[arch-commits] Commit in sagemath/repos (24 files)
Antonio Rojas
arojas at archlinux.org
Thu Jan 12 06:54:02 UTC 2017
Date: Thursday, January 12, 2017 @ 06:54:01
Author: arojas
Revision: 206903
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 206902, sagemath/trunk/PKGBUILD)
sagemath/repos/community-staging-i686/cython-sys-path.patch
(from rev 206902, sagemath/trunk/cython-sys-path.patch)
sagemath/repos/community-staging-i686/disable-fes.patch
(from rev 206902, sagemath/trunk/disable-fes.patch)
sagemath/repos/community-staging-i686/ecm-7.patch
(from rev 206902, sagemath/trunk/ecm-7.patch)
sagemath/repos/community-staging-i686/env.patch
(from rev 206902, sagemath/trunk/env.patch)
sagemath/repos/community-staging-i686/increase-rtol.patch
(from rev 206902, sagemath/trunk/increase-rtol.patch)
sagemath/repos/community-staging-i686/is-package-installed.patch
(from rev 206902, sagemath/trunk/is-package-installed.patch)
sagemath/repos/community-staging-i686/jupyter-path.patch
(from rev 206902, sagemath/trunk/jupyter-path.patch)
sagemath/repos/community-staging-i686/package.patch
(from rev 206902, sagemath/trunk/package.patch)
sagemath/repos/community-staging-i686/skip-check.patch
(from rev 206902, sagemath/trunk/skip-check.patch)
sagemath/repos/community-staging-i686/test-optional.patch
(from rev 206902, sagemath/trunk/test-optional.patch)
sagemath/repos/community-staging-x86_64/
sagemath/repos/community-staging-x86_64/PKGBUILD
(from rev 206902, sagemath/trunk/PKGBUILD)
sagemath/repos/community-staging-x86_64/cython-sys-path.patch
(from rev 206902, sagemath/trunk/cython-sys-path.patch)
sagemath/repos/community-staging-x86_64/disable-fes.patch
(from rev 206902, sagemath/trunk/disable-fes.patch)
sagemath/repos/community-staging-x86_64/ecm-7.patch
(from rev 206902, sagemath/trunk/ecm-7.patch)
sagemath/repos/community-staging-x86_64/env.patch
(from rev 206902, sagemath/trunk/env.patch)
sagemath/repos/community-staging-x86_64/increase-rtol.patch
(from rev 206902, sagemath/trunk/increase-rtol.patch)
sagemath/repos/community-staging-x86_64/is-package-installed.patch
(from rev 206902, sagemath/trunk/is-package-installed.patch)
sagemath/repos/community-staging-x86_64/jupyter-path.patch
(from rev 206902, sagemath/trunk/jupyter-path.patch)
sagemath/repos/community-staging-x86_64/package.patch
(from rev 206902, sagemath/trunk/package.patch)
sagemath/repos/community-staging-x86_64/skip-check.patch
(from rev 206902, sagemath/trunk/skip-check.patch)
sagemath/repos/community-staging-x86_64/test-optional.patch
(from rev 206902, sagemath/trunk/test-optional.patch)
-----------------------------------------------------+
community-staging-i686/PKGBUILD | 148 ++++++++
community-staging-i686/cython-sys-path.patch | 10
community-staging-i686/disable-fes.patch | 19 +
community-staging-i686/ecm-7.patch | 79 ++++
community-staging-i686/env.patch | 93 +++++
community-staging-i686/increase-rtol.patch | 37 ++
community-staging-i686/is-package-installed.patch | 328 ++++++++++++++++++
community-staging-i686/jupyter-path.patch | 22 +
community-staging-i686/package.patch | 38 ++
community-staging-i686/skip-check.patch | 22 +
community-staging-i686/test-optional.patch | 25 +
community-staging-x86_64/PKGBUILD | 148 ++++++++
community-staging-x86_64/cython-sys-path.patch | 10
community-staging-x86_64/disable-fes.patch | 19 +
community-staging-x86_64/ecm-7.patch | 79 ++++
community-staging-x86_64/env.patch | 93 +++++
community-staging-x86_64/increase-rtol.patch | 37 ++
community-staging-x86_64/is-package-installed.patch | 328 ++++++++++++++++++
community-staging-x86_64/jupyter-path.patch | 22 +
community-staging-x86_64/package.patch | 38 ++
community-staging-x86_64/skip-check.patch | 22 +
community-staging-x86_64/test-optional.patch | 25 +
22 files changed, 1642 insertions(+)
Copied: sagemath/repos/community-staging-i686/PKGBUILD (from rev 206902, sagemath/trunk/PKGBUILD)
===================================================================
--- community-staging-i686/PKGBUILD (rev 0)
+++ community-staging-i686/PKGBUILD 2017-01-12 06:54:01 UTC (rev 206903)
@@ -0,0 +1,148 @@
+# $Id$
+# Maintainer: Evgeniy Alekseev <arcanis.arch at gmail dot com>
+# Maintainer: Antonio Rojas <arojas at archlinux.org>
+# Contributor: Daniel Wallace <danielwallace at gtmanfred dot com>
+# Contributor: Thomas Dziedzic <gostrc at gmail dot com>
+# Contributor: Osman Ugus <ugus11 at yahoo dot com>
+# Contributor: Stefan Husmann <stefan-husmann at t-online dot de>
+# Special thanks to Nareto for moving the compile from the .install to the PKGBUILD
+
+pkgbase=sagemath
+pkgname=(sagemath sagemath-jupyter)
+pkgver=7.5
+pkgrel=1
+pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab"
+arch=(i686 x86_64)
+url="http://www.sagemath.org"
+license=(GPL)
+depends=(ipython2 ppl palp brial cliquer maxima-ecl gfan sympow tachyon nauty python2-rpy2 python2-fpylll python2-psutil
+ python2-matplotlib python2-scipy python2-sympy python2-networkx python2-pillow python2-future libgap flintqs lcalc lrcalc arb
+ eclib gmp-ecm zn_poly gd python2-cvxopt pynac linbox rubiks pari-galdata pari-seadata-small planarity rankwidth
+ sage-data-combinatorial_designs sage-data-elliptic_curves sage-data-graphs sage-data-polytopes_db sage-data-conway_polynomials)
+optdepends=('cython2: to compile cython code' 'python2-pkgconfig: to compile cython code'
+ 'jmol: 3D plots' 'sage-notebook: Browser-based (flask) notebook interface'
+ 'sagemath-doc: Documentation and inline help' 'python2-igraph: igraph backend for graph theory'
+ 'coin-or-cbc: COIN backend for numerical computations' 'coin-or-csdp: for computing Lovász theta-function of graphs'
+ 'buckygen: for generating fullerene graphs' 'plantri: for generating some classes of graphs' 'benzene: for generating fusenes and benzenoids'
+ 'modular_decomposition: modular decomposition of graphs' 'ffmpeg: to export animations to video' 'imagemagick: to show animations'
+ 'coxeter3: Coxeter groups implementation' 'cryptominisat2: SAT solver' 'gap-data: for computing Galois groups'
+ 'lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes'
+ 'libhomfly: for computing the homfly polynomial of links' 'libbraiding: for computing in braid groups'
+ 'python2-pynormaliz: Normaliz backend for polyhedral computations')
+makedepends=(cython2 boost ratpoints symmetrica fflas-ffpack python2-jinja coin-or-cbc libhomfly libbraiding
+ mcqd coxeter3 cryptominisat2 modular_decomposition bliss-graphs tdlib python2-pkgconfig meataxe) # libfes
+source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"
+ env.patch skip-check.patch cython-sys-path.patch is-package-installed.patch package.patch disable-fes.patch
+ jupyter-path.patch test-optional.patch ecm-7.patch increase-rtol.patch)
+md5sums=('bff1fb8793ebc2934d14cf1efdcfbea3'
+ '784ba3fca83f24ed0bbf62e01fa4e967'
+ '6cafcb381437d4751fd55b25d5090987'
+ '0de8f29a99a48e2ca2a13045f122c386'
+ '409b0a2c520eb33281b5f262afcb6c76'
+ 'ccfd5b1bc4796f414f1531be52504dd7'
+ '06a67e611d10aa2381efe1f08ea4ffd9'
+ '0d88207416dfb98a17bf8886257d9a02'
+ '921017fd2d9dadbb6b602ac0476bfd58'
+ '0c9a57d35de80c2cd418ebec912efbbb'
+ '39d3fded716d2a7ae0ab03e0896b7497')
+
+prepare(){
+ cd sage-$pkgver
+
+# Arch-specific patches
+# assume all optional packages are installed
+ patch -p0 -i ../package.patch
+# set env variables
+ patch -p0 -i ../env.patch
+# skip checking build status
+ patch -p0 -i ../skip-check.patch
+# don't list optional packages when running tests
+ patch -p0 -i ../test-optional.patch
+# set jupyter path
+ patch -p0 -i ../jupyter-path.patch
+# search system paths for cython includes
+ patch -p1 -i ../cython-sys-path.patch
+# fix regressions with ECM 7
+ patch -p1 -i ../ecm-7.patch
+# increase numerical tolerance, needed by scipy 0.18
+ patch -p1 -i ../increase-rtol.patch
+
+# Upstream patches
+# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209
+# patch -p0 -i ../fes02.patch
+# disable fes module, fails to compile
+ patch -p0 -i ../disable-fes.patch
+# replace is_package_installed usage http://trac.sagemath.org/ticket/20377
+ patch -p1 -i ../is-package-installed.patch
+
+# use python2
+ sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' -e 's|exec python|exec python2|' -i src/bin/*
