vertex_adjacency(intro, data):
++ if '_V_adjacency_matrix' in self.__dict__:
++ raise NotImplementedError("can not replace internal representation as this breaks caching")
++ N = len(self._Vrepresentation)
++ self._V_adjacency_matrix = parse_adjacency(intro, data, N, self._cdd_V_to_sage_V)
++ for i, v in enumerate(self._Vrepresentation):
+ # cdd reports that lines are never adjacent to anything.
+- # I disagree, they are adjacent to everything!
+- if self._Vrepresentation[i].is_line():
+- for j in range(n):
++ # we disagree, they are adjacent to everything.
++ if v.is_line():
++ for j in range(len(self._Vrepresentation)):
+ self._V_adjacency_matrix[i,j] = 1
+ self._V_adjacency_matrix[j,i] = 1
+- self._V_adjacency_matrix[i,i] = 0
+- if suppressed_vertex: # cdd implied that there is only one vertex
+- for i in range(n-1):
+- self._V_adjacency_matrix[i,n-1] = 1
+- self._V_adjacency_matrix[n-1,i] = 1
++ self._V_adjacency_matrix[i,i] = 0
+ self._V_adjacency_matrix.set_immutable()
+- expect_in_cddout('end')
+-
+- if find_in_cddout('Facet graph'):
+- n = len(self._Hrepresentation);
+- self._H_adjacency_matrix = matrix(ZZ, n, n, 0)
+- if not find_in_cddout('begin'):
+- raise ValueError('Error while parsing cdd output: could not '
+- 'find "begin" after "Facet graph"')
+- l = cddout.pop(0).split()
+- assert int(l[0]) == n, "Not enough H-adjacencies in cdd output?"
+- for i in range(n):
+- for a in cdd_adjacencies():
+- self._H_adjacency_matrix[i,a] = 1
++ self.vertex_adjacency_matrix.set_cache(self._V_adjacency_matrix)
++
++ def parse_facet_adjacency(intro, data):
++ if '_H_adjacency_matrix' in self.__dict__:
++ raise NotImplementedError("can not replace internal representation as this breaks caching")
++ N = len(self._Hrepresentation)
++ self._H_adjacency_matrix = parse_adjacency(intro, data, N, self._cdd_H_to_sage_H)
+ self._H_adjacency_matrix.set_immutable()
+- expect_in_cddout('end')
++ self.facet_adjacency_matrix.set_cache(self._H_adjacency_matrix)
++
++ Polyhedron_cdd._parse_block(cddout, 'H-representation', parse_H_representation)
++ Polyhedron_cdd._parse_block(cddout, 'V-representation', parse_V_representation)
++ Polyhedron_cdd._parse_block(cddout, 'Facet adjacency', parse_facet_adjacency)
++ Polyhedron_cdd._parse_block(cddout, 'Vertex adjacency', parse_vertex_adjacency)
+
+
+-#########################################################################
+ class Polyhedron_QQ_cdd(Polyhedron_cdd, Polyhedron_QQ):
+ """
+ Polyhedra over QQ with cdd
+@@ -350,7 +359,7 @@ class Polyhedron_QQ_cdd(Polyhedron_cdd, Polyhedron_QQ):
+
+ _cdd_type = 'rational'
+
+- _cdd_executable = 'cdd_both_reps_gmp'
++ _cdd_executable = 'cddexec_gmp'
+
+ def __init__(self, parent, Vrep, Hrep, **kwds):
+ """
+@@ -369,7 +378,6 @@ class Polyhedron_QQ_cdd(Polyhedron_cdd, Polyhedron_QQ):
+ Polyhedron_cdd.__init__(self, parent, Vrep, Hrep, **kwds)
+
+
+-#########################################################################
+ class Polyhedron_RDF_cdd(Polyhedron_cdd, Polyhedron_RDF):
+ """
+ Polyhedra over RDF with cdd
+@@ -392,7 +400,7 @@ class Polyhedron_RDF_cdd(Polyhedron_cdd, Polyhedron_RDF):
+ """
+ _cdd_type = 'real'
+
+- _cdd_executable = 'cdd_both_reps'
++ _cdd_executable = 'cddexec'
+
+ def __init__(self, parent, Vrep, Hrep, **kwds):
+ """
+diff --git a/src/sage/geometry/polyhedron/base.py b/src/sage/geometry/polyhedron/base.py
+index 34f0a3f..a8ca502 100644
+--- a/src/sage/geometry/polyhedron/base.py
++++ b/src/sage/geometry/polyhedron/base.py
+@@ -47,10 +47,9 @@ from sage.categories.sets_cat import EmptySetError
+ # * derive from Polyhedron_base
+ #
+ # * you must implement _init_from_Vrepresentation and
+-# _init_from_Vrepresentationa
++# _init_from_Hrepresentation
+ #
+-# * You might want to override _init_empty_polyhedron,
+-# _init_facet_adjacency_matrix, _init_vertex_adjacency_matrix, and
++# * You might want to override _init_empty_polyhedron and
+ # _make_polyhedron_face.
