commit: 31948f21ddfb503f0c25d80ee1f38ba348fbc69d
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 23 10:34:09 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Sep 23 10:34:09 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=31948f21
Drop unnecessary die from emake
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
dev-cpp/eigen/eigen-3.2.2.ebuild | 118 ++++++++++-
dev-cpp/eigen/eigen-3.2.4.ebuild | 118 ++++++++++-
.../arrayfire-python-3.0.20150914.ebuild | 31 ++-
dev-python/brewer2mpl/brewer2mpl-1.4.1.ebuild | 26 ++-
dev-python/ipykernel/ipykernel-4.0.3.ebuild | 40 +++-
dev-python/ipyparallel/ipyparallel-4.0.0-r1.ebuild | 63 +++++-
.../ipython_genutils/ipython_genutils-0.1.0.ebuild | 35 +++-
dev-python/ipywidgets/ipywidgets-4.0.2-r1.ebuild | 43 +++-
.../matlab_wrapper/matlab_wrapper-0.9.6.ebuild | 26 ++-
.../matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild | 31 ++-
dev-python/pickleshare/pickleshare-0.5.ebuild | 40 +++-
.../prettyplotlib/prettyplotlib-0.1.7.ebuild | 31 ++-
dev-python/python-ivi/python-ivi-0.14.9.ebuild | 31 ++-
dev-python/python-vxi11/python-vxi11-0.7.ebuild | 23 ++-
dev-python/python-vxi11/python-vxi11-0.8.ebuild | 23 ++-
dev-python/qtconsole/qtconsole-4.0.1-r1.ebuild | 68 +++++-
dev-python/simplepam/simplepam-0.1.5.ebuild | 23 ++-
dev-python/traitlets/traitlets-4.0.0.ebuild | 60 +++++-
media-gfx/brlcad/brlcad-7.22.0.ebuild | 2 +-
media-gfx/brlcad/brlcad-7.24.0.ebuild | 2 +-
media-gfx/brlcad/brlcad-7.24.2.ebuild | 4 +-
media-gfx/brlcad/brlcad-9999.ebuild | 2 +-
sci-astronomy/missfits/missfits-2.8.0.ebuild | 34 ++-
sci-astronomy/psfex/psfex-3.17.0.ebuild | 71 ++++++-
sci-astronomy/psfex/psfex-3.9.1.ebuild | 71 ++++++-
sci-astronomy/sextractor/sextractor-2.19.5.ebuild | 74 ++++++-
sci-astronomy/skymaker/skymaker-3.10.5.ebuild | 36 +++-
sci-astronomy/stiff/stiff-2.4.0.ebuild | 44 +++-
sci-astronomy/stuff/stuff-1.26.0.ebuild | 36 +++-
sci-astronomy/swarp/swarp-2.38.0.ebuild | 42 +++-
.../weightwatcher/weightwatcher-1.12.ebuild | 36 +++-
sci-biology/biopieces/biopieces-0.51.ebuild | 73 ++++++-
sci-biology/blasr/blasr-9999.ebuild | 2 +-
sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild | 2 +-
sci-biology/mgblast/mgblast-0.1.ebuild | 2 +-
sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild | 157 +++++++++++++-
sci-biology/pileup/pileup-0.6.ebuild | 4 +-
sci-biology/tablet/tablet-1.14.04.10.ebuild | 50 ++++-
sci-libs/asl/asl-0.1.5.ebuild | 49 ++++-
.../blas-reference-20131116-r1.ebuild | 119 ++++++++++-
sci-libs/fox/fox-4.1.2-r2.ebuild | 4 +-
.../lapack-reference/lapack-reference-3.4.2.ebuild | 140 ++++++++++++-
.../lapack-reference/lapack-reference-3.5.0.ebuild | 140 ++++++++++++-
.../lapacke-reference-3.4.2.ebuild | 104 +++++++++-
.../lapacke-reference-3.5.0.ebuild | 104 +++++++++-
sci-libs/libsc/libsc-1.1.ebuild | 72 ++++++-
sci-libs/openblas/openblas-0.2.12.ebuild | 228 ++++++++++++++++++++-
sci-libs/openblas/openblas-0.2.14.ebuild | 228 ++++++++++++++++++++-
sci-libs/p4est/p4est-1.1.ebuild | 100 ++++++++-
sci-mathematics/htk/htk-3.4.1.ebuild | 2 +-
sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild | 2 +-
sci-mathematics/yorick/yorick-2.1.06.ebuild | 2 +-
sci-physics/abinit/abinit-7.10.4.ebuild | 2 +-
sci-physics/genfit/genfit-02.00.00.ebuild | 60 +++++-
sys-cluster/openmpi/openmpi-1.6.5.ebuild | 4 +-
55 files changed, 2875 insertions(+), 59 deletions(-)
diff --git a/dev-cpp/eigen/eigen-3.2.2.ebuild b/dev-cpp/eigen/eigen-3.2.2.ebuild
deleted file mode 120000
index eafd774..0000000
--- a/dev-cpp/eigen/eigen-3.2.2.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-eigen-9999.ebuild
\ No newline at end of file
diff --git a/dev-cpp/eigen/eigen-3.2.2.ebuild b/dev-cpp/eigen/eigen-3.2.2.ebuild
new file mode 100644
index 0000000..64caa71
--- /dev/null
+++ b/dev-cpp/eigen/eigen-3.2.2.ebuild
@@ -0,0 +1,117 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+FORTRAN_NEEDED=fortran
+
+if [[ ${PV} == "9999" ]] ; then
+ inherit mercurial
+ EHG_REPO_URI="https://bitbucket.org/eigen/eigen";
+ SRC_URI=""
+ KEYWORDS=""
+else
+ inherit vcs-snapshot
+ SRC_URI="
+ http://bitbucket.org/eigen/eigen/get/${PV}.tar.bz2 ->
${P}.tar.bz2
+
https://bitbucket.org/eigen/eigen/commits/1d71b1341c03a7c485289be2c8bd906a259c0487/raw/
-> ${P}-cmake.patch
+ "
+ PATCHES=( "${DISTDIR}"/${P}-cmake.patch )
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+inherit alternatives-2 cmake-utils fortran-2 multilib
+
+DESCRIPTION="C++ template library for linear algebra"
+HOMEPAGE="http://eigen.tuxfamily.org/";
+
+SLOT="3"
+LICENSE="MPL-2.0"
+IUSE="adolc doc fortran fftw gmp metis mkl pastix sparse static-libs test"
+
+CDEPEND="
+ adolc? ( sci-libs/adolc[sparse?] )
+ fftw? ( sci-libs/fftw:3.0 )
+ gmp? ( dev-libs/gmp:0 dev-libs/mpfr:0 )
+ metis? ( sci-libs/metis )
+ mkl? ( sci-libs/mkl )
+ pastix? ( sci-libs/pastix )
+ sparse? (
+ dev-cpp/sparsehash
+ sci-libs/cholmod[metis?]
+ sci-libs/spqr
+ sci-libs/superlu
+ sci-libs/umfpack )"
+DEPEND="
+ doc? ( app-doc/doxygen[dot,latex] )
+ test? ( ${CDEPEND} )"
+
+RDEPEND="
+ !dev-cpp/eigen:0
+ ${CDEPEND}"
+
+src_prepare() {
+ sed -i \
+ -e "s:/usr:${EPREFIX}/usr:g" \
+ -e "s:/bin/bash:${EPREFIX}/bin/bash:g" \
+ cmake/*.cmake || die
+ sed -i \
+ -e "/DESTINATION/s:lib:$(get_libdir):g" \
+ {blas,lapack}/CMakeLists.txt || die
+
+ # TOFIX: static-libs for blas are always built with PIC
+ use static-libs || sed -i \
+ -e "/add_dependencies/s/eigen_[a-z]*_static//g" \
+ -e "/TARGETS/s/eigen_[a-z]*_static//g" \
+ -e "/add_library(eigen_[a-z]*_static/d" \
+ -e "/target_link_libraries(eigen_[a-z]*_static/d" \
+ {blas,lapack}/CMakeLists.txt || die
+ cmake-utils_src_prepare
+}
+
+src_configure() {
+ # TOFIX: is it worth fixing all the automagic given no library is built?
+ # cmake has buggy disable_testing feature, so leave it for now
+ local mycmakeargs=(
+ -DDART_TESTING_TIMEOUT=300
+ -DEIGEN_BUILD_BTL=OFF
+ )
+ export VARTEXFONTS="${T}/fonts"
+ CMAKE_BUILD_TYPE="release" cmake-utils_src_configure
+ # use fortran && FORTRAN_LIBS="blas lapack" not ready
+ use fortran && FORTRAN_LIBS="blas"
+}
+
+src_compile() {
+ local targets="${FORTRAN_LIBS}"
+ use doc && targets+=" doc"
+ use test && targets+=" check"
+ cmake-utils_src_compile ${targets}
+}
+
+src_install() {
+ cmake-utils_src_install
+ use doc && dohtml -r "${BUILD_DIR}"/doc/html/*
+ local x
+ for x in ${FORTRAN_LIBS}; do
+ local libname="eigen_${x}"
+ emake DESTDIR="${D}" -C "${BUILD_DIR}/${x}" install ${libname}
+ cat > ${libname}.pc <<-EOF
+ prefix=${EPREFIX}/usr
+ libdir=\${prefix}/$(get_libdir)
+ includedir=\${prefix}/include
+ Name: ${PN}
+ Description: ${DESCRIPTION} ${x^^} implementation
+ Version: ${PV}
+ URL: ${HOMEPAGE}
+ Libs: -L\${libdir} -l${libname}
+ Libs.private: -lm
+ $([[ ${x} == lapack ]] && echo "Requires: blas")
+ EOF
+ alternatives_for ${x} eigen 0 \
+ /usr/$(get_libdir)/pkgconfig/${x}.pc ${libname}.pc
+ insinto /usr/$(get_libdir)/pkgconfig
+ doins ${libname}.pc
+ done
+}
diff --git a/dev-cpp/eigen/eigen-3.2.4.ebuild b/dev-cpp/eigen/eigen-3.2.4.ebuild
deleted file mode 120000
index eafd774..0000000
--- a/dev-cpp/eigen/eigen-3.2.4.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-eigen-9999.ebuild
\ No newline at end of file
diff --git a/dev-cpp/eigen/eigen-3.2.4.ebuild b/dev-cpp/eigen/eigen-3.2.4.ebuild
new file mode 100644
index 0000000..64caa71
--- /dev/null
+++ b/dev-cpp/eigen/eigen-3.2.4.ebuild
@@ -0,0 +1,117 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+FORTRAN_NEEDED=fortran
+
+if [[ ${PV} == "9999" ]] ; then
+ inherit mercurial
+ EHG_REPO_URI="https://bitbucket.org/eigen/eigen";
+ SRC_URI=""
+ KEYWORDS=""
+else
+ inherit vcs-snapshot
+ SRC_URI="
+ http://bitbucket.org/eigen/eigen/get/${PV}.tar.bz2 ->
${P}.tar.bz2
+
https://bitbucket.org/eigen/eigen/commits/1d71b1341c03a7c485289be2c8bd906a259c0487/raw/
-> ${P}-cmake.patch
+ "
+ PATCHES=( "${DISTDIR}"/${P}-cmake.patch )
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+inherit alternatives-2 cmake-utils fortran-2 multilib
+
+DESCRIPTION="C++ template library for linear algebra"
+HOMEPAGE="http://eigen.tuxfamily.org/";
+
+SLOT="3"
+LICENSE="MPL-2.0"
+IUSE="adolc doc fortran fftw gmp metis mkl pastix sparse static-libs test"
+
+CDEPEND="
+ adolc? ( sci-libs/adolc[sparse?] )
+ fftw? ( sci-libs/fftw:3.0 )
+ gmp? ( dev-libs/gmp:0 dev-libs/mpfr:0 )
+ metis? ( sci-libs/metis )
+ mkl? ( sci-libs/mkl )
+ pastix? ( sci-libs/pastix )
+ sparse? (
+ dev-cpp/sparsehash
+ sci-libs/cholmod[metis?]
+ sci-libs/spqr
+ sci-libs/superlu
+ sci-libs/umfpack )"
+DEPEND="
+ doc? ( app-doc/doxygen[dot,latex] )
+ test? ( ${CDEPEND} )"
+
+RDEPEND="
+ !dev-cpp/eigen:0
+ ${CDEPEND}"
+
+src_prepare() {
+ sed -i \
+ -e "s:/usr:${EPREFIX}/usr:g" \
+ -e "s:/bin/bash:${EPREFIX}/bin/bash:g" \
+ cmake/*.cmake || die
+ sed -i \
+ -e "/DESTINATION/s:lib:$(get_libdir):g" \
+ {blas,lapack}/CMakeLists.txt || die
+
+ # TOFIX: static-libs for blas are always built with PIC
+ use static-libs || sed -i \
+ -e "/add_dependencies/s/eigen_[a-z]*_static//g" \
+ -e "/TARGETS/s/eigen_[a-z]*_static//g" \
+ -e "/add_library(eigen_[a-z]*_static/d" \
+ -e "/target_link_libraries(eigen_[a-z]*_static/d" \
+ {blas,lapack}/CMakeLists.txt || die
+ cmake-utils_src_prepare
+}
+
+src_configure() {
+ # TOFIX: is it worth fixing all the automagic given no library is built?
