Date: Monday, September 11, 2017 @ 18:20:56 Author: arojas Revision: 256959
archrelease: copy trunk to community-staging-i686, community-staging-x86_64 Added: sagemath/repos/community-staging-i686/ sagemath/repos/community-staging-i686/PKGBUILD (from rev 256958, sagemath/trunk/PKGBUILD) sagemath/repos/community-staging-i686/env.patch (from rev 256958, sagemath/trunk/env.patch) sagemath/repos/community-staging-i686/fes02.patch (from rev 256958, sagemath/trunk/fes02.patch) sagemath/repos/community-staging-i686/jupyter-path.patch (from rev 256958, sagemath/trunk/jupyter-path.patch) sagemath/repos/community-staging-i686/latte-count.patch (from rev 256958, sagemath/trunk/latte-count.patch) sagemath/repos/community-staging-i686/package.patch (from rev 256958, sagemath/trunk/package.patch) sagemath/repos/community-staging-i686/r-no-readline.patch (from rev 256958, sagemath/trunk/r-no-readline.patch) sagemath/repos/community-staging-i686/sagemath-cython-0.26.patch (from rev 256958, sagemath/trunk/sagemath-cython-0.26.patch) sagemath/repos/community-staging-i686/sagemath-ecl-no-sigfpe.patch (from rev 256958, sagemath/trunk/sagemath-ecl-no-sigfpe.patch) sagemath/repos/community-staging-i686/sagemath-pynac-0.7.11.patch (from rev 256958, sagemath/trunk/sagemath-pynac-0.7.11.patch) sagemath/repos/community-staging-i686/sagemath-python3-notebook.patch (from rev 256958, sagemath/trunk/sagemath-python3-notebook.patch) sagemath/repos/community-staging-i686/test-optional.patch (from rev 256958, sagemath/trunk/test-optional.patch) sagemath/repos/community-staging-x86_64/ sagemath/repos/community-staging-x86_64/PKGBUILD (from rev 256958, sagemath/trunk/PKGBUILD) sagemath/repos/community-staging-x86_64/env.patch (from rev 256958, sagemath/trunk/env.patch) sagemath/repos/community-staging-x86_64/fes02.patch (from rev 256958, sagemath/trunk/fes02.patch) sagemath/repos/community-staging-x86_64/jupyter-path.patch (from rev 256958, sagemath/trunk/jupyter-path.patch) sagemath/repos/community-staging-x86_64/latte-count.patch (from rev 256958, sagemath/trunk/latte-count.patch) sagemath/repos/community-staging-x86_64/package.patch (from rev 256958, sagemath/trunk/package.patch) sagemath/repos/community-staging-x86_64/r-no-readline.patch (from rev 256958, sagemath/trunk/r-no-readline.patch) sagemath/repos/community-staging-x86_64/sagemath-cython-0.26.patch (from rev 256958, sagemath/trunk/sagemath-cython-0.26.patch) sagemath/repos/community-staging-x86_64/sagemath-ecl-no-sigfpe.patch (from rev 256958, sagemath/trunk/sagemath-ecl-no-sigfpe.patch) sagemath/repos/community-staging-x86_64/sagemath-pynac-0.7.11.patch (from rev 256958, sagemath/trunk/sagemath-pynac-0.7.11.patch) sagemath/repos/community-staging-x86_64/sagemath-python3-notebook.patch (from rev 256958, sagemath/trunk/sagemath-python3-notebook.patch) sagemath/repos/community-staging-x86_64/test-optional.patch (from rev 256958, sagemath/trunk/test-optional.patch) ----------------------------------------------------------+ community-staging-i686/PKGBUILD | 161 +++++++++++++ community-staging-i686/env.patch | 93 +++++++ community-staging-i686/fes02.patch | 57 ++++ community-staging-i686/jupyter-path.patch | 22 + community-staging-i686/latte-count.patch | 71 +++++ community-staging-i686/package.patch | 38 +++ community-staging-i686/r-no-readline.patch | 11 community-staging-i686/sagemath-cython-0.26.patch | 26 ++ community-staging-i686/sagemath-ecl-no-sigfpe.patch | 12 community-staging-i686/sagemath-pynac-0.7.11.patch | 21 + community-staging-i686/sagemath-python3-notebook.patch | 27 ++ community-staging-i686/test-optional.patch | 25 ++ community-staging-x86_64/PKGBUILD | 161 +++++++++++++ community-staging-x86_64/env.patch | 93 +++++++ community-staging-x86_64/fes02.patch | 57 ++++ community-staging-x86_64/jupyter-path.patch | 22 + community-staging-x86_64/latte-count.patch | 71 +++++ community-staging-x86_64/package.patch | 38 +++ community-staging-x86_64/r-no-readline.patch | 11 community-staging-x86_64/sagemath-cython-0.26.patch | 26 ++ community-staging-x86_64/sagemath-ecl-no-sigfpe.patch | 12 community-staging-x86_64/sagemath-pynac-0.7.11.patch | 21 + community-staging-x86_64/sagemath-python3-notebook.patch | 27 ++ community-staging-x86_64/test-optional.patch | 25 ++ 24 files changed, 1128 insertions(+) Copied: sagemath/repos/community-staging-i686/PKGBUILD (from rev 256958, sagemath/trunk/PKGBUILD) =================================================================== --- community-staging-i686/PKGBUILD (rev 0) +++ community-staging-i686/PKGBUILD 2017-09-11 18:20:56 UTC (rev 256959) @@ -0,0 +1,161 @@ +# Maintainer: Antonio Rojas <aro...@archlinux.org> +# Contributor: Evgeniy Alekseev <arcanis.arch at gmail dot com> +# Contributor: Daniel Wallace <danielwallace at gtmanfred dot com> +# Contributor: Thomas Dziedzic <gostrc at gmail dot com> +# Contributor: Osman Ugus <ugus11 at yahoo dot com> +# Contributor: Stefan Husmann <stefan-husmann at t-online dot de> +# Special thanks to Nareto for moving the compile from the .install to the PKGBUILD + +pkgbase=sagemath +pkgname=(sagemath sagemath-jupyter) +pkgver=8.0 +pkgrel=3 +pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab" +arch=(i686 x86_64) +url="http://www.sagemath.org" +license=(GPL) +depends=(ipython2 ppl palp brial cliquer maxima-ecl gfan sympow 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 + 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' + 'modular_decomposition: modular decomposition of graphs' 'ffmpeg: to export animations to video' 'imagemagick: to show animations' + 'coxeter3: Coxeter