+ #
+ # * You can of course also override any other method for which you
+diff --git a/src/sage/geometry/polyhedron/library.py b/src/sage/geometry/polyhedron/library.py
+index bbadbb3..2cdc728 100644
+--- a/src/sage/geometry/polyhedron/library.py
++++ b/src/sage/geometry/polyhedron/library.py
+@@ -1100,18 +1100,23 @@ class Polytopes():
+
+ EXAMPLES::
+
+- sage: td = polytopes.truncated_dodecahedron() # long time - 6secs
+- sage: td.f_vector() # long time
++ sage: td = polytopes.truncated_dodecahedron()
++ sage: td.f_vector()
+ (1, 60, 90, 32, 1)
+- sage: td.base_ring() # long time
++ sage: td.base_ring()
+ Number Field in sqrt5 with defining polynomial x^2 - 5
+
+- A much faster implementation using floating point approximations::
++ The faster implementation using floating point approximations does not
++ work unfortunately, see https://github.com/cddlib/cddlib/pull/7 for a
++ detailed discussion of this case::
+
+ sage: td = polytopes.truncated_dodecahedron(exact=False)
+- sage: td.f_vector()
++ Traceback (most recent call last):
++ ...
++ ValueError: polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data
++ sage: td.f_vector() # not tested
+ (1, 60, 90, 32, 1)
+- sage: td.base_ring()
++ sage: td.base_ring() # not tested
+ Real Double Field
+
+ Its faces are 20 triangles and 12 regular decagons::
+@@ -1323,21 +1328,25 @@ class Polytopes():
+ sage: ti.base_ring() # long time
+ Number Field in sqrt5 with defining polynomial x^2 - 5
+
+- A much faster implementation using floating point approximations::
++ The faster implementation using floating point approximations does not
++ work unfortunately::
+
+ sage: ti = polytopes.truncated_icosidodecahedron(exact=False)
+- sage: ti.f_vector()
++ Traceback (most recent call last):
++ ...
++ ValueError: polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data
++ sage: ti.f_vector() # not tested
+ (1, 120, 180, 62, 1)
+- sage: ti.base_ring()
++ sage: ti.base_ring() # not tested
+ Real Double Field
+
+ Its faces are 30 squares, 20 hexagons and 12 decagons::
+
+- sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 4)
++ sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 4) # long time
+ 30
+- sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 6)
++ sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 6) # long time
+ 20
+- sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 10)
++ sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 10) # long time
+ 12
+ """
+ if base_ring is None and exact:
+@@ -1382,26 +1391,32 @@ class Polytopes():
+
+ - ``backend`` -- the backend to use to create the polytope.
+
+- EXAMPLES::
++ EXAMPLES:
++
++ Unfortunately, no polyhedra backend supports the construction of the
++ snub dodecahedron at the moment::
+
+ sage: sd = polytopes.snub_dodecahedron()
+- sage: sd.f_vector()
++ Traceback (most recent call last):
++ ...
++ ValueError: *Error: Numerical inconsistency is found. Use the GMP exact arithmetic.