+ sed -e 's|cython {OPT}|cython2 {OPT}|' -e 's|python setup.py|python2 setup.py|' -i src/sage/misc/cython.py
+ sed -e 's|exec ipython|exec ipython2|' -e 's|cygdb|cygdb2|g' -i src/bin/sage
+ sed -e "s|'cython'|'cython2'|" -i src/bin/sage-cython
+ sed -e 's|bin/python|bin/python2|g' -i src/bin/sage-env
+}
+
+
+build() {
+ cd sage-$pkgver/src
+
+ export SAGE_LOCAL="/usr"
+ export SAGE_ROOT="$PWD"
+ export SAGE_SRC="$PWD"
+ export CC=gcc
+
+ python2 setup.py build
+}
+
+package_sagemath() {
+ optdepends+=('sagemath-jupyter: Jupyter kernel')
+ conflicts=(sage-mathematics)
+ replaces=(sage-mathematics)
+ provides=(sage-mathematics)
+
+ cd sage-$pkgver/src
+
+ export SAGE_ROOT="$PWD"
+ export SAGE_LOCAL="/usr"
+ export JUPYTER_PATH="$pkgdir"/usr/share/jupyter
+
+ python2 setup.py install --root="$pkgdir" --optimize=1 --skip-build
+
+ mkdir -p "$pkgdir"/usr/bin
+ cp bin/sage "$pkgdir"/usr/bin
+ for _i in arch-env banner cachegrind callgrind cleaner coverage coverageall cython env eval grep grepdoc inline-fortran ipython \
+ massif maxima.lisp native-execute notebook num-threads.py omega open preparse python rst2sws rst2txt run run-cython runtests startuptime.py \
+ sws2rst valgrind version.sh
+ do
+ cp bin/sage-$_i "$pkgdir"/usr/bin
+ done
+ cp bin/math-readline "$pkgdir"/usr/bin
+
+ mkdir -p "$pkgdir"/usr/share/sage
+ cp -r ext "$pkgdir"/usr/share/sage
+
+# Create SAGE_SRC, needed for the notebook and help
+ mkdir "$pkgdir"/usr/share/sage/source
+ ln -s /usr/share/doc/sage "$pkgdir"/usr/share/sage/source/doc
+
+# Remove sage_setup
+ rm -r "$pkgdir"/usr/lib/python2.7/site-packages/sage_setup
+
+# Split jupyter kernel
+ rm -r "$pkgdir"/usr/share/jupyter
+}
+
+package_sagemath-jupyter() {
+ pkgdesc='Jupyter kernel for SageMath'
+ depends=(sagemath python2-jupyter_client python2-ipywidgets jupyter-notebook mathjax)
+ optdepends=('sage-notebook-exporter: convert flask notebooks to Jupyter')
+
+ cd sage-$pkgver/src
+
+ export SAGE_ROOT="$PWD"
+ export SAGE_LOCAL="/usr"
+ export JUPYTER_PATH="$pkgdir"/usr/share/jupyter
+
+ python2 -c "from sage.repl.ipython_kernel.install import SageKernelSpec; SageKernelSpec.update()"
+}
Copied: sagemath/repos/community-staging-i686/cython-sys-path.patch (from rev 206902, sagemath/trunk/cython-sys-path.patch)
===================================================================
--- community-staging-i686/cython-sys-path.patch (rev 0)
+++ community-staging-i686/cython-sys-path.patch 2017-01-12 06:54:01 UTC (rev 206903)
@@ -0,0 +1,10 @@
+--- sage-7.1/src/setup.py.orig 2016-04-08 16:59:24.691349473 +0000
++++ sage-7.1/src/setup.py 2016-04-08 17:03:03.847153796 +0000
+@@ -414,6 +414,7 @@
+ build_dir=SAGE_CYTHONIZED,
+ force=force,
+ aliases=aliases,
++ include_path=sys.path,
+ compiler_directives={
+ 'autotestdict': False,
+ 'cdivision': True,
Copied: sagemath/repos/community-staging-i686/disable-fes.patch (from rev 206902, sagemath/trunk/disable-fes.patch)
===================================================================
--- community-staging-i686/disable-fes.patch (rev 0)
+++ community-staging-i686/disable-fes.patch 2017-01-12 06:54:01 UTC (rev 206903)
@@ -0,0 +1,19 @@
+--- src/module_list.py.orig 2015-06-07 11:29:30.710612146 +0200
++++ src/module_list.py 2015-06-07 11:30:21.877506106 +0200
+@@ -564,11 +564,11 @@
+ sources = ["sage/libs/ecl.pyx"],
+ libraries = ["ecl"]),
+
+- OptionalExtension("sage.libs.fes",
+- ["sage/libs/fes.pyx"],
+- language = "c",
+- libraries = ['fes'],
+- package = 'fes'),
++# OptionalExtension("sage.libs.fes",
++# ["sage/libs/fes.pyx"],
++# language = "c",
++# libraries = ['fes'],
++# package = 'fes'),
+
+ Extension('sage.libs.flint.flint',
+ sources = ["sage/libs/flint/flint.pyx"],
Copied: sagemath/repos/community-staging-i686/ecm-7.patch (from rev 206902, sagemath/trunk/ecm-7.patch)
===================================================================
--- community-staging-i686/ecm-7.patch (rev 0)
+++ community-staging-i686/ecm-7.patch 2017-01-12 06:54:01 UTC (rev 206903)
@@ -0,0 +1,79 @@
+--- a/src/sage/interfaces/ecm.py.orig 2016-05-16 22:18:03.894827738 +0200
++++ b/src/sage/interfaces/ecm.py 2016-05-16 22:19:14.674904932 +0200
+@@ -140,9 +140,6 @@
+ - ``ve`` -- integer `n`. Verbosely show short (`< n`
+ character) expressions on each loop
+
+- - ``cofdec`` -- boolean. Force cofactor output in decimal
+- (even if expressions are used )
+-
+ - ``B2scale`` -- integer. Multiplies the default B2 value
+
+ - ``go`` -- integer. Preload with group order val, which can
+@@ -395,15 +392,15 @@
+ if m is not None:
+ factor = m.group('factor')
+ primality = m.group('primality')
+- assert primality in ['probable prime', 'composite']
+- result += [(ZZ(factor), primality == 'probable prime')]
++ assert primality in ['prime', 'composite']
++ result += [(ZZ(factor), primality == 'prime')]
+ continue # cofactor on the next line
+ m = self._found_cofactor_re.match(line)
+ if m is not None:
+ cofactor = m.group('cofactor')
+ primality = m.group('primality')
+- assert primality in ['Probable prime', 'Composite']
+- result += [(ZZ(cofactor), primality == 'Probable prime')]
++ assert primality in ['Prime', 'Composite']
++ result += [(ZZ(cofactor), primality == 'Prime')]
+ # assert len(result) == 2
+ return result
+ raise ValueError('failed to parse ECM output')
+@@ -501,7 +498,6 @@
+ if factor_digits is not None:
+ B1 = self.recommended_B1(factor_digits)
+ kwds['one'] = True
+- kwds['cofdec'] = True
+ cmd = self._make_cmd(B1, None, kwds)
+ out = self._run_ecm(cmd, n)
+ return self._parse_output(n, out)
+@@ -828,8 +828,8 @@
+ Step 1 took 12ms
+ Step 2 took 17ms
+ ********** Factor found in step 2: 79792266297612017
+-Found probable prime factor of 17 digits: 79792266297612017
+-Probable prime cofactor 6366805760909027985741435139224233 has 34 digits
++Found prime factor of 17 digits: 79792266297612017
++Prime cofactor 6366805760909027985741435139224233 has 34 digits
+ """
+
+ TEST_ECM_OUTPUT_2 = """
+@@ -839,8 +839,8 @@
+ Step 1 took 2ms
+ Step 2 took 3ms
+ ********** Factor found in step 2: 179424673
+-Found probable prime factor of 9 digits: 179424673
+-Probable prime cofactor 179424673 has 9 digits
++Found prime factor of 9 digits: 179424673
++Prime cofactor 179424673 has 9 digits
+ """
+
+ TEST_ECM_OUTPUT_3 = """
+@@ -858,7 +858,7 @@
+ Step 1 took 5ms
+ Step 2 took 4ms
+ ********** Factor found in step 2: 197002597249
+-Found probable prime factor of 12 digits: 197002597249
++Found prime factor of 12 digits: 197002597249
+ Composite cofactor 339872432034468861533158743041639097889948066859 has 48 digits
+ """
+
+@@ -870,5 +870,5 @@
+ Step 2 took 2ms
+ ********** Factor found in step 2: 265748496095531068869578877937
+ Found composite factor of 30 digits: 265748496095531068869578877937
+-Probable prime cofactor 251951573867253012259144010843 has 30 digits
++Prime cofactor 251951573867253012259144010843 has 30 digits
+ """
+
Copied: sagemath/repos/community-staging-i686/env.patch (from rev 206902, sagemath/trunk/env.patch)
===================================================================
--- community-staging-i686/env.patch (rev 0)
+++ community-staging-i686/env.patch 2017-01-12 06:54:01 UTC (rev 206903)
@@ -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
+@@ -110,41 +110,7 @@
+ }
+
+
+-# New value for SAGE_ROOT: either SAGE_ROOT (if given)
+-# or a guessed value based on pwd.
+-if [ -n "$SAGE_ROOT" ]; then
+- NEW_SAGE_ROOT="$SAGE_ROOT"
+-elif [ -f sage -a -d build ]; then
+- NEW_SAGE_ROOT="."
+-elif [ -f ../../sage -a -d ../../build ]; then
+- NEW_SAGE_ROOT="../.."
+-else
+- # No idea what SAGE_ROOT should be...
+- echo >&2 "Error: You must set the SAGE_ROOT environment variable or run this"
+- echo >&2 "script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory."
+- return 1
+-fi
+-
+-# Make NEW_SAGE_ROOT absolute
+-NEW_SAGE_ROOT=`cd "$NEW_SAGE_ROOT" && pwd -P`
+-
+-# Sanity check NEW_SAGE_ROOT
+-if [ -f "$NEW_SAGE_ROOT/sage" -a -d "$NEW_SAGE_ROOT/build" ]; then
+- :
+-else
+- echo >&2 "Error: SAGE_ROOT is set to a bad value:"
+- echo >&2 "SAGE_ROOT=$SAGE_ROOT"
+- echo >&2 "You must correct it or erase it and run this script from the SAGE_ROOT"
+- echo >&2 "or SAGE_ROOT/local/bin/ directory."