groups implementation' 'cryptominisat5: SAT solver' 'gap-data: for computing Galois groups' + 'lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes' + 'libhomfly: for computing the homfly polynomial of links' 'libbraiding: for computing in braid groups' + 'libfes: exhaustive search of solutions for boolean equations' 'python2-pynormaliz: Normaliz backend for polyhedral computations' + 'latte-integrale: integral point count in polyhedra' 'polymake: polymake backend for polyhedral computations' + 'sirocco: for computing the fundamental group of the complement of a plane curve' + 'three.js: alternative 3D plots engine' 'tachyon: alternative 3D plots engine') +makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc libhomfly libbraiding sirocco + mcqd coxeter3 modular_decomposition bliss-graphs tdlib python2-pkgconfig meataxe libfes) +source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz" + env.patch package.patch latte-count.patch jupyter-path.patch sagemath-python3-notebook.patch test-optional.patch + r-no-readline.patch fes02.patch sagemath-ecl-no-sigfpe.patch sagemath-cython-0.26.patch + sagemath-pynac-0.7.11.patch) +sha256sums=('91df3e303add71616e24b38c04789f66d57ada7b1017e5369e850c42d5e8753d' + 'e0b5b8673300857fde823209a7e90faecf9e754ab812cc5e54297eddc0c79571' + '4a2297e4d9d28f0b3a1f58e1b463e332affcb109eafde44837b1657e309c8212' + 'c6836783251d94c00f0229c1e671de86c58c6c6fb0f6959725317817abc64ca8' + '775051aa9076ebf631c8a291af38b6ec4a13c904740dc9da831641d592d8bcd8' + '27aa73d427d92aeb2c181a233aa3a574a4158cd7dee33832808f69edaec55ea2' + '81d08c6a760f171f3381455b66a6c84789c9f0eefddbe6ca5794075514ad8c3a' + 'ef9f401fa84fe1772af9efee6816643534f2896da4c23b809937b19771bdfbbf' + 'a39da083c038ada797ffc5bedc9ba47455a3f77057d42f86484ae877ef9172ea' + 'c31809f887bf9acc45c5bd9dd30bb93e73601d3efbf3016594c3c1d241731c8a' + '2953ef15d957a2f3304a5584c154bf4777bcb4b461414d3a2178423257539755' + '3e23ff449a5a3a032684287722455633762636b93ecfc35fb00e875c69eff240') + +prepare(){ + cd sage-$pkgver + +# Arch-specific patches +# assume all optional packages are installed + patch -p0 -i ../package.patch +# set env variables + patch -p0 -i ../env.patch +# 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 + +# Upstream patches +# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209 + patch -p1 -i ../fes02.patch +# disable SIGFPE for ecl https://trac.sagemath.org/ticket/22191 + patch -p1 -i ../sagemath-ecl-no-sigfpe.patch +# disable auto_picke for cython 0.26 https://trac.sagemath.org/ticket/23360 + patch -p1 -i ../sagemath-cython-0.26.patch +# fix build with pynac 0.7.11 https://trac.sagemath.org/ticket/23820 + patch -p1 -i ../sagemath-pynac-0.7.11.patch + +# use python2 + sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' -e 's|exec python|exec python2|' -i src/bin/* + sed -e 's|cython {OPT}|cython2 {OPT}|' -e 's|python setup.py|python2 setup.py|' -i src/sage/misc/cython.py + sed -e 's|exec ipython|exec ipython2|' -e 's|cygdb|cygdb2|g' -i src/bin/sage + sed -e "s|'cython'|'cython2'|" -i src/bin/sage-cython + sed -e 's|bin/python|bin/python2|g' -i src/bin/sage-env +} + + +build() { + cd sage-$pkgver + autoreconf -vi + ./configure --prefix=/usr || true + + cd src + export SAGE_LOCAL="/usr" + export SAGE_ROOT="$PWD" + export SAGE_SRC="$PWD" + export CC=gcc + + python2 setup.py build +} + +package_sagemath() { + optdepends+=('sagemath-jupyter: Jupyter kernel') + conflicts=(sage-mathematics) + replaces=(sage-mathematics) + provides=(sage-mathematics) + + cd sage-$pkgver/src + + export SAGE_ROOT="$PWD" + export SAGE_LOCAL="/usr" + export JUPYTER_PATH="$pkgdir"/usr/share/jupyter + + python2 setup.py install --root="$pkgdir" --optimize=1 + + mkdir -p "$pkgdir"/usr/bin + cp bin/sage "$pkgdir"/usr/bin + for _i in arch-env banner cachegrind callgrind cleaner coverage coverageall cython env env-config eval grep grepdoc inline-fortran \ + ipython massif maxima.lisp native-execute notebook num-threads.py omega open preparse python rst2ipynb rst2sws rst2txt run \ + run-cython runtests startuptime.py sws2rst valgrind version.sh + do + cp bin/sage-$_i "$pkgdir"/usr/bin + done + cp bin/math-readline "$pkgdir"/usr/bin + + mkdir -p "$pkgdir"/usr/share/sage + cp -r ext "$pkgdir"/usr/share/sage + +# Create SAGE_SRC, needed for the notebook and help + mkdir "$pkgdir"/usr/share/sage/source + ln -s /usr/share/doc/sage "$pkgdir"/usr/share/sage/source/doc + +# Remove sage_setup + rm -r "$pkgdir"/usr/lib/python2.7/site-packages/sage_setup + +# Split jupyter kernel + rm -r "$pkgdir"/usr/share/jupyter + +# Drop meataxe extension, it segfaults + rm "$pkgdir"/usr/lib/python2.7/site-packages/sage/matrix/matrix_gfpn_dense.* +} + +package_sagemath-jupyter() { + pkgdesc='Jupyter kernel for SageMath' + depends=(sagemath python2-jupyter_client python2-ipywidgets mathjax) + optdepends=('sage-notebook-exporter: convert flask notebooks to Jupyter') + + cd sage-$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-staging-i686/env.patch (from rev 256958, sagemath/trunk/env.patch) =================================================================== --- community-staging-i686/env.patch (rev 0) +++ community-staging-i686/env.