++ sage: sd.f_vector() # not tested
+ (1, 60, 150, 92, 1)
+- sage: sd.base_ring()
++ sage: sd.base_ring() # not tested
+ Real Double Field
+
+ Its faces are 80 triangles and 12 pentagons::
+
+- sage: sum(1 for f in sd.faces(2) if len(f.vertices()) == 3)
++ sage: sum(1 for f in sd.faces(2) if len(f.vertices()) == 3) # not tested
+ 80
+- sage: sum(1 for f in sd.faces(2) if len(f.vertices()) == 5)
++ sage: sum(1 for f in sd.faces(2) if len(f.vertices()) == 5) # not tested
+ 12
+ """
+ if base_ring is None:
+ base_ring = RDF
+ phi = (1 + base_ring(5).sqrt()) / 2
+- xi = ((phi/2 + (phi - 5/27).sqrt()/2).nth_root(3) +
+- (phi/2 - (phi - 5/27).sqrt()/2).nth_root(3))
++ xi = ((phi/2 + (phi - 5/27).sqrt()/2)**(~ZZ(3)) +
++ (phi/2 - (phi - 5/27).sqrt()/2)**(~ZZ(3)))
+
+ alpha = xi - 1 / xi
+ beta = xi * phi + phi**2 + phi / xi
+@@ -1549,14 +1564,18 @@ class Polytopes():
+ sage: gap # not tested - very long time
+ A 4-dimensional polyhedron in (Number Field in sqrt5 with defining polynomial x^2 - 5)^4 defined as the convex hull of 100 vertices
+
+- Computation with approximated coordinates is much faster::
++ Computation with approximated coordinates would be much faster but is
++ not supported currently::
+
+ sage: gap = polytopes.grand_antiprism(exact=False)
+- sage: gap
++ Traceback (most recent call last):
++ ...
++ ValueError: polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data
++ sage: gap # not tested
+ A 4-dimensional polyhedron in RDF^4 defined as the convex hull of 100 vertices
+- sage: gap.f_vector()
++ sage: gap.f_vector() # not tested
+ (1, 100, 500, 720, 320, 1)
+- sage: len(list(gap.bounded_edges()))
++ sage: len(list(gap.bounded_edges())) # not tested
+ 500
+ """
+ from itertools import product
+diff --git a/src/sage/libs/ppl.pyx b/src/sage/libs/ppl.pyx
+index 5366c74..e318e86 100644
+--- a/src/sage/libs/ppl.pyx
++++ b/src/sage/libs/ppl.pyx
+@@ -110,14 +110,11 @@ basis vectors::
+ sage: C_Polyhedron(gs)
+ A 4-dimensional polyhedron in QQ^5 defined as the convex hull of 120 points
+
+-The above computation (using PPL) finishes without noticeable delay (timeit
+-measures it to be 90 microseconds on sage.math). Below we do the same
+-computation with cddlib, which needs more than 3 seconds on the same
+-hardware::
++The same computation with cddlib which is slightly slower::
+
+ sage: basis = list(range(5))
+ sage: gs = [ tuple(coeff) for coeff in Permutations(basis) ]
+- sage: Polyhedron(vertices=gs, backend='cdd') # long time (3s on sage.math, 2011)
++ sage: Polyhedron(vertices=gs, backend='cdd')
+ A 4-dimensional polyhedron in QQ^5 defined as the convex hull of 120 vertices
+
+ DIFFERENCES VS. C++
+diff --git a/src/sage/categories/finite_coxeter_groups.py b/src/sage/categories/finite_coxeter_groups.py
+index e0b2846..8395895 100644
+--- a/src/sage/categories/finite_coxeter_groups.py
++++ b/src/sage/categories/finite_coxeter_groups.py
+@@ -712,11 +712,15 @@ class FiniteCoxeterGroups(CategoryWithAxiom):
+ If function is too slow, switching the base ring to
+ :class:`RDF` will almost certainly speed things up.
+
+- EXAMPLES::
++ EXAMPLES:
++
++ Unfortunately, an inexact base ring can not always be used::
+
+ sage: W = CoxeterGroup(['H',3], base_ring=RDF)
+ sage: W.permutahedron()
+- A 3-dimensional polyhedron in RDF^3 defined as the convex hull of 120 vertices
++ Traceback (most recent call last):
++ ...
