Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

* 'master' of git+ssh://git.gentoo.org/proj/sci: (90 commits) sci-chemistry/coot: Don't set LD_LIBRARY_PATH www-client/casjerjs: Fix installation of casperjs executable dev-python/metakernel_bash: Install missing kernel spec dev-python/metakernel_python: Install missing kernel spec dev-python/metakernel_bash: New package, ebuild written by me dev-python/metakernel: New package, ebuild written by me dev-python/metakernel_python: New package, ebuild written by me sci-chemistry/votca-csgapps: sync with gx86 sci-chemistry/votca-csg: sync with gx86 sci-libs/votca-tools: sync with gx86 sys-cluster/openmpi: bump 1.10.0 Ban EAPI=4 Use default functions sci-biology/augustus: Use default functions sci-physics/mc-tester: Use default functions sci-biology/Atlas2: Use default functions sci-physics/tauola: Use default functions media-libs/libgfx: Use default functions dev-util/nvidia-cuda-gdk: Use default functions dev-java/netcdf: Bump to EAPI=5 ...
author: Justin Lecher <jlec@gentoo.org> 2015-09-25 18:22:42 +0200
committer: Justin Lecher <jlec@gentoo.org> 2015-09-25 18:22:42 +0200
commit: e3417554a48f19740c35e981c3a67a341e88d3c1 (patch)
tree: 4ea71ccc921da9cce2ebe845418eae33b93c8b59
parent: Add local USE description (diff)
parent: Merge remote-tracking branch 'github/master' (diff)
download: sci-e3417554.tar.gz
sci-e3417554.tar.bz2
sci-e3417554.zip
254 files changed, 4153 insertions, 1402 deletions
diff --git a/app-admin/eselect/eselect-1.4.5-r101.ebuild b/app-admin/eselect/eselect-1.4.5-r101.ebuild
index e37ea64b7..b1e138bb6 100644
--- a/app-admin/eselect/eselect-1.4.5-r101.ebuild
+++ b/app-admin/eselect/eselect-1.4.5-r101.ebuild
@@ -38,12 +38,12 @@ src_prepare() {
 }
 
 src_compile() {
-	emake
+	default
 	use doc && emake html
 }
 
 src_install() {
-	emake DESTDIR="${D}" install
+	default
 	newbashcomp misc/${PN}.bashcomp ${PN}
 	dodoc AUTHORS ChangeLog NEWS README TODO doc/*.txt
 	use doc && dohtml *.html doc/*
diff --git a/app-admin/eselect/eselect-9999.ebuild b/app-admin/eselect/eselect-9999.ebuild
index 595077517..33e6a1575 100644
--- a/app-admin/eselect/eselect-9999.ebuild
+++ b/app-admin/eselect/eselect-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -37,12 +37,12 @@ src_prepare() {
 }
 
 src_compile() {
-	emake
+	default
 	use doc && emake html
 }
 
 src_install() {
-	emake DESTDIR="${D}" install
+	default
 	newbashcomp misc/${PN}.bashcomp ${PN}
 	dodoc AUTHORS ChangeLog NEWS README TODO doc/*.txt
 	use doc && dohtml *.html doc/*
diff --git a/dev-cpp/eigen/eigen-3.2.2.ebuild b/dev-cpp/eigen/eigen-3.2.2.ebuild
index eafd77401..64caa7165 120000..100644
--- a/dev-cpp/eigen/eigen-3.2.2.ebuild
+++ b/dev-cpp/eigen/eigen-3.2.2.ebuild
@@ -1 +1,117 @@
-eigen-9999.ebuild
-\ No newline at end of file
+# 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
index eafd77401..64caa7165 120000..100644
--- a/dev-cpp/eigen/eigen-3.2.4.ebuild
+++ b/dev-cpp/eigen/eigen-3.2.4.ebuild
@@ -1 +1,117 @@
-eigen-9999.ebuild
-\ No newline at end of file
+# 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-java/jeuclid-core/jeuclid-core-3.1.9-r1.ebuild b/dev-java/jeuclid-core/jeuclid-core-3.1.9-r1.ebuild
index 0c19b16fe..97b7b0487 100644
--- a/dev-java/jeuclid-core/jeuclid-core-3.1.9-r1.ebuild
+++ b/dev-java/jeuclid-core/jeuclid-core-3.1.9-r1.ebuild
@@ -6,7 +6,7 @@ EAPI=5
 JAVA_PKG_IUSE="source"
 inherit eutils java-pkg-2 java-ant-2
 
-DESCRIPTION="Core module of MathML rendering solution."
+DESCRIPTION="Core module of MathML rendering solution"
 HOMEPAGE="http://jeuclid.sourceforge.net/"
 SRC_URI="mirror://sourceforge/jeuclid/jeuclid-parent-${PV}-src.zip"
 
diff --git a/dev-java/netcdf/metadata.xml b/dev-java/netcdf/metadata.xml
index 0f61886d7..c75f192cc 100644
--- a/dev-java/netcdf/metadata.xml
+++ b/dev-java/netcdf/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci</herd>
-<longdescription lang='en'>
+  <herd>sci</herd>
+  <longdescription lang="en">
   The NetCDF-Java Library is a Java interface to NetCDF files,
   as well as to many other types of scientific data formats.
 </longdescription>
diff --git a/dev-java/netcdf/netcdf-4.2.ebuild b/dev-java/netcdf/netcdf-4.2.ebuild
index b4fcb2d56..b3e3e8570 100644
--- a/dev-java/netcdf/netcdf-4.2.ebuild
+++ b/dev-java/netcdf/netcdf-4.2.ebuild
@@ -1,8 +1,9 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
+
 JAVA_PKG_IUSE="doc examples source test"
 inherit eutils java-pkg-2 java-ant-2
 
@@ -15,14 +16,15 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-CDEPEND="dev-java/commons-codec
+CDEPEND="
+	dev-java/commons-codec
 	dev-java/commons-httpclient
 	dev-java/commons-logging
-	dev-java/ehcache
+	dev-java/ehcache:*
 	dev-java/jcommon
-	dev-java/jdom
+	dev-java/jdom:*
 	dev-java/jfreechart
-	dev-java/jgoodies-forms
+	dev-java/jgoodies-forms:*
 	dev-java/joda-time
 	dev-java/log4j
 	dev-java/slf4j-api
@@ -35,7 +37,8 @@ DEPEND="${CDEPEND}
 	>=virtual/jdk-1.5
 	test? (
 		dev-java/ant-junit4
-		dev-java/hamcrest-core )"
+		dev-java/hamcrest-core
+	)"
 
 # There is a from-source maven package in java-overlay, but it hasn't
 # been merged into the Portage trunk yet.
diff --git a/dev-lang/julia/julia-9999.ebuild b/dev-lang/julia/julia-9999.ebuild
index 03d3bb04b..e86777c8a 100644
--- a/dev-lang/julia/julia-9999.ebuild
+++ b/dev-lang/julia/julia-9999.ebuild
@@ -147,15 +147,11 @@ src_configure() {
 src_compile() {
 	emake julia-release
 	pax-mark m $(file usr/bin/julia* | awk -F : '/ELF/ {print $1}')
-	emake
+	default
 	use doc && emake -C doc html
 	use emacs && elisp-compile contrib/julia-mode.el
 }
 
-src_test() {
-	emake test
-}
-
 src_install() {
 	emake install prefix="${ED}/usr"
 	cat > 99julia <<-EOF
diff --git a/dev-lang/julia/metadata.xml b/dev-lang/julia/metadata.xml
index 095766014..abfa1f580 100644
--- a/dev-lang/julia/metadata.xml
+++ b/dev-lang/julia/metadata.xml
@@ -14,8 +14,8 @@
   around defining functions, and overloading them for different combinations
   of argument types (which can also be user-defined).
 </longdescription>
-<use>
-  <flag name="int64">Build with 64 bits integer blas and lapack (needs
+  <use>
+    <flag name="int64">Build with 64 bits integer blas and lapack (needs
   <pkg>sci-libs/openblas</pkg> and <pkg>sci-libs/lapack-reference</pkg>)</flag>
-</use>
+  </use>
 </pkgmetadata>
diff --git a/dev-libs/fortrancl/fortrancl-0.1_alpha3.ebuild b/dev-libs/fortrancl/fortrancl-0.1_alpha3.ebuild
index 5d44cdd31..179fc4fc3 100644
--- a/dev-libs/fortrancl/fortrancl-0.1_alpha3.ebuild
+++ b/dev-libs/fortrancl/fortrancl-0.1_alpha3.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 AUTOTOOLS_AUTORECONF=1
 
diff --git a/dev-libs/libunzip/libunzip-5.52.ebuild b/dev-libs/libunzip/libunzip-5.52.ebuild
index 5cc3b0497..16929dad5 100644
--- a/dev-libs/libunzip/libunzip-5.52.ebuild
+++ b/dev-libs/libunzip/libunzip-5.52.ebuild
@@ -15,14 +15,15 @@ SRC_URI="mirror://gentoo/${MY_PN}${PV/.}.tar.gz"
 LICENSE="Info-ZIP"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
+IUSE="static-libs"
 