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -0,0 +1,93 @@ +--- 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=$NEW_SAGE_ROOT" +-fi ++NEW_SAGE_ROOT="/usr" + + # Display the Sage startup banner, used in src/bin/sage + sage_banner() { +@@ -151,6 +151,7 @@ + export SAGE_ENV_SOURCED=$SAGE_ENV_VERSION + + export SAGE_ROOT="$NEW_SAGE_ROOT" ++export SAGE_LOCAL='/usr' + + # sage-env must know where the Sage's script files are. + +@@ -233,8 +233,9 @@ + export SAGE_EXTCODE="$SAGE_SHARE/sage/ext" + export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed" + export SAGE_LOGS="$SAGE_ROOT/logs/pkgs" +-export SAGE_SRC="$SAGE_ROOT/src" +-export SAGE_DOC_SRC="$SAGE_SRC/doc" ++export GAP_ROOT_DIR="/usr/lib/gap" ++export SAGE_SRC="$SAGE_SHARE/sage/source" ++export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage" + export SAGE_DOC="$SAGE_SHARE/doc/sage" + + if [ -z "${SAGE_ORIG_PATH_SET}" ]; then +@@ -374,6 +337,9 @@ + export SAGE_STARTUP_FILE + fi + ++export LIBMTX="$DOT_SAGE/meataxe" ++[[ -d $LIBMTX ]] || mkdir -p $LIBMTX # Create meataxe data dir ++ + if [ -z "$IPYTHONDIR" ]; then + # We hardcode a version number in the directory name. The idea is + # that we keep using the same version number as long as that is +@@ -468,7 +400,6 @@ + fi + fi + fi +-export MAXIMA_PREFIX="$SAGE_LOCAL" + + PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB + +@@ -629,9 +608,6 @@ + LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH + fi + +-# See trac 7186 -- this is needed if ecl is moved +-ECLDIR="$SAGE_LOCAL/lib/ecl/" && export ECLDIR +- + # Handle parallel building/testing/... + # See Trac Ticket #12016 + # First, figure out the right values for SAGE_NUM_THREADS (default Copied: sagemath/repos/community-staging-i686/fes02.patch (from rev 256958, sagemath/trunk/fes02.patch) =================================================================== --- community-staging-i686/fes02.patch (rev 0) +++ community-staging-i686/fes02.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -0,0 +1,57 @@ +From b1f5e3ecc789db674fe17552812f2d0e2ab84be0 Mon Sep 17 00:00:00 2001 +From: Charles Bouillaguet <charles.bouillag...@lifl.fr> +Date: Thu, 19 Sep 2013 10:31:11 +0200 +Subject: updating the libFES binding to match a change in the interface + +--- + src/sage/libs/fes.pyx | 12 +++++++----- + 1 file changed, 7 insertions(+), 5 deletions(-) + +diff --git a/src/sage/libs/fes.pyx b/src/sage/libs/fes.pyx +index 40b9c23..d188cf0 100644 +--- a/src/sage/libs/fes.pyx ++++ b/src/sage/libs/fes.pyx +@@ -1,17 +1,19 @@ + """ +-Binding for the FES library. ++Binding for the libFES library. + + Finding solutions of systems of boolean equations by exhaustive + search, via the fes library. This is usually (much) faster than + computing a Groebner basis, except in special cases where the latter + is particularly easy. + +-The FES library is presently only able to deal with polynomials in 64 ++More information is available at [http://www.lifl.fr/~bouillag/fes]. ++ ++The libFES library is presently only able to deal with polynomials in 64 + variables. Performing a full exhaustive search over 64 variables will + take a **long** time. The number of variables can be artificially + reduced to 64 by specializing some of them. + +-Note that the FES library **requires** at least of the equations to be ++Note that the libFES library **requires** at least of the equations to be + non-linear. + + AUTHORS: +@@ -71,7 +73,7 @@ from libc.stdint cimport uint64_t + cdef extern from "fes_interface.h": + ctypedef int (*solution_callback_t)(void *, uint64_t) + +- void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose) ++ void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose, int T) + + + include 'sage/ext/interrupt.pxi' #sig_on(), sig_off() +@@ -219,7 +221,7 @@ def exhaustive_search(eqs, max_sols=Infinity, verbose=False): + + # ------- runs the library + sig_on() +- exhaustive_search_wrapper(n, len(eqs), degree, coeffs, report_solution, <void *> internal_state, verbose) ++ exhaustive_search_wrapper(n, len(eqs), degree, coeffs, report_solution, <void *> internal_state, verbose, 0) + sig_off() + + # ------- frees memory occupied by the dense representation of the equations +-- +cgit v1.0-1-gd88e + Copied: sagemath/repos/community-staging-i686/jupyter-path.patch (from rev 256958, sagemath/trunk/jupyter-path.patch) =================================================================== --- community-staging-i686/jupyter-path.patch (rev 0) +++ community-staging-i686/jupyter-path.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -0,0 +1,22 @@ +--- src/sage/repl/ipython_kernel/install.py.orig 2015-10-23 19:23:39.728456590 +0000 ++++ src/sage/repl/ipython_kernel/install.py 2015-10-23 19:24:00.965018978 +0000 +@@ -13,8 +13,7 @@ + SAGE_ROOT, SAGE_DOC, SAGE_LOCAL, SAGE_EXTCODE, + SAGE_VERSION + ) +-from jupyter_core.paths import ENV_JUPYTER_PATH +-JUPYTER_PATH = ENV_JUPYTER_PATH[0] ++JUPYTER_PATH = os.environ.get('JUPYTER_PATH') + + class SageKernelSpec(object): + +@@ -208,7 +208,7 @@ + sage: spec._symlink_resources() # not tested + """ + path = os.path.join(SAGE_EXTCODE, 'notebook-ipython') +- for filename in os.listdir(path): ++ for filename in os.listdir('ext/notebook-ipython'): + self.symlink( + os.path.join(path, filename), + os.path.join(self.kernel_dir, filename) + Copied: sagemath/repos/community-staging-i686/latte-count.patch (from rev 256958, sagemath/trunk/latte-count.patch) =================================================================== --- community-staging-i686/latte-count.patch (rev 0) +++ community-staging-i686/latte-count.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -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 +@@ -228,7 +228,7 @@ 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 +@@ -236,7 +236,7 @@ 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 +@@ -244,7 +244,7 @@ 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 +@@ -252,7 +252,7 @@ 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 +@@ -264,7 +264,7 @@ 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 +@@ -86,7 +86,7 @@ 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: ... +@@ -106,7 +106,7 @@ 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-staging-i686/package.patch (from rev 256958, sagemath/trunk/package.patch) =================================================================== --- community-staging-i686/package.patch (rev 0) +++ community-staging-i686/package.