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# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI="3"
PYTHON_DEPEND="2:2.6"
PYTHON_USE_WITH="sqlite"
inherit distutils eutils flag-o-matic python
MY_P="sage-${PV}"
DESCRIPTION="Math software for algebra, geometry, number theory, cryptography and numerical computation"
HOMEPAGE="http://www.sagemath.org"
SRC_URI="mirror://sage/spkg/standard/${MY_P}.spkg -> ${P}.tar.bz2"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~ppc ~x86"
IUSE="examples latex testsuite X"
CDEPEND="|| ( =dev-lang/python-2.6.4-r99
=dev-lang/python-2.6.5-r99 )
dev-libs/gmp
>=dev-libs/mpfr-2.4.2
>=dev-libs/ntl-5.5.2
>=dev-lisp/ecls-10.2.1[-unicode]
>=dev-python/numpy-1.4.1[lapack]
>=sci-mathematics/eclib-20100711
>=sci-mathematics/ecm-6.2.1
>=sci-libs/flint-1.5.0[ntl]
>=sci-libs/fplll-3.0.12
=sci-libs/givaro-3.2*
>=sci-libs/gsl-1.14
>=sci-libs/iml-1.0.1
>=sci-libs/libcliquer-1.2_p6
>=sci-libs/linbox-1.1.6[ntl,sage]
>=sci-libs/m4ri-20100701
>=sci-libs/mpfi-1.4
>=sci-libs/pynac-0.2.0_p5
>=sci-libs/symmetrica-2.0
>=sci-libs/zn_poly-0.9
>=sci-mathematics/glpk-4.43[gmp]
>=sci-mathematics/lcalc-1.23[pari]
>=sci-mathematics/pari-2.3.5[data,gmp]
>=sci-mathematics/polybori-0.6.5-r2[sage]
>=sci-mathematics/ratpoints-2.1.3
~sci-mathematics/sage-baselayout-${PV}[testsuite=]
~sci-mathematics/sage-clib-${PV}
~sci-mathematics/singular-3.1.1.4[libsingular]
media-libs/gd
media-libs/libpng
>=sys-libs/readline-6.0
sys-libs/zlib
virtual/cblas"
DEPEND="${CDEPEND}
=dev-python/cython-0.12*"
RDEPEND="${CDEPEND}
>=dev-lang/R-2.10.1[lapack,readline]
>=dev-python/cvxopt-0.9
>=dev-python/gdmodule-0.56
>=dev-python/ipython-0.9.1
>=dev-python/jinja-2.1.1
>=dev-python/matplotlib-1.0.0
~dev-python/mpmath-0.15
>=dev-python/networkx-1.2
~dev-python/pexpect-2.0
>=dev-python/pycrypto-2.1.0
>=dev-python/python-gnutls-1.1.4
>=dev-python/rpy-2.0.6
>=dev-python/sphinx-0.6.3
dev-python/sqlalchemy
~dev-python/sympy-0.6.6
>=media-gfx/tachyon-0.98
>=net-zope/zodb-3.7.0
>=sci-libs/cddlib-094f
=sci-libs/scipy-0.8*
>=sci-mathematics/flintqs-20070817_p4
>=sci-mathematics/gap-4.4.12
>=sci-mathematics/gap-guava-3.4
>=sci-mathematics/genus2reduction-0.3
>=sci-mathematics/gfan-0.4
>=sci-mathematics/cu2-20060223
>=sci-mathematics/cubex-20060128
>=sci-mathematics/dikcube-20070912_p12
~sci-mathematics/maxima-5.20.1[ecl]
>=sci-mathematics/mcube-20051209
>=sci-mathematics/optimal-20040603
>=sci-mathematics/palp-1.1
~sci-mathematics/sage-data-conway_polynomials-0.2
~sci-mathematics/sage-data-elliptic_curves-0.1
~sci-mathematics/sage-data-graphs-20070722_p1
~sci-mathematics/sage-data-polytopes_db-20100210
>=sci-mathematics/sage-doc-${PV}
~sci-mathematics/sage-extcode-${PV}
~sci-mathematics/sage-notebook-0.8.2
>=sci-mathematics/sympow-1.018.1_p8
examples? ( ~sci-mathematics/sage-examples-${PV} )
testsuite? (
~sci-mathematics/sage-doc-${PV}[html]
~sci-mathematics/sage-examples-${PV}
)
latex? ( ~dev-tex/sage-latex-2.2.5 )"
# TODO: check if use flags are necessary
src_prepare() {
# ATLAS independence
local cblaslibs=\'$(pkg-config --libs-only-l cblas | sed \
-e 's/^-l//' \
-e "s/ -l/\',\'/g" \
-e 's/,.pthread//g' \
-e "s: ::")\'