++ ValueError: polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data
+
+ sage: W = CoxeterGroup(['I',7])
+ sage: W.permutahedron()
+diff --git a/src/sage/geometry/polyhedron/backend_cdd.py b/src/sage/geometry/polyhedron/backend_cdd.py
+index 85f6632..aaae546 100644
+--- a/src/sage/geometry/polyhedron/backend_cdd.py
++++ b/src/sage/geometry/polyhedron/backend_cdd.py
+@@ -115,6 +115,10 @@ class Polyhedron_cdd(Polyhedron_base):
+ s = self._run_cdd(s, '--repall', verbose=verbose)
+ self._init_from_cdd_output(s)
+ if not self.base_ring().is_exact():
++ if len(self._Vrepresentation) == 0:
++ # cdd (reasonably) refuses to handle empty polyhedra, so we
++ # skip this check
++ return
+ # cdd's parser can not handle the full output of --repall, so we
+ # need to extract the first block before we feed it back into cdd
+ s = s.splitlines()
+diff --git a/src/sage/graphs/generators/smallgraphs.py b/src/sage/graphs/generators/smallgraphs.py
+index bae02d7..084ed43 100644
+--- a/src/sage/graphs/generators/smallgraphs.py
++++ b/src/sage/graphs/generators/smallgraphs.py
+@@ -4454,14 +4454,19 @@ def TruncatedIcosidodecahedralGraph():
+ and 180 edges. For more information, see the
+ :wikipedia:`Truncated_icosidodecahedron`.
+
+- EXAMPLES::
++ EXAMPLES:
++
++ Unfortunately, this graph can not be constructed currently, due to numerical issues::
+
+ sage: g = graphs.TruncatedIcosidodecahedralGraph(); g
+- Truncated Icosidodecahedron: Graph on 120 vertices
+- sage: g.order(), g.size()
++ Traceback (most recent call last):
++ ...
++ ValueError: *Error: Numerical inconsistency is found. Use the GMP exact arithmetic.
++ sage: g.order(), g.size() # not tested
+ (120, 180)
+ """
+ from sage.geometry.polyhedron.library import polytopes
++ # note that dropping exact=False here makes the construction take forever
+ G = polytopes.icosidodecahedron(exact=False).truncation().graph()
+ G.name("Truncated Icosidodecahedron")
+ return G
+--
+cgit v1.0-1-gd88e
+
+
+From c4048677393f7088d1aa9a2c1392ed95d809d31c Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Julian=20R=C3=BCth?= <julian.rueth at fsfe.org>
+Date: Thu, 14 Jun 2018 12:00:27 +0200
+Subject: Relax cddlib sanity checks
+
+sometimes cddlib's output is useful even if it fails to transform back and forth
+---
+ src/sage/categories/finite_coxeter_groups.py | 9 ++---
+ src/sage/geometry/polyhedron/backend_cdd.py | 6 ++-
+ src/sage/geometry/polyhedron/library.py | 56 +++++++++++++---------------
+ 3 files changed, 33 insertions(+), 38 deletions(-)
+
+diff --git a/src/sage/categories/finite_coxeter_groups.py b/src/sage/categories/finite_coxeter_groups.py
+index 8395895..78a89fd 100644
+--- a/src/sage/categories/finite_coxeter_groups.py
++++ b/src/sage/categories/finite_coxeter_groups.py
+@@ -712,15 +712,14 @@ class FiniteCoxeterGroups(CategoryWithAxiom):
+ If function is too slow, switching the base ring to
+ :class:`RDF` will almost certainly speed things up.
+
+- EXAMPLES:
+-
+- Unfortunately, an inexact base ring can not always be used::
++ EXAMPLES::
+
+ sage: W = CoxeterGroup(['H',3], base_ring=RDF)
+ sage: W.permutahedron()
+- Traceback (most recent call last):
++ doctest:warning
+ ...
+- ValueError: polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data
++ UserWarning: This polyhedron data is numerically complicated; cdd could not convert between the inexact V and H representation without loss of data. The resulting object might show inconsistencies.
++ A 3-dimensional polyhedron in RDF^3 defined as the convex hull of 120 vertices
+
+ sage: W = CoxeterGroup(['I',7])
+ sage: W.permutahedron()
+diff --git a/src/sage/geometry/polyhedron/backend_cdd.py b/src/sage/geometry/polyhedron/backend_cdd.py
+index aaae546..64f3002 100644
+--- a/src/sage/geometry/polyhedron/backend_cdd.py
++++ b/src/sage/geometry/polyhedron/backend_cdd.py
+@@ -82,7 +82,8 @@ class Polyhedron_cdd(Polyhedron_base):
+ # somewhat random numerical choices. (But I am not an
+ # expert in that field by any means.) See also
+ # https://github.com/cddlib/cddlib/pull/7.