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -0,0 +1,38 @@ +--- src/sage/misc/package.py.orig 2014-11-23 15:58:13.000000000 +0100 ++++ src/sage/misc/package.py 2015-01-22 20:32:25.651383902 +0100 +@@ -343,7 +343,7 @@ + sage: for pkg in list_packages('pip', local=True): + ....: assert not is_package_installed(pkg) + """ +- return any(p.split('-')[0] == package for p in installed_packages(exclude_pip)) ++ return True + + def package_versions(package_type, local=False): + r""" +--- src/sage_setup/optional_extension.py.orig 2016-10-19 18:35:10.092577510 +0000 ++++ src/sage_setup/optional_extension.py 2016-10-19 18:38:13.514765366 +0000 +@@ -21,8 +21,6 @@ + from distutils.extension import Extension + from sage.misc.package import is_package_installed, list_packages + +-all_packages = list_packages(local=True) +- + + class CythonizeExtension(Extension): + """ +@@ -76,14 +74,7 @@ + condition = kwds.pop("condition") + except KeyError: + pkg = kwds.pop("package") +- try: +- pkginfo = all_packages[pkg] +- except KeyError: +- # Might be an installed old-style package +- condition = is_package_installed(pkg) +- else: +- condition = (pkginfo["installed_version"] == pkginfo["remote_version"]) +- ++ condition = True + if condition: + return Extension(*args, **kwds) + else: Copied: sagemath/repos/community-staging-i686/r-no-readline.patch (from rev 256958, sagemath/trunk/r-no-readline.patch) =================================================================== --- community-staging-i686/r-no-readline.patch (rev 0) +++ community-staging-i686/r-no-readline.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -0,0 +1,11 @@ +--- a/src/sage/interfaces/r.py ++++ b/src/sage/interfaces/r.py +@@ -331,7 +331,7 @@ + prompt = '> ', #default, later comes the change + + # This is the command that starts up your program +- command = "R --vanilla --quiet", ++ command = "R --no-readline --vanilla --quiet", + + server=server, + server_tmpdir=server_tmpdir, Copied: sagemath/repos/community-staging-i686/sagemath-cython-0.26.patch (from rev 256958, sagemath/trunk/sagemath-cython-0.26.patch) =================================================================== --- community-staging-i686/sagemath-cython-0.26.patch (rev 0) +++ community-staging-i686/sagemath-cython-0.26.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -0,0 +1,26 @@ +diff --git a/src/setup.py b/src/setup.py +index 2215379..ddca1eb 100755 +--- a/src/setup.py ++++ b/src/setup.py +@@ -95,7 +95,12 @@ library_dirs = [os.path.join(SAGE_LOCAL, "lib")] + + # Manually add -fno-strict-aliasing, which is needed to compile Cython + # and disappears from the default flags if the user has set CFLAGS. +-extra_compile_args = [ "-fno-strict-aliasing" ] ++# ++# Add -DCYTHON_CLINE_IN_TRACEBACK=1 which causes the .c line number to ++# always appear in exception tracebacks (by default, this is a runtime ++# setting in Cython which causes some overhead every time an exception ++# is raised). ++extra_compile_args = ["-fno-strict-aliasing", "-DCYTHON_CLINE_IN_TRACEBACK=1"] + extra_link_args = [ ] + + DEVEL = False +@@ -336,6 +341,7 @@ class sage_build_cython(Command): + + # Cython compiler directives + self.cython_directives = dict( ++ auto_pickle=False, + autotestdict=False, + cdivision=True, + embedsignature=True, Copied: sagemath/repos/community-staging-i686/sagemath-ecl-no-sigfpe.patch (from rev 256958, sagemath/trunk/sagemath-ecl-no-sigfpe.patch) =================================================================== --- community-staging-i686/sagemath-ecl-no-sigfpe.patch (rev 0) +++ community-staging-i686/sagemath-ecl-no-sigfpe.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -0,0 +1,12 @@ +diff --git a/src/sage/libs/ecl.pyx b/src/sage/libs/ecl.pyx +index 1fafb6c..4f730ad 100644 +--- a/src/sage/libs/ecl.pyx ++++ b/src/sage/libs/ecl.pyx +@@ -314,6 +314,7 @@ def init_ecl(): + """)) + safe_funcall_clobj=cl_eval(string_to_object("(symbol-function 'sage-safe-funcall)")) + ++ cl_eval(string_to_object("(si::trap-fpe T NIL)")) + ecl_has_booted = 1 + + cdef cl_object ecl_safe_eval(cl_object form) except NULL: Copied: sagemath/repos/community-staging-i686/sagemath-pynac-0.7.11.patch (from rev 256958, sagemath/trunk/sagemath-pynac-0.7.11.patch) =================================================================== --- community-staging-i686/sagemath-pynac-0.7.11.patch (rev 0) +++ community-staging-i686/sagemath-pynac-0.7.11.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -0,0 +1,21 @@ +--- a/src/sage/libs/pynac/pynac.pxd ++++ b/src/sage/libs/pynac/pynac.pxd +@@ -302,7 +302,6 @@ cdef extern from "sage/libs/pynac/wrap.h": + bint is_a_fderivative "is_a<GiNaC::fderivative>" (GEx e) + bint is_a_function "is_a<GiNaC::function>" (GEx e) + bint is_exactly_a_function "is_exactly_a<GiNaC::function>" (GEx e) +- bint is_a_ncmul "is_a<GiNaC::ncmul>" (GEx e) + + # Arithmetic + int ginac_error() +--- a/src/sage/symbolic/expression.pyx ++++ b/src/sage/symbolic/expression.pyx +@@ -5536,7 +5536,7 @@ cdef class Expression(CommutativeRingElement): + cdef unsigned serial + if is_a_add(self._gobj): + return add_vararg +- elif is_a_mul(self._gobj) or is_a_ncmul(self._gobj): ++ elif is_a_mul(self._gobj): + return mul_vararg + elif is_a_power(self._gobj): + return operator.pow Copied: sagemath/repos/community-staging-i686/sagemath-python3-notebook.patch (from rev 256958, sagemath/trunk/sagemath-python3-notebook.patch) =================================================================== --- community-staging-i686/sagemath-python3-notebook.patch (rev 0) +++ community-staging-i686/sagemath-python3-notebook.