+ # cmake has buggy disable_testing feature, so leave it for now
+ local mycmakeargs=(
+ -DDART_TESTING_TIMEOUT=300
+ -DEIGEN_BUILD_BTL=OFF
+ )
+ export VARTEXFONTS="${T}/fonts"
+ CMAKE_BUILD_TYPE="release" cmake-utils_src_configure
+ # use fortran && FORTRAN_LIBS="blas lapack" not ready
+ use fortran && FORTRAN_LIBS="blas"
+}
+
+src_compile() {
+ local targets="${FORTRAN_LIBS}"
+ use doc && targets+=" doc"
+ use test && targets+=" check"
+ cmake-utils_src_compile ${targets}
+}
+
+src_install() {
+ cmake-utils_src_install
+ use doc && dohtml -r "${BUILD_DIR}"/doc/html/*
+ local x
+ for x in ${FORTRAN_LIBS}; do
+ local libname="eigen_${x}"
+ emake DESTDIR="${D}" -C "${BUILD_DIR}/${x}" install ${libname}
+ cat > ${libname}.pc <<-EOF
+ prefix=${EPREFIX}/usr
+ libdir=\${prefix}/$(get_libdir)
+ includedir=\${prefix}/include
+ Name: ${PN}
+ Description: ${DESCRIPTION} ${x^^} implementation
+ Version: ${PV}
+ URL: ${HOMEPAGE}
+ Libs: -L\${libdir} -l${libname}
+ Libs.private: -lm
+ $([[ ${x} == lapack ]] && echo "Requires: blas")
+ EOF
+ alternatives_for ${x} eigen 0 \
+ /usr/$(get_libdir)/pkgconfig/${x}.pc ${libname}.pc
+ insinto /usr/$(get_libdir)/pkgconfig
+ doins ${libname}.pc
+ done
+}
diff --git a/dev-python/arrayfire-python/arrayfire-python-3.0.20150914.ebuild
b/dev-python/arrayfire-python/arrayfire-python-3.0.20150914.ebuild
deleted file mode 120000
index a61966c..0000000
--- a/dev-python/arrayfire-python/arrayfire-python-3.0.20150914.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-arrayfire-python-9999.ebuild
\ No newline at end of file
diff --git a/dev-python/arrayfire-python/arrayfire-python-3.0.20150914.ebuild
b/dev-python/arrayfire-python/arrayfire-python-3.0.20150914.ebuild
new file mode 100644
index 0000000..c4d561b
--- /dev/null
+++ b/dev-python/arrayfire-python/arrayfire-python-3.0.20150914.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+PYTHON_COMPAT=( python{2_7,3_3,3_4} )
+
+inherit distutils-r1
+
+DESCRIPTION="Python bindings for ArrayFire"
+HOMEPAGE="http://www.arrayfire.com";
+
+MY_PN="arrayfire"
+
+if [ ${PV} == "9999" ] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/arrayfire/${PN}.git
git://github.com/arrayfire/${PN}.git"
+else
+ SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_PN}-${PV}.tar.gz"
+ KEYWORDS="~amd64"
+ S="${WORKDIR}/${MY_PN}-${PV}"
+fi
+
+LICENSE="BSD"
+SLOT="0"
+
+RDEPEND="
+ >=sci-libs/arrayfire-3.0.0
+ "
+DEPEND="${RDEPEND}"
diff --git a/dev-python/brewer2mpl/brewer2mpl-1.4.1.ebuild
b/dev-python/brewer2mpl/brewer2mpl-1.4.1.ebuild
deleted file mode 120000
index 2ab86f8..0000000
--- a/dev-python/brewer2mpl/brewer2mpl-1.4.1.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-brewer2mpl-9999.ebuild
\ No newline at end of file
diff --git a/dev-python/brewer2mpl/brewer2mpl-1.4.1.ebuild
b/dev-python/brewer2mpl/brewer2mpl-1.4.1.ebuild
new file mode 100644
index 0000000..d74308c
--- /dev/null
+++ b/dev-python/brewer2mpl/brewer2mpl-1.4.1.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+PYTHON_COMPAT=( python{2_7,3_3,3_4} )
+
+inherit distutils-r1
+
+DESCRIPTION="Connect colorbrewer2.org color maps to Python and matplotlib"
+HOMEPAGE="https://github.com/jiffyclub/brewer2mpl";
+
+if [ ${PV} == "9999" ] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/jiffyclub/${PN}.git
git://github.com/jiffyclub/${PN}.git"
+else
+ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+
+RDEPEND="dev-python/matplotlib[${PYTHON_USEDEP}]"
+DEPEND="${RDEPEND}"
diff --git a/dev-python/ipykernel/ipykernel-4.0.3.ebuild
b/dev-python/ipykernel/ipykernel-4.0.3.ebuild
deleted file mode 120000
index 6bb3cdb..0000000
--- a/dev-python/ipykernel/ipykernel-4.0.3.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-ipykernel-9999.ebuild
\ No newline at end of file
diff --git a/dev-python/ipykernel/ipykernel-4.0.3.ebuild
b/dev-python/ipykernel/ipykernel-4.0.3.ebuild
new file mode 100644
index 0000000..f44668a
--- /dev/null
+++ b/dev-python/ipykernel/ipykernel-4.0.3.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+PYTHON_COMPAT=( python2_7 python{3_3,3_4} )
+
+inherit distutils-r1
+
+DESCRIPTION="IPython Kernel for Jupyter"
+HOMEPAGE="https://github.com/ipython/ipykernel";
+
+if [ ${PV} == "9999" ] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/ipython/${PN}.git
git://github.com/ipython/${PN}.git"
+else
+ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="test"
+
+RDEPEND="
+ dev-python/traitlets[${PYTHON_USEDEP}]"
+ #dev-python/jupyter_client[${PYTHON_USEDEP}]
+ #>=dev-python/ipython-4.0.0[${PYTHON_USEDEP}]
+DEPEND="${RDEPEND}
+ test? (
+ dev-python/coverage[${PYTHON_USEDEP}]
+ >=dev-python/ipython-4.0.0[${PYTHON_USEDEP}]
+ dev-python/nose[${PYTHON_USEDEP}]
+ )
+ "
+
+python_test() {
+ nosetests --with-coverage --cover-package ipykernel ipykernel || die
+}
diff --git a/dev-python/ipyparallel/ipyparallel-4.0.0-r1.ebuild
b/dev-python/ipyparallel/ipyparallel-4.0.0-r1.ebuild
deleted file mode 120000
index 1db7c42..0000000
--- a/dev-python/ipyparallel/ipyparallel-4.0.0-r1.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-ipyparallel-9999.ebuild
\ No newline at end of file
diff --git a/dev-python/ipyparallel/ipyparallel-4.0.0-r1.ebuild
b/dev-python/ipyparallel/ipyparallel-4.0.0-r1.ebuild
new file mode 100644
index 0000000..b1c0267
--- /dev/null
+++ b/dev-python/ipyparallel/ipyparallel-4.0.0-r1.ebuild
@@ -0,0 +1,62 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+PYTHON_COMPAT=( python2_7 python{3_3,3_4} )
+
+inherit distutils-r1
+
+DESCRIPTION="Interactive Parallel Computing with IPython"
+HOMEPAGE="http://ipython.org/";
+
+if [ ${PV} == "9999" ] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/ipython/${PN}.git
git://github.com/ipython/${PN}.git"
+else
+ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="doc test"
+
+RDEPEND="
+ dev-python/ipython_genutils[${PYTHON_USEDEP}]
+ dev-python/decorator[${PYTHON_USEDEP}]
+ >=dev-python/pyzmq-14.4.0[${PYTHON_USEDEP}]
+ dev-python/ipykernel[${PYTHON_USEDEP}]
+ >=dev-python/ipython-4.0.0[${PYTHON_USEDEP}]
+ dev-python/jupyter_client[${PYTHON_USEDEP}]
+ "
+DEPEND="${RDEPEND}
+ doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
+ test? (
+ dev-python/nose[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-python/coverage[${PYTHON_USEDEP}]
+ )
+ "
+
+python_prepare_all() {
+ # Prevent un-needed download during build
+ if use doc; then
+ sed -e "/^ 'sphinx.ext.intersphinx',/d" -i
docs/source/conf.py || die
+ fi
+
+ distutils-r1_python_prepare_all
+}
+
+python_compile_all() {
+ use doc && emake -C docs html
+}
+
+python_test() {
+ iptest --coverage xml ipyparallel.tests || die
+}
+
+python_install_all() {
+ use doc && HTML_DOCS=( docs/build/html/. )
+ distutils-r1_python_install_all
+}
diff --git a/dev-python/ipython_genutils/ipython_genutils-0.1.0.ebuild
b/dev-python/ipython_genutils/ipython_genutils-0.1.0.ebuild
deleted file mode 120000
index 66350df..0000000
--- a/dev-python/ipython_genutils/ipython_genutils-0.1.0.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-ipython_genutils-9999.ebuild
\ No newline at end of file
diff --git a/dev-python/ipython_genutils/ipython_genutils-0.1.0.ebuild
b/dev-python/ipython_genutils/ipython_genutils-0.1.0.ebuild
new file mode 100644
index 0000000..3c7b157
--- /dev/null
+++ b/dev-python/ipython_genutils/ipython_genutils-0.1.0.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+PYTHON_COMPAT=( python2_7 python{3_3,3_4} )
+
+inherit distutils-r1
+
+DESCRIPTION="Vestigial utilities from IPython"
+HOMEPAGE="https://github.com/ipython/ipython_genutils";
+
+if [ ${PV} == "9999" ] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/ipython/${PN}.git
git://github.com/ipython/${PN}.git"
+else
+ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="test"
+
+DEPEND="
+ test? (
+ dev-python/nose[${PYTHON_USEDEP}]
+ dev-python/coverage[${PYTHON_USEDEP}]
+ )
+ "
+
+python_test() {
+ nosetests --with-coverage --cover-package=ipython_genutils
ipython_genutils || die
+}
diff --git a/dev-python/ipywidgets/ipywidgets-4.0.2-r1.ebuild
b/dev-python/ipywidgets/ipywidgets-4.0.2-r1.ebuild
deleted file mode 120000
index e3cd5c1..0000000
--- a/dev-python/ipywidgets/ipywidgets-4.0.2-r1.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-ipywidgets-9999.ebuild
\ No newline at end of file
diff --git a/dev-python/ipywidgets/ipywidgets-4.0.2-r1.ebuild
b/dev-python/ipywidgets/ipywidgets-4.0.2-r1.ebuild
new file mode 100644
index 0000000..3c3d216
--- /dev/null
+++ b/dev-python/ipywidgets/ipywidgets-4.0.2-r1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+PYTHON_COMPAT=( python2_7 python{3_3,3_4} )
+
+inherit distutils-r1
+
+DESCRIPTION="IPython HTML widgets for Jupyter"
+HOMEPAGE="http://ipython.org/";
+
+if [ ${PV} == "9999" ] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/ipython/${PN}.git
git://github.com/ipython/${PN}.git"
+else
+ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="test"
+
+RDEPEND="
+ dev-python/traitlets[${PYTHON_USEDEP}]
+ dev-python/ipykernel[${PYTHON_USEDEP}]
+ "
+DEPEND="${RDEPEND}
+ test? (
+ $(python_gen_cond_dep 'dev-python/mock[${PYTHON_USEDEP}]'
python2_7)
+ dev-python/nose[${PYTHON_USEDEP}]
+ dev-python/coverage[${PYTHON_USEDEP}]
+ www-client/casperjs
+ )
+ "
+
+python_test() {
+ nosetests --with-coverage --cover-package=ipywidgets ipywidgets || die
+
+ "${PYTHON}" -m ipywidgets.jstest || die
+}
diff --git a/dev-python/matlab_wrapper/matlab_wrapper-0.9.6.ebuild
b/dev-python/matlab_wrapper/matlab_wrapper-0.9.6.ebuild
deleted file mode 120000
index 09a5074..0000000
--- a/dev-python/matlab_wrapper/matlab_wrapper-0.9.6.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-matlab_wrapper-9999.ebuild
\ No newline at end of file
diff --git a/dev-python/matlab_wrapper/matlab_wrapper-0.9.6.ebuild
b/dev-python/matlab_wrapper/matlab_wrapper-0.9.6.ebuild
new file mode 100644
index 0000000..42a4c47
--- /dev/null
+++ b/dev-python/matlab_wrapper/matlab_wrapper-0.9.6.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+PYTHON_COMPAT=( python2_7 )
+
+inherit distutils-r1
+
+DESCRIPTION="MATLAB wrapper for Python"
+HOMEPAGE="https://github.com/mrkrd/matlab_wrapper";
+
+if [ ${PV} == "9999" ] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/mrkrd/${PN}.git
git://github.com/mrkrd/${PN}.git"
+else
+ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3+"
+SLOT="0"
+
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+DEPEND="${RDEPEND}"
diff --git a/dev-python/matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild
b/dev-python/matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild
deleted file mode 120000
index 49bc235..0000000
--- a/dev-python/matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-matplotlib2tikz-9999.ebuild
\ No newline at end of file
diff --git a/dev-python/matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild
b/dev-python/matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild
new file mode 100644
index 0000000..20ab8da
--- /dev/null
+++ b/dev-python/matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 python3_{3,4} )
+
+inherit distutils-r1
+
+DESCRIPTION="Python script for converting matplotlib figures into native
Pgfplots (TikZ) figures"
+HOMEPAGE="https://github.com/nschloe/matplotlib2tikz";
+
+if [ ${PV} = "9999" ] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/nschloe/${PN}.git
git://github.com/nschloe/${PN}.git"
+ KEYWORDS=""
+else
+
SRC_URI="https://github.com/nschloe/matplotlib2tikz/archive/v${PV}.tar.gz ->
${P}.tar.gz"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="LGPL-3"
+SLOT="0"
+IUSE=""
+
+RDEPEND="dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-texlive/texlive-pictures"
+DEPEND="${RDEPEND}"
+ #test? ( dev-python/pytest[${PYTHON_USEDEP}] )"
diff --git a/dev-python/pickleshare/pickleshare-0.5.ebuild
b/dev-python/pickleshare/pickleshare-0.5.ebuild
deleted file mode 120000
index 16ddbe4..0000000
--- a/dev-python/pickleshare/pickleshare-0.5.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-pickleshare-9999.ebuild
\ No newline at end of file
diff --git a/dev-python/pickleshare/pickleshare-0.5.ebuild
b/dev-python/pickleshare/pickleshare-0.5.ebuild
new file mode 100644
index 0000000..c295d4e
--- /dev/null
+++ b/dev-python/pickleshare/pickleshare-0.5.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 python{3_3,3_4} )
+
+inherit distutils-r1
+
+DESCRIPTION="A small 'shelve' like datastore with concurrency support"
+HOMEPAGE="https://github.com/pickleshare/pickleshare";
+
+if [ ${PV} == "9999" ] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/${PN}/${PN}.git
git://github.com/${PN}/${PN}.git"
+else
+ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+ # test_pickleshare.py is not included in the pickleshare-0.5 source
+ # we fetched from pipy
+ RESTRICT="test"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+IUSE="test"
+
+RDEPEND="
+ dev-python/path-py[${PYTHON_USEDEP}]"
+DEPEND="${RDEPEND}
+ test? ( dev-python/pytest[${PYTHON_USEDEP}] )"
+
+python_test() {
+ distutils_install_for_testing
+ cd "${TEST_DIR}"/lib || die
+ cp "${S}"/test_pickleshare.py "${TEST_DIR}"/lib/ || die
+ py.test || die
+}
diff --git a/dev-python/prettyplotlib/prettyplotlib-0.1.7.ebuild
b/dev-python/prettyplotlib/prettyplotlib-0.1.7.ebuild
deleted file mode 120000
index 46a331d..0000000
--- a/dev-python/prettyplotlib/prettyplotlib-0.1.7.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-prettyplotlib-9999.ebuild
\ No newline at end of file
diff --git a/dev-python/prettyplotlib/prettyplotlib-0.1.7.ebuild
b/dev-python/prettyplotlib/prettyplotlib-0.1.7.ebuild
new file mode 100644
index 0000000..8680ca7
--- /dev/null
+++ b/dev-python/prettyplotlib/prettyplotlib-0.1.7.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+PYTHON_COMPAT=( python{2_7,3_3,3_4} )
+
+inherit distutils-r1
+
+DESCRIPTION="Painlessly create beautiful matplotlib plots"
+HOMEPAGE="http://blog.olgabotvinnik.com/prettyplotlib/";
+
+if [ ${PV} == "9999" ] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/olgabot/${PN}.git
git://github.com/olgabot/${PN}.git"
+else
+ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+
+RDEPEND="
+ sci-libs/scipy[${PYTHON_USEDEP}]
+ >=dev-python/matplotlib-1.4.0[${PYTHON_USEDEP}]
+ dev-python/brewer2mpl[${PYTHON_USEDEP}]
+ dev-python/six[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]"
+DEPEND="${RDEPEND}"
diff --git a/dev-python/python-ivi/python-ivi-0.14.9.ebuild
b/dev-python/python-ivi/python-ivi-0.14.9.ebuild
deleted file mode 120000
index 267b209..0000000
--- a/dev-python/python-ivi/python-ivi-0.14.9.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-python-ivi-9999.ebuild
\ No newline at end of file
diff --git a/dev-python/python-ivi/python-ivi-0.14.9.ebuild
b/dev-python/python-ivi/python-ivi-0.14.9.ebuild
new file mode 100644
index 0000000..f0a5176
--- /dev/null
+++ b/dev-python/python-ivi/python-ivi-0.14.9.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+PYTHON_COMPAT=( python{2_7,3_4} )
+
+inherit distutils-r1
+
+DESCRIPTION="Python-based interpretation of the Interchangeable Virtual
Instrument standard"
+HOMEPAGE="https://github.com/python-ivi/python-ivi";
+
+if [ ${PV} == "9999" ] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/${PN}/${PN}.git
git://github.com/${PN}/${PN}.git"
+else
+ SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz ->
${P}.tar.gz"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+
+RDEPEND="
+ || (
+ dev-python/python-vxi11[${PYTHON_USEDEP}]
+ sci-libs/linux-gpib
+ )
+ dev-python/numpy[${PYTHON_USEDEP}]"
+DEPEND="${RDEPEND}"
diff --git a/dev-python/python-vxi11/python-vxi11-0.7.ebuild
b/dev-python/python-vxi11/python-vxi11-0.7.ebuild
deleted file mode 120000
index ed718af..0000000
--- a/dev-python/python-vxi11/python-vxi11-0.7.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-python-vxi11-9999.ebuild
\ No newline at end of file
diff --git a/dev-python/python-vxi11/python-vxi11-0.7.ebuild
b/dev-python/python-vxi11/python-vxi11-0.7.ebuild
new file mode 100644
index 0000000..fd6fcc9
--- /dev/null