############################################################################
# Fixes to Sage's build system
############################################################################
# Fix startup issue and python-2.6.5 problem
append-flags -fno-strict-aliasing -DNDEBUG
# fix build file to make it compile without other Sage components
epatch "${FILESDIR}"/${PN}-4.3.4-site-packages.patch
# add pari and gmp to everything.
sed -i "s:\['stdc++', 'ntl'\]:\['stdc++', 'ntl','pari','gmp'\]:g" setup.py \
|| die "failed to add pari and gmp everywhere"
# remove annoying std=c99 from a c++ file.
epatch "${FILESDIR}"/${PN}-4.4.4-extra-stdc99.patch
# Fix ecls bug for ppc see #308909. This has to be done before sed is applied to module_list.py
if use ppc ; then
epatch "${FILESDIR}"/${P}-ecls_ppc.patch
fi
# upgrade to numpy-1.4.1/scipy-0.8
epatch "${FILESDIR}"/trac_9808_numpy_doctest_change.patch
# use already installed csage
rm -rf c_lib || die "failed to remove c library directory"
# patch SAGE_LOCAL
sed -i "s:SAGE_LOCAL = SAGE_ROOT + '/local/':SAGE_LOCAL = os.environ['SAGE_LOCAL']:g" \
module_list.py setup.py || die "failed to patch SAGE_LOCAL"
# fix include paths
sed -i \
-e "s:SAGE_ROOT[[:space:]]*+[[:space:]]*\([\'\"]\)/local/include/\([^\1]*\)\1:SAGE_LOCAL + \1/include/\2\1:g" \
-e "s:sage/c_lib/include/:${EPREFIX}/usr/include/csage/:g" \
module_list.py || die "failed to patch paths for libraries"
sed -i "s:'%s/sage/sage/ext'%SAGE_DEVEL:'sage/ext':g" \
setup.py || die "failed to patch extensions path"
# fix png library name
sed -i "s:png12:$(libpng-config --libs | cut -dl -f2):g" \
module_list.py || die "failed to patch png library name"
# fix numpy path
sed -i "s:SAGE_ROOT+'/local/lib/python/site-packages/numpy/core/include':'$(python_get_sitedir)/numpy/core/include':g" \
module_list.py || die "failed to patch path for numpy include directory"
# fix cython path
sed -i "s:SAGE_LOCAL + '/lib/python/site-packages/Cython/Includes/':'$(python_get_sitedir)/Cython/Includes/':g" \
setup.py || die "failed to patch path for cython include directory"
# fix lcalc path
sed -i "s:include/lcalc/:include/Lfunction/:g" module_list.py \
|| die "failed to patch path for lcalc include directory"
# rebuild in place
sed -i "s:SAGE_DEVEL + 'sage/sage/ext/interpreters':'sage/ext/interpreters':g" \
setup.py || die "failed to patch interpreters path"
# fix include paths and CBLAS/ATLAS
sed -i \
-e "s:'%s/include/csage'%SAGE_LOCAL:'${EPREFIX}/usr/include/csage':g" \
-e "s:'%s/sage/sage/ext'%SAGE_DEVEL:'sage/ext':g" \
setup.py || die "failed to patch include paths"
sed -i \
-e "s:BLAS, BLAS2:${cblaslibs}:g" \
-e "s:,BLAS:,${cblaslibs}:g" \
module_list.py || die "failed to patch module_list.py for ATLAS"
# enable glpk
sed -i "s:is_package_installed('glpk'):True:g" module_list.py \
|| die "failed to enable glpk"
# TODO: why does Sage fail with linbox commentator ?
############################################################################
# Fixes to Sage itself
############################################################################
# gmp-5 compatibility - works with gmp-4.3 as well
sed -i "s:__GMP_BITS_PER_MP_LIMB:GMP_LIMB_BITS:g" sage/rings/integer.pyx \
|| die "failed to patch for gmp-5"
# run maxima with ecl
sed -i \
-e "s:maxima-noreadline:maxima -l ecl:g" \
-e "s:maxima --very-quiet:maxima -l ecl --very-quiet:g" \
sage/interfaces/maxima.py || die "failed to patch maxima commands"
# Uses singular internal copy of the factory header
sed -i "s:factory.h:singular/factory.h:" sage/libs/singular/singular-cdefs.pxi \
|| die "failed to patch factory header"""