+- return 1
+-fi
+-
+-# Warn if NEW_SAGE_ROOT does not equal the old SAGE_ROOT
+-if [ "$SAGE_ROOT" != "$NEW_SAGE_ROOT" -a -n "$SAGE_ROOT" ]; then
+- echo >&2 "Warning: overwriting SAGE_ROOT environment variable:"
+- echo >&2 "Old SAGE_ROOT=$SAGE_ROOT"
+- echo >&2 "New SAGE_ROOT=$NEW_SAGE_ROOT"
+-fi
++NEW_SAGE_ROOT="/usr"
+
+ # Display the Sage startup banner, used in src/bin/sage
+ sage_banner() {
+@@ -187,7 +187,7 @@
+
+ # SAGE_LOCAL is the installation prefix and can be customized
+ if [ -z "$SAGE_LOCAL" ]; then
+- export SAGE_LOCAL="$SAGE_ROOT/local"
++ export SAGE_LOCAL="/usr"
+ fi
+
+ # sage-env must know where the Sage's script files are
+@@ -233,8 +233,8 @@
+ 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="$SAGE_SRC/doc"
++export SAGE_SRC="$SAGE_SHARE/sage/source"
++export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage"
+ export SAGE_DOC="$SAGE_SHARE/doc/sage"
+
+ if [ -z "${SAGE_ORIG_PATH_SET}" ]; then
+@@ -374,6 +337,9 @@
+ export SAGE_STARTUP_FILE
+ fi
+
++export LIBMTX="$DOT_SAGE/meataxe"
++[[ -d $LIBMTX ]] || mkdir $LIBMTX # Create meataxe data dir
++
+ if [ -z "$IPYTHONDIR" ]; then
+ # We hardcode a version number in the directory name. The idea is
+ # that we keep using the same version number as long as that is
+@@ -468,7 +400,6 @@
+ fi
+ fi
+ fi
+-export MAXIMA_PREFIX="$SAGE_LOCAL"
+
+ PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB
+
+@@ -629,9 +608,6 @@
+ LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH
+ fi
+
+-# See trac 7186 -- this is needed if ecl is moved
+-ECLDIR="$SAGE_LOCAL/lib/ecl/" && export ECLDIR
+-
+ # Handle parallel building/testing/...
+ # See Trac Ticket #12016
+ # First, figure out the right values for SAGE_NUM_THREADS (default
Copied: sagemath/repos/community-staging-i686/increase-rtol.patch (from rev 206902, sagemath/trunk/increase-rtol.patch)
===================================================================
--- community-staging-i686/increase-rtol.patch (rev 0)
+++ community-staging-i686/increase-rtol.patch 2017-01-12 06:54:01 UTC (rev 206903)
@@ -0,0 +1,37 @@
+diff -ru sage-7.3.orig/src/sage/coding/code_bounds.py sage-7.3/src/sage/coding/code_bounds.py
+--- sage-7.3.orig/src/sage/coding/code_bounds.py 2016-08-05 20:26:10.033204091 +0200
++++ sage-7.3/src/sage/coding/code_bounds.py 2016-08-05 20:32:27.276579565 +0200
+@@ -554,7 +554,7 @@
+ if q < 2: # Here we check that q is actually at least 2
+ raise ValueError("The value q must be an integer greater than 1")
+
+- eps = 4.5e-16 # find_root has about this as the default xtol
++ eps = 4.5e-15 # find_root has about this as the default xtol
+ ymax = 1 - 1/q
+ if x <= eps:
+ return 0
+diff -ru sage-7.3.orig/src/sage/numerical/optimize.py sage-7.3/src/sage/numerical/optimize.py
+--- sage-7.3.orig/src/sage/numerical/optimize.py 2016-08-05 20:26:10.816536625 +0200
++++ sage-7.3/src/sage/numerical/optimize.py 2016-08-05 20:32:21.449907130 +0200
+@@ -15,7 +15,7 @@
+ from sage.rings.real_double import RDF
+
+
+-def find_root(f, a, b, xtol=10e-13, rtol=4.5e-16, maxiter=100, full_output=False):
++def find_root(f, a, b, xtol=10e-13, rtol=4.5e-15, maxiter=100, full_output=False):
+ """
+ Numerically find a root of ``f`` on the closed interval `[a,b]`
+ (or `[b,a]`) if possible, where ``f`` is a function in the one variable.
+diff -ru sage-7.3.orig/src/sage/symbolic/expression.pyx sage-7.3/src/sage/symbolic/expression.pyx
+--- sage-7.3.orig/src/sage/symbolic/expression.pyx 2016-08-05 20:26:11.333202767 +0200
++++ sage-7.3/src/sage/symbolic/expression.pyx 2016-08-05 20:32:14.236566826 +0200
+@@ -10884,7 +10884,7 @@
+ ret = ret[0]
+ return ret
+
+- def find_root(self, a, b, var=None, xtol=10e-13, rtol=4.5e-16, maxiter=100, full_output=False):
++ def find_root(self, a, b, var=None, xtol=10e-13, rtol=4.5e-15, maxiter=100, full_output=False):
+ """
+ Numerically find a root of self on the closed interval [a,b] (or
+ [b,a]) if possible, where self is a function in the one variable.
+
Copied: sagemath/repos/community-staging-i686/is-package-installed.patch (from rev 206902, sagemath/trunk/is-package-installed.patch)
===================================================================
--- community-staging-i686/is-package-installed.patch (rev 0)
+++ community-staging-i686/is-package-installed.patch 2017-01-12 06:54:01 UTC (rev 206903)
@@ -0,0 +1,328 @@
+diff --git a/src/sage/databases/cremona.py b/src/sage/databases/cremona.py
+index 0a5f794..2969d92 100644
+--- a/src/sage/databases/cremona.py
++++ b/src/sage/databases/cremona.py
+@@ -53,7 +53,6 @@ from sage.misc.prandom import randint
+
+ import sage.schemes.elliptic_curves.constructor as elliptic
+ from .sql_db import SQLDatabase, verify_column
+-from sage.misc.package import is_package_installed
+ from sage.env import SAGE_SHARE
+ from sage.misc.all import walltime
+
+@@ -824,7 +823,7 @@ class MiniCremonaDatabase(SQLDatabase):
+ if N < self.largest_conductor():
+ message = "There is no elliptic curve with label " + label \
+ + " in the database"
+- elif is_package_installed('database_cremona_ellcurve'):
++ elif os.path.isfile(os.path.join(SAGE_SHARE, "cremona", "cremona.db")):
+ message = "There is no elliptic curve with label " + label \
+ + " in the currently available databases"
+ else:
+@@ -1673,7 +1672,7 @@ def CremonaDatabase(name=None,mini=None,set_global=None):
+ if name is None and not set_global:
+ return _db
+ if set_global and name is None:
+- if is_package_installed('database_cremona_ellcurve'):
++ if os.path.isfile(os.path.join(SAGE_SHARE, "cremona", "cremona.db")):
+ name = 'cremona'
+ else:
+ name = 'cremona mini'
+diff --git a/src/sage/game_theory/normal_form_game.py b/src/sage/game_theory/normal_form_game.py
+index b917d2a..80fb20c 100644
+--- a/src/sage/game_theory/normal_form_game.py
++++ b/src/sage/game_theory/normal_form_game.py
+@@ -614,8 +614,9 @@ from sage.rings.all import QQ
+ from sage.structure.sage_object import SageObject
+ from sage.matrix.constructor import matrix
+ from sage.matrix.constructor import vector
+-from sage.misc.package import is_package_installed
+ from sage.misc.temporary_file import tmp_filename
++import os
++from sage.env import SAGE_LOCAL
+
+ try:
+ from gambit import Game
+@@ -1317,13 +1318,13 @@ class NormalFormGame(SageObject, MutableMapping):
+ raise ValueError("utilities have not been populated")
+
+ if not algorithm:
+- if is_package_installed('lrslib'):
++ if os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'lrs')):
+ algorithm = "lrs"
+ else:
+ algorithm = "enumeration"
+
+ if algorithm == "lrs":
+- if not is_package_installed('lrslib'):
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'lrs')):
+ raise NotImplementedError("lrslib is not installed")
+
+ return self._solve_lrs(maximization)
+diff --git a/src/sage/geometry/polyhedron/base.py b/src/sage/geometry/polyhedron/base.py
+index 2f58d8b..eb519a2 100644
+--- a/src/sage/geometry/polyhedron/base.py
++++ b/src/sage/geometry/polyhedron/base.py
+@@ -21,7 +21,6 @@ import six
+ from sage.structure.element import Element, coerce_binop, is_Vector
+
+ from sage.misc.all import cached_method, prod
+-from sage.misc.package import is_package_installed
+
+ from sage.rings.all import QQ, ZZ
+ from sage.rings.real_double import RDF
+@@ -3691,7 +3690,9 @@ class Polyhedron_base(Element):
+
+ David Avis's lrs program.
+ """
+- if not is_package_installed('lrslib'):
++ import os
++ from sage.env import SAGE_LOCAL
++ if os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'lrs')) != True:
+ raise NotImplementedError('You must install the optional lrslib package '
+ 'for this function to work')
+
+diff --git a/src/sage/graphs/generators/classical_geometries.py b/src/sage/graphs/generators/classical_geometries.py
+index e80f2a5..04cd9ce 100644
+--- a/src/sage/graphs/generators/classical_geometries.py
++++ b/src/sage/graphs/generators/classical_geometries.py
+@@ -1287,10 +1287,9 @@ def CossidentePenttilaGraph(q):
+ raise ValueError('q(={}) must be an odd prime power'.format(q))
+
+ from sage.libs.gap.libgap import libgap
+- from sage.misc.package import is_package_installed, PackageNotFoundError
++ from sage.interfaces.gap import gap
+
+- if not is_package_installed('gap_packages'):
+- raise PackageNotFoundError('gap_packages')
++ gap.load_package("grape")
+
+ adj_list=libgap.function_factory("""function(q)
+ local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x;
+diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
+index 252984f..ce19682 100644
+--- a/src/sage/graphs/generic_graph.py
++++ b/src/sage/graphs/generic_graph.py
+@@ -7858,7 +7858,6 @@ class GenericGraph(GenericGraph_pyx):
+ sage: abs(flow_ff-flow_igraph) < 0.00001 # optional python_igraph
+ True
+ """
+- from sage.misc.package import is_package_installed
+ self._scream_if_not_simple(allow_loops=True)
+ if vertex_bound and algorithm in ["FF", "igraph"]:
+ raise ValueError("This method does not support both " +
+@@ -7876,10 +7875,12 @@ class GenericGraph(GenericGraph_pyx):
+ if algorithm is None:
+ if vertex_bound:
+ algorithm = "LP"
+- elif is_package_installed("python_igraph"):
+- algorithm = "igraph"
+ else:
+- algorithm = "FF"
++ algorithm = "igraph"
++ try:
++ import igraph
++ except ImportError:
++ algorithm = "FF"
+
+ if (algorithm == "FF"):
+ return self._ford_fulkerson(x,y, value_only=value_only, integer=integer, use_edge_labels=use_edge_labels)
+diff --git a/src/sage/graphs/graph_generators.py b/src/sage/graphs/graph_generators.py
+index 5919ab3..1766796 100644
+--- a/src/sage/graphs/graph_generators.py
++++ b/src/sage/graphs/graph_generators.py
+@@ -1195,8 +1195,9 @@ class GraphGenerators():
+ .. [buckygen] \G. Brinkmann, J. Goedgebeur and B.D. McKay, Generation of Fullerenes,
+ Journal of Chemical Information and Modeling, 52(11):2910-2918, 2012.