 S="${WORKDIR}/${MY_PN}-${PV}"
 
 src_prepare() {
-	epatch "${FILESDIR}"/${P}-no-exec-stack.patch
-	epatch "${FILESDIR}"/${P}-CVE-2008-0888.patch #213761
-	epatch "${FILESDIR}"/${P}-Makefile.patch
+	epatch \
+		"${FILESDIR}"/${P}-no-exec-stack.patch \
+		"${FILESDIR}"/${P}-CVE-2008-0888.patch \
+		"${FILESDIR}"/${P}-Makefile.patch
 	sed -i \
 		-e 's:-O3:$(CFLAGS) $(CPPFLAGS):' \
 		-e 's:-O :$(CFLAGS) $(CPPFLAGS) :' \
@@ -45,10 +46,7 @@ src_compile() {
 }
 
 src_install() {
-	dolib.so ${PN}.so.0.4
-	dolib.so ${PN}.so.0
-	dolib.so ${PN}.so
-	dolib.a ${PN}.a
-	insinto /usr/include
-	doins unzip.h
+	dolib.so ${PN}.so*
+	use static-libs && dolib.a ${PN}.a
+	doheader unzip.h
 }
diff --git a/dev-ml/lacaml/lacaml-7.0.3.ebuild b/dev-ml/lacaml/lacaml-7.0.3.ebuild
index 07f9ca915..a7b3743ec 100644
--- a/dev-ml/lacaml/lacaml-7.0.3.ebuild
+++ b/dev-ml/lacaml/lacaml-7.0.3.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 OASIS_BUILD_DOCS=1
 
diff --git a/dev-perl/Log-Cabin/Log-Cabin-0.06.ebuild b/dev-perl/Log-Cabin/Log-Cabin-0.06.ebuild
index ac5bcf200..2d8369e36 100644
--- a/dev-perl/Log-Cabin/Log-Cabin-0.06.ebuild
+++ b/dev-perl/Log-Cabin/Log-Cabin-0.06.ebuild
@@ -10,7 +10,7 @@ MODULE_SECTION="Log-Cabin"
 
 inherit perl-module
 
-DESCRIPTION="Partial implementation of Log::Log4perl with reduced disk IO."
+DESCRIPTION="Partial implementation of Log::Log4perl with reduced disk IO"
 
 LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
 SLOT="0"
diff --git a/dev-perl/Time-Progress/Time-Progress-1.7.ebuild b/dev-perl/Time-Progress/Time-Progress-1.7.ebuild
index 4197eaa03..89cc66564 100644
--- a/dev-perl/Time-Progress/Time-Progress-1.7.ebuild
+++ b/dev-perl/Time-Progress/Time-Progress-1.7.ebuild
@@ -8,7 +8,7 @@ MODULE_AUTHOR="CADE"
 
 inherit perl-module
 
-DESCRIPTION="Elapsed and estimated finish time reporting."
+DESCRIPTION="Elapsed and estimated finish time reporting"
 
 LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
 SLOT="0"
diff --git a/dev-python/arrayfire-python/arrayfire-python-3.0.20150914.ebuild b/dev-python/arrayfire-python/arrayfire-python-3.0.20150914.ebuild
index a61966cf0..c4d561b8d 120000..100644
--- a/dev-python/arrayfire-python/arrayfire-python-3.0.20150914.ebuild
+++ b/dev-python/arrayfire-python/arrayfire-python-3.0.20150914.ebuild
@@ -1 +1,30 @@
-arrayfire-python-9999.ebuild
-\ No newline at end of file
+# 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
index 2ab86f848..d74308cf6 120000..100644
--- a/dev-python/brewer2mpl/brewer2mpl-1.4.1.ebuild
+++ b/dev-python/brewer2mpl/brewer2mpl-1.4.1.ebuild
@@ -1 +1,25 @@
-brewer2mpl-9999.ebuild
-\ No newline at end of file
+# 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
index 6bb3cdbda..f44668a79 120000..100644
--- a/dev-python/ipykernel/ipykernel-4.0.3.ebuild
+++ b/dev-python/ipykernel/ipykernel-4.0.3.ebuild
@@ -1 +1,39 @@
-ipykernel-9999.ebuild
-\ No newline at end of file
+# 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
index 1db7c42ea..b1c026781 120000..100644
--- a/dev-python/ipyparallel/ipyparallel-4.0.0-r1.ebuild
+++ b/dev-python/ipyparallel/ipyparallel-4.0.0-r1.ebuild
@@ -1 +1,62 @@
-ipyparallel-9999.ebuild
-\ No newline at end of file
+# 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
index 66350df81..3c7b157e8 120000..100644
--- a/dev-python/ipython_genutils/ipython_genutils-0.1.0.ebuild
+++ b/dev-python/ipython_genutils/ipython_genutils-0.1.0.ebuild
@@ -1 +1,34 @@
-ipython_genutils-9999.ebuild
-\ No newline at end of file
+# 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/ChangeLog b/dev-python/ipywidgets/ChangeLog
index 747b0b3cc..7b0819da0 100644
--- a/dev-python/ipywidgets/ChangeLog
+++ b/dev-python/ipywidgets/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  03 Sep 2015; Sean Vig <sean.v.775@gmail.com> ipywidgets-4.0.3,
+  ipywidgets-9999.ebuild:
+  dev-python/ipywidgets: Add javascript tests
+
   22 Sep 2015; Marius Brehler <marbre@linux.sungazer.de>
   ipywidgets-4.0.3.ebuild:
   dev-python/ipywidgets: Add ~x86 to KEYWORDS
diff --git a/dev-python/ipywidgets/ipywidgets-4.0.2-r1.ebuild b/dev-python/ipywidgets/ipywidgets-4.0.2-r1.ebuild
index e3cd5c19f..3c3d2165a 120000..100644
--- a/dev-python/ipywidgets/ipywidgets-4.0.2-r1.ebuild
+++ b/dev-python/ipywidgets/ipywidgets-4.0.2-r1.ebuild
@@ -1 +1,42 @@
-ipywidgets-9999.ebuild
-\ No newline at end of file
+# 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
+
+	"${PYTHON}" -m ipywidgets.jstest || die
+}
diff --git a/dev-python/ipywidgets/ipywidgets-4.0.3.ebuild b/dev-python/ipywidgets/ipywidgets-4.0.3.ebuild
index a295a6959..3c3d2165a 100644
--- a/dev-python/ipywidgets/ipywidgets-4.0.3.ebuild
+++ b/dev-python/ipywidgets/ipywidgets-4.0.3.ebuild
@@ -31,9 +31,12 @@ DEPEND="${RDEPEND}
 		$(python_gen_cond_dep 'dev-python/mock[${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
+
+	"${PYTHON}" -m ipywidgets.jstest || die
 }
diff --git a/dev-python/ipywidgets/ipywidgets-9999.ebuild b/dev-python/ipywidgets/ipywidgets-9999.ebuild
index a295a6959..3c3d2165a 100644
--- a/dev-python/ipywidgets/ipywidgets-9999.ebuild
+++ b/dev-python/ipywidgets/ipywidgets-9999.ebuild
@@ -31,9 +31,12 @@ DEPEND="${RDEPEND}
 		$(python_gen_cond_dep 'dev-python/mock[${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/jupyter/jupyter-1.0.0.ebuild b/dev-python/jupyter/jupyter-1.0.0.ebuild
index e1142bd7c..6f6ef69f7 100644
--- a/dev-python/jupyter/jupyter-1.0.0.ebuild
+++ b/dev-python/jupyter/jupyter-1.0.0.ebuild
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 python3_{3,4} )
 
 inherit distutils-r1
 
-DESCRIPTION="Jupyter metapackage. Install all the Jupyter components in one go."
+DESCRIPTION="Jupyter metapackage. Install all the Jupyter components in one go"
 HOMEPAGE="http://jupyter.org"
 SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
 
diff --git a/dev-python/line_profiler/line_profiler-1.0.ebuild b/dev-python/line_profiler/line_profiler-1.0.ebuild
index fb2359a76..bec34f593 120000..100644
--- a/dev-python/line_profiler/line_profiler-1.0.ebuild
+++ b/dev-python/line_profiler/line_profiler-1.0.ebuild
@@ -1 +1,29 @@
-line_profiler-9999.ebuild
-\ No newline at end of file
+# 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="Line-by-line profiling for Python"
+HOMEPAGE="https://github.com/rkern/line_profiler"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+KEYWORDS="~amd64"
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="test"
+
+DEPEND="
+	test? ( dev-python/pytest[${PYTHON_USEDEP}] )
+	"
+
+python_test() {
+	distutils_install_for_testing
+	cd "${TEST_DIR}"/lib || die
+	cp "${S}"/setup.py "${TEST_DIR}"/lib/ || die
+	cp -r "${S}"/tests "${TEST_DIR}"/lib/ || die
+	py.test || die
+}
diff --git a/dev-python/line_profiler/line_profiler-9999.ebuild b/dev-python/line_profiler/line_profiler-9999.ebuild
index 51b1bd9c9..52f8cef60 100644
--- a/dev-python/line_profiler/line_profiler-9999.ebuild
+++ b/dev-python/line_profiler/line_profiler-9999.ebuild
@@ -5,18 +5,11 @@
 EAPI=5
 PYTHON_COMPAT=( python{2_7,3_3,3_4} )
 
-inherit distutils-r1
+inherit distutils-r1 git-r3
 
 DESCRIPTION="Line-by-line profiling for Python"
 HOMEPAGE="https://github.com/rkern/line_profiler"
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/rkern/${PN}.git git://github.com/rkern/${PN}.git"
-else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
+EGIT_REPO_URI="https://github.com/rkern/${PN}.git git://github.com/rkern/${PN}.git"
 