+++ b/dev-python/python-vxi11/python-vxi11-0.7.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+PYTHON_COMPAT=( python{2_7,3_4} )
+
+inherit distutils-r1
+
+DESCRIPTION="Provides a pure Python VXI-11 driver for controlling instruments
over Ethernet"
+HOMEPAGE="https://github.com/python-ivi/python-vxi11";
+
+if [ ${PV} == "9999" ] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/python-ivi/${PN}.git
git://github.com/python-ivi/${PN}.git"
+else
+ SRC_URI="https://github.com/python-ivi/${PN}/archive/v${PV}.tar.gz ->
${P}.tar.gz"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="MIT"
+SLOT="0"
diff --git a/dev-python/python-vxi11/python-vxi11-0.8.ebuild
b/dev-python/python-vxi11/python-vxi11-0.8.ebuild
deleted file mode 120000
index ed718af..0000000
--- a/dev-python/python-vxi11/python-vxi11-0.8.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-python-vxi11-9999.ebuild
\ No newline at end of file
diff --git a/dev-python/python-vxi11/python-vxi11-0.8.ebuild
b/dev-python/python-vxi11/python-vxi11-0.8.ebuild
new file mode 100644
index 0000000..fd6fcc9
--- /dev/null
+++ b/dev-python/python-vxi11/python-vxi11-0.8.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+PYTHON_COMPAT=( python{2_7,3_4} )
+
+inherit distutils-r1
+
+DESCRIPTION="Provides a pure Python VXI-11 driver for controlling instruments
over Ethernet"
+HOMEPAGE="https://github.com/python-ivi/python-vxi11";
+
+if [ ${PV} == "9999" ] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/python-ivi/${PN}.git
git://github.com/python-ivi/${PN}.git"
+else
+ SRC_URI="https://github.com/python-ivi/${PN}/archive/v${PV}.tar.gz ->
${P}.tar.gz"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="MIT"
+SLOT="0"
diff --git a/dev-python/qtconsole/qtconsole-4.0.1-r1.ebuild
b/dev-python/qtconsole/qtconsole-4.0.1-r1.ebuild
deleted file mode 120000
index 6170cda..0000000
--- a/dev-python/qtconsole/qtconsole-4.0.1-r1.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-qtconsole-9999.ebuild
\ No newline at end of file
diff --git a/dev-python/qtconsole/qtconsole-4.0.1-r1.ebuild
b/dev-python/qtconsole/qtconsole-4.0.1-r1.ebuild
new file mode 100644
index 0000000..8ac99f4
--- /dev/null
+++ b/dev-python/qtconsole/qtconsole-4.0.1-r1.ebuild
@@ -0,0 +1,67 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+PYTHON_COMPAT=( python2_7 python{3_3,3_4} )
+
+inherit distutils-r1
+
+DESCRIPTION="Qt-based console for Jupyter with support for rich media output"
+HOMEPAGE="http://jupyter.org";
+
+if [ ${PV} == "9999" ] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/jupyter/${PN}.git
git://github.com/jupyter/${PN}.git"
+else
+ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="doc test"
+
+RDEPEND="
+ dev-python/ipykernel[${PYTHON_USEDEP}]
+ dev-python/jupyter_client[${PYTHON_USEDEP}]
+ "
+DEPEND="${RDEPEND}
+ doc? (
+ dev-python/ipython[${PYTHON_USEDEP}]
+ dev-python/sphinx[${PYTHON_USEDEP}]
+ )
+ test? (
+ >=dev-python/nose-0.10.1[${PYTHON_USEDEP}]
+ )
+ || (
+ dev-python/PyQt4[${PYTHON_USEDEP},svg]
+ dev-python/PyQt5[${PYTHON_USEDEP},svg]
+ dev-python/pyside[${PYTHON_USEDEP},svg]
+ )
+ dev-python/pygments[${PYTHON_USEDEP}]
+ >=dev-python/pyzmq-13[${PYTHON_USEDEP}]
+ "
+PDEPEND="dev-python/ipython[${PYTHON_USEDEP}]"
+
+python_prepare_all() {
+ # Prevent un-needed download during build
+ if use doc; then
+ sed -e "/^ 'sphinx.ext.intersphinx',/d" -i
docs/source/conf.py || die
+ fi
+
+ distutils-r1_python_prepare_all
+}
+
+python_compile_all() {
+ use doc && emake -C docs html
+}
+
+python_test() {
+ nosetests --with-coverage --cover-package qtconsole qtconsole || die
+}
+
+python_install_all() {
+ use doc && HTML_DOCS=( docs/build/html/. )
+ distutils-r1_python_install_all
+}
diff --git a/dev-python/simplepam/simplepam-0.1.5.ebuild
b/dev-python/simplepam/simplepam-0.1.5.ebuild
deleted file mode 120000
index 5878361..0000000
--- a/dev-python/simplepam/simplepam-0.1.5.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-simplepam-9999.ebuild
\ No newline at end of file
diff --git a/dev-python/simplepam/simplepam-0.1.5.ebuild
b/dev-python/simplepam/simplepam-0.1.5.ebuild
new file mode 100644
index 0000000..155232e
--- /dev/null
+++ b/dev-python/simplepam/simplepam-0.1.5.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+PYTHON_COMPAT=( python{2_7,3_3,3_4} )
+
+inherit distutils-r1
+
+DESCRIPTION="A pure python interface to the PAM library"
+HOMEPAGE="https://github.com/leonnnn/python3-simplepam";
+
+if [ ${PV} == "9999" ] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/leonnnn/python3-${PN}.git
git://github.com/leonnnn/python3-${PN}.git"
+else
+ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="MIT"
+SLOT="0"
diff --git a/dev-python/traitlets/traitlets-4.0.0.ebuild
b/dev-python/traitlets/traitlets-4.0.0.ebuild
deleted file mode 120000
index 6d6a41b..0000000
--- a/dev-python/traitlets/traitlets-4.0.0.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-traitlets-9999.ebuild
\ No newline at end of file
diff --git a/dev-python/traitlets/traitlets-4.0.0.ebuild
b/dev-python/traitlets/traitlets-4.0.0.ebuild
new file mode 100644
index 0000000..afcdfa0
--- /dev/null
+++ b/dev-python/traitlets/traitlets-4.0.0.ebuild
@@ -0,0 +1,59 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+PYTHON_COMPAT=( python2_7 python{3_3,3_4} )
+
+inherit distutils-r1
+
+DESCRIPTION="A configuration system for Python applications"
+HOMEPAGE="https://github.com/ipython/traitlets";
+
+if [ ${PV} == "9999" ] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/ipython/${PN}.git
git://github.com/ipython/${PN}.git"
+else
+ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="doc test"
+
+RDEPEND="
+ dev-python/decorator[${PYTHON_USEDEP}]
+ dev-python/ipython_genutils[${PYTHON_USEDEP}]
+ "
+DEPEND="
+ doc? (
+ dev-python/ipython_genutils[${PYTHON_USEDEP}]
+ dev-python/sphinx[${PYTHON_USEDEP}]
+ )
+ test? (
+ dev-python/nose[${PYTHON_USEDEP}]
+ dev-python/coverage[${PYTHON_USEDEP}]
+ )"
+
+python_prepare_all() {
+ # Prevent un-needed download during build
+ if use doc; then
+ sed -e "/^ 'sphinx.ext.intersphinx',/d" -i
docs/source/conf.py || die
+ fi
+
+ distutils-r1_python_prepare_all
+}
+
+python_compile_all() {
+ use doc && emake -C docs html
+}
+
+python_test() {
+ nosetests --with-coverage --cover-package traitlets traitlets || die
+}
+
+python_install_all() {
+ use doc && HTML_DOCS=( docs/build/html/. )
+ distutils-r1_python_install_all
+}
diff --git a/media-gfx/brlcad/brlcad-7.22.0.ebuild
b/media-gfx/brlcad/brlcad-7.22.0.ebuild
index e301a42..98fb810 100644
--- a/media-gfx/brlcad/brlcad-7.22.0.ebuild
+++ b/media-gfx/brlcad/brlcad-7.22.0.ebuild
@@ -95,7 +95,7 @@ src_test() {
cmake-utils_src_test
#emake check || die "emake check failed"
if use benchmarks; then
- emake benchmark || die "emake benchmark failed"
+ emake benchmark
fi
}
diff --git a/media-gfx/brlcad/brlcad-7.24.0.ebuild
b/media-gfx/brlcad/brlcad-7.24.0.ebuild
index e1235bb..1933ed4 100644
--- a/media-gfx/brlcad/brlcad-7.24.0.ebuild
+++ b/media-gfx/brlcad/brlcad-7.24.0.ebuild
@@ -95,7 +95,7 @@ src_test() {
cmake-utils_src_test
#emake check || die "emake check failed"
if use benchmarks; then
- emake benchmark || die "emake benchmark failed"
+ emake benchmark
fi
}
diff --git a/media-gfx/brlcad/brlcad-7.24.2.ebuild
b/media-gfx/brlcad/brlcad-7.24.2.ebuild
index e37cdaa..09399be 100644
--- a/media-gfx/brlcad/brlcad-7.24.2.ebuild
+++ b/media-gfx/brlcad/brlcad-7.24.2.ebuild
@@ -92,9 +92,9 @@ src_compile() {
src_test() {
cmake-utils_src_test
- emake check || die "emake check failed"
+ emake check
if use benchmarks; then
- emake benchmark || die "emake benchmark failed"
+ emake benchmark
fi
}
diff --git a/media-gfx/brlcad/brlcad-9999.ebuild
b/media-gfx/brlcad/brlcad-9999.ebuild
index cdd393e..06de13d 100644
--- a/media-gfx/brlcad/brlcad-9999.ebuild
+++ b/media-gfx/brlcad/brlcad-9999.ebuild
@@ -90,7 +90,7 @@ src_test() {
cmake-utils_src_test
#emake check || die "emake check failed"
if use benchmarks; then
- emake benchmark || die "emake benchmark failed"
+ emake benchmark
fi
}
diff --git a/sci-astronomy/missfits/missfits-2.8.0.ebuild
b/sci-astronomy/missfits/missfits-2.8.0.ebuild
deleted file mode 120000
index b8cfc90..0000000
--- a/sci-astronomy/missfits/missfits-2.8.0.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-missfits-9999.ebuild
\ No newline at end of file
diff --git a/sci-astronomy/missfits/missfits-2.8.0.ebuild
b/sci-astronomy/missfits/missfits-2.8.0.ebuild
new file mode 100644
index 0000000..19b75a8
--- /dev/null
+++ b/sci-astronomy/missfits/missfits-2.8.0.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+if [[ ${PV} == "9999" ]] ; then
+ inherit subversion
+ ESVN_REPO_URI="https://astromatic.net/pubsvn/software/${PN}/trunk";
+ SRC_URI=""
+ KEYWORDS=""
+ AUTOTOOLS_AUTORECONF=1
+else
+ SRC_URI="http://www.astromatic.net/download/${PN}/${P}.tar.gz";
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+inherit autotools-utils
+
+DESCRIPTION="Performs basic maintenance and packaging tasks on FITS files"
+HOMEPAGE="http://www.astromatic.net/software/missfits/";
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="doc"
+
+RDEPEND=""
+DEPEND="${RDEPEND}"
+
+src_install () {
+ autotools-utils_src_install
+ use doc && dodoc doc/*
+}
diff --git a/sci-astronomy/psfex/psfex-3.17.0.ebuild
b/sci-astronomy/psfex/psfex-3.17.0.ebuild
deleted file mode 120000
index 1942f52..0000000
--- a/sci-astronomy/psfex/psfex-3.17.0.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-psfex-9999.ebuild
\ No newline at end of file
diff --git a/sci-astronomy/psfex/psfex-3.17.0.ebuild
b/sci-astronomy/psfex/psfex-3.17.0.ebuild
new file mode 100644
index 0000000..db23a21
--- /dev/null
+++ b/sci-astronomy/psfex/psfex-3.17.0.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+if [[ ${PV} == "9999" ]] ; then
+ inherit subversion
+ ESVN_REPO_URI="https://astromatic.net/pubsvn/software/${PN}/trunk";
+ SRC_URI=""
+ KEYWORDS=""
+else
+ SRC_URI="http://www.astromatic.net/download/${PN}/${P}.tar.gz";
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+AUTOTOOLS_AUTORECONF=1
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+inherit autotools-utils multilib
+
+DESCRIPTION="Extracts models of the Point Spread Function from FITS images"
+HOMEPAGE="http://www.astromatic.net/software/psfex";
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="doc threads plplot"
+
+RDEPEND="
+ sci-libs/atlas[lapack,threads=]
+ sci-libs/fftw:3.0
+ plplot? ( sci-libs/plplot:= )"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+ local mycblas=atlcblas myclapack=atlclapack
+ if use threads; then
+ [[ -e ${EPREFIX}/usr/$(get_libdir)/libptcblas.so ]] && \
+ mycblas=ptcblas
+ [[ -e ${EPREFIX}/usr/$(get_libdir)/libptclapack.so ]] &&
+ myclapack=ptclapack
+ fi
+ # fix the configure and not the acx_atlas.m4. the eautoreconf will
+ # produce a configure giving a wrong install Makefile target (to fix)
+ sed -i \
+ -e "s/-lcblas/-l${mycblas}/g" \
+ -e "s/AC_CHECK_LIB(cblas/AC_CHECK_LIB(${mycblas}/g" \
+ -e "s/-llapack/-l${myclapack}/g" \
+ -e "s/\(lapack_lib=\).*/\1${myclapack}/g" \
+ -e "s/AC_CHECK_LIB(lapack/AC_CHECK_LIB(${myclapack}/g" \
+ acx_atlas.m4 || die
+
+ # fix for newer plplot
+ sed -i -e 's/plcol(/plcol0(/g' src/cplot.c || die
+ autotools-utils_src_prepare
+}
+
+src_configure() {
+ local myeconfargs=(
+ --with-atlas-incdir="${EPREFIX}/usr/include/atlas"
+ $(use_enable plplot)
+ $(use_enable threads)
+ )
+ autotools-utils_src_configure
+}
+
+src_install () {
+ autotools-utils_src_install
+ use doc && dodoc doc/*
+}
diff --git a/sci-astronomy/psfex/psfex-3.9.1.ebuild
b/sci-astronomy/psfex/psfex-3.9.1.ebuild
deleted file mode 120000
index 1942f52..0000000
--- a/sci-astronomy/psfex/psfex-3.9.1.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-psfex-9999.ebuild
\ No newline at end of file
diff --git a/sci-astronomy/psfex/psfex-3.9.1.ebuild
b/sci-astronomy/psfex/psfex-3.9.1.ebuild
new file mode 100644
index 0000000..db23a21
--- /dev/null
+++ b/sci-astronomy/psfex/psfex-3.9.1.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+if [[ ${PV} == "9999" ]] ; then
+ inherit subversion
+ ESVN_REPO_URI="https://astromatic.net/pubsvn/software/${PN}/trunk";
+ SRC_URI=""
+ KEYWORDS=""
+else
+ SRC_URI="http://www.astromatic.net/download/${PN}/${P}.tar.gz";
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+AUTOTOOLS_AUTORECONF=1
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+inherit autotools-utils multilib
+
+DESCRIPTION="Extracts models of the Point Spread Function from FITS images"
+HOMEPAGE="http://www.astromatic.net/software/psfex";
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="doc threads plplot"
+
+RDEPEND="
+ sci-libs/atlas[lapack,threads=]
+ sci-libs/fftw:3.0
+ plplot? ( sci-libs/plplot:= )"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+ local mycblas=atlcblas myclapack=atlclapack
+ if use threads; then
+ [[ -e ${EPREFIX}/usr/$(get_libdir)/libptcblas.so ]] && \
+ mycblas=ptcblas
+ [[ -e ${EPREFIX}/usr/$(get_libdir)/libptclapack.so ]] &&
+ myclapack=ptclapack
+ fi
+ # fix the configure and not the acx_atlas.m4. the eautoreconf will
+ # produce a configure giving a wrong install Makefile target (to fix)
+ sed -i \
+ -e "s/-lcblas/-l${mycblas}/g" \
+ -e "s/AC_CHECK_LIB(cblas/AC_CHECK_LIB(${mycblas}/g" \
+ -e "s/-llapack/-l${myclapack}/g" \
+ -e "s/\(lapack_lib=\).*/\1${myclapack}/g" \
+ -e "s/AC_CHECK_LIB(lapack/AC_CHECK_LIB(${myclapack}/g" \
+ acx_atlas.m4 || die
+
+ # fix for newer plplot
+ sed -i -e 's/plcol(/plcol0(/g' src/cplot.c || die
+ autotools-utils_src_prepare
+}
+
+src_configure() {
+ local myeconfargs=(
+ --with-atlas-incdir="${EPREFIX}/usr/include/atlas"
+ $(use_enable plplot)
+ $(use_enable threads)
+ )
+ autotools-utils_src_configure
+}
+
+src_install () {
+ autotools-utils_src_install
+ use doc && dodoc doc/*
+}
diff --git a/sci-astronomy/sextractor/sextractor-2.19.5.ebuild
b/sci-astronomy/sextractor/sextractor-2.19.5.ebuild
deleted file mode 120000
index 8b8a275..0000000
--- a/sci-astronomy/sextractor/sextractor-2.19.5.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-sextractor-9999.ebuild
\ No newline at end of file
diff --git a/sci-astronomy/sextractor/sextractor-2.19.5.ebuild
b/sci-astronomy/sextractor/sextractor-2.19.5.ebuild
new file mode 100644
index 0000000..6515bca
--- /dev/null
+++ b/sci-astronomy/sextractor/sextractor-2.19.5.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+if [[ ${PV} == "9999" ]] ; then
+ inherit subversion
+ ESVN_REPO_URI="https://astromatic.net/pubsvn/software/${PN}/trunk";
+ SRC_URI=""
+ KEYWORDS=""
+else
+ SRC_URI="http://www.astromatic.net/download/${PN}/${P}.tar.gz";
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+inherit autotools-utils multilib
+
+DESCRIPTION="Extract catalogs of sources from astronomical FITS images"
+HOMEPAGE="http://www.astromatic.net/software/sextractor";
+
+LICENSE="GPL-3"
+SLOT="0"
+
+IUSE="doc modelfit threads"
+
+RDEPEND="
+ modelfit? ( sci-libs/atlas[lapack,threads=] sci-libs/fftw:3.0 )"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+ if use modelfit; then
+ local mycblas=atlcblas myclapack=atlclapack
+ if use threads; then
+ [[ -e "${EPREFIX}"/usr/$(get_libdir)/libptcblas.so ]]
&& \
+ mycblas=ptcblas
+ [[ -e "${EPREFIX}"/usr/$(get_libdir)/libptclapack.so ]]
&& \
+ myclapack=ptclapack
+ fi
+ sed -i \
+ -e "s/-lcblas/-l${mycblas}/g" \
+ -e "s/AC_CHECK_LIB(cblas/AC_CHECK_LIB(${mycblas}/g" \
+ -e "s/-llapack/-l${myclapack}/g" \
+ -e "s/AC_CHECK_LIB(lapack/AC_CHECK_LIB(${myclapack}/g" \
+ acx_atlas.m4 || die
+ AUTOTOOLS_AUTORECONF=1
+ fi
+ autotools-utils_src_prepare
+}
+
+src_configure() {
+ local myeconfargs=(
+ --with-atlas-incdir="${EPREFIX}/usr/include/atlas"
+ $(use_enable modelfit model-fitting)
+ $(use_enable threads)
+ )
+ autotools-utils_src_configure
+}
+
+src_install () {
+ autotools-utils_src_install
+ CONFDIR=/usr/share/sextractor
+ insinto ${CONFDIR}
+ doins config/*
+ use doc && dodoc doc/*
+}
+
+pkg_postinst() {
+ elog "SExtractor examples configuration files are located in"
+ elog "${EROOT%/}/${CONFDIR} and are not loaded anymore by default."