+ """
+- from sage.misc.package import is_package_installed
+- if not is_package_installed("buckygen"):
++ import os
++ from sage.env import SAGE_LOCAL
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'buckygen')):
+ raise TypeError("the optional buckygen package is not installed")
+
+ # number of vertices should be positive
+@@ -1280,8 +1281,9 @@ class GraphGenerators():
+ .. [benzene] \G. Brinkmann, G. Caporossi and P. Hansen, A Constructive Enumeration of Fusenes and Benzenoids,
+ Journal of Algorithms, 45:155-166, 2002.
+ """
+- from sage.misc.package import is_package_installed
+- if not is_package_installed("benzene"):
++ import os
++ from sage.env import SAGE_LOCAL
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'benzene')):
+ raise TypeError("the optional benzene package is not installed")
+
+ # number of hexagons should be positive
+@@ -1433,8 +1435,9 @@ class GraphGenerators():
+ .. [plantri] \G. Brinkmann and B.D. McKay, Fast generation of planar graphs,
+ MATCH-Communications in Mathematical and in Computer Chemistry, 58(2):323-357, 2007.
+ """
+- from sage.misc.package import is_package_installed
+- if not is_package_installed("plantri"):
++ import os
++ from sage.env import SAGE_LOCAL
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'plantri')):
+ raise TypeError("the optional plantri package is not installed")
+
+ # number of vertices should be positive
+@@ -1632,8 +1635,9 @@ class GraphGenerators():
+ sage: [g.size() for g in graphs.triangulations(6, minimum_connectivity=3)] # optional plantri
+ [12, 12]
+ """
+- from sage.misc.package import is_package_installed
+- if not is_package_installed("plantri"):
++ import os
++ from sage.env import SAGE_LOCAL
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'plantri')):
+ raise TypeError("the optional plantri package is not installed")
+
+ # number of vertices should be positive
+@@ -1786,8 +1790,9 @@ class GraphGenerators():
+ sage: [len(g) for g in graphs.quadrangulations(12, no_nonfacial_quadrangles=True, dual=True)] # optional plantri
+ [10, 10]
+ """
+- from sage.misc.package import is_package_installed
+- if not is_package_installed("plantri"):
++ import os
++ from sage.env import SAGE_LOCAL
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'plantri')):
+ raise TypeError("the optional plantri package is not installed")
+
+ # number of vertices should be positive
+diff --git a/src/sage/graphs/lovasz_theta.py b/src/sage/graphs/lovasz_theta.py
+index 0d345c9..60948d2 100644
+--- a/src/sage/graphs/lovasz_theta.py
++++ b/src/sage/graphs/lovasz_theta.py
+@@ -65,10 +65,9 @@ def lovasz_theta(graph):
+ from sage.misc.temporary_file import tmp_filename
+ import os, subprocess
+ from sage.env import SAGE_LOCAL
+- from sage.misc.package import is_package_installed, PackageNotFoundError
+
+- if not is_package_installed('csdp'):
+- raise PackageNotFoundError("csdp")
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'theta')):
++ raise NotImplementedError("You must install csdp before using this function")
+
+ g = graph.relabel(inplace=False, perm=range(1,n+1)).networkx_graph()
+ tf_name = tmp_filename()
+diff --git a/src/sage/groups/generic.py b/src/sage/groups/generic.py
+index c801636..f43e6d9 100644
+--- a/src/sage/groups/generic.py
++++ b/src/sage/groups/generic.py
+@@ -1400,15 +1400,15 @@ def structure_description(G, latex=False):
+ sage: groups.matrix.GL(4,2).structure_description() # optional - database_gap
+ 'A8'
+ """
+- import re
+- from sage.misc.package import is_package_installed
++ import re, os
++ from sage.env import SAGE_LOCAL
+ def correct_dihedral_degree(match):
+ return "%sD%d" % (match.group(1), int(match.group(2))/2)
+
+ try:
+ description = str(G._gap_().StructureDescription())
+ except RuntimeError:
+- if not is_package_installed('database_gap'):
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, "lib", "gap", "small", "readsml.g")):
+ raise RuntimeError("You must install the optional database_gap package first.")
+ raise
+
+diff --git a/src/sage/groups/perm_gps/permgroup.py b/src/sage/groups/perm_gps/permgroup.py
+index e42db61..d4d5684 100644
+--- a/src/sage/groups/perm_gps/permgroup.py
++++ b/src/sage/groups/perm_gps/permgroup.py
+@@ -145,7 +145,6 @@ from sage.groups.perm_gps.permgroup_element import PermutationGroupElement, stan
+ from sage.groups.abelian_gps.abelian_group import AbelianGroup
+ from sage.misc.cachefunc import cached_method
+ from sage.groups.class_function import ClassFunction
+-from sage.misc.package import is_package_installed
+ from sage.sets.finite_enumerated_set import FiniteEnumeratedSet
+ from sage.categories.all import FiniteEnumeratedSets
+ from sage.groups.conjugacy_classes import ConjugacyClassGAP
+@@ -190,8 +189,6 @@ def hap_decorator(f):
+ """
+ @wraps(f)
+ def wrapped(self, n, p=0):
+- if not is_package_installed('gap_packages'):
+- raise RuntimeError("You must install the optional gap_packages package.")
+ load_hap()
+ from sage.arith.all import is_prime
+ if not (p == 0 or is_prime(p)):
+@@ -1682,9 +1679,7 @@ class PermutationGroup_generic(group.FiniteGroup):
+ try:
+ return [Integer(n) for n in self._gap_().IdGroup()]
+ except RuntimeError:
+- if not is_package_installed('database_gap'):
+- raise RuntimeError("You must install the optional database_gap package first.")
+- raise
++ raise RuntimeError("You must install the optional gap_packages package.")
+
+ def id(self):
+ """
+@@ -1735,9 +1730,7 @@ class PermutationGroup_generic(group.FiniteGroup):
+ try:
+ return Integer(self._gap_().PrimitiveIdentification())
+ except RuntimeError:
+- if not is_package_installed('database_gap'):
+- raise RuntimeError("You must install the optional database_gap package first.")
+- raise
++ raise RuntimeError("You must install the optional gap_packages package.")
+
+ def center(self):
+ """
+@@ -4113,8 +4106,6 @@ class PermutationGroup_generic(group.FiniteGroup):
+ - David Joyner and Graham Ellis
+
+ """
+- if not is_package_installed('gap_packages'):
+- raise RuntimeError("You must install the optional gap_packages package.")
+ load_hap()
+ from sage.arith.all import is_prime
+ if not (p == 0 or is_prime(p)):
+diff --git a/src/sage/misc/all.py b/src/sage/misc/all.py
+index 90e6985..21daeb0 100644
+--- a/src/sage/misc/all.py
++++ b/src/sage/misc/all.py
+@@ -53,10 +53,6 @@ from fpickle import pickle_function, unpickle_function
+
+ from .dist import install_scripts
+
+-from .package import (installed_packages, is_package_installed,
+- standard_packages, optional_packages, experimental_packages,
+- package_versions)
+-
+ from .pager import pager
+
+ lazy_import('sage.misc.sagedoc', ['browse_sage_doc',
+diff --git a/src/sage/rings/polynomial/multi_polynomial_sequence.py b/src/sage/rings/polynomial/multi_polynomial_sequence.py
+index da41cb0..49cae0b 100644
+--- a/src/sage/rings/polynomial/multi_polynomial_sequence.py
++++ b/src/sage/rings/polynomial/multi_polynomial_sequence.py
+@@ -163,7 +163,6 @@ from sage.misc.cachefunc import cached_method
+
+ from types import GeneratorType
+ from sage.misc.converting_dict import KeyConvertingDict
+-from sage.misc.package import is_package_installed
+
+ from sage.structure.sequence import Sequence, Sequence_generic
+
+@@ -1433,10 +1432,11 @@ class PolynomialSequence_gf2(PolynomialSequence_generic):
+
+ if S != []:
+ if algorithm == "exhaustive_search":
+- if not is_package_installed('fes'):
+- from sage.misc.package import PackageNotFoundError
+- raise PackageNotFoundError("fes")
+- from sage.libs.fes import exhaustive_search
++ try:
++ from sage.libs.fes import exhaustive_search
++ except ImportError:
++ raise RuntimeError("You must install the optional fes package.")
++
+ solutions = exhaustive_search(S, max_sols=n, verbose=verbose, **kwds)
+
+ elif algorithm == "polybori":
Copied: sagemath/repos/community-staging-i686/jupyter-path.patch (from rev 206902, sagemath/trunk/jupyter-path.patch)
===================================================================
--- community-staging-i686/jupyter-path.patch (rev 0)
+++ community-staging-i686/jupyter-path.patch 2017-01-12 06:54:01 UTC (rev 206903)
@@ -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/package.patch (from rev 206902, sagemath/trunk/package.patch)
===================================================================
--- community-staging-i686/package.patch (rev 0)
+++ community-staging-i686/package.patch 2017-01-12 06:54:01 UTC (rev 206903)
@@ -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/skip-check.patch (from rev 206902, sagemath/trunk/skip-check.patch)
===================================================================
--- community-staging-i686/skip-check.patch (rev 0)
+++ community-staging-i686/skip-check.patch 2017-01-12 06:54:01 UTC (rev 206903)
@@ -0,0 +1,22 @@
+--- src/bin/sage.orig 2014-12-18 09:47:27.354829070 +0100
++++ src/bin/sage 2014-12-18 09:48:00.041563401 +0100
+@@ -352,18 +352,6 @@
+
+ # Prepare for running Sage, either interactively or non-interactively.