 LICENSE="BSD"
 SLOT="0"
diff --git a/dev-python/matlab_wrapper/matlab_wrapper-0.9.6.ebuild b/dev-python/matlab_wrapper/matlab_wrapper-0.9.6.ebuild
index 09a507433..42a4c47a8 120000..100644
--- a/dev-python/matlab_wrapper/matlab_wrapper-0.9.6.ebuild
+++ b/dev-python/matlab_wrapper/matlab_wrapper-0.9.6.ebuild
@@ -1 +1,25 @@
-matlab_wrapper-9999.ebuild
-\ No newline at end of file
+# 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
index 49bc235a9..20ab8da5e 120000..100644
--- a/dev-python/matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild
+++ b/dev-python/matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild
@@ -1 +1,30 @@
-matplotlib2tikz-9999.ebuild
-\ No newline at end of file
+# 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/metakernel/ChangeLog b/dev-python/metakernel/ChangeLog
new file mode 100644
index 000000000..e7392d391
--- /dev/null
+++ b/dev-python/metakernel/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for dev-python/metakernel
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Id$
+
+*metakernel-0.11.0 (24 Sep 2015)
+
+  24 Sep 2015; Marius Brehler <marbre@linux.sungazer.de> +metadata.xml,
+  +metakernel-0.11.0.ebuild:
+  dev-python/metakernel: New package, ebuild written by me
diff --git a/dev-python/metakernel/Manifest b/dev-python/metakernel/Manifest
new file mode 100644
index 000000000..bcbedb65f
--- /dev/null
+++ b/dev-python/metakernel/Manifest
@@ -0,0 +1 @@
+DIST metakernel-0.11.0.tar.gz 88834 SHA256 8b030de8477b532b9c871413ccd6cd853319f842f7bcee12de2413ea4afc0572 SHA512 d9dabf1dcbc6075af7c03949d8ffeaf2d8f8381972c9b18f25b50423492084ffe2afe3357d27576c1f36387508ca27d8a0fc54abe7e0f72ab206822ed402aad2 WHIRLPOOL bf67d360366f7c80ce2b4d0f18a6979ca789cf96aa79ff998bbad722c2bd4a50c2561840aa931b0558049aaefead2dee01b0b04dc7b4c00fa4a819b222c461ab
diff --git a/dev-python/metakernel/metadata.xml b/dev-python/metakernel/metadata.xml
new file mode 100644
index 000000000..be095aee3
--- /dev/null
+++ b/dev-python/metakernel/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci</herd>
+  <longdescription>
+    A Jupyter/IPython kernel template which includes core magic
+    functions (including help, command and file path completion,
+    parallel and distributed processing, downloads, and much more).
+  </longdescription>
+  <upstream>
+    <remote-id type="pypi">metakernel</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/dev-python/metakernel/metakernel-0.11.0.ebuild b/dev-python/metakernel/metakernel-0.11.0.ebuild
new file mode 100644
index 000000000..f02b935f9
--- /dev/null
+++ b/dev-python/metakernel/metakernel-0.11.0.ebuild
@@ -0,0 +1,37 @@
+# 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="Metakernel for Jupyter"
+HOMEPAGE="https://github.com/Calysto/metakernel"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+KEYWORDS="~amd64"
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="test"
+
+RDEPEND="
+	>=dev-python/ipython-3.0[${PYTHON_USEDEP}]
+	"
+DEPEND="${RDEPEND}
+	test? (
+		dev-python/nose[${PYTHON_USEDEP}]
+		dev-python/coverage[${PYTHON_USEDEP}]
+		>=dev-python/metakernel_python-0.11.3[${PYTHON_USEDEP}]
+	)
+"
+
+# tests currently fail and the dying/stopping of ipcluster needs to be fixed
+RESTRICT="test"
+
+python_test() {
+	ipcluster start -n=3 &
+	nosetests --with-doctest --with-coverage --cover-package metakernel || die
+	ipcluster stop
+}
diff --git a/dev-python/metakernel_bash/ChangeLog b/dev-python/metakernel_bash/ChangeLog
new file mode 100644
index 000000000..ec1c1a02f
--- /dev/null
+++ b/dev-python/metakernel_bash/ChangeLog
@@ -0,0 +1,15 @@
+# ChangeLog for dev-python/metakernel_bash
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Id$
+
+*metakernel_bash-0.11.3-r1 (24 Sep 2015)
+
+  24 Sep 2015; Marius Brehler <marbre@linux.sungazer.de> +files/kernel.json,
+  +metakernel_bash-0.11.3-r1.ebuild, -metakernel_bash-0.11.3.ebuild:
+  dev-python/metakernel_bash: Install missing kernel spec
+
+*metakernel_bash-0.11.3 (24 Sep 2015)
+
+  24 Sep 2015; Marius Brehler <marbre@linux.sungazer.de> +metadata.xml,
+  +metakernel_bash-0.11.3.ebuild:
+  dev-python/metakernel_bash: New package, ebuild written by me
diff --git a/dev-python/metakernel_bash/Manifest b/dev-python/metakernel_bash/Manifest
new file mode 100644
index 000000000..b24fc1061
--- /dev/null
+++ b/dev-python/metakernel_bash/Manifest
@@ -0,0 +1 @@
+DIST metakernel_bash-0.11.3.tar.gz 1801 SHA256 e86087b9fe6aa86d5f33f394db98dddc759fea5b0ef65061d0adc9e02105f919 SHA512 8a96580d7bbb409c461c227d5255d9075968c4c423a4e7fc329713dcf097c0194031a8a9c747146e18ccdcf58958478e99233f586b715601514741ceb1b67c75 WHIRLPOOL 54dc704783666f73793ab62836d91882936eadb5baf0ee2b7a47ecd51ac3b7a3d4496ea08e817e568b335ab75929812bb4cbeb433a2b72097d967f2041ccb126
diff --git a/dev-python/metakernel_bash/files/kernel.json b/dev-python/metakernel_bash/files/kernel.json
new file mode 100644
index 000000000..a8e06d478
--- /dev/null
+++ b/dev-python/metakernel_bash/files/kernel.json
@@ -0,0 +1 @@
+{"argv": ["/usr/bin/python", "-m", "metakernel_bash", "-f", "{connection_file}"], "display_name": "MetaKernel Bash", "language": "bash", "name": "metakernel_bash"}
diff --git a/dev-python/metakernel_bash/metadata.xml b/dev-python/metakernel_bash/metadata.xml
new file mode 100644
index 000000000..9e6119aea
--- /dev/null
+++ b/dev-python/metakernel_bash/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci</herd>
+  <longdescription>
+    A Bash kernel for Jupyter/IPython, based on MetaKernel.
+  </longdescription>
+  <upstream>
+    <remote-id type="pypi">metakernel_bash</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/dev-python/metakernel_bash/metakernel_bash-0.11.3-r1.ebuild b/dev-python/metakernel_bash/metakernel_bash-0.11.3-r1.ebuild
new file mode 100644
index 000000000..9bd8f0b7f
--- /dev/null
+++ b/dev-python/metakernel_bash/metakernel_bash-0.11.3-r1.ebuild
@@ -0,0 +1,28 @@
+# 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 Bash kernel for Jupyter/IPython"
+HOMEPAGE="https://github.com/Calysto/metakernel"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+KEYWORDS="~amd64"
+
+LICENSE="BSD"
+SLOT="0"
+
+RDEPEND="
+	>=dev-python/metakernel-0.11.0[${PYTHON_USEDEP}]
+	"
+DEPEND="${RDEPEND}"
+
+python_install_all() {
+	insinto /usr/share/jupyter/kernels/${PN}
+	doins "${FILESDIR}"/kernel.json
+
+	distutils-r1_python_install_all
+}
+\ No newline at end of file
diff --git a/dev-python/metakernel_python/ChangeLog b/dev-python/metakernel_python/ChangeLog
new file mode 100644
index 000000000..c26be8420
--- /dev/null
+++ b/dev-python/metakernel_python/ChangeLog
@@ -0,0 +1,15 @@
+# ChangeLog for dev-python/metakernel_python
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Id$
+
+*metakernel_python-0.11.3-r1 (24 Sep 2015)
+
+  24 Sep 2015; Marius Brehler <marbre@linux.sungazer.de> +files/kernel.json,
+  +metakernel_python-0.11.3-r1.ebuild, -metakernel_python-0.11.3.ebuild:
+  dev-python/metakernel_python: Install missing kernel spec
+
+*metakernel_python-0.11.3 (24 Sep 2015)
+
+  24 Sep 2015; Marius Brehler <marbre@linux.sungazer.de> +metadata.xml,
+  +metakernel_python-0.11.3.ebuild:
+  dev-python/metakernel_python: New package, ebuild written by me
diff --git a/dev-python/metakernel_python/Manifest b/dev-python/metakernel_python/Manifest
new file mode 100644
index 000000000..269c992fa
--- /dev/null
+++ b/dev-python/metakernel_python/Manifest
@@ -0,0 +1 @@
+DIST metakernel_python-0.11.3.tar.gz 1856 SHA256 ae596a14f1914db5448500b0ca691dee4b1637f96d36184a8e5afd3f5f4e2f34 SHA512 13cc9ee62047a6048b1ea469a3850c34e369a426a16b6c43e002427601f07a585f109c4162bfd30e6607186233affbff7333ae84b12ca6749ecbbc2cea2a1915 WHIRLPOOL 36bf4dddb9f4550bfd4c8815eb896d1c185b95bae9a8bfb89c87bfe9564dbab9c83e0a96f3db2bad756ed9c28c636422407089250c7a5108ef8162c1410a7078
diff --git a/dev-python/metakernel_python/files/kernel.json b/dev-python/metakernel_python/files/kernel.json
new file mode 100644
index 000000000..0a561584a
--- /dev/null
+++ b/dev-python/metakernel_python/files/kernel.json
@@ -0,0 +1 @@
+{"argv": ["/usr/bin/python", "-m", "metakernel_python", "-f", "{connection_file}"], "display_name": "MetaKernel Python", "language": "python", "name": "metakernel_python"}
diff --git a/dev-python/metakernel_python/metadata.xml b/dev-python/metakernel_python/metadata.xml
new file mode 100644
index 000000000..8bebad5bc
--- /dev/null
+++ b/dev-python/metakernel_python/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci</herd>
+  <longdescription>
+    A Python kernel for Jupyter/IPython, based on MetaKernel.
+  </longdescription>
+  <upstream>
+    <remote-id type="pypi">metakernel_python</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/dev-python/metakernel_python/metakernel_python-0.11.3-r1.ebuild b/dev-python/metakernel_python/metakernel_python-0.11.3-r1.ebuild
new file mode 100644
index 000000000..9b4def176
--- /dev/null
+++ b/dev-python/metakernel_python/metakernel_python-0.11.3-r1.ebuild
@@ -0,0 +1,29 @@
+# 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 Python kernel for Jupyter/IPython"
+HOMEPAGE="https://github.com/Calysto/metakernel"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+KEYWORDS="~amd64"
+
+LICENSE="BSD"
+SLOT="0"
+
+RDEPEND="
+	>=dev-python/metakernel-0.11.0[${PYTHON_USEDEP}]
+	dev-python/jedi[${PYTHON_USEDEP}]
+	"
+DEPEND="${RDEPEND}"
+
+python_install_all() {
+	insinto /usr/share/jupyter/kernels/${PN}
+	doins "${FILESDIR}"/kernel.json
+
+	distutils-r1_python_install_all
+}
+\ No newline at end of file
diff --git a/dev-python/nbconvert/nbconvert-4.0.0-r1.ebuild b/dev-python/nbconvert/nbconvert-4.0.0-r1.ebuild
index ac4dd4146..9e298f39c 120000..100644
--- a/dev-python/nbconvert/nbconvert-4.0.0-r1.ebuild
+++ b/dev-python/nbconvert/nbconvert-4.0.0-r1.ebuild
@@ -1 +1,78 @@
-nbconvert-9999.ebuild
-\ No newline at end of file
+# 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
+
+MY_PN="nbconvert"
+
+DESCRIPTION="Converting Jupyter Notebooks"
+HOMEPAGE="http://jupyter.org"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+KEYWORDS="~amd64 ~x86"
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="doc test"
+
+PATCHES=(
+	"${FILESDIR}/${P}"-docs-Makefile.patch
+	"${FILESDIR}/${P}"-pandoc-highlighting.patch
+)
+
+RDEPEND="
+	dev-python/jupyter_core[${PYTHON_USEDEP}]
+	dev-python/nbformat[${PYTHON_USEDEP}]
+	dev-python/mistune[${PYTHON_USEDEP}]
+	dev-python/jinja[${PYTHON_USEDEP}]
+	dev-python/pygments[${PYTHON_USEDEP}]
+	dev-python/traitlets[${PYTHON_USEDEP}]
+	"
+DEPEND="${RDEPEND}
+	doc? (
+		dev-python/ipython[${PYTHON_USEDEP}]
+		dev-python/jupyter_client[${PYTHON_USEDEP}]
+		dev-python/sphinx[${PYTHON_USEDEP}]
+		app-text/pandoc
+	)
+	test? (
+		dev-python/nose[${PYTHON_USEDEP}]
+		dev-python/coverage[${PYTHON_USEDEP}]
+		dev-python/ipykernel[${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() {
+	distutils_install_for_testing
+	cd "${TEST_DIR}"/lib || die
+	nosetests --with-coverage --cover-package=nbconvert nbconvert || die
+}
+
+python_install_all() {
+	use doc && HTML_DOCS=( docs/build/html/. )
+	distutils-r1_python_install_all
+}
+
+pkg_postinst() {
+	if ! has_version app-text/pandoc ; then
+		einfo "Pandoc is required for converting to formats other than Python,"
+		einfo "HTML, and Markdown. If you need this functionality, install"
+		einfo "app-text/pandoc."
+	fi
+}
diff --git a/dev-python/nbconvert/nbconvert-9999.ebuild b/dev-python/nbconvert/nbconvert-9999.ebuild
index 297f7bf04..c97ed8a75 100644
--- a/dev-python/nbconvert/nbconvert-9999.ebuild
+++ b/dev-python/nbconvert/nbconvert-9999.ebuild
@@ -5,27 +5,20 @@
 EAPI=5
 PYTHON_COMPAT=( python2_7 python{3_3,3_4} )
 