+}
diff --git a/sci-astronomy/skymaker/skymaker-3.10.5.ebuild
b/sci-astronomy/skymaker/skymaker-3.10.5.ebuild
deleted file mode 120000
index bae5406..0000000
--- a/sci-astronomy/skymaker/skymaker-3.10.5.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-skymaker-9999.ebuild
\ No newline at end of file
diff --git a/sci-astronomy/skymaker/skymaker-3.10.5.ebuild
b/sci-astronomy/skymaker/skymaker-3.10.5.ebuild
new file mode 100644
index 0000000..f44f47f
--- /dev/null
+++ b/sci-astronomy/skymaker/skymaker-3.10.5.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+if [[ ${PV} == "9999" ]] ; then
+ inherit subversion
+ ESVN_REPO_URI="https://astromatic.net/pubsvn/software/${PN}/trunk";
+ SRC_URI=""
+ KEYWORDS=""
+else
+ SRC_URI="http://www.astromatic.net/download/${PN}/${P}.tar.gz";
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+#AUTOTOOLS_AUTORECONF=1
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+inherit autotools-utils
+
+DESCRIPTION="Program that simulates astronomical images"
+HOMEPAGE="http://www.astromatic.net/software/skymaker";
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="threads"
+
+RDEPEND="sci-libs/fftw:3.0"
+DEPEND="${RDEPEND}"
+
+src_configure() {
+ local myeconfargs=( $(use_enable threads) )
+ autotools-utils_src_configure
+}
diff --git a/sci-astronomy/stiff/stiff-2.4.0.ebuild
b/sci-astronomy/stiff/stiff-2.4.0.ebuild
deleted file mode 120000
index 5f7f899..0000000
--- a/sci-astronomy/stiff/stiff-2.4.0.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-stiff-9999.ebuild
\ No newline at end of file
diff --git a/sci-astronomy/stiff/stiff-2.4.0.ebuild
b/sci-astronomy/stiff/stiff-2.4.0.ebuild
new file mode 100644
index 0000000..33c0767
--- /dev/null
+++ b/sci-astronomy/stiff/stiff-2.4.0.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+if [[ ${PV} == "9999" ]] ; then
+ inherit subversion
+ ESVN_REPO_URI="https://astromatic.net/pubsvn/software/${PN}/trunk";
+ SRC_URI=""
+ KEYWORDS=""
+else
+ SRC_URI="http://www.astromatic.net/download/${PN}/${P}.tar.gz";
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+#AUTOTOOLS_AUTORECONF=1
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+inherit autotools-utils
+
+DESCRIPTION="Converts astronomical FITS images to the TIFF format"
+HOMEPAGE="http://astromatic.iap.fr/software/stiff";
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="doc threads"
+
+RDEPEND="
+ media-libs/tiff:0=
+ virtual/jpeg:0
+ sys-libs/zlib:0="
+DEPEND="${RDEPEND}"
+
+src_configure() {
+ local myeconfargs=( $(use_enable threads) )
+ autotools-utils_src_configure
+}
+
+src_install () {
+ use doc && DOCS=( doc/. )
+ autotools-utils_src_install
+}
diff --git a/sci-astronomy/stuff/stuff-1.26.0.ebuild
b/sci-astronomy/stuff/stuff-1.26.0.ebuild
deleted file mode 120000
index 181cfcc..0000000
--- a/sci-astronomy/stuff/stuff-1.26.0.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-stuff-9999.ebuild
\ No newline at end of file
diff --git a/sci-astronomy/stuff/stuff-1.26.0.ebuild
b/sci-astronomy/stuff/stuff-1.26.0.ebuild
new file mode 100644
index 0000000..1f57f85
--- /dev/null
+++ b/sci-astronomy/stuff/stuff-1.26.0.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+if [[ ${PV} == "9999" ]] ; then
+ inherit subversion
+ ESVN_REPO_URI="https://astromatic.net/pubsvn/software/${PN}/trunk";
+ SRC_URI=""
+ KEYWORDS=""
+else
+ SRC_URI="http://www.astromatic.net/download/${PN}/${P}.tar.gz";
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+#AUTOTOOLS_AUTORECONF=1
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+inherit autotools-utils
+
+DESCRIPTION="Tool for automatic generation of astronomical catalogs"
+HOMEPAGE="http://www.astromatic.net/software/stuff/";
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="threads"
+
+RDEPEND="sci-libs/fftw:3.0"
+DEPEND="${RDEPEND}"
+
+src_configure() {
+ local myeconfargs=( $(use_enable threads) )
+ autotools-utils_src_configure
+}
diff --git a/sci-astronomy/swarp/swarp-2.38.0.ebuild
b/sci-astronomy/swarp/swarp-2.38.0.ebuild
deleted file mode 120000
index ffc97cb..0000000
--- a/sci-astronomy/swarp/swarp-2.38.0.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-swarp-9999.ebuild
\ No newline at end of file
diff --git a/sci-astronomy/swarp/swarp-2.38.0.ebuild
b/sci-astronomy/swarp/swarp-2.38.0.ebuild
new file mode 100644
index 0000000..71c254d
--- /dev/null
+++ b/sci-astronomy/swarp/swarp-2.38.0.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+if [[ ${PV} == "9999" ]] ; then
+ inherit subversion
+ ESVN_REPO_URI="https://astromatic.net/pubsvn/software/${PN}/trunk";
+ SRC_URI=""
+ KEYWORDS=""
+ AUTOTOOLS_AUTORECONF=1
+else
+ SRC_URI="http://www.astromatic.net/download/${PN}/${P}.tar.gz";
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+inherit autotools-utils
+
+DESCRIPTION="Resample and coadd astronomical FITS images"
+HOMEPAGE="http://astromatic.iap.fr/software/swarp";
+
+LICENSE="GPL-3"
+SLOT="0"
+
+IUSE="doc threads"
+
+RDEPEND=""
+DEPEND="${RDEPEND}"
+
+src_configure() {
+ local myeconfargs=( $(use_enable threads) )
+ autotools-utils_src_configure
+}
+
+src_install () {
+ autotools-utils_src_install
+ use doc && dodoc doc/*
+}
diff --git a/sci-astronomy/weightwatcher/weightwatcher-1.12.ebuild
b/sci-astronomy/weightwatcher/weightwatcher-1.12.ebuild
deleted file mode 120000
index fedc2e1..0000000
--- a/sci-astronomy/weightwatcher/weightwatcher-1.12.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-weightwatcher-9999.ebuild
\ No newline at end of file
diff --git a/sci-astronomy/weightwatcher/weightwatcher-1.12.ebuild
b/sci-astronomy/weightwatcher/weightwatcher-1.12.ebuild
new file mode 100644
index 0000000..9f90ed1
--- /dev/null
+++ b/sci-astronomy/weightwatcher/weightwatcher-1.12.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+if [[ ${PV} == "9999" ]] ; then
+ inherit subversion
+ ESVN_REPO_URI="https://astromatic.net/pubsvn/software/${PN}/trunk";
+ SRC_URI=""
+ KEYWORDS=""
+else
+ SRC_URI="http://www.astromatic.net/download/${PN}/${P}.tar.gz";
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+#AUTOTOOLS_AUTORECONF=1
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+inherit autotools-utils
+
+DESCRIPTION="Combine weight maps and polygon for astronomical images weighting"
+HOMEPAGE="http://www.astromatic.net/software/weightwatcher/";
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="doc"
+
+RDEPEND=""
+DEPEND="${RDEPEND}"
+
+src_install () {
+ autotools-utils_src_install
+ use doc && dodoc doc/*
+}
diff --git a/sci-biology/biopieces/biopieces-0.51.ebuild
b/sci-biology/biopieces/biopieces-0.51.ebuild
deleted file mode 120000
index f048b8a..0000000
--- a/sci-biology/biopieces/biopieces-0.51.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-biopieces-9999.ebuild
\ No newline at end of file
diff --git a/sci-biology/biopieces/biopieces-0.51.ebuild
b/sci-biology/biopieces/biopieces-0.51.ebuild
new file mode 100644
index 0000000..ed5a251
--- /dev/null
+++ b/sci-biology/biopieces/biopieces-0.51.ebuild
@@ -0,0 +1,72 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+USE_RUBY="ruby19"
+
+if [ "$PV" == "9999" ]; then
+ ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk";
+ KEYWORDS=""
+ inherit subversion
+else
+
SRC_URI="http://biopieces.googlecode.com/files/biopieces_installer-${PV}.sh";
+ KEYWORDS=""
+fi
+
+inherit ruby-fakegem python-single-r1
+
+DESCRIPTION="Toolkit to find and trim adaptors, plot read lengths, qualities,
map reads and submit to GenBank"
+HOMEPAGE="http://code.google.com/p/biopieces";
+SRC_URI=""
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="test"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+# Ruby terminal-table ?
+
+CDEPEND="${PYTHON_DEPS}
+ >=dev-lang/perl-5.8
+ dev-perl/libwww-perl
+ dev-perl/Bit-Vector
+ dev-perl/Carp-Clan
+ dev-perl/Class-Inspector
+ dev-perl/DBD-mysql
+ dev-perl/DBI
+ dev-perl/HTML-Parser
+ dev-perl/Inline
+ dev-perl/Parse-RecDescent
+ dev-perl/SOAP-Lite
+ dev-perl/SVG
+ dev-perl/TermReadKey
+ dev-perl/URI
+ dev-perl/XML-Parser
+ virtual/perl-version
+ virtual/perl-DB_File
+ virtual/perl-Time-HiRes"
+
+DEPEND="${CDEPEND}"
+
+ruby_add_bdepend "dev-ruby/RubyInline"
+ruby_add_rdepend "dev-ruby/gnuplot dev-ruby/narray"
+
+# sci-biology/vmatch # http://www.vmatch.de/ # fecth restrict
+# sci-biology/usearch-bin # http://www.drive5.com/usearch/ # fecth restrict
+
+RDEPEND="${CDEPEND}
+ sci-biology/ncbi-tools
+ sci-biology/muscle
+ sci-biology/mummer
+ sci-biology/blat
+ sci-biology/bowtie
+ sci-biology/bwa
+ sci-biology/velvet
+ sci-biology/idba
+ sci-biology/Ray
+ sci-biology/scan_for_matches"
diff --git a/sci-biology/blasr/blasr-9999.ebuild
b/sci-biology/blasr/blasr-9999.ebuild
index 1ad2412..ca4ff28 100644
--- a/sci-biology/blasr/blasr-9999.ebuild
+++ b/sci-biology/blasr/blasr-9999.ebuild
@@ -26,5 +26,5 @@ S="${WORKDIR}/blasr-${MY_HASH}"
src_install() {
dodir /usr/bin
- emake install ASSEMBLY_HOME="${ED}/usr" || die
+ emake install ASSEMBLY_HOME="${ED}/usr"
}
diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
index 0c17e48..216bdcb 100644
--- a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
+++ b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
@@ -61,7 +61,7 @@ src_prepare(){
#}
#
#src_compile(){
-# emake || die
+# emake
#}
src_install(){
diff --git a/sci-biology/mgblast/mgblast-0.1.ebuild
b/sci-biology/mgblast/mgblast-0.1.ebuild
index 9292f31..ff0693f 100644
--- a/sci-biology/mgblast/mgblast-0.1.ebuild
+++ b/sci-biology/mgblast/mgblast-0.1.ebuild
@@ -37,7 +37,7 @@ src_prepare(){
src_compile(){
cd "${S}"/mgblast || die
- emake || die "mgblast really needs an older ncbi-toolkit version so we
are out of luck, install the binary provided by upstream instead from
mgblast-bin package"
+ emake
}
src_install(){
diff --git a/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild
b/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild
deleted file mode 120000
index 9f0bb27..0000000
--- a/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-ngs_backbone-9999.ebuild
\ No newline at end of file
diff --git a/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild
b/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild
new file mode 100644
index 0000000..734e32d
--- /dev/null
+++ b/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild
@@ -0,0 +1,156 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit distutils-r1
+
+[ "$PV" == "9999" ] && inherit git-2
+
+DESCRIPTION="Assembly and annotation pipeline with web interface for
EST/chromosomal sequences"
+HOMEPAGE="http://bioinf.comav.upv.es/ngs_backbone/index.html";
+if [ "$PV" == "9999" ]; then
+ EGIT_REPO_URI="https://github.com/JoseBlanca/franklin";
+ KEYWORDS=""
+else
+ SRC_URI="http://bioinf.comav.upv.es/_downloads/"${P}".tar.gz";
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ sci-biology/biopython[${PYTHON_USEDEP}]
+ sci-biology/samtools[${PYTHON_USEDEP}]
+ sci-biology/picard
+ sci-biology/mira
+ sci-biology/bwa
+ sci-biology/gatk
+ sci-biology/pysam[${PYTHON_USEDEP}]
+ sci-biology/estscan
+ sci-biology/ncbi-tools
+ sci-biology/lucy
+ sci-biology/gmap
+ sci-biology/emboss
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/psubprocess[${PYTHON_USEDEP}]
+ dev-python/configobj[${PYTHON_USEDEP}]"
+ # ( blast2GO || b2g4pipe )
+ # sci-biology/sputnik
+ # sci-biology/gsnap
+
+# blast2GO is http://www.blast2go.org/home
+# a non-GUI pipeline is called b2g4pipe, see
https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/b2g4pipe-2-5
+
+# TODO: drop the bundled binaries but ...
+# 1. the QA check did not find all bundled binaries, e.g. sputnik, lucy,
trimpoly
+# 2. until we have them all, maybe keep the installed
+#
+# * QA Notice: The following files contain writable and executable sections
+# * Files with such sections will not work properly (or at all!) on some
+# * architectures/operating systems. A bug should be filed at
+# * http://bugs.gentoo.org/ to make sure the issue is fixed.
+# * For more information, see http://hardened.gentoo.org/gnu-stack.xml
+# * Please include the following list of files in your report:
+# * Note: Bugs should be filed for the respective maintainers
+# * of the package in question and not [email protected].