+ sage_setup() {
+- # Check that we're not in a source tarball which hasn't been built yet (#13561).
+- if [ ! -d "$SAGE_LOCAL/lib/python/site-packages/sage" ]; then
+- echo >&2 '************************************************************************'
+- echo >&2 'It seems that you are attempting to run Sage from an unpacked source'
+- echo >&2 'tarball, but you have not compiled it yet (or maybe the build has not'
+- echo >&2 'finished). You should run `make` in the Sage root directory first.'
+- echo >&2 'If you did not intend to build Sage from source, you should download'
+- echo >&2 'a binary tarball instead. Read README.txt for more information.'
+- echo >&2 '************************************************************************'
+- exit 1
+- fi
+-
+ # Display the startup banner (unless SAGE_BANNER is explictly "no")
+ if [ "$SAGE_BANNER" != "no" ]; then
+ # can be 'bare', or 'yes', or unspecified
+
Copied: sagemath/repos/community-staging-i686/test-optional.patch (from rev 206902, sagemath/trunk/test-optional.patch)
===================================================================
--- community-staging-i686/test-optional.patch (rev 0)
+++ community-staging-i686/test-optional.patch 2017-01-12 06:54:01 UTC (rev 206903)
@@ -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 206902, sagemath/trunk/PKGBUILD)
===================================================================
--- community-staging-x86_64/PKGBUILD (rev 0)
+++ community-staging-x86_64/PKGBUILD 2017-01-12 06:54:01 UTC (rev 206903)
@@ -0,0 +1,148 @@
+# $Id$
+# Maintainer: Evgeniy Alekseev <arcanis.arch at gmail dot com>
+# Maintainer: Antonio Rojas <arojas at archlinux.org>
+# Contributor: Daniel Wallace <danielwallace at gtmanfred dot com>
+# Contributor: Thomas Dziedzic <gostrc at gmail dot com>
+# Contributor: Osman Ugus <ugus11 at yahoo dot com>
+# Contributor: Stefan Husmann <stefan-husmann at t-online dot de>
+# Special thanks to Nareto for moving the compile from the .install to the PKGBUILD
+
+pkgbase=sagemath
+pkgname=(sagemath sagemath-jupyter)
+pkgver=7.5
+pkgrel=1
+pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab"
+arch=(i686 x86_64)
+url="http://www.sagemath.org"
+license=(GPL)
+depends=(ipython2 ppl palp brial cliquer maxima-ecl gfan sympow tachyon nauty python2-rpy2 python2-fpylll python2-psutil
+ python2-matplotlib python2-scipy python2-sympy python2-networkx python2-pillow python2-future libgap flintqs lcalc lrcalc arb
+ eclib gmp-ecm zn_poly gd python2-cvxopt pynac linbox rubiks pari-galdata pari-seadata-small planarity rankwidth
+ sage-data-combinatorial_designs sage-data-elliptic_curves sage-data-graphs sage-data-polytopes_db sage-data-conway_polynomials)
+optdepends=('cython2: to compile cython code' 'python2-pkgconfig: to compile cython code'
+ 'jmol: 3D plots' 'sage-notebook: Browser-based (flask) notebook interface'
+ 'sagemath-doc: Documentation and inline help' 'python2-igraph: igraph backend for graph theory'
+ 'coin-or-cbc: COIN backend for numerical computations' 'coin-or-csdp: for computing Lovász theta-function of graphs'
+ 'buckygen: for generating fullerene graphs' 'plantri: for generating some classes of graphs' 'benzene: for generating fusenes and benzenoids'
+ 'modular_decomposition: modular decomposition of graphs' 'ffmpeg: to export animations to video' 'imagemagick: to show animations'
+ 'coxeter3: Coxeter groups implementation' 'cryptominisat2: SAT solver' 'gap-data: for computing Galois groups'
+ 'lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes'
+ 'libhomfly: for computing the homfly polynomial of links' 'libbraiding: for computing in braid groups'
+ 'python2-pynormaliz: Normaliz backend for polyhedral computations')
+makedepends=(cython2 boost ratpoints symmetrica fflas-ffpack python2-jinja coin-or-cbc libhomfly libbraiding
+ mcqd coxeter3 cryptominisat2 modular_decomposition bliss-graphs tdlib python2-pkgconfig meataxe) # libfes
+source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"
+ env.patch skip-check.patch cython-sys-path.patch is-package-installed.patch package.patch disable-fes.patch
+ jupyter-path.patch test-optional.patch ecm-7.patch increase-rtol.patch)
+md5sums=('bff1fb8793ebc2934d14cf1efdcfbea3'
+ '784ba3fca83f24ed0bbf62e01fa4e967'
+ '6cafcb381437d4751fd55b25d5090987'
+ '0de8f29a99a48e2ca2a13045f122c386'
+ '409b0a2c520eb33281b5f262afcb6c76'
+ 'ccfd5b1bc4796f414f1531be52504dd7'
+ '06a67e611d10aa2381efe1f08ea4ffd9'
+ '0d88207416dfb98a17bf8886257d9a02'
+ '921017fd2d9dadbb6b602ac0476bfd58'
+ '0c9a57d35de80c2cd418ebec912efbbb'
+ '39d3fded716d2a7ae0ab03e0896b7497')
+
+prepare(){
+ cd sage-$pkgver
+
+# Arch-specific patches
+# assume all optional packages are installed
+ patch -p0 -i ../package.patch
+# set env variables
+ patch -p0 -i ../env.patch
+# skip checking build status
+ patch -p0 -i ../skip-check.patch
+# don't list optional packages when running tests
+ patch -p0 -i ../test-optional.patch
+# set jupyter path
+ patch -p0 -i ../jupyter-path.patch
+# search system paths for cython includes
+ patch -p1 -i ../cython-sys-path.patch
+# fix regressions with ECM 7
+ patch -p1 -i ../ecm-7.patch
+# increase numerical tolerance, needed by scipy 0.18
+ patch -p1 -i ../increase-rtol.patch
+
+# Upstream patches
+# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209
+# patch -p0 -i ../fes02.patch
+# disable fes module, fails to compile
+ patch -p0 -i ../disable-fes.patch
+# replace is_package_installed usage http://trac.sagemath.org/ticket/20377
+ patch -p1 -i ../is-package-installed.patch
+
+# use python2
+ sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' -e 's|exec python|exec python2|' -i src/bin/*
+ sed -e 's|cython {OPT}|cython2 {OPT}|' -e 's|python setup.py|python2 setup.py|' -i src/sage/misc/cython.py
+ sed -e 's|exec ipython|exec ipython2|' -e 's|cygdb|cygdb2|g' -i src/bin/sage
+ sed -e "s|'cython'|'cython2'|" -i src/bin/sage-cython
+ sed -e 's|bin/python|bin/python2|g' -i src/bin/sage-env
+}
+
+
+build() {
+ cd sage-$pkgver/src
+
+ export SAGE_LOCAL="/usr"
+ export SAGE_ROOT="$PWD"
+ export SAGE_SRC="$PWD"
+ export CC=gcc
+
+ python2 setup.py build
+}
+
+package_sagemath() {
+ optdepends+=('sagemath-jupyter: Jupyter kernel')
+ conflicts=(sage-mathematics)
+ replaces=(sage-mathematics)
+ provides=(sage-mathematics)
+
+ cd sage-$pkgver/src
+
+ export SAGE_ROOT="$PWD"
+ export SAGE_LOCAL="/usr"
+ export JUPYTER_PATH="$pkgdir"/usr/share/jupyter
+
+ python2 setup.py install --root="$pkgdir" --optimize=1 --skip-build
+
+ mkdir -p "$pkgdir"/usr/bin
+ cp bin/sage "$pkgdir"/usr/bin
+ for _i in arch-env banner cachegrind callgrind cleaner coverage coverageall cython env eval grep grepdoc inline-fortran ipython \
+ massif maxima.lisp native-execute notebook num-threads.py omega open preparse python rst2sws rst2txt run run-cython runtests startuptime.py \
+ sws2rst valgrind version.sh
+ do
+ cp bin/sage-$_i "$pkgdir"/usr/bin
+ done
+ cp bin/math-readline "$pkgdir"/usr/bin
+
+ mkdir -p "$pkgdir"/usr/share/sage
+ cp -r ext "$pkgdir"/usr/share/sage
+
+# Create SAGE_SRC, needed for the notebook and help
+ mkdir "$pkgdir"/usr/share/sage/source
+ ln -s /usr/share/doc/sage "$pkgdir"/usr/share/sage/source/doc
+
+# Remove sage_setup
+ rm -r "$pkgdir"/usr/lib/python2.7/site-packages/sage_setup
+
+# Split jupyter kernel
+ rm -r "$pkgdir"/usr/share/jupyter
+}
+
+package_sagemath-jupyter() {
+ pkgdesc='Jupyter kernel for SageMath'
+ depends=(sagemath python2-jupyter_client python2-ipywidgets jupyter-notebook mathjax)
+ optdepends=('sage-notebook-exporter: convert flask notebooks to Jupyter')
+
+ cd sage-$pkgver/src
+
+ export SAGE_ROOT="$PWD"
+ export SAGE_LOCAL="/usr"
+ export JUPYTER_PATH="$pkgdir"/usr/share/jupyter
+