-inherit distutils-r1
+inherit distutils-r1 git-r3
 
 MY_PN="nbconvert"
 
 DESCRIPTION="Converting Jupyter Notebooks"
 HOMEPAGE="http://jupyter.org"
-
-PATCHES=( "${FILESDIR}/${PN}"-4.0.0-docs-Makefile.patch )
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/jupyter/${MY_PN}.git git://github.com/jupyter/${MY_PN}.git"
-	else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-	KEYWORDS="~amd64 ~x86"
-	PATCHES+=( "${FILESDIR}"/${P}-pandoc-highlighting.patch )
-fi
+EGIT_REPO_URI="https://github.com/jupyter/${MY_PN}.git git://github.com/jupyter/${MY_PN}.git"
 
 LICENSE="BSD"
 SLOT="0"
 IUSE="doc test"
 
+PATCHES=( "${FILESDIR}/${PN}"-4.0.0-docs-Makefile.patch )
+
 RDEPEND="
 	dev-python/jupyter_core[${PYTHON_USEDEP}]
 	dev-python/nbformat[${PYTHON_USEDEP}]
diff --git a/dev-python/nbformat/nbformat-4.0.0.ebuild b/dev-python/nbformat/nbformat-4.0.0.ebuild
index c2590aa3b..cc116c0dd 120000..100644
--- a/dev-python/nbformat/nbformat-4.0.0.ebuild
+++ b/dev-python/nbformat/nbformat-4.0.0.ebuild
@@ -1 +1,59 @@
-nbformat-9999.ebuild
-\ No newline at end of file
+# 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} )
+PYTHON_REQ_USE='sqlite'
+
+inherit distutils-r1
+
+DESCRIPTION="Reference implementation of the Jupyter Notebook format"
+HOMEPAGE="http://jupyter.org"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+KEYWORDS="~amd64 ~x86"
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="doc test"
+
+RDEPEND="
+	dev-python/jsonschema[${PYTHON_USEDEP}]
+	dev-python/ipython_genutils[${PYTHON_USEDEP}]
+	dev-python/traitlets[${PYTHON_USEDEP}]
+	dev-python/jupyter_core[${PYTHON_USEDEP}]
+	"
+DEPEND="${RDEPEND}
+	doc? (
+		dev-python/sphinx[${PYTHON_USEDEP}]
+		dev-python/numpydoc[${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/conf.py || die
+	fi
+
+	distutils-r1_python_prepare_all
+}
+
+python_compile_all() {
+	use doc && emake -C docs html
+}
+
+python_test() {
+	distutils_install_for_testing
+	cd "${TEST_DIR}"/lib || die
+	nosetests --with-coverage --cover-package=nbformat nbformat || die
+}
+
+python_install_all() {
+	use doc && HTML_DOCS=( docs/_build/html/. )
+	distutils-r1_python_install_all
+}
diff --git a/dev-python/nbformat/nbformat-9999.ebuild b/dev-python/nbformat/nbformat-9999.ebuild
index 34610904f..777cf59e6 100644
--- a/dev-python/nbformat/nbformat-9999.ebuild
+++ b/dev-python/nbformat/nbformat-9999.ebuild
@@ -6,18 +6,11 @@ EAPI=5
 PYTHON_COMPAT=( python2_7 python{3_3,3_4} )
 PYTHON_REQ_USE='sqlite'
 
-inherit distutils-r1
+inherit distutils-r1 git-r3
 
 DESCRIPTION="Reference implementation of the Jupyter Notebook format"
 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
+EGIT_REPO_URI="https://github.com/jupyter/${PN}.git git://github.com/jupyter/${PN}.git"
 
 LICENSE="BSD"
 SLOT="0"
diff --git a/dev-python/notebook/ChangeLog b/dev-python/notebook/ChangeLog
index 2d7e2ea93..215864292 100644
--- a/dev-python/notebook/ChangeLog
+++ b/dev-python/notebook/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  03 Sep 2015; Sean Vig <sean.v.775@gmail.com> notebook-4.0.5.ebuild,
+  notebook-9999.ebuild:
+  dev-python/notebook: Add javascript tests
+
 *notebook-4.0.5 (22 Sep 2015)
 
   22 Sep 2015; Marius Brehler <marbre@linux.sungazer.de> +notebook-4.0.5.ebuild:
diff --git a/dev-python/notebook/notebook-4.0.5.ebuild b/dev-python/notebook/notebook-4.0.5.ebuild
index 1989a1a0e..80fa9fc1f 100644
--- a/dev-python/notebook/notebook-4.0.5.ebuild
+++ b/dev-python/notebook/notebook-4.0.5.ebuild
@@ -35,6 +35,7 @@ DEPEND="${RDEPEND}
 		>=dev-python/nose-0.10.1[${PYTHON_USEDEP}]
 		dev-python/requests[${PYTHON_USEDEP}]
 		dev-python/coverage[${PYTHON_USEDEP}]
+		www-client/casperjs
 	)
 	doc? (
 		app-text/pandoc
@@ -66,6 +67,11 @@ python_compile_all() {
 
 python_test() {
 	nosetests --with-coverage --cover-package=notebook notebook || die
+
+	"${PYTHON}" -m notebook.jstest base || die
+	"${PYTHON}" -m notebook.jstest notebook || die
+	"${PYTHON}" -m notebook.jstest services || die
+	"${PYTHON}" -m notebook.jstest tree || die
 }
 
 python_install() {
diff --git a/dev-python/notebook/notebook-9999.ebuild b/dev-python/notebook/notebook-9999.ebuild
index 0d2e0f910..d5ab6df53 100644
--- a/dev-python/notebook/notebook-9999.ebuild
+++ b/dev-python/notebook/notebook-9999.ebuild
@@ -34,6 +34,7 @@ DEPEND="${RDEPEND}
 		>=dev-python/nose-0.10.1[${PYTHON_USEDEP}]
 		dev-python/requests[${PYTHON_USEDEP}]
 		dev-python/coverage[${PYTHON_USEDEP}]
+		www-client/casperjs
 	)
 	doc? (
 		app-text/pandoc
@@ -65,6 +66,11 @@ python_compile_all() {
 