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastx
+# * RWX --- ---
usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/makeblastdb
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastx
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastp
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastn
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastn
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastx
+# * RWX --- ---
usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/makeblastdb
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastx
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastp
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastn
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastn
+
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/bgzip
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastn
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastp
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastx
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/bwa
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/EBLOSUM62
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/EDNAFULL
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/codes.english
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/est2genome.acd
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/knowntypes.standard
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/water.acd
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/est2genome
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/estscan
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/fa_coords
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_build
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_compress
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_process
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_reassemble
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_setup
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_uncompress
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmapindex
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gsnap
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gsnap_tally
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/lucy
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/makeblastdb
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/md_coords
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/mdust
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/samtools
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/sputnik
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tabix
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastn
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastx
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/trimpoly
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/water
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/bgzip
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastn
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastp
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastx
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/bwa
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/EBLOSUM62
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/EDNAFULL
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/codes.english
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/est2genome.acd
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/knowntypes.standard
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/water.acd
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/est2genome
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/estscan
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/fa_coords
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_build
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_compress
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_process
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_reassemble
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_setup
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_uncompress
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmapindex
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gsnap
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gsnap_tally
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/lucy
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/makeblastdb
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/md_coords
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/mdust
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/samtools
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/sputnik
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tabix
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastn
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastx
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/trimpoly
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/water
+
+pkg_postinst(){
+ einfo "It is highly recommended to install blast2GO. Either the
commercial version with GUI"
+ einfo " or a non-GUI version called b2g4pipe. Either way, refer to
http://www.blast2go.org";
+ einfo " Brief installation process is at
http://bioinf.comav.upv.es/ngs_backbone/install.html";
+ einfo "Alternatively, a VirtualBox image with ngs_bakbone is at
http://bioinf.comav.upv.es/_downloads/ngs_machine_v3.tar.gz";
+}
diff --git a/sci-biology/pileup/pileup-0.6.ebuild
b/sci-biology/pileup/pileup-0.6.ebuild
index 433c1d7..064c48c 100644
--- a/sci-biology/pileup/pileup-0.6.ebuild
+++ b/sci-biology/pileup/pileup-0.6.ebuild
@@ -37,12 +37,12 @@ src_prepare(){
src_compile(){
cd ssaha_pileup/ssaha_pileup || die "Cannot cd to
"${S}"ssaha_pileup/ssaha_pileup"
- emake || die "emake failed"
+ emake
for d in get_seqreads ssaha_split ssaha_parseSNP search_read; do
cd "${S}"/ssaha_pileup/other_codes/$d || die "Cannot cd to
"${S}"ssaha_pileup/other_codes/"$d
make clean
- emake || die "emake failed"
+ emake
done
}
diff --git a/sci-biology/tablet/tablet-1.14.04.10.ebuild
b/sci-biology/tablet/tablet-1.14.04.10.ebuild
deleted file mode 120000
index a170f54..0000000
--- a/sci-biology/tablet/tablet-1.14.04.10.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-tablet-9999.ebuild
\ No newline at end of file
diff --git a/sci-biology/tablet/tablet-1.14.04.10.ebuild
b/sci-biology/tablet/tablet-1.14.04.10.ebuild
new file mode 100644
index 0000000..d8aa02c
--- /dev/null
+++ b/sci-biology/tablet/tablet-1.14.04.10.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit java-pkg-2 java-ant-2 python-r1
+
+# [ "$PV" == "9999" ] && inherit subversion
+inherit subversion
+
+DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
+HOMEPAGE="http://bioinf.scri.ac.uk/tablet/";
+if [ "$PV" == "9999" ]; then
+ ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/";
+ KEYWORDS=""
+else
+ ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}";
+ KEYWORDS=""
+fi
+
+LICENSE="Tablet"
+SLOT="0"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}
+ >=virtual/jdk-1.7:*"
+RDEPEND="${PYTHON_DEPS}
+ >=virtual/jre-1.7:*
+ sci-biology/samtools
+ sci-biology/picard
+ dev-db/sqlite:3"
+
+S="${WORKDIR}"
+
+src_install() {
+ java-pkg_dojar lib/tablet-resources.jar
+ java-pkg_dojar lib/tablet.jar
+ java-pkg_dojar lib/flamingo.jar
+ java-pkg_dojar lib/scri-commons.jar
+ java-pkg_dojar lib/samtools*.jar
+
+ echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
+ doenvd 99Tablet
+}
diff --git a/sci-libs/asl/asl-0.1.5.ebuild b/sci-libs/asl/asl-0.1.5.ebuild
deleted file mode 120000
index 2176c62..0000000
--- a/sci-libs/asl/asl-0.1.5.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-asl-9999.ebuild
\ No newline at end of file
diff --git a/sci-libs/asl/asl-0.1.5.ebuild b/sci-libs/asl/asl-0.1.5.ebuild
new file mode 100644
index 0000000..3163a5d
--- /dev/null
+++ b/sci-libs/asl/asl-0.1.5.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+MY_PN=ASL
+
+if [[ ${PV} == "9999" ]] ; then
+ inherit git-r3
+ EGIT_REPO_URI="git://github.com/AvtechScientific/${MY_PN}.git"
+else
+
SRC_URI="https://github.com/AvtechScientific/${MY_PN}/archive/v${PV}.tar.gz ->
${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+ S="${WORKDIR}/${MY_PN}-${PV}"
+fi
+
+CMAKE_MIN_VERSION=3.0.2
+CMAKE_MAKEFILE_GENERATOR="${CMAKE_MAKEFILE_GENERATOR:-ninja}"
+
+inherit cmake-utils
+
+DESCRIPTION="Advanced Simulation Library - multiphysics simulation software
package"
+HOMEPAGE="http://asl.org.il/";
+LICENSE="AGPL-3"
+SLOT="0"
+IUSE="doc examples matio"
+
+RDEPEND="
+ >=dev-libs/boost-1.55:=
+ >=sci-libs/vtk-6.1
+ >=virtual/opencl-0-r2
+"
+DEPEND="${RDEPEND}
+ doc? ( app-doc/doxygen[dot] )
+ matio? ( >=sci-libs/matio-1.5.2 )
+"
+
+src_configure() {
+ local mycmakeargs=(
+ -DCMAKE_INSTALL_DOCDIR=/usr/share/doc/${PF}
+ -DCMAKE_SKIP_RPATH=yes
+ $(cmake-utils_use_with doc API_DOC)
+ $(cmake-utils_use_with examples)
+ $(cmake-utils_use_with matio)
+ )
+ cmake-utils_src_configure
+}
diff --git a/sci-libs/blas-reference/blas-reference-20131116-r1.ebuild
b/sci-libs/blas-reference/blas-reference-20131116-r1.ebuild
deleted file mode 120000
index 28324bd..0000000
--- a/sci-libs/blas-reference/blas-reference-20131116-r1.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-blas-reference-99999999.ebuild
\ No newline at end of file
diff --git a/sci-libs/blas-reference/blas-reference-20131116-r1.ebuild
b/sci-libs/blas-reference/blas-reference-20131116-r1.ebuild
new file mode 100644
index 0000000..4b9d2ea
--- /dev/null
+++ b/sci-libs/blas-reference/blas-reference-20131116-r1.ebuild
@@ -0,0 +1,118 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EBASE_PROFNAME="refblas"
+ESTATIC_MULTIBUILD="true"
+inherit fortran-2 cmake-utils alternatives-2 multibuild multilib-build
toolchain-funcs fortran-int64
+
+LPN=lapack
+LPV=3.5.0
+
+if [[ ${PV} == "99999999" ]] ; then
+ ESVN_REPO_URI="https://icl.cs.utk.edu/svn/lapack-dev/${LPN}/trunk";
+ inherit subversion
+ KEYWORDS=""
+else
+ SRC_URI="http://www.netlib.org/${LPN}/${LPN}-${LPV}.tgz";
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+DESCRIPTION="Reference implementation of BLAS"
+HOMEPAGE="http://www.netlib.org/lapack/";
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="int64 static-libs test"
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
+PDEPEND=">=virtual/blas-2.1-r3[int64?]"
+
+S="${WORKDIR}/${LPN}-${LPV}"
+
+src_prepare() {
+ # rename library to avoid collision with other blas implementations
+ # ${LIBNAME} and ${PROFNAME} are not defined here, they are in single
+ # quotes in the following seds. They are later set by defining cmake
+ # variables with -DPROFNAME etc in src_configure
+ sed -i \
+ -e 's:\([^xc]\)blas:\1${LIBNAME}:g' \
+ CMakeLists.txt \
+ BLAS/SRC/CMakeLists.txt || die
+ sed -i \
+ -e '/Name: /s:blas:${PROFNAME}:' \
+ -e 's:-lblas:-l${LIBNAME}:g' \
+ BLAS/blas.pc.in || die
+ sed -i \
+ -e 's:blas):${LIBNAME}):' \
+ BLAS/TESTING/CMakeLists.txt || die
+ sed -i \
+ -e 's:BINARY_DIR}/blas:BINARY_DIR}/${PROFNAME}:' \
+ BLAS/CMakeLists.txt || die
+}
+
+src_configure() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ blas_configure() {
+ local profname=$(fortran-int64_get_profname)
+ local libname="${profname//-/_}"
+ local mycmakeargs=(
+ -Wno-dev
+ -DPROFNAME="${profname}"
+ -DLIBNAME="${libname}"
+ -DUSE_OPTIMIZED_BLAS=OFF
+ $(cmake-utils_use_build test TESTING)
+ -DCMAKE_Fortran_FLAGS="$($(tc-getPKG_CONFIG) --cflags
${blas_profname}) $(get_abi_CFLAGS)
$(fortran-int64_get_fortran_int64_abi_fflags) ${FCFLAGS}"
+
-DLAPACK_PKGCONFIG_FFLAGS="$(fortran-int64_get_fortran_int64_abi_fflags)"
+ )
+ if $(fortran-int64_is_static_build); then
+ mycmakeargs+=(
+ -DBUILD_SHARED_LIBS=OFF
+ -DBUILD_STATIC_LIBS=ON
+ )
+ else
+ mycmakeargs+=(
+ -DBUILD_SHARED_LIBS=ON
+ -DBUILD_STATIC_LIBS=OFF
+ )
+ fi
+ cmake-utils_src_configure
+ }
+ multibuild_foreach_variant fortran-int64_multilib_multibuild_wrapper
blas_configure
+}
+
+src_compile() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ multibuild_foreach_variant fortran-int64_multilib_multibuild_wrapper
cmake-utils_src_compile -C BLAS
+}
+
+src_test() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ blas_test() {
+ _check_build_dir
+ pushd "${BUILD_DIR}/BLAS" > /dev/null
+ local ctestargs
+ [[ -n ${TEST_VERBOSE} ]] && ctestargs="--extra-verbose
--output-on-failure"
+ ctest ${ctestargs} || die
+ popd > /dev/null
+ }
+ multibuild_foreach_variant fortran-int64_multilib_multibuild_wrapper
blas_test
+}
+
+src_install() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ my_src_install() {
+ cmake-utils_src_install -C BLAS
+ if ! $(fortran-int64_is_static_build); then
+ local profname=$(fortran-int64_get_profname)
+ local provider=$(fortran-int64_get_blas_provider)
+ alternatives_for ${provider}
$(fortran-int64_get_profname "reference") 0 \
+ /usr/$(get_libdir)/pkgconfig/${provider}.pc
${profname}.pc
+ fi
+ }
+ multibuild_foreach_variant fortran-int64_multilib_multibuild_wrapper
my_src_install
+}
diff --git a/sci-libs/fox/fox-4.1.2-r2.ebuild b/sci-libs/fox/fox-4.1.2-r2.ebuild
index 928deff..2c4659c 100644
--- a/sci-libs/fox/fox-4.1.2-r2.ebuild
+++ b/sci-libs/fox/fox-4.1.2-r2.ebuild
@@ -46,7 +46,7 @@ src_configure() {
}
src_compile() {
- emake -j1 || die "make failed"
+ emake -j1
}
src_test() {
@@ -60,7 +60,7 @@ src_install() {
-e's%\$libdir/lib\([^ ]\+\)\.a\>%-l\1%g' \
-e's%\(echo\( -I"$moddir"\)\?\) \$LIBS%\1 -L"$libdir" $LIBS%' \
FoX-config
- emake -j1 DESTDIR="${D}" install || die "make install failed"
+ emake -j1 DESTDIR="${D}" install
dodoc README.FoX.txt || die "dodoc failed"
if use doc; then
dodoc Changelog
diff --git a/sci-libs/lapack-reference/lapack-reference-3.4.2.ebuild
b/sci-libs/lapack-reference/lapack-reference-3.4.2.ebuild
deleted file mode 120000
index 0d81fdd..0000000
--- a/sci-libs/lapack-reference/lapack-reference-3.4.2.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-lapack-reference-9999.ebuild
\ No newline at end of file
diff --git a/sci-libs/lapack-reference/lapack-reference-3.4.2.ebuild
b/sci-libs/lapack-reference/lapack-reference-3.4.2.ebuild
new file mode 100644
index 0000000..e81c5a2
--- /dev/null
+++ b/sci-libs/lapack-reference/lapack-reference-3.4.2.ebuild
@@ -0,0 +1,139 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+EBASE_PROFNAME="reflapack"
+ESTATIC_MULTIBUILD=1
+inherit fortran-2 cmake-utils multibuild alternatives-2 multilib-build
toolchain-funcs fortran-int64
+
+if [[ ${PV} == "9999" ]] ; then
+ # The master ESVN_REPO_URI is difficult to access, the git mirror is
easier
+ # ESVN_REPO_URI="https://icl.cs.utk.edu/svn/lapack-dev/lapack/trunk";
+ # MY_PN=lapack
+ # inherit subversion
+ EGIT_REPO_URI="https://github.com/nschloe/lapack.git";
+ MY_PN=lapack-reference
+ MYP=${MY_PN}-${PV}
+ inherit git-r3
+ KEYWORDS=""
+else
+ MY_PN=lapack
+ MYP=${MY_PN}-${PV}
+ SRC_URI="http://www.netlib.org/lapack/${MYP}.tgz";
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+DESCRIPTION="Reference implementation of LAPACK"
+HOMEPAGE="http://www.netlib.org/lapack/";
+
+LICENSE="BSD"
+SLOT="0"
+
+IUSE="int64 static-libs test xblas"
+
+RDEPEND="
+ >=virtual/blas-2.1-r3[int64?]
+ xblas? ( sci-libs/xblas[fortran,int64?] )"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
+PDEPEND="
+ >=virtual/lapack-3.5-r2[int64?]"
+
+S="${WORKDIR}/${MYP}"
+
+src_prepare() {
+ fortran-int64_ensure_blas
+
+ # rename library to avoid collision with other lapack implementations
+ # ${PROFNAME}, ${LIBNAME} and ${BLAS_REQUIRES} are not defined here,
they
+ # are in single quotes in the following seds. They are set later by
+ # defining a cmake variables with -DPROFNAME etc in src_configure.
+ sed -i \
+ -e 's:BINARY_DIR}/lapack.pc:BINARY_DIR}/${PROFNAME}.pc:' \
+ -e '/ALL_TARGETS/s:lapack):${LIBNAME}):' \
+ -e '/LAPACK_LIBRARIES/s:lapack:${LIBNAME}:g' \
+ CMakeLists.txt || die
+ sed -i \
+ -e 's:(lapack:(${LIBNAME}:g' \
+ SRC/CMakeLists.txt || die
+ sed -i \
+ -e '/Name: /s:lapack:${PROFNAME}:' \
+ -e 's:-llapack:-l${LIBNAME}:g' \
+ -e '/Requires:
/s:blas:${BLAS_REQUIRES}\nFflags=${LAPACK_PKGCONFIG_FFLAGS}:' \
+ lapack.pc.in || die
+ # some string does not get passed properly
+ sed -i \
+ -e '/lapack_testing.py/d' \
+ CTestCustom.cmake.in || die
+ # separate ebuild to tmglib
+ sed -i \
+ -e '/lapack_install_library(tmglib)/d' \
+ TESTING/MATGEN/CMakeLists.txt || die
+}
+
+src_configure() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ my_src_configure() {
+ local profname=$(fortran-int64_get_profname)
+ local libname="${profname//-/_}"
+ local blas_profname=$(fortran-int64_get_blas_profname)
+ local xblas_profname=$(fortran-int64_get_xblas_profname)
+ local xblas_libname="${xblas_profname//-/_}"
+ local blas_requires="${blas_profname}"
+ use xblas && \
+ blas_requires+=" ${xblas_profname}"
+ local mycmakeargs=(
+ -DPROFNAME="${profname}"
+ -DBLAS_REQUIRES="${blas_requires}"
+ -DLIBNAME="${libname}"
+ -DUSE_OPTIMIZED_BLAS=ON
+ -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs
${blas_profname})"
+ $(cmake-utils_use_build test TESTING)
+ $(cmake-utils_use_use xblas XBLAS)
+ -DCMAKE_C_FLAGS="$($(tc-getPKG_CONFIG) --cflags
${blas_profname}) ${CFLAGS}"
+ -DCMAKE_CXX_FLAGS="$($(tc-getPKG_CONFIG) --cflags
${blas_profname}) ${CXXFLAGS}"
+ -DCMAKE_Fortran_FLAGS="$($(tc-getPKG_CONFIG) --cflags
${blas_profname}) $(get_abi_CFLAGS)
$(fortran-int64_get_fortran_int64_abi_fflags) ${FCFLAGS}"
+
-DLAPACK_PKGCONFIG_FFLAGS="$(fortran-int64_get_fortran_int64_abi_fflags)"
+ )
+ use xblas && \
+ mycmakeargs+=(
-DXBLAS_LIBRARY:FILEPATH="${EROOT}usr/$(get_libdir)/lib${xblas_libname}.so" )
+ if $(fortran-int64_is_static_build); then
+ mycmakeargs+=(
+ -DBUILD_SHARED_LIBS=OFF
+ -DBUILD_STATIC_LIBS=ON
+ )
+ else
+ mycmakeargs+=(
+ -DBUILD_SHARED_LIBS=ON
+ -DBUILD_STATIC_LIBS=OFF
+ )
+ fi
+ cmake-utils_src_configure
+ }
+ multibuild_foreach_variant fortran-int64_multilib_multibuild_wrapper
my_src_configure
+}
+
+src_compile() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ multibuild_foreach_variant fortran-int64_multilib_multibuild_wrapper
cmake-utils_src_compile
+}
+
+src_test() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ multibuild_foreach_variant fortran-int64_multilib_multibuild_wrapper
cmake-utils_src_test
+}
+
+src_install() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ my_src_install() {
+ cmake-utils_src_install
+ if ! $(fortran-int64_is_static_build); then
+ local profname=$(fortran-int64_get_profname)
+ local provider=$(fortran-int64_get_lapack_provider)
+ alternatives_for ${provider}
$(fortran-int64_get_profname "reference") 0 \
+ /usr/$(get_libdir)/pkgconfig/${provider}.pc
${profname}.pc
+ fi
+ }
+ multibuild_foreach_variant fortran-int64_multilib_multibuild_wrapper
my_src_install
+}
diff --git a/sci-libs/lapack-reference/lapack-reference-3.5.0.ebuild
b/sci-libs/lapack-reference/lapack-reference-3.5.0.ebuild
deleted file mode 120000
index 0d81fdd..0000000
--- a/sci-libs/lapack-reference/lapack-reference-3.5.0.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-lapack-reference-9999.ebuild
\ No newline at end of file
diff --git a/sci-libs/lapack-reference/lapack-reference-3.5.0.ebuild
b/sci-libs/lapack-reference/lapack-reference-3.5.0.ebuild
new file mode 100644
index 0000000..e81c5a2
--- /dev/null
+++ b/sci-libs/lapack-reference/lapack-reference-3.5.0.ebuild
@@ -0,0 +1,139 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+EBASE_PROFNAME="reflapack"
+ESTATIC_MULTIBUILD=1
+inherit fortran-2 cmake-utils multibuild alternatives-2 multilib-build
toolchain-funcs fortran-int64
+
+if [[ ${PV} == "9999" ]] ; then
+ # The master ESVN_REPO_URI is difficult to access, the git mirror is
easier
+ # ESVN_REPO_URI="https://icl.cs.utk.edu/svn/lapack-dev/lapack/trunk";
+ # MY_PN=lapack
+ # inherit subversion
+ EGIT_REPO_URI="https://github.com/nschloe/lapack.git";
+ MY_PN=lapack-reference
+ MYP=${MY_PN}-${PV}
+ inherit git-r3
+ KEYWORDS=""
+else
+ MY_PN=lapack
+ MYP=${MY_PN}-${PV}
+ SRC_URI="http://www.netlib.org/lapack/${MYP}.tgz";
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+DESCRIPTION="Reference implementation of LAPACK"
+HOMEPAGE="http://www.netlib.org/lapack/";
+
+LICENSE="BSD"
+SLOT="0"
+
+IUSE="int64 static-libs test xblas"
+
+RDEPEND="
+ >=virtual/blas-2.1-r3[int64?]