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -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 SageNBExport(NotebookJupyter): +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 +@@ -281,7 +281,6 @@ def have_prerequisites(debug=True): + True + """ + try: +- from notebook.notebookapp import NotebookApp + return True + except ImportError: + if debug: + Copied: sagemath/repos/community-staging-i686/test-optional.patch (from rev 256958, sagemath/trunk/test-optional.patch) =================================================================== --- community-staging-i686/test-optional.patch (rev 0) +++ community-staging-i686/test-optional.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -0,0 +1,25 @@ +--- src/sage/doctest/control.py.orig 2016-10-20 19:39:53.714618246 +0200 ++++ src/sage/doctest/control.py 2016-10-20 19:40:15.158049920 +0200 +@@ -307,22 +307,6 @@ + if "all" in options.optional: + # Special case to run all optional tests + options.optional = True +- else: +- # We replace the 'optional' tag by all optional +- # packages for which the installed version matches the +- # latest available version (this implies in particular +- # that the package is actually installed). +- if 'optional' in options.optional: +- options.optional.discard('optional') +- from sage.misc.package import list_packages +- for pkg in list_packages('optional', local=True).values(): +- if pkg['installed_version'] == pkg['remote_version']: +- options.optional.add(pkg['name']) +- +- # Check that all tags are valid +- for o in options.optional: +- if not optionaltag_regex.search(o): +- raise ValueError('invalid optional tag {!r}'.format(o)) + + self.options = options + self.files = args Copied: sagemath/repos/community-staging-x86_64/PKGBUILD (from rev 256958, sagemath/trunk/PKGBUILD) =================================================================== --- community-staging-x86_64/PKGBUILD (rev 0) +++ community-staging-x86_64/PKGBUILD 2017-09-11 18:20:56 UTC (rev 256959) @@ -0,0 +1,161 @@ +# Maintainer: Antonio Rojas <aro...@archlinux.org> +# Contributor: Evgeniy Alekseev <arcanis.arch at gmail dot com> +# Contributor: Daniel Wallace <danielwallace at gtmanfred dot com> +# Contributor: Thomas Dziedzic <gostrc at gmail dot com> +# Contributor: Osman Ugus <ugus11 at yahoo dot com> +# Contributor: Stefan Husmann <stefan-husmann at t-online dot de> +# Special thanks to Nareto for moving the compile from the .install to the PKGBUILD + +pkgbase=sagemath +pkgname=(sagemath sagemath-jupyter) +pkgver=8.0 +pkgrel=3 +pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab" +arch=(i686 x86_64) +url="http://www.sagemath.org" +license=(GPL) +depends=(ipython2 ppl palp brial cliquer maxima-ecl gfan sympow 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 + 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' + 'modular_decomposition: modular decomposition of graphs' 'ffmpeg: to export animations to video' 'imagemagick: to show animations' + 'coxeter3: Coxeter groups implementation' 'cryptominisat5: SAT solver' 'gap-data: for computing Galois groups' + 'lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes' + 'libhomfly: for computing the homfly polynomial of links' 'libbraiding: for computing in braid groups' + 'libfes: exhaustive search of solutions for boolean equations' 'python2-pynormaliz: Normaliz backend for polyhedral computations' + 'latte-integrale: integral point count in polyhedra' 'polymake: polymake backend for polyhedral computations' + 'sirocco: for computing the fundamental group of the complement of a plane curve' + 'three.js: alternative 3D plots engine' 'tachyon: alternative 3D plots engine') +makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc libhomfly libbraiding sirocco + mcqd coxeter3 modular_decomposition bliss-graphs tdlib python2-pkgconfig meataxe libfes) +source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz" + env.patch package.patch latte-count.patch jupyter-path.patch sagemath-python3-notebook.patch test-optional.patch + r-no-readline.patch fes02.patch sagemath-ecl-no-sigfpe.patch sagemath-cython-0.26.patch + sagemath-pynac-0.7.11.patch) +sha256sums=('91df3e303add71616e24b38c04789f66d57ada7b1017e5369e850c42d5e8753d' + 'e0b5b8673300857fde823209a7e90faecf9e754ab812cc5e54297eddc0c79571' + '4a2297e4d9d28f0b3a1f58e1b463e332affcb109eafde44837b1657e309c8212' + 'c6836783251d94c00f0229c1e671de86c58c6c6fb0f6959725317817abc64ca8' + '775051aa9076ebf631c8a291af38b6ec4a13c904740dc9da831641d592d8bcd8' + '27aa73d427d92aeb2c181a233aa3a574a4158cd7dee33832808f69edaec55ea2' + '81d08c6a760f171f3381455b66a6c84789c9f0eefddbe6ca5794075514ad8c3a' + 'ef9f401fa84fe1772af9efee6816643534f2896da4c23b809937b19771bdfbbf' + 'a39da083c038ada797ffc5bedc9ba47455a3f77057d42f86484ae877ef9172ea' + 'c31809f887bf9acc45c5bd9dd30bb93e73601d3efbf3016594c3c1d241731c8a' + '2953ef15d957a2f3304a5584c154bf4777bcb4b461414d3a2178423257539755' + '3e23ff449a5a3a032684287722455633762636b93ecfc35fb00e875c69eff240') + +prepare(){ + cd sage-$pkgver + +# Arch-specific patches +# assume all optional packages are installed + patch -p0 -i ../package.patch +# set env variables + patch -p0 -i ../env.patch +# 