 python_test() {
 	nosetests --with-coverage --cover-package=notebook notebook || die
+
+	"${PYTHON}" -m notebook.jstest base || die
+	"${PYTHON}" -m notebook.jstest notebook || die
+	"${PYTHON}" -m notebook.jstest services || die
+	"${PYTHON}" -m notebook.jstest tree || die
 }
 
 python_install() {
diff --git a/dev-python/pickleshare/pickleshare-0.5.ebuild b/dev-python/pickleshare/pickleshare-0.5.ebuild
index 16ddbe44b..c295d4eca 120000..100644
--- a/dev-python/pickleshare/pickleshare-0.5.ebuild
+++ b/dev-python/pickleshare/pickleshare-0.5.ebuild
@@ -1 +1,39 @@
-pickleshare-9999.ebuild
-\ No newline at end of file
+# 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
index 46a331dec..8680ca749 120000..100644
--- a/dev-python/prettyplotlib/prettyplotlib-0.1.7.ebuild
+++ b/dev-python/prettyplotlib/prettyplotlib-0.1.7.ebuild
@@ -1 +1,30 @@
-prettyplotlib-9999.ebuild
-\ No newline at end of file
+# 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/pyfftw/pyfftw-0.9.2.ebuild b/dev-python/pyfftw/pyfftw-0.9.2.ebuild
index c3e80cfca..6ccb3d359 120000..100644
--- a/dev-python/pyfftw/pyfftw-0.9.2.ebuild
+++ b/dev-python/pyfftw/pyfftw-0.9.2.ebuild
@@ -1 +1,36 @@
-pyfftw-9999.ebuild
-\ No newline at end of file
+# 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
+
+MY_PN="pyFFTW"
+
+DESCRIPTION="FFTW wrapper for python"
+HOMEPAGE="http://hgomersall.github.io/pyFFTW/"
+SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_PN}-${PV}.tar.gz"
+KEYWORDS="~amd64"
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="test"
+
+S="${WORKDIR}/${MY_PN}-${PV}"
+
+RDEPEND="
+	>=dev-python/numpy-1.8.0[${PYTHON_USEDEP}]
+	>=sci-libs/fftw-3.3.3
+	>=dev-python/cython-0.19.1[${PYTHON_USEDEP}]
+	"
+DEPEND="${RDEPEND}"
+
+python_test() {
+	distutils_install_for_testing
+	cd "${TEST_DIR}"/lib || die
+	cp "${S}"/setup.py "${TEST_DIR}"/lib/ || die
+	cp -r "${S}"/test "${TEST_DIR}"/lib/ || die
+	esetup.py test || die
+}
diff --git a/dev-python/pyfftw/pyfftw-9999.ebuild b/dev-python/pyfftw/pyfftw-9999.ebuild
index e1f59e97c..300828a7a 100644
--- a/dev-python/pyfftw/pyfftw-9999.ebuild
+++ b/dev-python/pyfftw/pyfftw-9999.ebuild
@@ -5,21 +5,13 @@
 EAPI=5
 PYTHON_COMPAT=( python{2_7,3_3,3_4} )
 
-inherit distutils-r1
+inherit distutils-r1 git-r3
 
 MY_PN="pyFFTW"
 
 DESCRIPTION="FFTW wrapper for python"
 HOMEPAGE="http://hgomersall.github.io/pyFFTW/"
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/hgomersall/${MY_PN}.git git://github.com/hgomersall/${MY_PN}.git"
-else
-	SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_PN}-${PV}.tar.gz"
-	KEYWORDS="~amd64"
-	S="${WORKDIR}/${MY_PN}-${PV}"
-fi
+EGIT_REPO_URI="https://github.com/hgomersall/${MY_PN}.git git://github.com/hgomersall/${MY_PN}.git"
 
 LICENSE="BSD"
 SLOT="0"
diff --git a/dev-python/python-ivi/python-ivi-0.14.9.ebuild b/dev-python/python-ivi/python-ivi-0.14.9.ebuild
index 267b2096a..f0a517681 120000..100644
--- a/dev-python/python-ivi/python-ivi-0.14.9.ebuild
+++ b/dev-python/python-ivi/python-ivi-0.14.9.ebuild
@@ -1 +1,30 @@
-python-ivi-9999.ebuild
-\ No newline at end of file
+# 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
index ed718af3a..fd6fcc97c 120000..100644
--- a/dev-python/python-vxi11/python-vxi11-0.7.ebuild
+++ b/dev-python/python-vxi11/python-vxi11-0.7.ebuild
@@ -1 +1,22 @@
-python-vxi11-9999.ebuild
-\ No newline at end of file
+# 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
index ed718af3a..fd6fcc97c 120000..100644
--- a/dev-python/python-vxi11/python-vxi11-0.8.ebuild
+++ b/dev-python/python-vxi11/python-vxi11-0.8.ebuild
@@ -1 +1,22 @@
-python-vxi11-9999.ebuild
-\ No newline at end of file
+# 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
index 6170cda91..8ac99f406 120000..100644
--- a/dev-python/qtconsole/qtconsole-4.0.1-r1.ebuild
+++ b/dev-python/qtconsole/qtconsole-4.0.1-r1.ebuild
@@ -1 +1,67 @@
-qtconsole-9999.ebuild
-\ No newline at end of file
+# 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
index 58783615d..155232e85 120000..100644
--- a/dev-python/simplepam/simplepam-0.1.5.ebuild
+++ b/dev-python/simplepam/simplepam-0.1.5.ebuild
@@ -1 +1,22 @@
-simplepam-9999.ebuild
-\ No newline at end of file
+# 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/testpath/testpath-0.2.ebuild b/dev-python/testpath/testpath-0.2.ebuild
index 07bd68e33..df61d9545 120000..100644
--- a/dev-python/testpath/testpath-0.2.ebuild
+++ b/dev-python/testpath/testpath-0.2.ebuild
@@ -1 +1,54 @@
-testpath-9999.ebuild
-\ No newline at end of file
+# 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="Test utilities for code working with files and commands"
+HOMEPAGE="http://jupyter.org"
+SRC_URI="https://github.com/jupyter/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
+KEYWORDS="~amd64 ~x86"
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="doc test"
+
+DEPEND="
+	test? (
+		dev-python/pathlib[${PYTHON_USEDEP}]
+		dev-python/pytest[${PYTHON_USEDEP}]
+	)
+	doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
+	"
+
+PATCHES=(
+	"${FILESDIR}/${P}"-setup.py.patch
+	)
+
+python_prepare_all() {
+	# Prevent un-needed download during build
+	if use doc; then
+		sed -e "/^    'sphinx.ext.intersphinx',/d" -i doc/conf.py || die
+	fi
+
+distutils-r1_python_prepare_all
+}
+
+python_compile_all() {
+	use doc && emake -C doc html
+}
+
+python_install_all() {
+	use doc && HTML_DOCS=( doc/_build/html/. )
+	distutils-r1_python_install_all
+	}
+
+python_test() {
+	distutils_install_for_testing
+	cd "${TEST_DIR}"/lib || die
+	cp -r "${S}"/tests "${TEST_DIR}"/lib/ || die
+	py.test || die
+}
diff --git a/dev-python/testpath/testpath-9999.ebuild b/dev-python/testpath/testpath-9999.ebuild
index 395bfd701..61ceb0cd4 100644
--- a/dev-python/testpath/testpath-9999.ebuild
+++ b/dev-python/testpath/testpath-9999.ebuild
@@ -5,18 +5,11 @@
 EAPI=5
 PYTHON_COMPAT=( python2_7 python{3_3,3_4} )
 
-inherit distutils-r1
+inherit distutils-r1 git-r3
 
 DESCRIPTION="Test utilities for code working with files and commands"
 HOMEPAGE="http://jupyter.org"
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/jupyter/${PN}.git git://github.com/jupyter/${PN}.git"
-else
-	SRC_URI="https://github.com/jupyter/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64 ~x86"
-fi
+EGIT_REPO_URI="https://github.com/jupyter/${PN}.git git://github.com/jupyter/${PN}.git"
 
 LICENSE="BSD"
 SLOT="0"
@@ -31,7 +24,7 @@ DEPEND="
 	"
 
 PATCHES=(
-	"${FILESDIR}/${P}"-setup.py.patch
+	"${FILESDIR}/${PN}"-0.2-setup.py.patch
 	)
 
 python_prepare_all() {
diff --git a/dev-python/traitlets/traitlets-4.0.0.ebuild b/dev-python/traitlets/traitlets-4.0.0.ebuild
index 6d6a41b5d..afcdfa056 120000..100644
--- a/dev-python/traitlets/traitlets-4.0.0.ebuild
+++ b/dev-python/traitlets/traitlets-4.0.0.ebuild
@@ -1 +1,59 @@
-traitlets-9999.ebuild
-\ No newline at end of file
+# 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/dev-util/amdapp/amdapp-2.9.1.ebuild b/dev-util/amdapp/amdapp-2.9.1.ebuild
index b483113f7..657a36245 100644
--- a/dev-util/amdapp/amdapp-2.9.1.ebuild
+++ b/dev-util/amdapp/amdapp-2.9.1.ebuild
@@ -67,7 +67,7 @@ src_prepare() {
 
 src_compile() {
 	MAKEOPTS+=" -j1"
-	use examples && cd samples/opencl && emake
+	use examples && cd samples/opencl && default
 }
 
 src_install() {
diff --git a/dev-util/amdapp/amdapp-2.9.ebuild b/dev-util/amdapp/amdapp-2.9.ebuild
index 1620a5403..9ad0debde 100644
--- a/dev-util/amdapp/amdapp-2.9.ebuild
+++ b/dev-util/amdapp/amdapp-2.9.ebuild
@@ -71,7 +71,7 @@ src_prepare() {
 
 src_compile() {
 	MAKEOPTS+=" -j1"
-	use examples && cd samples/opencl && emake
+	use examples && cd samples/opencl && default
 }
 
 src_install() {
diff --git a/dev-util/amdapp/amdapp-3.0_beta.ebuild b/dev-util/amdapp/amdapp-3.0_beta.ebuild
index e9c774043..db1a8e6a8 100644
--- a/dev-util/amdapp/amdapp-3.0_beta.ebuild
+++ b/dev-util/amdapp/amdapp-3.0_beta.ebuild
@@ -67,7 +67,7 @@ src_prepare() {
 
 src_compile() {
 	MAKEOPTS+=" -j1"
-	use examples && cd samples/opencl && emake
+	use examples && cd samples/opencl && default
 }
 
 src_install() {
diff --git a/dev-util/ndiff/ndiff-2.00.ebuild b/dev-util/ndiff/ndiff-2.00.ebuild
index 75b6ca697..fc7fa44da 100644
--- a/dev-util/ndiff/ndiff-2.00.ebuild
+++ b/dev-util/ndiff/ndiff-2.00.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 DESCRIPTION="A diff program that ignores small numeric differences"
 HOMEPAGE="http://www.math.utah.edu/~beebe/software/ndiff/"
@@ -13,7 +13,7 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="doc"
 