+ xblas? ( sci-libs/xblas[fortran,int64?] )"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
+PDEPEND="
+ >=virtual/lapack-3.5-r2[int64?]"
+
+S="${WORKDIR}/${MYP}"
+
+src_prepare() {
+ fortran-int64_ensure_blas
+
+ # rename library to avoid collision with other lapack implementations
+ # ${PROFNAME}, ${LIBNAME} and ${BLAS_REQUIRES} are not defined here,
they
+ # are in single quotes in the following seds. They are set later by
+ # defining a cmake variables with -DPROFNAME etc in src_configure.
+ sed -i \
+ -e 's:BINARY_DIR}/lapack.pc:BINARY_DIR}/${PROFNAME}.pc:' \
+ -e '/ALL_TARGETS/s:lapack):${LIBNAME}):' \
+ -e '/LAPACK_LIBRARIES/s:lapack:${LIBNAME}:g' \
+ CMakeLists.txt || die
+ sed -i \
+ -e 's:(lapack:(${LIBNAME}:g' \
+ SRC/CMakeLists.txt || die
+ sed -i \
+ -e '/Name: /s:lapack:${PROFNAME}:' \
+ -e 's:-llapack:-l${LIBNAME}:g' \
+ -e '/Requires:
/s:blas:${BLAS_REQUIRES}\nFflags=${LAPACK_PKGCONFIG_FFLAGS}:' \
+ lapack.pc.in || die
+ # some string does not get passed properly
+ sed -i \
+ -e '/lapack_testing.py/d' \
+ CTestCustom.cmake.in || die
+ # separate ebuild to tmglib
+ sed -i \
+ -e '/lapack_install_library(tmglib)/d' \
+ TESTING/MATGEN/CMakeLists.txt || die
+}
+
+src_configure() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ my_src_configure() {
+ local profname=$(fortran-int64_get_profname)
+ local libname="${profname//-/_}"
+ local blas_profname=$(fortran-int64_get_blas_profname)
+ local xblas_profname=$(fortran-int64_get_xblas_profname)
+ local xblas_libname="${xblas_profname//-/_}"
+ local blas_requires="${blas_profname}"
+ use xblas && \
+ blas_requires+=" ${xblas_profname}"
+ local mycmakeargs=(
+ -DPROFNAME="${profname}"
+ -DBLAS_REQUIRES="${blas_requires}"
+ -DLIBNAME="${libname}"
+ -DUSE_OPTIMIZED_BLAS=ON
+ -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs
${blas_profname})"
+ $(cmake-utils_use_build test TESTING)
+ $(cmake-utils_use_use xblas XBLAS)
+ -DCMAKE_C_FLAGS="$($(tc-getPKG_CONFIG) --cflags
${blas_profname}) ${CFLAGS}"
+ -DCMAKE_CXX_FLAGS="$($(tc-getPKG_CONFIG) --cflags
${blas_profname}) ${CXXFLAGS}"
+ -DCMAKE_Fortran_FLAGS="$($(tc-getPKG_CONFIG) --cflags
${blas_profname}) $(get_abi_CFLAGS)
$(fortran-int64_get_fortran_int64_abi_fflags) ${FCFLAGS}"
+
-DLAPACK_PKGCONFIG_FFLAGS="$(fortran-int64_get_fortran_int64_abi_fflags)"
+ )
+ use xblas && \
+ mycmakeargs+=(
-DXBLAS_LIBRARY:FILEPATH="${EROOT}usr/$(get_libdir)/lib${xblas_libname}.so" )
+ if $(fortran-int64_is_static_build); then
+ mycmakeargs+=(
+ -DBUILD_SHARED_LIBS=OFF
+ -DBUILD_STATIC_LIBS=ON
+ )
+ else
+ mycmakeargs+=(
+ -DBUILD_SHARED_LIBS=ON
+ -DBUILD_STATIC_LIBS=OFF
+ )
+ fi
+ cmake-utils_src_configure
+ }
+ multibuild_foreach_variant fortran-int64_multilib_multibuild_wrapper
my_src_configure
+}
+
+src_compile() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ multibuild_foreach_variant fortran-int64_multilib_multibuild_wrapper
cmake-utils_src_compile
+}
+
+src_test() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ multibuild_foreach_variant fortran-int64_multilib_multibuild_wrapper
cmake-utils_src_test
+}
+
+src_install() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ my_src_install() {
+ cmake-utils_src_install
+ if ! $(fortran-int64_is_static_build); then
+ local profname=$(fortran-int64_get_profname)
+ local provider=$(fortran-int64_get_lapack_provider)
+ alternatives_for ${provider}
$(fortran-int64_get_profname "reference") 0 \
+ /usr/$(get_libdir)/pkgconfig/${provider}.pc
${profname}.pc
+ fi
+ }
+ multibuild_foreach_variant fortran-int64_multilib_multibuild_wrapper
my_src_install
+}
diff --git a/sci-libs/lapacke-reference/lapacke-reference-3.4.2.ebuild
b/sci-libs/lapacke-reference/lapacke-reference-3.4.2.ebuild
deleted file mode 120000
index 19f551a..0000000
--- a/sci-libs/lapacke-reference/lapacke-reference-3.4.2.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-lapacke-reference-9999.ebuild
\ No newline at end of file
diff --git a/sci-libs/lapacke-reference/lapacke-reference-3.4.2.ebuild
b/sci-libs/lapacke-reference/lapacke-reference-3.4.2.ebuild
new file mode 100644
index 0000000..2c53640
--- /dev/null
+++ b/sci-libs/lapacke-reference/lapacke-reference-3.4.2.ebuild
@@ -0,0 +1,103 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit alternatives-2 cmake-utils eutils fortran-2 toolchain-funcs
+
+FORTRAN_NEEDED=test
+
+MYP=lapack-${PV}
+
+if [[ ${PV} == "9999" ]] ; then
+ ESVN_REPO_URI="https://icl.cs.utk.edu/svn/lapack-dev/lapack/trunk";
+ inherit subversion
+ KEYWORDS=""
+else
+ SRC_URI="http://www.netlib.org/lapack/${MYP}.tgz";
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+DESCRIPTION="C Interface to LAPACK"
+HOMEPAGE="http://www.netlib.org/lapack/";
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="static-libs test tmg xblas"
+
+RDEPEND="
+ virtual/blas
+ virtual/lapack
+ tmg? ( sci-libs/tmglib )
+ xblas? ( sci-libs/xblas )"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
+
+S="${WORKDIR}/${MYP}"
+
+src_prepare() {
+ # rename libraries to avoid collision with other lapacke
+ sed -i \
+ -e 's:BINARY_DIR}/lapacke.pc:BINARY_DIR}/reflapacke.pc:' \
+ -e '/export/s:lapacke:reflapacke:g' \
+ -e '/ALL_TARGETS/s:lapacke):reflapacke):' \
+ -e '/LAPACK_LIBRARIES/s:lapacke:reflapacke:g' \
+ CMakeLists.txt || die
+ sed -i \
+ -e '/librar/s:(lapacke:(reflapacke:g' \
+ lapacke/CMakeLists.txt || die
+ sed -i \
+ -e '/librar/s:lapacke:reflapacke:g' \
+ lapacke/example/CMakeLists.txt || die
+ local tmgpc; use tmg && tmgpc=" -ltmglib"
+ sed -i \
+ -e "s:-llapacke:-lreflapacke${tmgpc}:g" \
+ lapacke/lapacke.pc.in || die
+ use static-libs && mkdir "${WORKDIR}/${PN}_static"
+}
+
+src_configure() {
+ lapack_configure() {
+ local mycmakeargs=(
+ -DUSE_OPTIMIZED_BLAS=ON
+ -DUSE_OPTIMIZED_LAPACK=ON
+ -DLAPACKE=ON
+ -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)"
+ -DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs
lapack)"
+ $(cmake-utils_use tmg LAPACKE_WITH_TMG)
+ $(cmake-utils_use_build test TESTING)
+ $(cmake-utils_use_use xblas XBLAS)
+ $@
+ )
+ cmake-utils_src_configure
+ }
+
+ lapack_configure -DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=OFF
+ use static-libs && \
+ CMAKE_BUILD_DIR="${WORKDIR}/${PN}_static" lapack_configure \
+ -DBUILD_SHARED_LIBS=OFF -DBUILD_STATIC_LIBS=ON
+}
+
+src_compile() {
+ use test && cmake-utils_src_compile -C TESTING/MATGEN
+ cmake-utils_src_compile -C lapacke
+ use static-libs && CMAKE_BUILD_DIR="${WORKDIR}/${PN}_static" \
+ cmake-utils_src_compile -C lapacke
+}
+
+src_test() {
+ pushd "${CMAKE_BUILD_DIR}/lapacke" > /dev/null
+ local ctestargs
+ [[ -n ${TEST_VERBOSE} ]] && ctestargs="--extra-verbose
--output-on-failure"
+ ctest ${ctestargs} || die
+ popd > /dev/null
+}
+
+src_install() {
+ cmake-utils_src_install -C lapacke
+ use static-libs && CMAKE_BUILD_DIR="${WORKDIR}/${PN}_static" \
+ cmake-utils_src_install -C lapacke
+ alternatives_for lapacke reference 0 \
+ /usr/$(get_libdir)/pkgconfig/lapacke.pc reflapacke.pc
+}
diff --git a/sci-libs/lapacke-reference/lapacke-reference-3.5.0.ebuild
b/sci-libs/lapacke-reference/lapacke-reference-3.5.0.ebuild
deleted file mode 120000
index 19f551a..0000000
--- a/sci-libs/lapacke-reference/lapacke-reference-3.5.0.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-lapacke-reference-9999.ebuild
\ No newline at end of file
diff --git a/sci-libs/lapacke-reference/lapacke-reference-3.5.0.ebuild
b/sci-libs/lapacke-reference/lapacke-reference-3.5.0.ebuild
new file mode 100644
index 0000000..2c53640
--- /dev/null
+++ b/sci-libs/lapacke-reference/lapacke-reference-3.5.0.ebuild
@@ -0,0 +1,103 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit alternatives-2 cmake-utils eutils fortran-2 toolchain-funcs
+
+FORTRAN_NEEDED=test
+
+MYP=lapack-${PV}
+
+if [[ ${PV} == "9999" ]] ; then
+ ESVN_REPO_URI="https://icl.cs.utk.edu/svn/lapack-dev/lapack/trunk";
+ inherit subversion
+ KEYWORDS=""
+else
+ SRC_URI="http://www.netlib.org/lapack/${MYP}.tgz";
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+DESCRIPTION="C Interface to LAPACK"
+HOMEPAGE="http://www.netlib.org/lapack/";
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="static-libs test tmg xblas"
+
+RDEPEND="
+ virtual/blas
+ virtual/lapack
+ tmg? ( sci-libs/tmglib )
+ xblas? ( sci-libs/xblas )"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
+
+S="${WORKDIR}/${MYP}"
+
+src_prepare() {
+ # rename libraries to avoid collision with other lapacke
+ sed -i \
+ -e 's:BINARY_DIR}/lapacke.pc:BINARY_DIR}/reflapacke.pc:' \
+ -e '/export/s:lapacke:reflapacke:g' \
+ -e '/ALL_TARGETS/s:lapacke):reflapacke):' \
+ -e '/LAPACK_LIBRARIES/s:lapacke:reflapacke:g' \
+ CMakeLists.txt || die
+ sed -i \
+ -e '/librar/s:(lapacke:(reflapacke:g' \
+ lapacke/CMakeLists.txt || die
+ sed -i \
+ -e '/librar/s:lapacke:reflapacke:g' \
+ lapacke/example/CMakeLists.txt || die
+ local tmgpc; use tmg && tmgpc=" -ltmglib"
+ sed -i \
+ -e "s:-llapacke:-lreflapacke${tmgpc}:g" \
+ lapacke/lapacke.pc.in || die
+ use static-libs && mkdir "${WORKDIR}/${PN}_static"
+}
+
+src_configure() {
+ lapack_configure() {
+ local mycmakeargs=(
+ -DUSE_OPTIMIZED_BLAS=ON
+ -DUSE_OPTIMIZED_LAPACK=ON
+ -DLAPACKE=ON
+ -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)"
+ -DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs
lapack)"
+ $(cmake-utils_use tmg LAPACKE_WITH_TMG)
+ $(cmake-utils_use_build test TESTING)
+ $(cmake-utils_use_use xblas XBLAS)
+ $@
+ )
+ cmake-utils_src_configure
+ }
+
+ lapack_configure -DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=OFF
+ use static-libs && \
+ CMAKE_BUILD_DIR="${WORKDIR}/${PN}_static" lapack_configure \
+ -DBUILD_SHARED_LIBS=OFF -DBUILD_STATIC_LIBS=ON
+}
+
+src_compile() {
+ use test && cmake-utils_src_compile -C TESTING/MATGEN
+ cmake-utils_src_compile -C lapacke
+ use static-libs && CMAKE_BUILD_DIR="${WORKDIR}/${PN}_static" \
+ cmake-utils_src_compile -C lapacke
+}
+
+src_test() {
+ pushd "${CMAKE_BUILD_DIR}/lapacke" > /dev/null
+ local ctestargs
+ [[ -n ${TEST_VERBOSE} ]] && ctestargs="--extra-verbose
--output-on-failure"
+ ctest ${ctestargs} || die
+ popd > /dev/null
+}
+
+src_install() {
+ cmake-utils_src_install -C lapacke
+ use static-libs && CMAKE_BUILD_DIR="${WORKDIR}/${PN}_static" \
+ cmake-utils_src_install -C lapacke
+ alternatives_for lapacke reference 0 \
+ /usr/$(get_libdir)/pkgconfig/lapacke.pc reflapacke.pc
+}
diff --git a/sci-libs/libsc/libsc-1.1.ebuild b/sci-libs/libsc/libsc-1.1.ebuild
deleted file mode 120000
index 2541d9d..0000000
--- a/sci-libs/libsc/libsc-1.1.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-libsc-1.0.ebuild
\ No newline at end of file
diff --git a/sci-libs/libsc/libsc-1.1.ebuild b/sci-libs/libsc/libsc-1.1.ebuild
new file mode 100644
index 0000000..a922f6b
--- /dev/null
+++ b/sci-libs/libsc/libsc-1.1.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+WANT_AUTOMAKE=1.11
+
+inherit autotools-utils toolchain-funcs eutils multilib
+
+DESCRIPTION="Support for parallel scientific applications"
+HOMEPAGE="http://www.p4est.org/";
+SRC_URI="https://github.com/cburstedde/libsc/archive/v${PV}.tar.gz ->
${P}.tar.gz"
+
+LICENSE="LGPL-2.1+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="debug examples mpi romio static-libs"
+
+REQUIRED_USE="romio? ( mpi )"
+
+RDEPEND="
+ dev-lang/lua:*
+ sys-apps/util-linux
+ virtual/blas
+ virtual/lapack
+ mpi? ( virtual/mpi[romio?] )"
+
+DEPEND="
+ ${RDEPEND}
+ virtual/pkgconfig"
+
+DOCS=(AUTHORS NEWS README)
+
+AUTOTOOLS_AUTORECONF=true
+
+src_prepare() {
+ # Inject a version number into the build system
+ echo "${PV}" > ${S}/.tarball-version
+
+ autotools-utils_src_prepare
+}
+
+src_configure() {
+ local myeconfargs=(
+ $(use_enable debug)
+ $(use_enable mpi)
+ $(use_enable romio mpiio)
+ --with-blas="$($(tc-getPKG_CONFIG) --libs blas)"
+ --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)"
+ )
+ autotools-utils_src_configure
+}
+
+src_install() {
+ autotools-utils_src_install
+
+ if use examples; then
+ docinto examples
+ dodoc -r example/*
+ docompress -x /usr/share/doc/${PF}/examples
+ else
+ # Remove the compiled example binaries in case of -examples:
+ rm -r "${ED}"/usr/bin || die "rm failed"
+ fi
+
+ # Fix up some wrong installation paths:
+ dodir /usr/share/libsc
+ mv "${ED}"/etc/* "${ED}"/usr/share/libsc
+ rmdir "${ED}"/etc/
+}
diff --git a/sci-libs/openblas/openblas-0.2.12.ebuild
b/sci-libs/openblas/openblas-0.2.12.ebuild
deleted file mode 120000
index 2381753..0000000
--- a/sci-libs/openblas/openblas-0.2.12.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-openblas-9999.ebuild
\ No newline at end of file
diff --git a/sci-libs/openblas/openblas-0.2.12.ebuild
b/sci-libs/openblas/openblas-0.2.12.ebuild
new file mode 100644
index 0000000..91736c8
--- /dev/null
+++ b/sci-libs/openblas/openblas-0.2.12.ebuild
@@ -0,0 +1,227 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EBASE_PROFNAME="openblas"
+inherit alternatives-2 eutils multilib fortran-2 multibuild multilib-build
toolchain-funcs fortran-int64
+
+SRC_URI+="http://dev.gentoo.org/~gienah/distfiles/${PN}-0.2.11-gentoo.patch";
+if [[ ${PV} == "9999" ]] ; then
+ EGIT_REPO_URI="https://github.com/xianyi/OpenBLAS.git";
+ EGIT_BRANCH="develop"
+ inherit git-r3
+ KEYWORDS=""
+else
+ SRC_URI+=" http://github.com/xianyi/OpenBLAS/tarball/v${PV} ->
${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos ~ppc-macos
~x64-macos"
+fi
+
+DESCRIPTION="Optimized BLAS library based on GotoBLAS2"
+HOMEPAGE="http://xianyi.github.com/OpenBLAS/";
+LICENSE="BSD"
+SLOT="0"
+IUSE="dynamic int64 openmp static-libs threads"
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
+PDEPEND="
+ >=virtual/blas-2.1-r2[int64?]