+ python2 -c "from sage.repl.ipython_kernel.install import SageKernelSpec; SageKernelSpec.update()"
+}
Copied: sagemath/repos/community-staging-x86_64/cython-sys-path.patch (from rev 206902, sagemath/trunk/cython-sys-path.patch)
===================================================================
--- community-staging-x86_64/cython-sys-path.patch (rev 0)
+++ community-staging-x86_64/cython-sys-path.patch 2017-01-12 06:54:01 UTC (rev 206903)
@@ -0,0 +1,10 @@
+--- sage-7.1/src/setup.py.orig 2016-04-08 16:59:24.691349473 +0000
++++ sage-7.1/src/setup.py 2016-04-08 17:03:03.847153796 +0000
+@@ -414,6 +414,7 @@
+ build_dir=SAGE_CYTHONIZED,
+ force=force,
+ aliases=aliases,
++ include_path=sys.path,
+ compiler_directives={
+ 'autotestdict': False,
+ 'cdivision': True,
Copied: sagemath/repos/community-staging-x86_64/disable-fes.patch (from rev 206902, sagemath/trunk/disable-fes.patch)
===================================================================
--- community-staging-x86_64/disable-fes.patch (rev 0)
+++ community-staging-x86_64/disable-fes.patch 2017-01-12 06:54:01 UTC (rev 206903)
@@ -0,0 +1,19 @@
+--- src/module_list.py.orig 2015-06-07 11:29:30.710612146 +0200
++++ src/module_list.py 2015-06-07 11:30:21.877506106 +0200
+@@ -564,11 +564,11 @@
+ sources = ["sage/libs/ecl.pyx"],
+ libraries = ["ecl"]),
+
+- OptionalExtension("sage.libs.fes",
+- ["sage/libs/fes.pyx"],
+- language = "c",
+- libraries = ['fes'],
+- package = 'fes'),
++# OptionalExtension("sage.libs.fes",
++# ["sage/libs/fes.pyx"],
++# language = "c",
++# libraries = ['fes'],
++# package = 'fes'),
+
+ Extension('sage.libs.flint.flint',
+ sources = ["sage/libs/flint/flint.pyx"],
Copied: sagemath/repos/community-staging-x86_64/ecm-7.patch (from rev 206902, sagemath/trunk/ecm-7.patch)
===================================================================
--- community-staging-x86_64/ecm-7.patch (rev 0)
+++ community-staging-x86_64/ecm-7.patch 2017-01-12 06:54:01 UTC (rev 206903)
@@ -0,0 +1,79 @@
+--- a/src/sage/interfaces/ecm.py.orig 2016-05-16 22:18:03.894827738 +0200
++++ b/src/sage/interfaces/ecm.py 2016-05-16 22:19:14.674904932 +0200
+@@ -140,9 +140,6 @@
+ - ``ve`` -- integer `n`. Verbosely show short (`< n`
+ character) expressions on each loop
+
+- - ``cofdec`` -- boolean. Force cofactor output in decimal
+- (even if expressions are used )
+-
+ - ``B2scale`` -- integer. Multiplies the default B2 value
+
+ - ``go`` -- integer. Preload with group order val, which can
+@@ -395,15 +392,15 @@
+ if m is not None:
+ factor = m.group('factor')
+ primality = m.group('primality')
+- assert primality in ['probable prime', 'composite']
+- result += [(ZZ(factor), primality == 'probable prime')]
++ assert primality in ['prime', 'composite']
++ result += [(ZZ(factor), primality == 'prime')]
+ continue # cofactor on the next line
+ m = self._found_cofactor_re.match(line)
+ if m is not None:
+ cofactor = m.group('cofactor')
+ primality = m.group('primality')
+- assert primality in ['Probable prime', 'Composite']
+- result += [(ZZ(cofactor), primality == 'Probable prime')]
++ assert primality in ['Prime', 'Composite']
++ result += [(ZZ(cofactor), primality == 'Prime')]
+ # assert len(result) == 2
+ return result
+ raise ValueError('failed to parse ECM output')
+@@ -501,7 +498,6 @@
+ if factor_digits is not None:
+ B1 = self.recommended_B1(factor_digits)
+ kwds['one'] = True
+- kwds['cofdec'] = True
+ cmd = self._make_cmd(B1, None, kwds)
+ out = self._run_ecm(cmd, n)
+ return self._parse_output(n, out)
+@@ -828,8 +828,8 @@
+ Step 1 took 12ms
+ Step 2 took 17ms
+ ********** Factor found in step 2: 79792266297612017
+-Found probable prime factor of 17 digits: 79792266297612017
+-Probable prime cofactor 6366805760909027985741435139224233 has 34 digits
++Found prime factor of 17 digits: 79792266297612017
++Prime cofactor 6366805760909027985741435139224233 has 34 digits
+ """
+
+ TEST_ECM_OUTPUT_2 = """
+@@ -839,8 +839,8 @@
+ Step 1 took 2ms
+ Step 2 took 3ms
+ ********** Factor found in step 2: 179424673
+-Found probable prime factor of 9 digits: 179424673
+-Probable prime cofactor 179424673 has 9 digits
++Found prime factor of 9 digits: 179424673
++Prime cofactor 179424673 has 9 digits
+ """
+
+ TEST_ECM_OUTPUT_3 = """
+@@ -858,7 +858,7 @@
+ Step 1 took 5ms
+ Step 2 took 4ms
+ ********** Factor found in step 2: 197002597249
+-Found probable prime factor of 12 digits: 197002597249
++Found prime factor of 12 digits: 197002597249
+ Composite cofactor 339872432034468861533158743041639097889948066859 has 48 digits
+ """
+
+@@ -870,5 +870,5 @@
+ Step 2 took 2ms
+ ********** Factor found in step 2: 265748496095531068869578877937
+ Found composite factor of 30 digits: 265748496095531068869578877937
+-Probable prime cofactor 251951573867253012259144010843 has 30 digits
++Prime cofactor 251951573867253012259144010843 has 30 digits
+ """
+
Copied: sagemath/repos/community-staging-x86_64/env.patch (from rev 206902, sagemath/trunk/env.patch)
===================================================================
--- community-staging-x86_64/env.patch (rev 0)
+++ community-staging-x86_64/env.patch 2017-01-12 06:54:01 UTC (rev 206903)
@@ -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
+@@ -110,41 +110,7 @@
+ }
+
+
+-# New value for SAGE_ROOT: either SAGE_ROOT (if given)
+-# or a guessed value based on pwd.
+-if [ -n "$SAGE_ROOT" ]; then
+- NEW_SAGE_ROOT="$SAGE_ROOT"
+-elif [ -f sage -a -d build ]; then
+- NEW_SAGE_ROOT="."
+-elif [ -f ../../sage -a -d ../../build ]; then
+- NEW_SAGE_ROOT="../.."
+-else
+- # No idea what SAGE_ROOT should be...
+- echo >&2 "Error: You must set the SAGE_ROOT environment variable or run this"
+- echo >&2 "script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory."
+- return 1
+-fi
+-
+-# Make NEW_SAGE_ROOT absolute
+-NEW_SAGE_ROOT=`cd "$NEW_SAGE_ROOT" && pwd -P`
+-
+-# Sanity check NEW_SAGE_ROOT
+-if [ -f "$NEW_SAGE_ROOT/sage" -a -d "$NEW_SAGE_ROOT/build" ]; then
+- :
+-else
+- echo >&2 "Error: SAGE_ROOT is set to a bad value:"
+- echo >&2 "SAGE_ROOT=$SAGE_ROOT"
+- echo >&2 "You must correct it or erase it and run this script from the SAGE_ROOT"
+- echo >&2 "or SAGE_ROOT/local/bin/ directory."
+- return 1
+-fi
+-
+-# Warn if NEW_SAGE_ROOT does not equal the old SAGE_ROOT
+-if [ "$SAGE_ROOT" != "$NEW_SAGE_ROOT" -a -n "$SAGE_ROOT" ]; then
+- echo >&2 "Warning: overwriting SAGE_ROOT environment variable:"
+- echo >&2 "Old SAGE_ROOT=$SAGE_ROOT"
+- echo >&2 "New SAGE_ROOT=$NEW_SAGE_ROOT"
+-fi
++NEW_SAGE_ROOT="/usr"
+
+ # Display the Sage startup banner, used in src/bin/sage
+ sage_banner() {
+@@ -187,7 +187,7 @@
+
+ # SAGE_LOCAL is the installation prefix and can be customized
+ if [ -z "$SAGE_LOCAL" ]; then
+- export SAGE_LOCAL="$SAGE_ROOT/local"
++ export SAGE_LOCAL="/usr"
+ fi
+
+ # sage-env must know where the Sage's script files are
+@@ -233,8 +233,8 @@
+ 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="$SAGE_SRC/doc"
++export SAGE_SRC="$SAGE_SHARE/sage/source"
++export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage"
+ export SAGE_DOC="$SAGE_SHARE/doc/sage"
+
+ if [ -z "${SAGE_ORIG_PATH_SET}" ]; then
+@@ -374,6 +337,9 @@
+ export SAGE_STARTUP_FILE
+ fi
+
++export LIBMTX="$DOT_SAGE/meataxe"
++[[ -d $LIBMTX ]] || mkdir $LIBMTX # Create meataxe data dir
++
+ if [ -z "$IPYTHONDIR" ]; then
+ # We hardcode a version number in the directory name. The idea is
+ # that we keep using the same version number as long as that is
+@@ -468,7 +400,6 @@
+ fi
+ fi
+ fi
+-export MAXIMA_PREFIX="$SAGE_LOCAL"
+
+ PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB
+
+@@ -629,9 +608,6 @@
+ LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH
+ fi
+
+-# See trac 7186 -- this is needed if ecl is moved
+-ECLDIR="$SAGE_LOCAL/lib/ecl/" && export ECLDIR
+-
+ # Handle parallel building/testing/...