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 + +# Upstream patches +# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209 + patch -p1 -i ../fes02.patch +# disable SIGFPE for ecl https://trac.sagemath.org/ticket/22191 + patch -p1 -i ../sagemath-ecl-no-sigfpe.patch +# disable auto_picke for cython 0.26 https://trac.sagemath.org/ticket/23360 + patch -p1 -i ../sagemath-cython-0.26.patch +# fix build with pynac 0.7.11 https://trac.sagemath.org/ticket/23820 + patch -p1 -i ../sagemath-pynac-0.7.11.patch + +# use python2 + sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' -e 's|exec python|exec python2|' -i src/bin/* + sed -e 's|cython {OPT}|cython2 {OPT}|' -e 's|python setup.py|python2 setup.py|' -i src/sage/misc/cython.py + sed -e 's|exec ipython|exec ipython2|' -e 's|cygdb|cygdb2|g' -i src/bin/sage + sed -e "s|'cython'|'cython2'|" -i src/bin/sage-cython + sed -e 's|bin/python|bin/python2|g' -i src/bin/sage-env +} + + +build() { + cd sage-$pkgver + autoreconf -vi + ./configure --prefix=/usr || true + + cd src + export SAGE_LOCAL="/usr" + export SAGE_ROOT="$PWD" + export SAGE_SRC="$PWD" + export CC=gcc + + python2 setup.py build +} + +package_sagemath() { + optdepends+=('sagemath-jupyter: Jupyter kernel') + conflicts=(sage-mathematics) + replaces=(sage-mathematics) + provides=(sage-mathematics) + + cd sage-$pkgver/src + + export SAGE_ROOT="$PWD" + export SAGE_LOCAL="/usr" + export JUPYTER_PATH="$pkgdir"/usr/share/jupyter + + python2 setup.py install --root="$pkgdir" --optimize=1 + + mkdir -p "$pkgdir"/usr/bin + cp bin/sage "$pkgdir"/usr/bin + for _i in arch-env banner cachegrind callgrind cleaner coverage coverageall cython env env-config eval grep grepdoc inline-fortran \ + ipython massif maxima.lisp native-execute notebook num-threads.py omega open preparse python rst2ipynb rst2sws rst2txt run \ + run-cython runtests startuptime.py sws2rst valgrind version.sh + do + cp bin/sage-$_i "$pkgdir"/usr/bin + done + cp bin/math-readline "$pkgdir"/usr/bin + + mkdir -p "$pkgdir"/usr/share/sage + cp -r ext "$pkgdir"/usr/share/sage + +# Create SAGE_SRC, needed for the notebook and help + mkdir "$pkgdir"/usr/share/sage/source + ln -s /usr/share/doc/sage "$pkgdir"/usr/share/sage/source/doc + +# Remove sage_setup + rm -r "$pkgdir"/usr/lib/python2.7/site-packages/sage_setup + +# Split jupyter kernel + rm -r "$pkgdir"/usr/share/jupyter + +# Drop meataxe extension, it segfaults + rm "$pkgdir"/usr/lib/python2.7/site-packages/sage/matrix/matrix_gfpn_dense.* +} + +package_sagemath-jupyter() { + pkgdesc='Jupyter kernel for SageMath' + depends=(sagemath python2-jupyter_client python2-ipywidgets mathjax) + optdepends=('sage-notebook-exporter: convert flask notebooks to Jupyter') + + cd sage-$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-staging-x86_64/env.patch (from rev 256958, sagemath/trunk/env.patch) =================================================================== --- community-staging-x86_64/env.patch (rev 0) +++ community-staging-x86_64/env.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -0,0 +1,93 @@ +--- 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=$NEW_SAGE_ROOT" +-fi ++NEW_SAGE_ROOT="/usr" + + # Display the Sage startup banner, used in src/bin/sage + sage_banner() { +@@ -151,6 +151,7 @@ + export SAGE_ENV_SOURCED=$SAGE_ENV_VERSION + + export SAGE_ROOT="$NEW_SAGE_ROOT" ++export SAGE_LOCAL='/usr' + + # sage-env must know where the Sage's script files are. + +@@ -233,8 +233,9 @@ + export SAGE_EXTCODE="$SAGE_SHARE/sage/ext" + export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed" + export SAGE_LOGS="$SAGE_ROOT/logs/pkgs" +-export SAGE_SRC="$SAGE_ROOT/src" +-export SAGE_DOC_SRC="$SAGE_SRC/doc" ++export GAP_ROOT_DIR="/usr/lib/gap" ++export SAGE_SRC="$SAGE_SHARE/sage/source" ++export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage" + export SAGE_DOC="$SAGE_SHARE/doc/sage" + + if [ -z "${SAGE_ORIG_PATH_SET}" ]; then +@@ -374,6 +337,9 @@ + export SAGE_STARTUP_FILE + fi + ++export LIBMTX="$DOT_SAGE/meataxe" ++[[ -d $LIBMTX ]] || mkdir -p $LIBMTX # Create meataxe data dir ++ + if [ -z "$IPYTHONDIR" ]; then + # We hardcode a version number in the directory name. The idea is + # that we keep using the same version number as long as that is +@@ -468,7 +400,6 @@ + fi + fi + fi +-export MAXIMA_PREFIX="$SAGE_LOCAL" + + PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB + +@@ -629,9 +608,6 @@ + LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH + fi + +-# See trac 7186 -- this is needed if ecl is moved +-ECLDIR="$SAGE_LOCAL/lib/ecl/" && export ECLDIR +- + # Handle parallel building/testing/... + # See Trac Ticket #12016 + # First, figure out the right values for SAGE_NUM_THREADS (default Copied: sagemath/repos/community-staging-x86_64/fes02.patch (from rev 256958, sagemath/trunk/fes02.patch) =================================================================== --- community-staging-x86_64/fes02.patch (rev 0) +++ community-staging-x86_64/fes02.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -0,0 +1,57 @@ +From b1f5e3ecc789db674fe17552812f2d0e2ab84be0 Mon Sep 17 00:00:00 2001 +From: Charles Bouillaguet <charles.bouillag...