+ >=virtual/cblas-2.0-r1[int64?]"
+
+MULTILIB_WRAPPED_HEADERS=(
+ /usr/include/openblas/cblas.h
+ /usr/include/openblas/f77blas.h
+ /usr/include/openblas/openblas_config.h
+)
+
+get_openblas_flags() {
+ local openblas_flags=""
+ use dynamic && \
+ openblas_flags+=" DYNAMIC_ARCH=1 TARGET=GENERIC NUM_THREADS=64
NO_AFFINITY=1"
+ $(fortran-int64_is_int64_build) && \
+ openblas_flags+=" INTERFACE64=1"
+ # choose posix threads over openmp when the two are set
+ # yet to see the need of having the two profiles simultaneously
+ if use threads; then
+ openblas_flags+=" USE_THREAD=1 USE_OPENMP=0"
+ elif use openmp; then
+ openblas_flags+=" USE_OPENMP=1"
+ fi
+ local profname=$(fortran-int64_get_profname)
+ local libname="${profname//-/_}"
+ local underscoresuffix="${libname#${PN}}"
+ if [[ "${underscoresuffix}" != "_" ]]; then
+ local libnamesuffix="${underscoresuffix#_}"
+ openblas_flags+=" LIBNAMESUFFIX=${libnamesuffix}"
+ fi
+ echo "${openblas_flags}"
+}
+
+get_openblas_abi_cflags() {
+ local openblas_abi_cflags=""
+ if [[ "${ABI}" == "x86" ]]; then
+ openblas_abi_cflags="-DOPENBLAS_ARCH_X86=1
-DOPENBLAS___32BIT__=1"
+ else
+ openblas_abi_cflags="-DOPENBLAS_ARCH_X86_64=1
-DOPENBLAS___64BIT__=1"
+ fi
+ $(fortran-int64_is_int64_build) && \
+ openblas_abi_cflags+=" -DOPENBLAS_USE64BITINT"
+ echo "${openblas_abi_cflags}"
+}
+
+src_unpack() {
+ if [[ ${PV} == "9999" ]] ; then
+ git-r3_src_unpack
+ else
+ default
+ if [[ ${PV} != "9999" ]] ; then
+ find "${WORKDIR}" -maxdepth 1 -type d -name
\*OpenBLAS\* && \
+ mv "${WORKDIR}"/*OpenBLAS* "${S}"
+ fi
+ fi
+}
+
+src_prepare() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ epatch "${DISTDIR}/${PN}-0.2.11-gentoo.patch"
+ if [[ ${PV} == "0.2.11" ]] ; then
+ epatch "${FILESDIR}/${PN}-0.2.11-cpuid_x86.patch"
+ fi
+ # lapack and lapacke are not modified from upstream lapack
+ sed \
+ -e "s:^#\s*\(NO_LAPACK\)\s*=.*:\1=1:" \
+ -e "s:^#\s*\(NO_LAPACKE\)\s*=.*:\1=1:" \
+ -i Makefile.rule || die
+ multibuild_copy_sources
+}
+
+src_configure() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ my_configure() {
+ local openblas_abi_cflags="$(get_openblas_abi_cflags)"
+ local
internal_openblas_abi_cflags="${openblas_abi_cflags//OPENBLAS_}"
+ sed \
+ -e "s:^#\s*\(CC\)\s*=.*:\1=$(tc-getCC)
$(get_abi_CFLAGS):" \
+ -e "s:^#\s*\(FC\)\s*=.*:\1=$(tc-getFC)
$(get_abi_CFLAGS):" \
+ -e "s:^#\s*\(COMMON_OPT\)\s*=.*:\1=${CFLAGS}
${internal_openblas_abi_cflags}:" \
+ -i Makefile.rule || die
+ }
+ multibuild_foreach_variant run_in_build_dir
fortran-int64_multilib_multibuild_wrapper my_configure
+}
+
+src_compile() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ # openblas already does multi-jobs
+ MAKEOPTS+=" -j1"
+ my_src_compile () {
+ local openblas_flags=$(get_openblas_flags)
+ local profname=$(fortran-int64_get_profname)
+ local libname="${profname//-/_}"
+ einfo "Compiling profile ${profname}"
+ # cflags already defined twice
+ unset CFLAGS
+ emake clean
+ emake libs shared ${openblas_flags}
+ mkdir -p libs && mv libopenblas* libs/
+ # avoid pic when compiling static libraries, so re-compiling
+ if use static-libs; then
+ emake clean
+ emake libs ${openblas_flags} NO_SHARED=1 NEED_PIC=
+ mv libopenblas* libs/
+ fi
+ # Fix Bug 524612 - [science overlay] sci-libs/openblas-0.2.11 -
Assembler messages:
+ # ../kernel/x86_64/gemm_kernel_8x4_barcelona.S:451: Error:
missing ')'
+ # The problem is applying this patch in src_prepare() causes
build failures on
+ # assembler code as the assembler does not understand
sizeof(float). So
+ # delay applying the patch until after building the libraries.
+ epatch
"${FILESDIR}/${PN}-0.2.11-openblas_config_header_same_between_ABIs.patch"
+ rm -f config.h config_last.h
+ # Note: prints this spurious warning: make: Nothing to be done
for 'config.h'.
+ emake config.h
+ cp config.h config_last.h || die
+ cat <<-EOF > ${profname}.pc
+ prefix=${EPREFIX}/usr
+ libdir=\${prefix}/$(get_libdir)
+ includedir=\${prefix}/include
+ Name: ${profname}
+ Description: ${DESCRIPTION}
+ Version: ${PV}
+ URL: ${HOMEPAGE}
+ Libs: -L\${libdir} -l${libname}
+ Libs.private: -lm
+ EOF
+ local openblas_abi_cflags=$(get_openblas_abi_cflags)
+ local
openblas_abi_fflags=$(fortran-int64_get_fortran_int64_abi_fflags)
+ cat <<-EOF >> ${profname}.pc
+ Cflags: -I\${includedir}/${PN} ${openblas_abi_cflags}
+ Fflags=${openblas_abi_fflags}
+ EOF
+ mv libs/libopenblas* . || die
+ }
+ multibuild_foreach_variant run_in_build_dir
fortran-int64_multilib_multibuild_wrapper my_src_compile
+}
+
+src_test() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ my_src_test () {
+ local openblas_flags=$(get_openblas_flags)
+ emake tests ${openblas_flags}
+ }
+ multibuild_foreach_variant run_in_build_dir
fortran-int64_multilib_multibuild_wrapper my_src_test
+}
+
+src_install() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ my_src_install() {
+ local openblas_flags=$(get_openblas_flags)
+ local profname=$(fortran-int64_get_profname)
+ local pcfile
+ for pcfile in *.pc; do
+ local profname=${pcfile%.pc}
+ # The file /usr/include/openblas/openblas_config.h is
generated during the install.
+ # The sed on config_last.h removes the #define's
OPENBLAS_USE64BITINT
+ # OPENBLASS__32BIT__ OPENBLASS__64BIT__
OPENBLAS__ARCH_X86 OPENBLAS__ARCH_X86_64
+ # from /usr/include/openblas/openblas_config.h. We
then specify it in Cflags in
+ # the
/usr/lib64/pkg-config/openblas-int64-{threads,openmp}.pc file.
+ sed -e '/#define USE64BITINT/d' \
+ -e '/#define ARCH_X86/d' \
+ -e '/#define __\(32\|64\)BIT__/d' \
+ -i config_last.h \
+ || die "Could not ensure there is no definition
of USE64BITINT in config_last.h"
+ emake install \
+ PREFIX="${ED}"usr ${openblas_flags} \
+ OPENBLAS_INCLUDE_DIR="${ED}"usr/include/${PN} \
+ OPENBLAS_LIBRARY_DIR="${ED}"usr/$(get_libdir)
+ use static-libs || rm "${ED}"usr/$(get_libdir)/lib*.a
+ alternatives_for $(fortran-int64_get_blas_provider)
${profname} 0 \
+
/usr/$(get_libdir)/pkgconfig/$(fortran-int64_get_blas_provider).pc ${pcfile}
+ alternatives_for $(fortran-int64_get_cblas_provider)
${profname} 0 \
+
/usr/$(get_libdir)/pkgconfig/$(fortran-int64_get_cblas_provider).pc ${pcfile} \
+ /usr/include/cblas.h ${PN}/cblas.h
+ insinto /usr/$(get_libdir)/pkgconfig
+ doins ${pcfile}
+ done
+
+ if [[ ${CHOST} == *-darwin* ]] ; then
+ cd "${ED}"/usr/$(get_libdir)
+ local d
+ for d in *.dylib ; do
+ ebegin "Correcting install_name of ${d}"
+ install_name_tool -id
"${EPREFIX}/usr/$(get_libdir)/${d}" "${d}"
+ eend $?
+ done
+ fi
+ if [[ ${#MULTIBUILD_VARIANTS[@]} -gt 1 ]]; then
+ multilib_prepare_wrappers
+ multilib_check_headers
+ fi
+ }
+ multibuild_foreach_variant run_in_build_dir
fortran-int64_multilib_multibuild_wrapper my_src_install
+ multilib_install_wrappers
+
+ dodoc GotoBLAS_{01Readme,03FAQ,04FAQ,05LargePage,06WeirdPerformance}.txt
+ dodoc *md Changelog.txt
+}
diff --git a/sci-libs/openblas/openblas-0.2.14.ebuild
b/sci-libs/openblas/openblas-0.2.14.ebuild
deleted file mode 120000
index 2381753..0000000
--- a/sci-libs/openblas/openblas-0.2.14.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-openblas-9999.ebuild
\ No newline at end of file
diff --git a/sci-libs/openblas/openblas-0.2.14.ebuild
b/sci-libs/openblas/openblas-0.2.14.ebuild
new file mode 100644
index 0000000..91736c8
--- /dev/null
+++ b/sci-libs/openblas/openblas-0.2.14.ebuild
@@ -0,0 +1,227 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EBASE_PROFNAME="openblas"
+inherit alternatives-2 eutils multilib fortran-2 multibuild multilib-build
toolchain-funcs fortran-int64
+
+SRC_URI+="http://dev.gentoo.org/~gienah/distfiles/${PN}-0.2.11-gentoo.patch";
+if [[ ${PV} == "9999" ]] ; then
+ EGIT_REPO_URI="https://github.com/xianyi/OpenBLAS.git";
+ EGIT_BRANCH="develop"
+ inherit git-r3
+ KEYWORDS=""
+else
+ SRC_URI+=" http://github.com/xianyi/OpenBLAS/tarball/v${PV} ->
${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos ~ppc-macos
~x64-macos"
+fi
+
+DESCRIPTION="Optimized BLAS library based on GotoBLAS2"
+HOMEPAGE="http://xianyi.github.com/OpenBLAS/";
+LICENSE="BSD"
+SLOT="0"
+IUSE="dynamic int64 openmp static-libs threads"
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
+PDEPEND="
+ >=virtual/blas-2.1-r2[int64?]
+ >=virtual/cblas-2.0-r1[int64?]"
