sagemath-6.9-2.parabola1: updating version

* switch to atlas-lapack
* add python2-igraph dependency
* move lrs to depends

5 files changed, 19 insertions, 74 deletions

diff --git a/libre/sagemath/PKGBUILD b/libre/sagemath/PKGBUILD
index b6f87e544..ce369c9e8 100644
--- a/libre/sagemath/PKGBUILD
+++ b/libre/sagemath/PKGBUILD
@@ -1,4 +1,4 @@
-# $Id: PKGBUILD 143700 2015-10-11 19:15:19Z arojas $
+# $Id: PKGBUILD 143765 2015-10-12 11:53:35Z arojas $
 # Maintainer (Arch): Evgeniy Alekseev <arcanis.arch at gmail dot com>
 # Maintainer (Arch): Antonio Rojas <arojas@archlinux.org>
 # Contributor (Arch): Daniel Wallace <danielwallace at gtmanfred dot com>
@@ -10,22 +10,21 @@
 # Maintainer: André Silva <emulatorman@parabola.nu>
 
 pkgname=sagemath
-pkgver=6.8
-pkgrel=5.parabola1
+pkgver=6.9
+pkgrel=2.parabola1
 pkgdesc="Free Mathematics Software, free software replacement of Magma, Maple, Mathematica, and Matlab, without nonfree nauty recommendation"
 arch=(i686 x86_64)
 url="http://www.sagemath.org"
 license=(GPL)
-depends=(ipython2 ppl mpfi palp polybori singular libcliquer maxima-ecl gfan sympow tachyon python2-rpy2
-  python2-matplotlib python2-scipy python2-sympy python2-networkx libgap gap flintqs lcalc lrcalc
+depends=(ipython2 atlas-lapack ppl mpfi palp brial singular libcliquer maxima-ecl gfan sympow tachyon python2-rpy2
+  python2-matplotlib python2-scipy python2-sympy python2-networkx python2-igraph libgap gap flintqs lcalc lrcalc lrs
   eclib gmp-ecm zn_poly gd python2-cvxopt pynac linbox gsl 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' 'jmol: 3D plots' 'sage-notebook: Browser-based (flask) notebook interface'
   'sagemath-doc: Documentation and inline help' 'ipython2-notebook: Jupyter notebook interface' 'mathjax: Jupyter notebook interface'
   'coin-or-cbc: COIN backend for numerical computations'
   'buckygen: for generating fullerene graphs' 'plantri: for generating some classes of graphs' 'benzene: for generating fusenes and benzenoids'
-  'modular_decomposition: modular decomposition of graphs'
-  'lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes' 'imagemagick: to show animations'
+  'modular_decomposition: modular decomposition of graphs' 'ffmpeg: to export animations to video' 'imagemagick: to show animations'
   'coxeter3: Coxeter groups implementation' 'cryptominisat: SAT solver' 'arb: floating-point ball arithmetic')
 makedepends=(cython2 boost ratpoints symmetrica fflas-ffpack python2-jinja coin-or-cbc
   mcqd coxeter3 cryptominisat arb modular_decomposition bliss-graphs) # libfes
@@ -36,21 +35,19 @@ source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgv
 # "http://www.sagemath.org/packages/upstream/pexpect/pexpect-2.0.tar.bz2" 
 "http://mirrors.mit.edu/sage/spkg/upstream/pexpect/pexpect-2.0.tar.bz2" 'kernel.json'
 'anal.h' 'package.patch' 'env.patch' 'paths.patch' 'clean.patch' 'skip-check.patch' 
-'pexpect-env.patch' 'pexpect-del.patch' 'disable-fes.patch' 'cython-0.23.patch' 'ipython-4.patch')
-md5sums=('943780ef4460e38f28fefe95e3138981'
+'pexpect-env.patch' 'pexpect-del.patch' 'disable-fes.patch')
+md5sums=('847ad447eaef17b2bc81bb4fae69c190'
          'd9a3e113ed147dcee8f89962a8dccd43'
          '4cee4f96bcd877587e7efc40c20adba7'
          'a906a180d198186a39820b0a2f9a9c63'
-         'f72e544032b1a3f952b7ddafc3a49d63'
-         '843a6cc3b17a1850604593813321418e'
+         '9ba81f717ffd4e20b8b2f2a318307488'
+         '5ebdb6e6ac541f040a39f8d3fd9c8ee1'
          'fd8e3e07f5b7318e6a7200a3c64f5bc2'
          '23e972753be1e5d0f761a7f82a95cebf'
          '5947a420a0b1483f0cbc74c76895789b'
          'a83a3b1bc7fcb7cbf752a83a8311fc42'
          'f333939ea6c41377b66407c81016cee4'
-         '4eb23a3c7363258bc9ba764d6e5512ba'
-         '1b8dfa047115180aa0afbeaf19d97762'
-         '41aa997ad9f00afdc3357b37fc70f0e6')
+         '4eb23a3c7363258bc9ba764d6e5512ba')
 