-DEPEND="dev-libs/gmp"
+DEPEND="dev-libs/gmp:0="
 RDEPEND="${DEPEND}"
 
 # Rename the files from ndiff to numdiff, since /usr/bin/ndiff used to be
diff --git a/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-340.29.ebuild b/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-340.29.ebuild
index b6b736b71..9a4687257 100644
--- a/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-340.29.ebuild
+++ b/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-340.29.ebuild
@@ -41,7 +41,7 @@ src_unpack() {
 src_compile() {
 	use examples || return
 	cd "${S}"/nvml/example || die
-	emake
+	default
 }
 
 src_install() {
diff --git a/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-346.46.ebuild b/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-346.46.ebuild
index 20c6d53ce..d858f8e15 100644
--- a/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-346.46.ebuild
+++ b/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-346.46.ebuild
@@ -38,7 +38,7 @@ src_unpack() {
 src_compile() {
 	use examples || return
 	cd "${S}"/nvml/example || die
-	emake
+	default
 }
 
 src_install() {
diff --git a/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-352.07.ebuild b/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-352.07.ebuild
index 6b59192fd..f119a6c36 100644
--- a/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-352.07.ebuild
+++ b/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-352.07.ebuild
@@ -55,7 +55,7 @@ src_unpack() {
 src_compile() {
 	use examples || return
 	cd "${S}"/nvml/example || die
-	emake
+	default
 }
 
 src_install() {
diff --git a/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-352.39.ebuild b/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-352.39.ebuild
index 9e3c4e6e0..13ca6d7de 100644
--- a/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-352.39.ebuild
+++ b/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-352.39.ebuild
@@ -56,7 +56,7 @@ src_unpack() {
 src_compile() {
 	use examples || return
 	cd "${S}"/nvml/example || die
-	emake
+	default
 }
 
 src_install() {
diff --git a/media-gfx/brlcad/brlcad-7.22.0.ebuild b/media-gfx/brlcad/brlcad-7.22.0.ebuild
index e301a427d..98fb81098 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 e1235bba3..1933ed4c9 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 e37cdaa9a..09399be15 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 cdd393eb5..06de13dea 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/media-libs/OpenMOIV/OpenMOIV-1.0.3a.ebuild b/media-libs/OpenMOIV/OpenMOIV-1.0.3a.ebuild
index df3b692c6..af43459d7 100644
--- a/media-libs/OpenMOIV/OpenMOIV-1.0.3a.ebuild
+++ b/media-libs/OpenMOIV/OpenMOIV-1.0.3a.ebuild
@@ -6,7 +6,7 @@ EAPI=5
 
 inherit cmake-utils
 
-DESCRIPTION="Object-oriented 3D toolkit that facilitates the rendering and interaction of chemical systems."
+DESCRIPTION="Object-oriented 3D toolkit that facilitates the rendering and interaction of chemical systems"
 HOMEPAGE="http://www.tecn.upf.es/openMOIV/"
 SRC_URI="http://www.tecn.upf.es/openMOIV/download/1.0.3/${PN}.src.${PV}.tar.bz2"
 
diff --git a/media-libs/libgfx/libgfx-1.1.0.ebuild b/media-libs/libgfx/libgfx-1.1.0.ebuild
index 6e3b92711..baac528c6 100644
--- a/media-libs/libgfx/libgfx-1.1.0.ebuild
+++ b/media-libs/libgfx/libgfx-1.1.0.ebuild
@@ -13,6 +13,7 @@ SRC_URI="http://mgarland.org/dist/${P}.tar.gz"
 LICENSE="LGPL-2.1"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
 
 src_prepare() {
 	epatch "${FILESDIR}"/${PV}-gcc4.3.patch
@@ -20,13 +21,12 @@ src_prepare() {
 
 src_compile() {
 	cd src || die
-	emake
+	default
 }
 
 src_install() {
-	dolib.a src/*.a
-	insinto /usr/include/
-	doins include/gfx/gfx.h
+	use static-libs && dolib.a src/*.a
+	doheader include/gfx/gfx.h
 
 	dohtml doc/*
 }
diff --git a/media-libs/libgfx/metadata.xml b/media-libs/libgfx/metadata.xml
index b229aec85..d369d068f 100644
--- a/media-libs/libgfx/metadata.xml
+++ b/media-libs/libgfx/metadata.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci</herd>
+	<herd>sci</herd>
 </pkgmetadata>
diff --git a/metadata/layout.conf b/metadata/layout.conf
index c3e0be38e..f07e25117 100644
--- a/metadata/layout.conf
+++ b/metadata/layout.conf
@@ -7,7 +7,7 @@ manifest-hashes = SHA256 SHA512 WHIRLPOOL
 
 # 2013-04-09 gentoo's council says to deprecate EAPIs 1 and 2 (bug #470670).
 # 2014-02-25 council meeting deprecated EAPIs 0 and 3.
-eapis-banned = 0 1 2 3
+eapis-banned = 0 1 2 3 4
 eapis-deprecated = 0 1 2 3 4
 
 # Bug #337853 - gentoo's council says to enable
diff --git a/sci-astronomy/lephare/lephare-2.2.ebuild b/sci-astronomy/lephare/lephare-2.2.ebuild
index 5834609c8..4d047340a 100644
--- a/sci-astronomy/lephare/lephare-2.2.ebuild
+++ b/sci-astronomy/lephare/lephare-2.2.ebuild
@@ -1,8 +1,9 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
+
 inherit eutils check-reqs fortran-2 versionator
 
 MYP=${PN}_dev_v$(replace_version_separator 2 '')
@@ -16,9 +17,6 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="doc"
 
-RDEPEND=""
-DEPEND="${RDEPEND}"
-
 S="${WORKDIR}/${PN}_dev/source"
 
 CHECKREQS_DISK_BUILD="400M"
@@ -26,14 +24,14 @@ CHECKREQS_DISK_BUILD="400M"
 src_prepare() {
 	export LEPHAREDIR="${WORKDIR}/${PN}_dev" LEPHAREWORK="${WORKDIR}"
 	# clean up mac left over crap
-	find . -name ._\* -delete
+	find . -name ._\* -delete || die
 	# respect user flags and compiler
 	sed -i -e '/^FC/d' -e '/^FFLAGS/d' Makefile || die
 }
 
 src_test() {
 	# from pdf manual
-	cd ${LEPHAREDIR}/test
+	cd ${LEPHAREDIR}/test || die
 	${LEPHAREDIR}/source/sedtolib -t S -c ../config/zphot.para || die
 	${LEPHAREDIR}/source/sedtolib -t Q -c ../config/zphot.para || die
 	${LEPHAREDIR}/source/sedtolib -t G -c ../config/zphot.para || die
@@ -57,7 +55,7 @@ src_install() {
 		mag_zform
 	dodoc README_TECH
 	insinto /usr/share/${PN}
-	cd ..
+	cd .. || die
 	doins -r {ext,filt,config,opa,sed,simul,test,tools,vega}
 	echo "LEPHAREDIR=${EPREFIX}/usr/share/${PN}" > 99lephare
 	doenvd 99lephare
diff --git a/sci-astronomy/lephare/metadata.xml b/sci-astronomy/lephare/metadata.xml
index e68e8f647..665c2abc4 100644
--- a/sci-astronomy/lephare/metadata.xml
+++ b/sci-astronomy/lephare/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-astronomy</herd>
-<longdescription lang="en">
+  <herd>sci-astronomy</herd>
+  <longdescription lang="en">
   Le Photometric Analysis for Redshift Estimate is a set of commands
   to compute photometric redshifts and to perform SED fitting.
 </longdescription>
diff --git a/sci-astronomy/missfits/missfits-2.8.0.ebuild b/sci-astronomy/missfits/missfits-2.8.0.ebuild
index b8cfc9035..19b75a881 120000..100644
--- a/sci-astronomy/missfits/missfits-2.8.0.ebuild
+++ b/sci-astronomy/missfits/missfits-2.8.0.ebuild
@@ -1 +1,33 @@
-missfits-9999.ebuild
-\ No newline at end of file
+# 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
index 1942f52c3..db23a2197 120000..100644
--- a/sci-astronomy/psfex/psfex-3.17.0.ebuild
+++ b/sci-astronomy/psfex/psfex-3.17.0.ebuild
@@ -1 +1,70 @@
-psfex-9999.ebuild
-\ No newline at end of file
+# 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
index 1942f52c3..db23a2197 120000..100644
--- a/sci-astronomy/psfex/psfex-3.9.1.ebuild
+++ b/sci-astronomy/psfex/psfex-3.9.1.ebuild
@@ -1 +1,70 @@
-psfex-9999.ebuild
-\ No newline at end of file
+# 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
index 8b8a27578..6515bca3a 120000..100644
--- a/sci-astronomy/sextractor/sextractor-2.19.5.ebuild
+++ b/sci-astronomy/sextractor/sextractor-2.19.5.ebuild
@@ -1 +1,73 @@
-sextractor-9999.ebuild
-\ No newline at end of file
+# 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
index bae540666..f44f47f96 120000..100644
--- a/sci-astronomy/skymaker/skymaker-3.10.5.ebuild
+++ b/sci-astronomy/skymaker/skymaker-3.10.5.ebuild
@@ -1 +1,35 @@
-skymaker-9999.ebuild
-\ No newline at end of file
+# 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
index 5f7f899eb..33c0767fd 120000..100644
--- a/sci-astronomy/stiff/stiff-2.4.0.ebuild
+++ b/sci-astronomy/stiff/stiff-2.4.0.ebuild
@@ -1 +1,43 @@
-stiff-9999.ebuild
-\ No newline at end of file
+# 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
index 181cfccd3..1f57f85a8 120000..100644
--- a/sci-astronomy/stuff/stuff-1.26.0.ebuild
+++ b/sci-astronomy/stuff/stuff-1.26.0.ebuild
@@ -1 +1,35 @@
-stuff-9999.ebuild
-\ No newline at end of file
+# 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
index ffc97cbfa..71c254dee 120000..100644
--- a/sci-astronomy/swarp/swarp-2.38.0.ebuild
+++ b/sci-astronomy/swarp/swarp-2.38.0.ebuild
@@ -1 +1,41 @@
-swarp-9999.ebuild
-\ No newline at end of file
+# 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
index fedc2e16f..9f90ed11f 120000..100644
--- a/sci-astronomy/weightwatcher/weightwatcher-1.12.ebuild
+++ b/sci-astronomy/weightwatcher/weightwatcher-1.12.ebuild
@@ -1 +1,35 @@
-weightwatcher-9999.ebuild
-\ No newline at end of file
+# 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="${RDEPEND}"
+
+src_install () {
+	autotools-utils_src_install
+	use doc && dodoc doc/*
+}
diff --git a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
index fe3583583..4e27e89ca 100644
--- a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
+++ b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
@@ -28,7 +28,7 @@ S="${WORKDIR}"/all/"${PN}"_v"${PV}"
 