+
+MULTILIB_WRAPPED_HEADERS=(
+ /usr/include/openblas/cblas.h
+ /usr/include/openblas/f77blas.h
+ /usr/include/openblas/openblas_config.h
+)
+
+get_openblas_flags() {
+ local openblas_flags=""
+ use dynamic && \
+ openblas_flags+=" DYNAMIC_ARCH=1 TARGET=GENERIC NUM_THREADS=64
NO_AFFINITY=1"
+ $(fortran-int64_is_int64_build) && \
+ openblas_flags+=" INTERFACE64=1"
+ # choose posix threads over openmp when the two are set
+ # yet to see the need of having the two profiles simultaneously
+ if use threads; then
+ openblas_flags+=" USE_THREAD=1 USE_OPENMP=0"
+ elif use openmp; then
+ openblas_flags+=" USE_OPENMP=1"
+ fi
+ local profname=$(fortran-int64_get_profname)
+ local libname="${profname//-/_}"
+ local underscoresuffix="${libname#${PN}}"
+ if [[ "${underscoresuffix}" != "_" ]]; then
+ local libnamesuffix="${underscoresuffix#_}"
+ openblas_flags+=" LIBNAMESUFFIX=${libnamesuffix}"
+ fi
+ echo "${openblas_flags}"
+}
+
+get_openblas_abi_cflags() {
+ local openblas_abi_cflags=""
+ if [[ "${ABI}" == "x86" ]]; then
+ openblas_abi_cflags="-DOPENBLAS_ARCH_X86=1
-DOPENBLAS___32BIT__=1"
+ else
+ openblas_abi_cflags="-DOPENBLAS_ARCH_X86_64=1
-DOPENBLAS___64BIT__=1"
+ fi
+ $(fortran-int64_is_int64_build) && \
+ openblas_abi_cflags+=" -DOPENBLAS_USE64BITINT"
+ echo "${openblas_abi_cflags}"
+}
+
+src_unpack() {
+ if [[ ${PV} == "9999" ]] ; then
+ git-r3_src_unpack
+ else
+ default
+ if [[ ${PV} != "9999" ]] ; then
+ find "${WORKDIR}" -maxdepth 1 -type d -name
\*OpenBLAS\* && \
+ mv "${WORKDIR}"/*OpenBLAS* "${S}"
+ fi
+ fi
+}
+
+src_prepare() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ epatch "${DISTDIR}/${PN}-0.2.11-gentoo.patch"
+ if [[ ${PV} == "0.2.11" ]] ; then
+ epatch "${FILESDIR}/${PN}-0.2.11-cpuid_x86.patch"
+ fi
+ # lapack and lapacke are not modified from upstream lapack
+ sed \
+ -e "s:^#\s*\(NO_LAPACK\)\s*=.*:\1=1:" \
+ -e "s:^#\s*\(NO_LAPACKE\)\s*=.*:\1=1:" \
+ -i Makefile.rule || die
+ multibuild_copy_sources
+}
+
+src_configure() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ my_configure() {
+ local openblas_abi_cflags="$(get_openblas_abi_cflags)"
+ local
internal_openblas_abi_cflags="${openblas_abi_cflags//OPENBLAS_}"
+ sed \
+ -e "s:^#\s*\(CC\)\s*=.*:\1=$(tc-getCC)
$(get_abi_CFLAGS):" \
+ -e "s:^#\s*\(FC\)\s*=.*:\1=$(tc-getFC)
$(get_abi_CFLAGS):" \
+ -e "s:^#\s*\(COMMON_OPT\)\s*=.*:\1=${CFLAGS}
${internal_openblas_abi_cflags}:" \
+ -i Makefile.rule || die
+ }
+ multibuild_foreach_variant run_in_build_dir
fortran-int64_multilib_multibuild_wrapper my_configure
+}
+
+src_compile() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ # openblas already does multi-jobs
+ MAKEOPTS+=" -j1"
+ my_src_compile () {
+ local openblas_flags=$(get_openblas_flags)
+ local profname=$(fortran-int64_get_profname)
+ local libname="${profname//-/_}"
+ einfo "Compiling profile ${profname}"
+ # cflags already defined twice
+ unset CFLAGS
+ emake clean
+ emake libs shared ${openblas_flags}
+ mkdir -p libs && mv libopenblas* libs/
+ # avoid pic when compiling static libraries, so re-compiling
+ if use static-libs; then
+ emake clean
+ emake libs ${openblas_flags} NO_SHARED=1 NEED_PIC=
+ mv libopenblas* libs/
+ fi
+ # Fix Bug 524612 - [science overlay] sci-libs/openblas-0.2.11 -
Assembler messages:
+ # ../kernel/x86_64/gemm_kernel_8x4_barcelona.S:451: Error:
missing ')'
+ # The problem is applying this patch in src_prepare() causes
build failures on
+ # assembler code as the assembler does not understand
sizeof(float). So
+ # delay applying the patch until after building the libraries.
+ epatch
"${FILESDIR}/${PN}-0.2.11-openblas_config_header_same_between_ABIs.patch"
+ rm -f config.h config_last.h
+ # Note: prints this spurious warning: make: Nothing to be done
for 'config.h'.
+ emake config.h
+ cp config.h config_last.h || die
+ cat <<-EOF > ${profname}.pc
+ prefix=${EPREFIX}/usr
+ libdir=\${prefix}/$(get_libdir)
+ includedir=\${prefix}/include
+ Name: ${profname}
+ Description: ${DESCRIPTION}
+ Version: ${PV}
+ URL: ${HOMEPAGE}
+ Libs: -L\${libdir} -l${libname}
+ Libs.private: -lm
+ EOF
+ local openblas_abi_cflags=$(get_openblas_abi_cflags)
+ local
openblas_abi_fflags=$(fortran-int64_get_fortran_int64_abi_fflags)
+ cat <<-EOF >> ${profname}.pc
+ Cflags: -I\${includedir}/${PN} ${openblas_abi_cflags}
+ Fflags=${openblas_abi_fflags}
+ EOF
+ mv libs/libopenblas* . || die
+ }
+ multibuild_foreach_variant run_in_build_dir
fortran-int64_multilib_multibuild_wrapper my_src_compile
+}
+
+src_test() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ my_src_test () {
+ local openblas_flags=$(get_openblas_flags)
+ emake tests ${openblas_flags}
+ }
+ multibuild_foreach_variant run_in_build_dir
fortran-int64_multilib_multibuild_wrapper my_src_test
+}
+
+src_install() {
+ local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) )
+ my_src_install() {
+ local openblas_flags=$(get_openblas_flags)
+ local profname=$(fortran-int64_get_profname)
+ local pcfile
+ for pcfile in *.pc; do
+ local profname=${pcfile%.pc}
+ # The file /usr/include/openblas/openblas_config.h is
generated during the install.
+ # The sed on config_last.h removes the #define's
OPENBLAS_USE64BITINT
+ # OPENBLASS__32BIT__ OPENBLASS__64BIT__
OPENBLAS__ARCH_X86 OPENBLAS__ARCH_X86_64
+ # from /usr/include/openblas/openblas_config.h. We
then specify it in Cflags in
+ # the
/usr/lib64/pkg-config/openblas-int64-{threads,openmp}.pc file.
+ sed -e '/#define USE64BITINT/d' \
+ -e '/#define ARCH_X86/d' \
+ -e '/#define __\(32\|64\)BIT__/d' \
+ -i config_last.h \
+ || die "Could not ensure there is no definition
of USE64BITINT in config_last.h"
+ emake install \
+ PREFIX="${ED}"usr ${openblas_flags} \
+ OPENBLAS_INCLUDE_DIR="${ED}"usr/include/${PN} \
+ OPENBLAS_LIBRARY_DIR="${ED}"usr/$(get_libdir)
+ use static-libs || rm "${ED}"usr/$(get_libdir)/lib*.a
+ alternatives_for $(fortran-int64_get_blas_provider)
${profname} 0 \
+
/usr/$(get_libdir)/pkgconfig/$(fortran-int64_get_blas_provider).pc ${pcfile}
+ alternatives_for $(fortran-int64_get_cblas_provider)
${profname} 0 \
+
/usr/$(get_libdir)/pkgconfig/$(fortran-int64_get_cblas_provider).pc ${pcfile} \
+ /usr/include/cblas.h ${PN}/cblas.h
+ insinto /usr/$(get_libdir)/pkgconfig
+ doins ${pcfile}
+ done
+
+ if [[ ${CHOST} == *-darwin* ]] ; then
+ cd "${ED}"/usr/$(get_libdir)
+ local d
+ for d in *.dylib ; do
+ ebegin "Correcting install_name of ${d}"
+ install_name_tool -id
"${EPREFIX}/usr/$(get_libdir)/${d}" "${d}"
+ eend $?
+ done
+ fi
+ if [[ ${#MULTIBUILD_VARIANTS[@]} -gt 1 ]]; then
+ multilib_prepare_wrappers
+ multilib_check_headers
+ fi
+ }
+ multibuild_foreach_variant run_in_build_dir
fortran-int64_multilib_multibuild_wrapper my_src_install
+ multilib_install_wrappers
+
+ dodoc GotoBLAS_{01Readme,03FAQ,04FAQ,05LargePage,06WeirdPerformance}.txt
+ dodoc *md Changelog.txt
+}
diff --git a/sci-libs/p4est/p4est-1.1.ebuild b/sci-libs/p4est/p4est-1.1.ebuild
deleted file mode 120000
index 89804b2..0000000
--- a/sci-libs/p4est/p4est-1.1.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-p4est-1.0.ebuild
\ No newline at end of file
diff --git a/sci-libs/p4est/p4est-1.1.ebuild b/sci-libs/p4est/p4est-1.1.ebuild
new file mode 100644
index 0000000..e686b86
--- /dev/null
+++ b/sci-libs/p4est/p4est-1.1.ebuild
@@ -0,0 +1,99 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+WANT_AUTOMAKE=1.11
+
+inherit autotools-utils toolchain-funcs eutils multilib
+
+DESCRIPTION="Scalable Algorithms for Parallel Adaptive Mesh Refinement on
Forests of Octrees"
+HOMEPAGE="http://www.p4est.org/";
+SRC_URI="
+ https://github.com/cburstedde/p4est/archive/v${PV}.tar.gz -> ${P}.tar.gz
+ https://github.com/cburstedde/libsc/archive/v${PV}.tar.gz ->
libsc-${PV}.tar.gz"
+
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+LICENSE="GPL-2+"
+SLOT="0"
+
+IUSE="debug doc examples mpi romio static-libs +vtk-binary"
+REQUIRED_USE="romio? ( mpi )"
+
+RDEPEND="
+ >=sci-libs/libsc-1.0[mpi,romio]
+ dev-lang/lua:*
+ sys-apps/util-linux
+ virtual/blas
+ virtual/lapack
+ mpi? ( virtual/mpi[romio?] )"
+
+DEPEND="
+ ${RDEPEND}
+ sys-devel/automake:1.11
+ virtual/pkgconfig"
+
+DOCS=( AUTHORS NEWS README )
+
+AT_M4DIR="${WORKDIR}/${P}/config ${WORKDIR}/${P}/sc/config"
+AUTOTOOLS_AUTORECONF=true
+
+src_prepare() {
+ # Inject libsc to get all parts of the build system...
+ rmdir "${S}/sc" || die "rmdir failed"
+ mv "${WORKDIR}/libsc-${PV}" "${S}/sc" || die "mv failed"
+
+ # Inject a version number into the build system
+ echo "${PV}" > ${S}/.tarball-version
+
+ autotools-utils_src_prepare
+
+ sed -i \
+ "s/P4EST_SC_DIR\/etc/P4EST_SC_DIR\/share\/libsc/" \
+ "${S}"/configure || die "sed failed"
+
+ sed -i \
+ "s/libsc\.la/libsc\.so/" \
+ "${S}"/configure || die "sed failed"
+
+}
+
+src_configure() {
+ # Somehow --with-sc=$EPREFIX/usr does not work...
+ LDFLAGS="${LDFLAGS} -lsc"
+
+ local myeconfargs=(
+ $(use_enable debug)
+ $(use_enable mpi)
+ $(use_enable romio mpiio)
+ $(use_enable vtk-binary)
+ --with-blas="$($(tc-getPKG_CONFIG) --libs blas)"
+ --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)"
+ --with-sc="${EPREFIX}/usr"
+ )
+ autotools-utils_src_configure
+}
+
+src_install() {
+ autotools-utils_src_install
+
+ use doc && dodoc -r doc/*
+
+ if use examples
+ then
+ docinto examples
+ dodoc -r example/*
+ docompress -x /usr/share/doc/${PF}/examples
+ else
+ # Remove the compiled example binaries in case of -examples:
+ rm -r "${ED}"/usr/bin || die "rm failed"
+ fi
+
+ # Fix up some wrong installation paths:
+ dodir /usr/share/p4est
+ mv "${ED}"/usr/share/data "${ED}"/usr/share/p4est/data
+ mv "${ED}"/etc/* "${ED}"/usr/share/p4est
+ rmdir "${ED}"/etc/
+}
diff --git a/sci-mathematics/htk/htk-3.4.1.ebuild
b/sci-mathematics/htk/htk-3.4.1.ebuild
index 99d9adc..ceae8db 100644
--- a/sci-mathematics/htk/htk-3.4.1.ebuild
+++ b/sci-mathematics/htk/htk-3.4.1.ebuild
@@ -50,7 +50,7 @@ src_configure() {
src_compile() {
if use hlmtools || use hdecode; then
- emake -j1 || die "Cannot compile"
+ emake -j1
else
emake
fi
diff --git a/sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild
b/sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild
index 10e83c7..38b4c31 100644
--- a/sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild
+++ b/sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild
@@ -21,7 +21,7 @@ src_compile() {
-e "s/CC=gcc/#CC=gcc/g" \
-e "s/CFLAGS= -O3 -ansi -DNXT/CFLAGS+= -ansi -DNXT/g"
- emake || die "emake failed"
+ emake
}
src_install() {
diff --git a/sci-mathematics/yorick/yorick-2.1.06.ebuild
b/sci-mathematics/yorick/yorick-2.1.06.ebuild
index 0ba5b87..e0020b1 100644
--- a/sci-mathematics/yorick/yorick-2.1.06.ebuild
+++ b/sci-mathematics/yorick/yorick-2.1.06.ebuild
@@ -36,7 +36,7 @@ src_configure() {
src_compile() {
# makefiles are not robust. (not interested in fixing)
emake prefix=/usr ysite Y_HOME=/usr/$(get_libdir)/yorick
- emake config || die
+ emake config
emake -j1
}
diff --git a/sci-physics/abinit/abinit-7.10.4.ebuild
b/sci-physics/abinit/abinit-7.10.4.ebuild
index 44625ff..40f2d15 100644
--- a/sci-physics/abinit/abinit-7.10.4.ebuild
+++ b/sci-physics/abinit/abinit-7.10.4.ebuild
@@ -351,7 +351,7 @@ src_install() {
#autotools-utils_src_install() expanded
_check_build_dir
pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
- emake DESTDIR="${D}" install || die "make install failed"
+ emake DESTDIR="${D}" install
use libabinit && dolib libabinit.a
diff --git a/sci-physics/genfit/genfit-02.00.00.ebuild
b/sci-physics/genfit/genfit-02.00.00.ebuild
deleted file mode 120000
index c4f24f2..0000000
--- a/sci-physics/genfit/genfit-02.00.00.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-genfit-9999.ebuild
\ No newline at end of file
diff --git a/sci-physics/genfit/genfit-02.00.00.ebuild
b/sci-physics/genfit/genfit-02.00.00.ebuild
new file mode 100644
index 0000000..a449b62
--- /dev/null
+++ b/sci-physics/genfit/genfit-02.00.00.ebuild
@@ -0,0 +1,59 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit cmake-utils versionator
+
+if [[ ${PV} == *9999* ]]; then
+ inherit subversion
+ ESVN_REPO_URI="https://svn.code.sf.net/p/${PN}/code/trunk";
+ ESVN_PROJECT="${PN}.${PV}"
+ KEYWORDS=""
+else
+ # .zip-snapshot can be recreated by visiting
+ #
http://sourceforge.net/p/${PN}/code/${COMMIT}/tarball?path=/tags/v$(replace_all_version_separators
'-')
+ TAG_VER=${PN}-code-1688-tags-v$(replace_all_version_separators '-')
+
#SRC_URI="http://sourceforge.net/code-snapshots/svn/g/ge/genfit/code/${TAG_VER}.zip";
+ SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${TAG_VER}.zip";
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+ S=${WORKDIR}/${TAG_VER}
+fi
+
+DESCRIPTION="Generic toolkit for track reconstruction in physics experiments"
+HOMEPAGE="http://genfit.sourceforge.net/Main.html";
+
+LICENSE="LGPL-3"
+SLOT="0"
+IUSE="doc examples"
+
+RDEPEND="
+ sci-physics/root:=
+ dev-libs/boost:="
+DEPEND="${RDEPEND}
+ doc? ( app-doc/doxygen[dot] )"
+
+src_compile() {
+ cmake-utils_src_compile
+ use doc && cmake-utils_src_compile doc
+ use examples && cmake-utils_src_compile tests
+}
+
+src_install() {
+ cmake-utils_src_install
+ if use examples; then
+ insinto /usr/share/doc/${PF}
+ doins -r "${BUILD_DIR}/bin"
+ doins test/makeGeom.C
+ doins test/README
+ fi
+ use doc && dohtml -r doc/html/*
+ echo
+ elog "Note that there is no support in this ebuild for RAVE yet,"
+ elog "which is also not in portage."
+ elog "It should be possible to use a local installation of RAVE"
+ elog "and set:"
+ elog " export RAVEPATH=<yourRaveDirectory>"
+ echo
+}
diff --git a/sys-cluster/openmpi/openmpi-1.6.5.ebuild
b/sys-cluster/openmpi/openmpi-1.6.5.ebuild
index c454e37..ab58af6 100644
--- a/sys-cluster/openmpi/openmpi-1.6.5.ebuild
+++ b/sys-cluster/openmpi/openmpi-1.6.5.ebuild
@@ -147,7 +147,7 @@ src_configure() {
}
src_install () {
- emake DESTDIR="${D}" install || die "make install failed"
+ emake DESTDIR="${D}" install
# From USE=vt see #359917
rm "${ED}"/$(mpi_root)/usr/share/libtool &> /dev/null
mpi_dodoc README AUTHORS NEWS VERSION || die
@@ -158,5 +158,5 @@ src_test() {
# Doesn't work with the default src_test as the dry run (-n) fails.
# Do not override malloc during build. Works around #462602
- emake -j1 check || die "emake check failed"
+ emake -j1 check
}