 prepare(){
   cd sage-$pkgver
@@ -66,8 +63,6 @@ prepare(){
   patch -p0 -i ../env.patch
 # fix paths in python imports
   patch -p0 -i ../paths.patch
-# fix cython linking
-  sed -e "s| atlas(),||" -i src/sage/misc/cython.py
 # don't try to remove installed files
   patch -p0 -i ../clean.patch
 # skip checking build status
@@ -81,16 +76,12 @@ prepare(){
   sed -e 's|graph.hh|bliss/graph.hh|' -i src/sage/graphs/bliss.pyx
 # fix opening docs from Jupyter notebook
   sed -e "s|SageKernelSpec.identifier()|'SageMath'|g" -i src/sage/repl/ipython_kernel/kernel.py
-# fix IPython 4 compatibility
-  patch -p0 -i ../ipython-4.patch
 
 # Upstream patches  
 # fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209
 #  patch -p0 -i "$srcdir"/fes02.patch
 # disable fes module, fails to compile
   patch -p0 -i ../disable-fes.patch
-# fix build with cython 0.23
-  patch -p1 -i "$srcdir"/cython-0.23.patch
 
 # use python2
   sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' -e 's|exec python|exec python2|' -i src/bin/*
@@ -139,7 +130,7 @@ package() {
   export SAGE_LOCAL="$SAGE_ROOT"
   export SAGE_SRC="$PWD"
 
-  python2 setup.py install --root="$pkgdir" --optimize=1
+  python2 setup.py install --root="$pkgdir" --optimize=1 --skip-build
 
   mkdir -p "$pkgdir"/usr/bin
   cp bin/sage "$pkgdir"/usr/bin
diff --git a/libre/sagemath/cython-0.23.patch b/libre/sagemath/cython-0.23.patch
deleted file mode 100644
index 2ae14ad57..000000000
--- a/libre/sagemath/cython-0.23.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff --git a/src/sage/libs/polybori/decl.pxd b/src/sage/libs/polybori/decl.pxd
-index b8fcc6e..6ec4bce 100644
---- a/src/sage/libs/polybori/decl.pxd
-+++ b/src/sage/libs/polybori/decl.pxd
-@@ -10,8 +10,8 @@ cdef extern from "sage/libs/polybori/pb_wrap.h":
-         pbdp_asc        "CTypes::dp_asc"
-         pbblock_dlex    "CTypes::block_dlex"
-         pbblock_dp_asc  "CTypes::block_dp_asc"
--        pbdp            "17"
--        pbblock_dp      "19"
-+        pbdp            "static_cast<COrderEnums::ordercodes>(17)"
-+        pbblock_dp      "static_cast<COrderEnums::ordercodes>(19)"
- 
-     cdef enum comparecodes "CCompareEnums::comparecodes":
-         less_than               "CTypes::less_than"
-
diff --git a/libre/sagemath/env.patch b/libre/sagemath/env.patch
index d1429e35e..b8ca1eb4d 100644
--- a/libre/sagemath/env.patch
+++ b/libre/sagemath/env.patch
@@ -80,7 +80,7 @@
  if [ -z "$SAGE_REPO_ANONYMOUS" ]; then
      SAGE_REPO_ANONYMOUS="git://trac.sagemath.org/sage.git"
      export SAGE_REPO_ANONYMOUS
-@@ -363,25 +318,17 @@
+@@ -363,30 +318,17 @@
      export SAGE_STARTUP_FILE
  fi
  