 src_compile(){
 	cd SOLiD-SNP-caller || die
-	emake
+	default
 
 	cd ../vcfPrinter
 	# TODO: install the *.rb files
diff --git a/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild b/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
index 39e10af29..df99ed3b2 100644
--- a/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
+++ b/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
@@ -29,7 +29,7 @@ src_prepare(){
 
 src_compile(){
 	cd src || die
-	emake
+	default
 }
 
 src_install(){
diff --git a/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild b/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild
index 47849a1c3..def9b355a 100644
--- a/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild
+++ b/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild
@@ -37,19 +37,19 @@ src_configure(){
 
 src_compile(){
 	cd jellyfish || die
-	emake
+	default
 
 	cd ../CA/kmer || die
-	emake
+	default
 
 	cd ../../CA/src || die
-	emake
+	default
 
 	cd ../SuperReads || die
-	emake
+	default
 
 	cd ../quorum || die
-	emake
+	default
 }
 
 src_install(){
diff --git a/sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild b/sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild
index 504b76cd8..f5d99485e 100644
--- a/sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild
+++ b/sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit toolchain-funcs versionator java-pkg-2
 
@@ -10,8 +10,9 @@ MY_PV=$(replace_all_version_separators '-')
 
 DESCRIPTION="Java-based editor optimized for the OBO biological ontology file format"
 HOMEPAGE="http://www.oboedit.org/"
-SRC_URI="http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%20"${PV}"/"${MY_PV}"_unix_install4j.sh/download -> OBO-Edit_unix_install4j-"${PV}".sh
-		http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%20"${PV}"/ReleaseNotes-"${PV}".txt"
+SRC_URI="
+	http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%20"${PV}"/"${MY_PV}"_unix_install4j.sh/download -> OBO-Edit_unix_install4j-"${PV}".sh
+	http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%20"${PV}"/ReleaseNotes-"${PV}".txt"
 
 LICENSE="OBO-Edit" # Artistic-like
 SLOT="0"
@@ -29,8 +30,8 @@ src_install(){
 	sed "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${D}"/../temp -Dinstall4j.jvmDir#" -i "${DISTDIR}"/OBO-Edit_unix_install4j-"${PV}".sh || die "failed to set userHome value"
 
 	sh "${DISTDIR}"/OBO-Edit_unix_install4j-"${PV}".sh -q -overwrite --varfile="${D}"/opt/OBO-Edit2/.install4j/response.varfile --destination="${D}"/opt/OBO-Edit2 -dir "${D}"/opt/OBO-Edit2 || die "Failed to run the self-extracting "${DISTDIR}"/OBO-Edit_unix_install4j-"${PV}".sh file"
-	find . -name firstrun -delete
-	find . -name .svn -exec rm -rf '{}' \;
+	find . -name firstrun -delete || die
+	find . -name .svn -exec rm -rf '{}' \; || die
 
 	insinto /opt/
 	doins -r OBO-Edit2
diff --git a/sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild b/sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild
index 2c0ac7b4b..0a3ca5d30 100644
--- a/sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild
+++ b/sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit toolchain-funcs versionator java-pkg-2
 
@@ -13,8 +13,9 @@ MY_PV=$(replace_all_version_separators '-')
 
 DESCRIPTION="Java-based editor optimized for the OBO biological ontology file format"
 HOMEPAGE="http://www.oboedit.org/"
-SRC_URI="http://downloads.sourceforge.net/project/geneontology/OBO-Edit%202%20%5BLatest%20versions%5D/"${MY_VER}"/"${MY_PV}"_unix_install4j.sh -> "${PN}"_unix_install4j-"${PV}".sh
-		http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/"${MY_PV}"/ReleaseNotes-"${MY_VER}".txt -> "${PN}"_ReleaseNotes-"${PV}".txt"
+SRC_URI="
+	http://downloads.sourceforge.net/project/geneontology/OBO-Edit%202%20%5BLatest%20versions%5D/"${MY_VER}"/"${MY_PV}"_unix_install4j.sh -> "${PN}"_unix_install4j-"${PV}".sh
+	http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/"${MY_PV}"/ReleaseNotes-"${MY_VER}".txt -> "${PN}"_ReleaseNotes-"${PV}".txt"
 
 LICENSE="OBO-Edit" # Artistic-like
 SLOT="0"
diff --git a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
index 7ac63ae53..b7a1bcbec 100644
--- a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
+++ b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild
@@ -7,7 +7,7 @@ EAPI=5
 PERL_EXPORT_PHASE_FUNCTIONS=no
 inherit perl-module eutils
 
-DESCRIPTION="Optimise three primary parameter options (K, -exp_cov, -cov_cutoff) for Velvet sequence assembler."
+DESCRIPTION="Optimise three primary parameter options (K, -exp_cov, -cov_cutoff) for Velvet sequence assembler"
 HOMEPAGE="http://www.vicbioinformatics.com/software.velvetoptimiser.shtml"
 SRC_URI="http://www.vicbioinformatics.com/"${P}".tar.gz"
 
diff --git a/sci-biology/abyss/abyss-1.3.3-r1.ebuild b/sci-biology/abyss/abyss-1.3.3-r1.ebuild
index 5afbdd0b7..76f15b496 100644
--- a/sci-biology/abyss/abyss-1.3.3-r1.ebuild
+++ b/sci-biology/abyss/abyss-1.3.3-r1.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI="4"
+EAPI=5
 
 inherit autotools eutils toolchain-funcs
 
diff --git a/sci-biology/apollo/apollo-9999.ebuild b/sci-biology/apollo/apollo-9999.ebuild
index 9c776166f..c00cdcc83 100644
--- a/sci-biology/apollo/apollo-9999.ebuild
+++ b/sci-biology/apollo/apollo-9999.ebuild
@@ -8,7 +8,7 @@ inherit java-pkg-2 java-ant-2
 
 [ "$PV" == "9999" ] && inherit subversion
 
-DESCRIPTION="Apollo genome editor is Java-based application for browsing and annotation of genomic sequences."
+DESCRIPTION="Apollo genome editor is Java-based application for browsing and annotation of genomic sequences"
 HOMEPAGE="http://gmod.org/wiki/Apollo"
 if [ "$PV" == "9999" ]; then
 	#SRC_URI="http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/?view=tar" # Apollo_unix.sh
diff --git a/sci-biology/augustus/augustus-3.1.ebuild b/sci-biology/augustus/augustus-3.1.ebuild
index 6e1883169..e67723d48 100644
--- a/sci-biology/augustus/augustus-3.1.ebuild
+++ b/sci-biology/augustus/augustus-3.1.ebuild
@@ -32,7 +32,7 @@ src_prepare() {
 }
 
 src_compile() {
-	emake clean && emake
+	emake clean && default
 }
 
 src_install() {
diff --git a/sci-biology/bambino/bambino-1.02.ebuild b/sci-biology/bambino/bambino-1.02.ebuild
index afeb2f18d..bfc859a1b 100644
--- a/sci-biology/bambino/bambino-1.02.ebuild
+++ b/sci-biology/bambino/bambino-1.02.ebuild
@@ -27,8 +27,8 @@ RDEPEND="${DEPEND}
 
 src_install(){
 	insinto "${DESTDIR}"/usr/share/"${PN}"/lib
-	doins "${DISTDIR}"/bambino_core_"${PV}".jar || die
-	doins "${DISTDIR}"/bambino_bundle_"${PV}".jar || die
+	doins "${DISTDIR}"/bambino_core_"${PV}".jar
+	doins "${DISTDIR}"/bambino_bundle_"${PV}".jar
 
 	einfo "bambino can be run using 'java -jar /usr/share/bambino/lib/bambino_bundle_1.02.jar'"
 	einfo "  or 'java -jar /usr/share/bambino/lib/bambino_core_1.02.jar'"
diff --git a/sci-biology/bambino/bambino-1.06.ebuild b/sci-biology/bambino/bambino-1.06.ebuild
index cc46f29f8..fa16a700f 100644
--- a/sci-biology/bambino/bambino-1.06.ebuild
+++ b/sci-biology/bambino/bambino-1.06.ebuild
@@ -27,8 +27,8 @@ RDEPEND="${DEPEND}
 
 src_install(){
 	insinto "${DESTDIR}"/usr/share/"${PN}"/lib
-	doins "${DISTDIR}"/bambino_core_"${PV}".jar || die
-	doins "${DISTDIR}"/bambino_bundle_"${PV}".jar || die
+	doins "${DISTDIR}"/bambino_core_"${PV}".jar
+	doins "${DISTDIR}"/bambino_bundle_"${PV}".jar
 
 	einfo "bambino can be run using 'java -jar /usr/share/bambino/lib/bambino_bundle_1.06.jar'"
 	einfo "  or 'java -jar /usr/share/bambino/lib/bambino_core_1.06.jar'"
diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33.ebuild
index d5b7c7f7d..13b7b6216 100644
--- a/sci-biology/bambus/bambus-2.33.ebuild
+++ b/sci-biology/bambus/bambus-2.33.ebuild
@@ -8,10 +8,12 @@ PERL_EXPORT_PHASE_FUNCTIONS=no
 inherit perl-module eutils toolchain-funcs
 