# upgrade to matplotlib-1.0.0 as it is now marked stable
epatch "${FILESDIR}"/trac-9221-matplotlib-update.patch
# use delaunay from matplotlib (see ticket #6946)
epatch "${FILESDIR}"/${PN}-4.3.3-delaunay-from-matplotlib.patch
# use arpack from scipy (see also scipy ticket #231)
epatch "${FILESDIR}"/${PN}-4.3.3-arpack-from-scipy.patch
# Fix portage QA warning. Potentially prevent some leaking.
epatch "${FILESDIR}"/${PN}-4.4.2-flint.patch
sed -i "s:cblas(), atlas():${cblaslibs}:" sage/misc/cython.py \
|| die "failed to patch cython.py for ATLAS"
# patch for optional glpk
sed -i "s:\.\./\.\./local/include/glpk\.h:${EPREFIX}/usr/include/glpk.h:g" \
sage/numerical/mip_glpk.pxd || die "failed to patch mip_glpk.pxd"
sed -i "s:\.\./\.\./\.\./\.\./devel/sage/sage:..:g" \
sage/numerical/mip_glpk.pyx || die "failed to patch mip_glpk.pyx"
# Ticket #5155:
# save gap_stamp to directory where sage is able to write
sed -i "s:GAP_STAMP = '%s/local/bin/gap_stamp'%SAGE_ROOT:GAP_STAMP = '%s/gap_stamp'%DOT_SAGE:g" \
sage/interfaces/gap.py || die "patch to patch gap interface"
# fix qepcad paths
epatch "${FILESDIR}"/${PN}-4.5.1-fix-qepcad-path.patch
# fix save path (for testing only)
sed -i "s:save(w,'test'):save(w,tmp_filename('test')):g" \
sage/combinat/words/morphism.py || die "failed to patch path for save"
# Ticket #8898:
# make sure line endings are unix ones so as not to confuse python-2.6.5
edos2unix sage/libs/mpmath/ext_impl.pxd
edos2unix sage/libs/mpmath/ext_main.pyx
edos2unix sage/libs/mpmath/ext_main.pxd
edos2unix sage/libs/mpmath/ext_libmp.pyx
# replace SAGE_ROOT/local with SAGE_LOCAL
epatch "${FILESDIR}"/${PN}-4.5.1-fix-SAGE_LOCAL.patch
# patch path for saving sessions
sed -i "s:save_session('tmp_f', :save_session(tmp_f, :g" \
sage/misc/session.pyx || die "failed to patch session path"
# patch lie library path
sed -i "s:open(SAGE_LOCAL + 'lib/lie/INFO\.0'):open(SAGE_LOCAL + '/share/lie/INFO.0'):g" \
sage/interfaces/lie.py || die "failed to patch lie library path"
# Patch to singular info file shipped with sage-doc
sed -i "s:os.environ\[\"SAGE_LOCAL\"\]+\"/share/singular/\":os.environ\[\"SAGE_DOC\"\]+\"/\":g" \
sage/interfaces/singular.py || die "failed to patch singular.hlp path"
# fix test paths
sed -i \
-e "s:'my_animation.gif':tmp_filename('my_animation')+'.gif':g" \
-e "s:'wave.gif':tmp_filename('wave')+'.gif':g" \
-e "s:'wave0.sobj':tmp_filename('wave0')+'.sobj':g" \
-e "s:'wave1.sobj':tmp_filename('wave1')+'.sobj':g" \
sage/plot/animate.py
# do not forget to run distutils
distutils_src_prepare
}
src_configure() {
export SAGE_LOCAL="${EPREFIX}"/usr
export SAGE_ROOT="${EPREFIX}"/usr/share/sage
export SAGE_VERSION=${PV}
export MAKE=${MAKEOPTS}
# files are not built unless they are touched
find sage -name "*pyx" -exec touch '{}' \; \
|| die "failed to touch *pyx files"
}
src_install() {
distutils_src_install
if use testsuite ; then
# install testable sources and sources needed for testing
find sage ! \( -name "*.py" -o -name "*.pyx" -o -name "*.pxd" -o \
-name "*.pxi" \) -type f -delete \
|| die "failed to remove non-testable sources"
insinto "${SAGE_ROOT}"/devel/sage-main
doins -r sage || die
fi
}
pkg_postinst() {
einfo "If you use Sage's browser interface ('Sage Notebook') and experience"
einfo "an 'Internal Server Error' you should append the following line to"
einfo "your ~/.bashrc (replace firefox with your favorite browser and note"
einfo "that it your case it WILL NOT WORK with xdg-open):"
einfo ""
einfo " export SAGE_BROWSER=/usr/bin/firefox"
einfo ""
einfo "Sage comes with the 'Standard' set of Sage Packages, i.e. those"
einfo "listed at: http://sagemath.org/packages/standard/ which are now"
einfo "already installed."
einfo "There are also some packages of the 'Optional' set (which consists"
einfo "of the these: http://sagemath.org/packages/optional/) available"
einfo "which may be installed with portage as usual."
if use testsuite ; then
einfo "You have installed Sage's testsuite. In order to test Sage run the"
einfo "following command in a directory where Sage may write to:"
einfo ""
einfo " sage -testall"
einfo ""
einfo "Note that testing Sage may take more than 4 hours. If you want to"
einfo "compare your results look at the list of known failures:"
einfo ""
einfo " http://github.com/cschwan/sage-on-gentoo/wiki/Known-test-failures"
fi
}
|