+ # See Trac Ticket #12016
+ # First, figure out the right values for SAGE_NUM_THREADS (default
Copied: sagemath/repos/community-staging-x86_64/increase-rtol.patch (from rev 206902, sagemath/trunk/increase-rtol.patch)
===================================================================
--- community-staging-x86_64/increase-rtol.patch (rev 0)
+++ community-staging-x86_64/increase-rtol.patch 2017-01-12 06:54:01 UTC (rev 206903)
@@ -0,0 +1,37 @@
+diff -ru sage-7.3.orig/src/sage/coding/code_bounds.py sage-7.3/src/sage/coding/code_bounds.py
+--- sage-7.3.orig/src/sage/coding/code_bounds.py 2016-08-05 20:26:10.033204091 +0200
++++ sage-7.3/src/sage/coding/code_bounds.py 2016-08-05 20:32:27.276579565 +0200
+@@ -554,7 +554,7 @@
+ if q < 2: # Here we check that q is actually at least 2
+ raise ValueError("The value q must be an integer greater than 1")
+
+- eps = 4.5e-16 # find_root has about this as the default xtol
++ eps = 4.5e-15 # find_root has about this as the default xtol
+ ymax = 1 - 1/q
+ if x <= eps:
+ return 0
+diff -ru sage-7.3.orig/src/sage/numerical/optimize.py sage-7.3/src/sage/numerical/optimize.py
+--- sage-7.3.orig/src/sage/numerical/optimize.py 2016-08-05 20:26:10.816536625 +0200
++++ sage-7.3/src/sage/numerical/optimize.py 2016-08-05 20:32:21.449907130 +0200
+@@ -15,7 +15,7 @@
+ from sage.rings.real_double import RDF
+
+
+-def find_root(f, a, b, xtol=10e-13, rtol=4.5e-16, maxiter=100, full_output=False):
++def find_root(f, a, b, xtol=10e-13, rtol=4.5e-15, maxiter=100, full_output=False):
+ """
+ Numerically find a root of ``f`` on the closed interval `[a,b]`
+ (or `[b,a]`) if possible, where ``f`` is a function in the one variable.
+diff -ru sage-7.3.orig/src/sage/symbolic/expression.pyx sage-7.3/src/sage/symbolic/expression.pyx
+--- sage-7.3.orig/src/sage/symbolic/expression.pyx 2016-08-05 20:26:11.333202767 +0200
++++ sage-7.3/src/sage/symbolic/expression.pyx 2016-08-05 20:32:14.236566826 +0200
+@@ -10884,7 +10884,7 @@
+ ret = ret[0]
+ return ret
+
+- def find_root(self, a, b, var=None, xtol=10e-13, rtol=4.5e-16, maxiter=100, full_output=False):
++ def find_root(self, a, b, var=None, xtol=10e-13, rtol=4.5e-15, maxiter=100, full_output=False):
+ """
+ Numerically find a root of self on the closed interval [a,b] (or
+ [b,a]) if possible, where self is a function in the one variable.
+
Copied: sagemath/repos/community-staging-x86_64/is-package-installed.patch (from rev 206902, sagemath/trunk/is-package-installed.patch)
===================================================================
--- community-staging-x86_64/is-package-installed.patch (rev 0)
+++ community-staging-x86_64/is-package-installed.patch 2017-01-12 06:54:01 UTC (rev 206903)
@@ -0,0 +1,328 @@
+diff --git a/src/sage/databases/cremona.py b/src/sage/databases/cremona.py
+index 0a5f794..2969d92 100644
+--- a/src/sage/databases/cremona.py
++++ b/src/sage/databases/cremona.py
+@@ -53,7 +53,6 @@ from sage.misc.prandom import randint
+
+ import sage.schemes.elliptic_curves.constructor as elliptic
+ from .sql_db import SQLDatabase, verify_column
+-from sage.misc.package import is_package_installed
+ from sage.env import SAGE_SHARE
+ from sage.misc.all import walltime
+
+@@ -824,7 +823,7 @@ class MiniCremonaDatabase(SQLDatabase):
+ if N < self.largest_conductor():
+ message = "There is no elliptic curve with label " + label \
+ + " in the database"
+- elif is_package_installed('database_cremona_ellcurve'):
++ elif os.path.isfile(os.path.join(SAGE_SHARE, "cremona", "cremona.db")):
+ message = "There is no elliptic curve with label " + label \
+ + " in the currently available databases"
+ else:
+@@ -1673,7 +1672,7 @@ def CremonaDatabase(name=None,mini=None,set_global=None):
+ if name is None and not set_global:
+ return _db
+ if set_global and name is None:
+- if is_package_installed('database_cremona_ellcurve'):
++ if os.path.isfile(os.path.join(SAGE_SHARE, "cremona", "cremona.db")):
+ name = 'cremona'
+ else:
+ name = 'cremona mini'
+diff --git a/src/sage/game_theory/normal_form_game.py b/src/sage/game_theory/normal_form_game.py
+index b917d2a..80fb20c 100644
+--- a/src/sage/game_theory/normal_form_game.py
++++ b/src/sage/game_theory/normal_form_game.py
+@@ -614,8 +614,9 @@ from sage.rings.all import QQ
+ from sage.structure.sage_object import SageObject
+ from sage.matrix.constructor import matrix
+ from sage.matrix.constructor import vector
+-from sage.misc.package import is_package_installed
+ from sage.misc.temporary_file import tmp_filename
++import os
++from sage.env import SAGE_LOCAL
+
+ try:
+ from gambit import Game
+@@ -1317,13 +1318,13 @@ class NormalFormGame(SageObject, MutableMapping):
+ raise ValueError("utilities have not been populated")
+
+ if not algorithm:
+- if is_package_installed('lrslib'):
++ if os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'lrs')):
+ algorithm = "lrs"
+ else:
+ algorithm = "enumeration"
+
+ if algorithm == "lrs":
+- if not is_package_installed('lrslib'):
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'lrs')):
+ raise NotImplementedError("lrslib is not installed")
+
+ return self._solve_lrs(maximization)
+diff --git a/src/sage/geometry/polyhedron/base.py b/src/sage/geometry/polyhedron/base.py
+index 2f58d8b..eb519a2 100644
+--- a/src/sage/geometry/polyhedron/base.py
++++ b/src/sage/geometry/polyhedron/base.py
+@@ -21,7 +21,6 @@ import six
+ from sage.structure.element import Element, coerce_binop, is_Vector
+
+ from sage.misc.all import cached_method, prod
+-from sage.misc.package import is_package_installed
+
+ from sage.rings.all import QQ, ZZ
+ from sage.rings.real_double import RDF
+@@ -3691,7 +3690,9 @@ class Polyhedron_base(Element):
+
+ David Avis's lrs program.
+ """
+- if not is_package_installed('lrslib'):
++ import os
++ from sage.env import SAGE_LOCAL
++ if os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'lrs')) != True:
+ raise NotImplementedError('You must install the optional lrslib package '
+ 'for this function to work')
+
+diff --git a/src/sage/graphs/generators/classical_geometries.py b/src/sage/graphs/generators/classical_geometries.py
+index e80f2a5..04cd9ce 100644
+--- a/src/sage/graphs/generators/classical_geometries.py
++++ b/src/sage/graphs/generators/classical_geometries.py
+@@ -1287,10 +1287,9 @@ def CossidentePenttilaGraph(q):
+ raise ValueError('q(={}) must be an odd prime power'.format(q))
+
+ from sage.libs.gap.libgap import libgap
+- from sage.misc.package import is_package_installed, PackageNotFoundError
++ from sage.interfaces.gap import gap
+
+- if not is_package_installed('gap_packages'):
+- raise PackageNotFoundError('gap_packages')
++ gap.load_package("grape")
+
+ adj_list=libgap.function_factory("""function(q)
+ local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x;
+diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
+index 252984f..ce19682 100644
+--- a/src/sage/graphs/generic_graph.py
++++ b/src/sage/graphs/generic_graph.py
+@@ -7858,7 +7858,6 @@ class GenericGraph(GenericGraph_pyx):
+ sage: abs(flow_ff-flow_igraph) < 0.00001 # optional python_igraph
+ True
+ """
+- from sage.misc.package import is_package_installed
+ self._scream_if_not_simple(allow_loops=True)
+ if vertex_bound and algorithm in ["FF", "igraph"]:
+ raise ValueError("This method does not support both " +
+@@ -7876,10 +7875,12 @@ class GenericGraph(GenericGraph_pyx):
+ if algorithm is None:
+ if vertex_bound:
+ algorithm = "LP"
+- elif is_package_installed("python_igraph"):
+- algorithm = "igraph"
+ else:
+- algorithm = "FF"
++ algorithm = "igraph"
++ try:
++ import igraph
++ except ImportError:
++ algorithm = "FF"
+
+ if (algorithm == "FF"):
+ return self._ford_fulkerson(x,y, value_only=value_only, integer=integer, use_edge_labels=use_edge_labels)
+diff --git a/src/sage/graphs/graph_generators.py b/src/sage/graphs/graph_generators.py
+index 5919ab3..1766796 100644
+--- a/src/sage/graphs/graph_generators.py
++++ b/src/sage/graphs/graph_generators.py
+@@ -1195,8 +1195,9 @@ class GraphGenerators():
+ .. [buckygen] \G. Brinkmann, J. Goedgebeur and B.D. McKay, Generation of Fullerenes,
+ Journal of Chemical Information and Modeling, 52(11):2910-2918, 2012.
+ """
+- from sage.misc.package import is_package_installed
+- if not is_package_installed("buckygen"):
++ import os
++ from sage.env import SAGE_LOCAL
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'buckygen')):
+ raise TypeError("the optional buckygen package is not installed")
+
+ # number of vertices should be positive
+@@ -1280,8 +1281,9 @@ class GraphGenerators():
+ .. [benzene] \G. Brinkmann, G. Caporossi and P. Hansen, A Constructive Enumeration of Fusenes and Benzenoids,
+ Journal of Algorithms, 45:155-166, 2002.
+ """
+- from sage.misc.package import is_package_installed
+- if not is_package_installed("benzene"):
++ import os
++ from sage.env import SAGE_LOCAL
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'benzene')):
+ raise TypeError("the optional benzene package is not installed")
+
+ # number of hexagons should be positive
+@@ -1433,8 +1435,9 @@ class GraphGenerators():
+ .. [plantri] \G. Brinkmann and B.D. McKay, Fast generation of planar graphs,
+ MATCH-Communications in Mathematical and in Computer Chemistry, 58(2):323-357, 2007.