@@ -101,8 +101,13 @@
 -        PYTHONPATH="$SAGE_PATH:$PYTHONPATH"
 -    fi
 -    PYTHONHOME="$SAGE_LOCAL"
+-    # Set PYTHONNOUSERSITE to avoid picking up non-Sage versions of
+-    # Matplotlib, numpy, etc. See http://trac.sagemath.org/ticket/14243
+-    # and http://trac.sagemath.org/ticket/18955.
+-    PYTHONNOUSERSITE=yes
 -    export PYTHONPATH
 -    export PYTHONHOME
+-    export PYTHONNOUSERSITE
 -fi
 +PYTHONPATH="/usr/lib/sage/site-packages:$PYTHONPATH"
 +PYTHONHOME="$SAGE_ROOT"
diff --git a/libre/sagemath/ipython-4.patch b/libre/sagemath/ipython-4.patch
deleted file mode 100644
index a3b17563d..000000000
--- a/libre/sagemath/ipython-4.patch
+++ /dev/null
@@ -1,35 +0,0 @@
---- src/sage/repl/interpreter.py.orig	2015-08-16 14:57:55.571128473 +0200
-+++ src/sage/repl/interpreter.py	2015-08-16 14:58:06.647849803 +0200
-@@ -104,8 +104,8 @@
- import sys
- from sage.repl.preparse import preparse
- 
--from IPython import Config
--from IPython.utils.traitlets import Bool, Type
-+from traitlets.config.loader import Config
-+from traitlets import Bool, Type
- 
- from sage.env import SAGE_LOCAL
- 
---- src/sage/repl/ipython_kernel/__main__.py.orig  2015-08-22 12:32:58.595605714 +0200
-+++ src/sage/repl/ipython_kernel/__main__.py       2015-08-22 12:33:36.065900491 +0200
-@@ -1,3 +1,3 @@
--from IPython.kernel.zmq.kernelapp import IPKernelApp
-+from ipykernel.kernelapp import IPKernelApp
- from sage.repl.ipython_kernel.kernel import SageKernel
- IPKernelApp.launch_instance(kernel_class=SageKernel)
---- src/sage/repl/ipython_kernel/kernel.py.orig    2015-08-22 12:35:08.709928354 +0200
-+++ src/sage/repl/ipython_kernel/kernel.py 2015-08-22 12:35:31.983429208 +0200
-@@ -15,9 +15,9 @@
- #*****************************************************************************
- 
- import sys
--from IPython.kernel.zmq.ipkernel import IPythonKernel
--from IPython.kernel.zmq.zmqshell import ZMQInteractiveShell
--from IPython.utils.traitlets import Type
-+from ipykernel.ipkernel import IPythonKernel
-+from ipykernel.zmqshell import ZMQInteractiveShell
-+from traitlets import Type
- 
- from sage.env import SAGE_VERSION, SAGE_EXTCODE, SAGE_DOC
- from sage.repl.interpreter import SageNotebookInteractiveShell
diff --git a/libre/sagemath/package.patch b/libre/sagemath/package.patch
index 0b219ddeb..b2a0d2dcf 100644
--- a/libre/sagemath/package.patch
+++ b/libre/sagemath/package.patch
@@ -4,7 +4,7 @@
      Otherwise, installing "pillow" will cause this function to think
      that "pil" is installed, for example.
      """
--    return any(p.split('-')[0] == package for p in install_package())
+-    return any(p.split('-')[0] == package for p in installed_packages())
 +    return True
  
  def package_versions(package_type, local=False):