+- raise ValueError("polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data")
++ from warnings import warn
++ warn("This polyhedron data is numerically complicated; cdd could not convert between the inexact V and H representation without loss of data. The resulting object might show inconsistencies.")
+ Polyhedron_cdd._parse_block(t.splitlines(), 'V-representation', parse)
+
+ def _init_from_Hrepresentation(self, ieqs, eqns, verbose=False):
+@@ -137,7 +138,8 @@ class Polyhedron_cdd(Polyhedron_base):
+ # optimized for numerical stability, and makes some
+ # somewhat random numerical choices. (But I am not an
+ # expert in that field by any means.)
+- raise ValueError("polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data")
++ from warnings import warn
++ warn("This polyhedron data is numerically complicated; cdd could not convert between the inexact V and H representation without loss of data. The resulting object might show inconsistencies.")
+ Polyhedron_cdd._parse_block(t.splitlines(), 'H-representation', parse)
+
+ def _run_cdd(self, cdd_input_string, cmdline_arg, verbose=False):
+diff --git a/src/sage/geometry/polyhedron/library.py b/src/sage/geometry/polyhedron/library.py
+index 2cdc728..1115978 100644
+--- a/src/sage/geometry/polyhedron/library.py
++++ b/src/sage/geometry/polyhedron/library.py
+@@ -1106,25 +1106,27 @@ class Polytopes():
+ sage: td.base_ring()
+ Number Field in sqrt5 with defining polynomial x^2 - 5
+
+- The faster implementation using floating point approximations does not
+- work unfortunately, see https://github.com/cddlib/cddlib/pull/7 for a
+- detailed discussion of this case::
+-
+- sage: td = polytopes.truncated_dodecahedron(exact=False)
+- Traceback (most recent call last):
+- ...
+- ValueError: polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data
+- sage: td.f_vector() # not tested
+- (1, 60, 90, 32, 1)
+- sage: td.base_ring() # not tested
+- Real Double Field
+-
+ Its faces are 20 triangles and 12 regular decagons::
+
+ sage: sum(1 for f in td.faces(2) if len(f.vertices()) == 3)
+ 20
+ sage: sum(1 for f in td.faces(2) if len(f.vertices()) == 10)
+ 12
++
++ The faster implementation using floating point approximations does not
++ fully work unfortunately, see https://github.com/cddlib/cddlib/pull/7
++ for a detailed discussion of this case::
++
++ sage: td = polytopes.truncated_dodecahedron(exact=False)
++ doctest:warning
++ ...
++ UserWarning: This polyhedron data is numerically complicated; cdd could not convert between the inexact V and H representation without loss of data. The resulting object might show inconsistencies.
++ sage: td.f_vector()
++ Traceback (most recent call last):
++ ...
++ KeyError: ...
++ sage: td.base_ring()
++ Real Double Field
+ """
+ if base_ring is None and exact:
+ from sage.rings.number_field.number_field import QuadraticField
+@@ -1328,25 +1330,21 @@ class Polytopes():
+ sage: ti.base_ring() # long time
+ Number Field in sqrt5 with defining polynomial x^2 - 5
+
+- The faster implementation using floating point approximations does not
+- work unfortunately::
++ The implementation using floating point approximations is much faster::
+
+ sage: ti = polytopes.truncated_icosidodecahedron(exact=False)
+- Traceback (most recent call last):
+- ...
+- ValueError: polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data
+- sage: ti.f_vector() # not tested
++ sage: ti.f_vector()
+ (1, 120, 180, 62, 1)
+- sage: ti.base_ring() # not tested
++ sage: ti.base_ring()
+ Real Double Field
+
+ Its faces are 30 squares, 20 hexagons and 12 decagons::
+
+- sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 4) # long time
++ sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 4)
+ 30
+- sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 6) # long time
++ sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 6)
+ 20
+- sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 10) # long time
++ sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 10)
+ 12
+ """
+ if base_ring is None and exact:
+@@ -1564,18 +1562,14 @@ class Polytopes():
+ sage: gap # not tested - very long time
+ A 4-dimensional polyhedron in (Number Field in sqrt5 with defining polynomial x^2 - 5)^4 defined as the convex hull of 100 vertices
+
+- Computation with approximated coordinates would be much faster but is
+- not supported currently::
++ Computation with approximated coordinates is much faster::
+
+ sage: gap = polytopes.grand_antiprism(exact=False)
+- Traceback (most recent call last):
+- ...