@lifl.fr> +Date: Thu, 19 Sep 2013 10:31:11 +0200 +Subject: updating the libFES binding to match a change in the interface + +--- + src/sage/libs/fes.pyx | 12 +++++++----- + 1 file changed, 7 insertions(+), 5 deletions(-) + +diff --git a/src/sage/libs/fes.pyx b/src/sage/libs/fes.pyx +index 40b9c23..d188cf0 100644 +--- a/src/sage/libs/fes.pyx ++++ b/src/sage/libs/fes.pyx +@@ -1,17 +1,19 @@ + """ +-Binding for the FES library. ++Binding for the libFES library. + + Finding solutions of systems of boolean equations by exhaustive + search, via the fes library. This is usually (much) faster than + computing a Groebner basis, except in special cases where the latter + is particularly easy. + +-The FES library is presently only able to deal with polynomials in 64 ++More information is available at [http://www.lifl.fr/~bouillag/fes]. ++ ++The libFES library is presently only able to deal with polynomials in 64 + variables. Performing a full exhaustive search over 64 variables will + take a **long** time. The number of variables can be artificially + reduced to 64 by specializing some of them. + +-Note that the FES library **requires** at least of the equations to be ++Note that the libFES library **requires** at least of the equations to be + non-linear. + + AUTHORS: +@@ -71,7 +73,7 @@ from libc.stdint cimport uint64_t + cdef extern from "fes_interface.h": + ctypedef int (*solution_callback_t)(void *, uint64_t) + +- void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose) ++ void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose, int T) + + + include 'sage/ext/interrupt.pxi' #sig_on(), sig_off() +@@ -219,7 +221,7 @@ def exhaustive_search(eqs, max_sols=Infinity, verbose=False): + + # ------- runs the library + sig_on() +- exhaustive_search_wrapper(n, len(eqs), degree, coeffs, report_solution, <void *> internal_state, verbose) ++ exhaustive_search_wrapper(n, len(eqs), degree, coeffs, report_solution, <void *> internal_state, verbose, 0) + sig_off() + + # ------- frees memory occupied by the dense representation of the equations +-- +cgit v1.0-1-gd88e + Copied: sagemath/repos/community-staging-x86_64/jupyter-path.patch (from rev 256958, sagemath/trunk/jupyter-path.patch) =================================================================== --- community-staging-x86_64/jupyter-path.patch (rev 0) +++ community-staging-x86_64/jupyter-path.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -0,0 +1,22 @@ +--- src/sage/repl/ipython_kernel/install.py.orig 2015-10-23 19:23:39.728456590 +0000 ++++ src/sage/repl/ipython_kernel/install.py 2015-10-23 19:24:00.965018978 +0000 +@@ -13,8 +13,7 @@ + SAGE_ROOT, SAGE_DOC, SAGE_LOCAL, SAGE_EXTCODE, + SAGE_VERSION + ) +-from jupyter_core.paths import ENV_JUPYTER_PATH +-JUPYTER_PATH = ENV_JUPYTER_PATH[0] ++JUPYTER_PATH = os.environ.get('JUPYTER_PATH') + + class SageKernelSpec(object): + +@@ -208,7 +208,7 @@ + sage: spec._symlink_resources() # not tested + """ + path = os.path.join(SAGE_EXTCODE, 'notebook-ipython') +- for filename in os.listdir(path): ++ for filename in os.listdir('ext/notebook-ipython'): + self.symlink( + os.path.join(path, filename), + os.path.join(self.kernel_dir, filename) + Copied: sagemath/repos/community-staging-x86_64/latte-count.patch (from rev 256958, sagemath/trunk/latte-count.patch) =================================================================== --- community-staging-x86_64/latte-count.patch (rev 0) +++ community-staging-x86_64/latte-count.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -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 +@@ -228,7 +228,7 @@ 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 +@@ -236,7 +236,7 @@ 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 +@@ -244,7 +244,7 @@ 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 +@@ -252,7 +252,7 @@ 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 +@@ -264,7 +264,7 @@ 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 +@@ -86,7 +86,7 @@ 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: ... +@@ -106,7 +106,7 @@ 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-staging-x86_64/package.patch (from rev 256958, sagemath/trunk/package.patch) =================================================================== --- community-staging-x86_64/package.patch (rev 0) +++ community-staging-x86_64/package.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -0,0 +1,38 @@ +--- src/sage/misc/package.py.orig 2014-11-23 15:58:13.000000000 +0100 ++++ src/sage/misc/package.py 2015-01-22 20:32:25.651383902 +0100 +@@ -343,7 +343,7 @@ + sage: for pkg in list_packages('pip', local=True): + ....: assert not is_package_installed(pkg) + """ +- return any(p.split('-')[0] == package for p in installed_packages(exclude_pip)) ++ return True + + def package_versions(package_type, local=False): + r""" +--- src/sage_setup/optional_extension.py.orig 2016-10-19 18:35:10.092577510 +0000 ++++ src/sage_setup/optional_extension.py 2016-10-19 18:38:13.514765366 +0000 +@@ -21,8 +21,6 @@ + from distutils.extension import Extension + from sage.misc.package import is_package_installed, list_packages + +-all_packages = list_packages(local=True) +- + + class CythonizeExtension(Extension): + """ +@@ -76,14 +74,7 @@ + condition = kwds.pop("condition") + except KeyError: + pkg = kwds.pop("package") +- try: +- pkginfo = all_packages[pkg] +- except KeyError: +- # Might be an installed old-style package +- condition = is_package_installed(pkg) +- else: +- condition = (pkginfo["installed_version"] == pkginfo["remote_version"]) +- ++ condition = True + if condition: + return Extension(*args, **kwds) + else: Copied: sagemath/repos/community-staging-x86_64/r-no-readline.patch (from rev 256958, sagemath/trunk/r-no-readline.patch) =================================================================== --- community-staging-x86_64/r-no-readline.patch (rev 0) +++ community-staging-x86_64/r-no-readline.