+ """
+- from sage.misc.package import is_package_installed
+- if not is_package_installed("plantri"):
++ import os
++ from sage.env import SAGE_LOCAL
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'plantri')):
+ raise TypeError("the optional plantri package is not installed")
+
+ # number of vertices should be positive
+@@ -1632,8 +1635,9 @@ class GraphGenerators():
+ sage: [g.size() for g in graphs.triangulations(6, minimum_connectivity=3)] # optional plantri
+ [12, 12]
+ """
+- from sage.misc.package import is_package_installed
+- if not is_package_installed("plantri"):
++ import os
++ from sage.env import SAGE_LOCAL
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'plantri')):
+ raise TypeError("the optional plantri package is not installed")
+
+ # number of vertices should be positive
+@@ -1786,8 +1790,9 @@ class GraphGenerators():
+ sage: [len(g) for g in graphs.quadrangulations(12, no_nonfacial_quadrangles=True, dual=True)] # optional plantri
+ [10, 10]
+ """
+- from sage.misc.package import is_package_installed
+- if not is_package_installed("plantri"):
++ import os
++ from sage.env import SAGE_LOCAL
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'plantri')):
+ raise TypeError("the optional plantri package is not installed")
+
+ # number of vertices should be positive
+diff --git a/src/sage/graphs/lovasz_theta.py b/src/sage/graphs/lovasz_theta.py
+index 0d345c9..60948d2 100644
+--- a/src/sage/graphs/lovasz_theta.py
++++ b/src/sage/graphs/lovasz_theta.py
+@@ -65,10 +65,9 @@ def lovasz_theta(graph):
+ from sage.misc.temporary_file import tmp_filename
+ import os, subprocess
+ from sage.env import SAGE_LOCAL
+- from sage.misc.package import is_package_installed, PackageNotFoundError
+
+- if not is_package_installed('csdp'):
+- raise PackageNotFoundError("csdp")
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, 'bin', 'theta')):
++ raise NotImplementedError("You must install csdp before using this function")
+
+ g = graph.relabel(inplace=False, perm=range(1,n+1)).networkx_graph()
+ tf_name = tmp_filename()
+diff --git a/src/sage/groups/generic.py b/src/sage/groups/generic.py
+index c801636..f43e6d9 100644
+--- a/src/sage/groups/generic.py
++++ b/src/sage/groups/generic.py
+@@ -1400,15 +1400,15 @@ def structure_description(G, latex=False):
+ sage: groups.matrix.GL(4,2).structure_description() # optional - database_gap
+ 'A8'
+ """
+- import re
+- from sage.misc.package import is_package_installed
++ import re, os
++ from sage.env import SAGE_LOCAL
+ def correct_dihedral_degree(match):
+ return "%sD%d" % (match.group(1), int(match.group(2))/2)
+
+ try:
+ description = str(G._gap_().StructureDescription())
+ except RuntimeError:
+- if not is_package_installed('database_gap'):
++ if not os.path.isfile(os.path.join(SAGE_LOCAL, "lib", "gap", "small", "readsml.g")):
+ raise RuntimeError("You must install the optional database_gap package first.")
+ raise
+
+diff --git a/src/sage/groups/perm_gps/permgroup.py b/src/sage/groups/perm_gps/permgroup.py
+index e42db61..d4d5684 100644
+--- a/src/sage/groups/perm_gps/permgroup.py
++++ b/src/sage/groups/perm_gps/permgroup.py
+@@ -145,7 +145,6 @@ from sage.groups.perm_gps.permgroup_element import PermutationGroupElement, stan
+ from sage.groups.abelian_gps.abelian_group import AbelianGroup
+ from sage.misc.cachefunc import cached_method
+ from sage.groups.class_function import ClassFunction
+-from sage.misc.package import is_package_installed
+ from sage.sets.finite_enumerated_set import FiniteEnumeratedSet
+ from sage.categories.all import FiniteEnumeratedSets
+ from sage.groups.conjugacy_classes import ConjugacyClassGAP
+@@ -190,8 +189,6 @@ def hap_decorator(f):
+ """
+ @wraps(f)
+ def wrapped(self, n, p=0):
+- if not is_package_installed('gap_packages'):
+- raise RuntimeError("You must install the optional gap_packages package.")
+ load_hap()
+ from sage.arith.all import is_prime
+ if not (p == 0 or is_prime(p)):
+@@ -1682,9 +1679,7 @@ class PermutationGroup_generic(group.FiniteGroup):
+ try:
+ return [Integer(n) for n in self._gap_().IdGroup()]
+ except RuntimeError:
+- if not is_package_installed('database_gap'):
+- raise RuntimeError("You must install the optional database_gap package first.")
+- raise
++ raise RuntimeError("You must install the optional gap_packages package.")
+
+ def id(self):
+ """
+@@ -1735,9 +1730,7 @@ class PermutationGroup_generic(group.FiniteGroup):
+ try:
+ return Integer(self._gap_().PrimitiveIdentification())
+ except RuntimeError:
+- if not is_package_installed('database_gap'):
+- raise RuntimeError("You must install the optional database_gap package first.")
+- raise
++ raise RuntimeError("You must install the optional gap_packages package.")
+
+ def center(self):
+ """
+@@ -4113,8 +4106,6 @@ class PermutationGroup_generic(group.FiniteGroup):
+ - David Joyner and Graham Ellis
+
+ """
+- if not is_package_installed('gap_packages'):
+- raise RuntimeError("You must install the optional gap_packages package.")
+ load_hap()
+ from sage.arith.all import is_prime
+ if not (p == 0 or is_prime(p)):
+diff --git a/src/sage/misc/all.py b/src/sage/misc/all.py
+index 90e6985..21daeb0 100644
+--- a/src/sage/misc/all.py
++++ b/src/sage/misc/all.py
+@@ -53,10 +53,6 @@ from fpickle import pickle_function, unpickle_function
+
+ from .dist import install_scripts
+
+-from .package import (installed_packages, is_package_installed,
+- standard_packages, optional_packages, experimental_packages,
+- package_versions)
+-
+ from .pager import pager
+
+ lazy_import('sage.misc.sagedoc', ['browse_sage_doc',
+diff --git a/src/sage/rings/polynomial/multi_polynomial_sequence.py b/src/sage/rings/polynomial/multi_polynomial_sequence.py
+index da41cb0..49cae0b 100644
+--- a/src/sage/rings/polynomial/multi_polynomial_sequence.py
++++ b/src/sage/rings/polynomial/multi_polynomial_sequence.py
+@@ -163,7 +163,6 @@ from sage.misc.cachefunc import cached_method
+
+ from types import GeneratorType
+ from sage.misc.converting_dict import KeyConvertingDict
+-from sage.misc.package import is_package_installed
+
+ from sage.structure.sequence import Sequence, Sequence_generic
+
+@@ -1433,10 +1432,11 @@ class PolynomialSequence_gf2(PolynomialSequence_generic):
+
+ if S != []:
+ if algorithm == "exhaustive_search":
+- if not is_package_installed('fes'):
+- from sage.misc.package import PackageNotFoundError
+- raise PackageNotFoundError("fes")
+- from sage.libs.fes import exhaustive_search
++ try:
++ from sage.libs.fes import exhaustive_search
++ except ImportError:
++ raise RuntimeError("You must install the optional fes package.")
++
+ solutions = exhaustive_search(S, max_sols=n, verbose=verbose, **kwds)
+
+ elif algorithm == "polybori":
Copied: sagemath/repos/community-staging-x86_64/jupyter-path.patch (from rev 206902, sagemath/trunk/jupyter-path.patch)
===================================================================
--- community-staging-x86_64/jupyter-path.patch (rev 0)
+++ community-staging-x86_64/jupyter-path.patch 2017-01-12 06:54:01 UTC (rev 206903)
@@ -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/package.patch (from rev 206902, sagemath/trunk/package.patch)
===================================================================
--- community-staging-x86_64/package.patch (rev 0)
+++ community-staging-x86_64/package.patch 2017-01-12 06:54:01 UTC (rev 206903)
@@ -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/skip-check.patch (from rev 206902, sagemath/trunk/skip-check.patch)
===================================================================
--- community-staging-x86_64/skip-check.patch (rev 0)
+++ community-staging-x86_64/skip-check.patch 2017-01-12 06:54:01 UTC (rev 206903)
@@ -0,0 +1,22 @@
+--- src/bin/sage.orig 2014-12-18 09:47:27.354829070 +0100
++++ src/bin/sage 2014-12-18 09:48:00.041563401 +0100
+@@ -352,18 +352,6 @@
+
+ # Prepare for running Sage, either interactively or non-interactively.
+ sage_setup() {
+- # Check that we're not in a source tarball which hasn't been built yet (#13561).
+- if [ ! -d "$SAGE_LOCAL/lib/python/site-packages/sage" ]; then
+- echo >&2 '************************************************************************'
+- echo >&2 'It seems that you are attempting to run Sage from an unpacked source'
+- echo >&2 'tarball, but you have not compiled it yet (or maybe the build has not'
+- echo >&2 'finished). You should run `make` in the Sage root directory first.'
+- echo >&2 'If you did not intend to build Sage from source, you should download'
+- echo >&2 'a binary tarball instead. Read README.txt for more information.'
+- echo >&2 '************************************************************************'
+- exit 1
+- fi
+-
+ # Display the startup banner (unless SAGE_BANNER is explictly "no")
+ if [ "$SAGE_BANNER" != "no" ]; then
+ # can be 'bare', or 'yes', or unspecified
+
Copied: sagemath/repos/community-staging-x86_64/test-optional.patch (from rev 206902, sagemath/trunk/test-optional.patch)
===================================================================
--- community-staging-x86_64/test-optional.patch (rev 0)
+++ community-staging-x86_64/test-optional.patch 2017-01-12 06:54:01 UTC (rev 206903)
@@ -0,0 +1,25 @@
+--- src/sage/doctest/control.py.orig 2016-10-20 19:39:53.714618246 +0200
++++ src/sage/doctest/control.py 2016-10-20 19:40:15.158049920 +0200
+@@ -307,22 +307,6 @@
+ if "all" in options.optional:
+ # Special case to run all optional tests
+ options.optional = True
+- else:
+- # We replace the 'optional' tag by all optional
+- # packages for which the installed version matches the
+- # latest available version (this implies in particular
+- # that the package is actually installed).
+- if 'optional' in options.optional:
+- options.optional.discard('optional')
+- from sage.misc.package import list_packages
+- for pkg in list_packages('optional', local=True).values():
+- if pkg['installed_version'] == pkg['remote_version']:
+- options.optional.add(pkg['name'])
+-
+- # Check that all tags are valid
+- for o in options.optional:
+- if not optionaltag_regex.search(o):
+- raise ValueError('invalid optional tag {!r}'.format(o))
+
+ self.options = options
+ self.files = args
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