+- ValueError: polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data
+- sage: gap # not tested
++ sage: gap
+ A 4-dimensional polyhedron in RDF^4 defined as the convex hull of 100 vertices
+- sage: gap.f_vector() # not tested
++ sage: gap.f_vector()
+ (1, 100, 500, 720, 320, 1)
+- sage: len(list(gap.bounded_edges())) # not tested
++ sage: len(list(gap.bounded_edges()))
+ 500
+ """
+ from itertools import product
+--
+cgit v1.0-1-gd88e
Deleted: sagemath-detect-igraph.patch
===================================================================
--- sagemath-detect-igraph.patch 2018-07-12 14:25:43 UTC (rev 357920)
+++ sagemath-detect-igraph.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 357920, sagemath/trunk/sagemath-detect-igraph.patch)
===================================================================
--- sagemath-detect-igraph.patch (rev 0)
+++ sagemath-detect-igraph.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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)
+
Copied: sagemath/repos/community-x86_64/sagemath-eclib-20180710.patch (from rev 357920, sagemath/trunk/sagemath-eclib-20180710.patch)
===================================================================
--- sagemath-eclib-20180710.patch (rev 0)
+++ sagemath-eclib-20180710.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -0,0 +1,24 @@
+diff --git a/src/sage/libs/eclib/wrap.cpp b/src/sage/libs/eclib/wrap.cpp
+index 5fd5693b53..d12468faa8 100644
+--- a/src/sage/libs/eclib/wrap.cpp
++++ b/src/sage/libs/eclib/wrap.cpp
+@@ -133,8 +133,8 @@ char* Curvedata_isogeny_class(struct Curvedata* E, int verbose)
+
+
+ int mw_process(struct Curvedata* curve, struct mw* m,
+- const struct bigint* x, const struct bigint* y,
+- const struct bigint* z, int sat)
++ const bigint* x, const bigint* y,
++ const bigint* z, int sat)
+ {
+ Point P(*curve, *x, *y, *z);
+ if (!P.isvalid())
+@@ -188,7 +188,7 @@ int mw_rank(struct mw* m)
+ }
+
+ /* Returns index and unsat long array, which user must deallocate */
+-int mw_saturate(struct mw* m, struct bigint* index, char** unsat,
++int mw_saturate(struct mw* m, bigint* index, char** unsat,
+ long sat_bd, int odd_primes_only)
+ {
+ vector<long> v;
Deleted: sagemath-env.patch
===================================================================
--- sagemath-env.patch 2018-07-12 14:25:43 UTC (rev 357920)
+++ sagemath-env.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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('$SAGE_SHARE','thebe'))
-
- # locate singular shared object
Copied: sagemath/repos/community-x86_64/sagemath-env.patch (from rev 357920, sagemath/trunk/sagemath-env.patch)
===================================================================
--- sagemath-env.patch (rev 0)
+++ sagemath-env.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -0,0 +1,149 @@
+--- src/bin/sage-env.orig 2015-01-06 10:46:04.469687605 +0100
++++ src/bin/sage-env 2015-01-06 10:49:59.547762019 +0100
+@@ -111,41 +111,7 @@
+ }
+
+
+-# New value for SAGE_ROOT: either SAGE_ROOT (if given)
+-# or a guessed value based on pwd.