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -0,0 +1,11 @@ +--- a/src/sage/interfaces/r.py ++++ b/src/sage/interfaces/r.py +@@ -331,7 +331,7 @@ + prompt = '> ', #default, later comes the change + + # This is the command that starts up your program +- command = "R --vanilla --quiet", ++ command = "R --no-readline --vanilla --quiet", + + server=server, + server_tmpdir=server_tmpdir, Copied: sagemath/repos/community-staging-x86_64/sagemath-cython-0.26.patch (from rev 256958, sagemath/trunk/sagemath-cython-0.26.patch) =================================================================== --- community-staging-x86_64/sagemath-cython-0.26.patch (rev 0) +++ community-staging-x86_64/sagemath-cython-0.26.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -0,0 +1,26 @@ +diff --git a/src/setup.py b/src/setup.py +index 2215379..ddca1eb 100755 +--- a/src/setup.py ++++ b/src/setup.py +@@ -95,7 +95,12 @@ library_dirs = [os.path.join(SAGE_LOCAL, "lib")] + + # Manually add -fno-strict-aliasing, which is needed to compile Cython + # and disappears from the default flags if the user has set CFLAGS. +-extra_compile_args = [ "-fno-strict-aliasing" ] ++# ++# Add -DCYTHON_CLINE_IN_TRACEBACK=1 which causes the .c line number to ++# always appear in exception tracebacks (by default, this is a runtime ++# setting in Cython which causes some overhead every time an exception ++# is raised). ++extra_compile_args = ["-fno-strict-aliasing", "-DCYTHON_CLINE_IN_TRACEBACK=1"] + extra_link_args = [ ] + + DEVEL = False +@@ -336,6 +341,7 @@ class sage_build_cython(Command): + + # Cython compiler directives + self.cython_directives = dict( ++ auto_pickle=False, + autotestdict=False, + cdivision=True, + embedsignature=True, Copied: sagemath/repos/community-staging-x86_64/sagemath-ecl-no-sigfpe.patch (from rev 256958, sagemath/trunk/sagemath-ecl-no-sigfpe.patch) =================================================================== --- community-staging-x86_64/sagemath-ecl-no-sigfpe.patch (rev 0) +++ community-staging-x86_64/sagemath-ecl-no-sigfpe.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -0,0 +1,12 @@ +diff --git a/src/sage/libs/ecl.pyx b/src/sage/libs/ecl.pyx +index 1fafb6c..4f730ad 100644 +--- a/src/sage/libs/ecl.pyx ++++ b/src/sage/libs/ecl.pyx +@@ -314,6 +314,7 @@ def init_ecl(): + """)) + safe_funcall_clobj=cl_eval(string_to_object("(symbol-function 'sage-safe-funcall)")) + ++ cl_eval(string_to_object("(si::trap-fpe T NIL)")) + ecl_has_booted = 1 + + cdef cl_object ecl_safe_eval(cl_object form) except NULL: Copied: sagemath/repos/community-staging-x86_64/sagemath-pynac-0.7.11.patch (from rev 256958, sagemath/trunk/sagemath-pynac-0.7.11.patch) =================================================================== --- community-staging-x86_64/sagemath-pynac-0.7.11.patch (rev 0) +++ community-staging-x86_64/sagemath-pynac-0.7.11.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -0,0 +1,21 @@ +--- a/src/sage/libs/pynac/pynac.pxd ++++ b/src/sage/libs/pynac/pynac.pxd +@@ -302,7 +302,6 @@ cdef extern from "sage/libs/pynac/wrap.h": + bint is_a_fderivative "is_a<GiNaC::fderivative>" (GEx e) + bint is_a_function "is_a<GiNaC::function>" (GEx e) + bint is_exactly_a_function "is_exactly_a<GiNaC::function>" (GEx e) +- bint is_a_ncmul "is_a<GiNaC::ncmul>" (GEx e) + + # Arithmetic + int ginac_error() +--- a/src/sage/symbolic/expression.pyx ++++ b/src/sage/symbolic/expression.pyx +@@ -5536,7 +5536,7 @@ cdef class Expression(CommutativeRingElement): + cdef unsigned serial + if is_a_add(self._gobj): + return add_vararg +- elif is_a_mul(self._gobj) or is_a_ncmul(self._gobj): ++ elif is_a_mul(self._gobj): + return mul_vararg + elif is_a_power(self._gobj): + return operator.pow Copied: sagemath/repos/community-staging-x86_64/sagemath-python3-notebook.patch (from rev 256958, sagemath/trunk/sagemath-python3-notebook.patch) =================================================================== --- community-staging-x86_64/sagemath-python3-notebook.patch (rev 0) +++ community-staging-x86_64/sagemath-python3-notebook.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -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 SageNBExport(NotebookJupyter): +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 +@@ -281,7 +281,6 @@ def have_prerequisites(debug=True): + True + """ + try: +- from notebook.notebookapp import NotebookApp + return True + except ImportError: + if debug: + Copied: sagemath/repos/community-staging-x86_64/test-optional.patch (from rev 256958, sagemath/trunk/test-optional.patch) =================================================================== --- community-staging-x86_64/test-optional.patch (rev 0) +++ community-staging-x86_64/test-optional.patch 2017-09-11 18:20:56 UTC (rev 256959) @@ -0,0 +1,25 @@ +--- src/sage/doctest/control.py.orig 2016-10-20 19:39:53.714618246 +0200 ++++ src/sage/doctest/control.py 2016-10-20 19:40:15.158049920 +0200 +@@ -307,22 +307,6 @@ + if "all" in options.optional: + # Special case to run all optional tests + options.optional = True +- else: +- # We replace the 'optional' tag by all optional +- # packages for which the installed version matches the +- # latest available version (this implies in particular +- # that the package is actually installed). +- if 'optional' in options.optional: +- options.optional.discard('optional') +- from sage.misc.package import list_packages +- for pkg in list_packages('optional', local=True).values(): +- if pkg['installed_version'] == pkg['remote_version']: +- options.optional.add(pkg['name']) +- +- # Check that all tags are valid +- for o in options.optional: +- if not optionaltag_regex.search(o): +- raise ValueError('invalid optional tag {!r}'.format(o)) + + self.options = options + self.files = args