+-if [ -n "$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('$SAGE_SHARE','thebe'))
+
+ # locate singular shared object
Deleted: sagemath-gap-4.8.patch
===================================================================
--- sagemath-gap-4.8.patch 2018-07-12 14:25:43 UTC (rev 357920)
+++ sagemath-gap-4.8.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -1,31 +0,0 @@
-diff --git a/src/sage/interfaces/gap.py b/src/sage/interfaces/gap.py
-index 177fc1b6eb..51c67bdd09 100644
---- a/src/sage/interfaces/gap.py
-+++ b/src/sage/interfaces/gap.py
-@@ -197,11 +197,11 @@ import string
-
- WORKSPACE = gap_workspace_file()
-
--GAP_BINARY = os.path.join(SAGE_LOCAL, 'bin', 'gap')
-+GAP_BINARY = os.path.join(SAGE_LOCAL, 'bin', 'gap-4.8')
-
- first_try = True
-
--gap_cmd = "gap -r"
-+gap_cmd = "gap-4.8 -r"
- if platform.processor() == 'ia64' and os.path.exists('/usr/bin/prctl'):
- # suppress unaligned access to 0x..., ip=0x... warnings
- gap_cmd = 'prctl --unaligned=silent ' + gap_cmd
-diff --git a/src/sage/libs/gap/util.pyx b/src/sage/libs/gap/util.pyx
-index 7bffcfc00d..51dad178d5 100644
---- a/src/sage/libs/gap/util.pyx
-+++ b/src/sage/libs/gap/util.pyx
-@@ -166,7 +166,7 @@ def gap_root():
- if os.path.exists(GAP_ROOT_DIR):
- return GAP_ROOT_DIR
- print('The gap-4.5.5.spkg (or later) seems to be not installed!')
-- gap_sh = open(os.path.join(SAGE_LOCAL, 'bin', 'gap')).read().splitlines()
-+ gap_sh = open(os.path.join(SAGE_LOCAL, 'bin', 'gap-4.8')).read().splitlines()
- gapdir = filter(lambda dir:dir.strip().startswith('GAP_DIR'), gap_sh)[0]
- gapdir = gapdir.split('"')[1]
- gapdir = gapdir.replace('$SAGE_LOCAL', SAGE_LOCAL)
Copied: sagemath/repos/community-x86_64/sagemath-gap-4.8.patch (from rev 357920, sagemath/trunk/sagemath-gap-4.8.patch)
===================================================================
--- sagemath-gap-4.8.patch (rev 0)
+++ sagemath-gap-4.8.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 2018-07-12 14:25:43 UTC (rev 357920)
+++ sagemath-ignore-warnings.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 <thansen at 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 357920, sagemath/trunk/sagemath-ignore-warnings.patch)
===================================================================
--- sagemath-ignore-warnings.patch (rev 0)
+++ sagemath-ignore-warnings.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 <thansen at 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 2018-07-12 14:25:43 UTC (rev 357920)
+++ sagemath-lcalc-c++11.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 357920, sagemath/trunk/sagemath-lcalc-c++11.patch)
===================================================================
--- sagemath-lcalc-c++11.patch (rev 0)
+++ sagemath-lcalc-c++11.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 2018-07-12 14:25:43 UTC (rev 357920)
+++ sagemath-lrs.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 357920, sagemath/trunk/sagemath-lrs.patch)
===================================================================
--- sagemath-lrs.patch (rev 0)
+++ sagemath-lrs.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 2018-07-12 14:25:43 UTC (rev 357920)
+++ sagemath-networkx2.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 357920, sagemath/trunk/sagemath-networkx2.patch)
===================================================================
--- sagemath-networkx2.patch (rev 0)
+++ sagemath-networkx2.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 2018-07-12 14:25:43 UTC (rev 357920)
+++ sagemath-python3-notebook.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 357920, sagemath/trunk/sagemath-python3-notebook.patch)
===================================================================
--- sagemath-python3-notebook.patch (rev 0)
+++ sagemath-python3-notebook.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 2018-07-12 14:25:43 UTC (rev 357920)
+++ sagemath-scipy-1.0.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 357920, sagemath/trunk/sagemath-scipy-1.0.patch)
===================================================================
--- sagemath-scipy-1.0.patch (rev 0)
+++ sagemath-scipy-1.0.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 2018-07-12 14:25:43 UTC (rev 357920)
+++ sagemath-singular-4.1.1.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 357920, sagemath/trunk/sagemath-singular-4.1.1.patch)
===================================================================
--- sagemath-singular-4.1.1.patch (rev 0)
+++ sagemath-singular-4.1.1.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 2018-07-12 14:25:43 UTC (rev 357920)
+++ sagemath-threejs.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 357920, sagemath/trunk/sagemath-threejs.patch)
===================================================================
--- sagemath-threejs.patch (rev 0)
+++ sagemath-threejs.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 2018-07-12 14:25:43 UTC (rev 357920)
+++ test-optional.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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 357920, sagemath/trunk/test-optional.patch)
===================================================================
--- test-optional.patch (rev 0)
+++ test-optional.patch 2018-07-12 14:26:44 UTC (rev 357921)
@@ -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
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