 DESCRIPTION="Scaffolding Polymorphic Genomes and Metagenomes, a part of AMOS bundle"
-HOMEPAGE="http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS
-		http://sourceforge.net/projects/amos/files/bambus
-		http://www.tigr.org/software/bambus"
-SRC_URI="http://sourceforge.net/projects/amos/files/bambus/${PV}/${P}.tar.gz
+HOMEPAGE="
+	http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS
+	http://sourceforge.net/projects/amos/files/bambus
+	http://www.tigr.org/software/bambus"
+SRC_URI="
+	http://sourceforge.net/projects/amos/files/bambus/${PV}/${P}.tar.gz
 	http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf"
 
 LICENSE="Artistic"
@@ -19,25 +21,25 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-DEPEND="sci-biology/tigr-foundation-libs"
-RDEPEND="${DEPEND}
-		dev-lang/perl
-		dev-lang/python
-		dev-perl/XML-Parser
-		dev-perl/Config-IniFiles
-		dev-perl/GraphViz"
+RDEPEND="
+	sci-biology/tigr-foundation-libs
+	dev-lang/perl
+	dev-perl/XML-Parser
+	dev-perl/Config-IniFiles
+	dev-perl/GraphViz"
+DEPEND="${RDEPEND}"
 
 src_prepare() {
 #	epatch "${FILESDIR}"/amos-2.0.8-gcc44.patch
 	sed -e 's:BASEDIR = /usr/local/packages/bambus:BASEDIR = /usr:' -i Makefile || die
 	sed -e 's:PERL = /usr/local/bin/perl:PERL = /usr/bin/perl:' -i Makefile || die
-	sed -e 's:INSTDIR:DESTDIR:g' -i Makefile || die
-	sed -e 's:INSTDIR:DESTDIR:g' -i src/Makefile || die
-	sed -e 's:INSTDIR:DESTDIR:g' -i doc/Makefile || die
+	sed \
+		-e 's:INSTDIR:DESTDIR:g' \
+			-i Makefile src/Makefile doc/Makefile || die
 	sed -e 's:make all;:make all || exit 255;:' -i src/Makefile || die
-	sed -e 's:INSTDIR:DESTDIR:g' -i src/IO/Makefile || die
-	sed -e 's:INSTDIR:DESTDIR:g' -i src/DotLib/Makefile || die
-	sed -e 's:INSTDIR:DESTDIR:g' -i src/grommit/Makefile || die
+	sed \
+		-e 's:INSTDIR:DESTDIR:g' \
+		-i src/IO/Makefile src/DotLib/Makefile src/grommit/Makefile || die
 	sed -e "s:^CC\t=:CC=$(tc-getCXX):" -i Makefile || die
 	sed -e "s:^CXX\t=:CXX=$(tc-getCXX):" -i Makefile || die
 	sed -e "s:^LD\t:LD=$(tc-getCXX):" -i Makefile || die
@@ -70,7 +72,7 @@ src_prepare() {
 }
 
 src_compile() {
-	emake DESTDIR="${D}/usr" || die "emake failed"
+	emake DESTDIR="${D}/usr"
 
 	# TODO:
 	#ld  -L../TIGR_Foundation_CC/ -shared -fPIC -o grommit grommit.o -L. -lgraph -lTigrFoundation
@@ -87,7 +89,7 @@ src_compile() {
 }
 
 src_install() {
-	emake DESTDIR="${D}/usr" install || die "emake install failed"
+	emake DESTDIR="${D}/usr" install
 	# cvs HEAD of amos now contains even more updated files: /usr/bin/printScaff /usr/bin/untangle /usr/lib/TIGR/AsmLib.pm
 	for f in FASTArecord.pm FASTAreader.pm Foundation.pm FASTAgrammar.pm AsmLib.pm; do rm "${D}"/usr/lib/TIGR/$f; done || die
 	for f in printScaff untangle; do rm "${D}"/usr/bin/$f; done || die
@@ -96,18 +98,18 @@ src_install() {
 	# link against the libTigrFoundation.a provided by sci-biology/tigr-foundation-libs package
 	for f in CategoryInformation.hh MessageLevel.hh ConfigFile.hh LogCategory.hh \
 			ConfigSection.hh TIGR_Foundation.hh OptionResult.hh Exceptions.hh \
-			LogMsg.hh Options.hh Logger.hh FileSystem.hh; do \
-				rm "${D}"/usr/include/$f; \
-	done || die
-	rm "${D}"/usr/lib/libTigrFoundation.a || die
+			LogMsg.hh Options.hh Logger.hh FileSystem.hh; do
+				rm "${ED}"/usr/include/$f || die
+	done
+	rm "${ED}"/usr/lib/libTigrFoundation.a || die
 
-	mkdir -p "${D}"/usr/share/doc/"${P}" || die
-	mv "${D}"/usr/doc/* "${D}"/usr/share/doc/"${P}" || die
-	rmdir "${D}"/usr/doc || die
+	dodir /usr/share/doc/${P}
+	mv "${ED}"/usr/doc/* "${ED}"/usr/share/doc/${PF} || die
+	rmdir "${ED}"/usr/doc || die
 
-	dobin "${FILESDIR}"/goBambus.pl || die "Failed to install the alternative of goBambus.py written in perl"
+	dobin "${FILESDIR}"/goBambus.pl
 	dodoc "${DISTDIR}"/scaffolding_MIRA_BAMBUS.pdf
-	rm -rf "${D}"/usr/lib
+	rm -rf "${ED}"/usr/lib || die
 }
 
 pkg_postinst(){
diff --git a/sci-biology/biopieces/biopieces-0.51.ebuild b/sci-biology/biopieces/biopieces-0.51.ebuild
index f048b8a7f..ed5a25108 120000..100644
--- a/sci-biology/biopieces/biopieces-0.51.ebuild
+++ b/sci-biology/biopieces/biopieces-0.51.ebuild
@@ -1 +1,72 @@
-biopieces-9999.ebuild
-\ No newline at end of file
+# 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 1ad2412f8..ca4ff2854 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/cap3-bin/cap3-bin-20071221.ebuild b/sci-biology/cap3-bin/cap3-bin-20071221.ebuild
index 025be4ee2..987b0e04f 100644
--- a/sci-biology/cap3-bin/cap3-bin-20071221.ebuild
+++ b/sci-biology/cap3-bin/cap3-bin-20071221.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 DESCRIPTION="CAP3 is for small-scale assembly of EST sequences with or without quality value"
 HOMEPAGE="http://seq.cs.iastate.edu"
diff --git a/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild b/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild
index 8adc908e2..306e195e5 100644
--- a/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild
+++ b/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit eutils flag-o-matic toolchain-funcs
 
@@ -11,7 +11,8 @@ RELEASE="${PN}-v${PV}-${RELDATE}"
 
 DESCRIPTION="Additional cd-hit itools: read-linker, cd-hit-lap and cd-hit-dup"
 HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
-SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz
+SRC_URI="
+	http://cdhit.googlecode.com/files/${RELEASE}.tgz
 	http://weizhong-lab.ucsd.edu/cd-hit/wiki/doku.php?id=cd-hit-auxtools-manual -> cd-hit-auxtools-manual.html"
 
 SLOT="0"
@@ -34,11 +35,10 @@ src_prepare() {
 src_compile() {
 	local myconf=
 	use openmp && myconf="openmp=yes"
-	make ${myconf} || die "If compilation failed try gcc-4.6.4 or older, newer versions are too picky about quality of the source code"
+	emake ${myconf}
 }
 
 src_install() {
-	dodir /usr/bin
 	dobin read-linker cd-hit-lap cd-hit-dup
 	use doc && dodoc "${DISTDIR}"/cd-hit-auxtools-manual.html
 }
diff --git a/sci-biology/cd-hit/cd-hit-4.6.1.ebuild b/sci-biology/cd-hit/cd-hit-4.6.1.ebuild
index cc009869d..aa5180115 100644
--- a/sci-biology/cd-hit/cd-hit-4.6.1.ebuild
+++ b/sci-biology/cd-hit/cd-hit-4.6.1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit eutils flag-o-matic toolchain-funcs
 
diff --git a/sci-biology/cluster/cluster-1.50-r1.ebuild b/sci-biology/cluster/cluster-1.50-r1.ebuild
index 4dddbd2b3..e638c96ca 100644
--- a/sci-biology/cluster/cluster-1.50-r1.ebuild
+++ b/sci-biology/cluster/cluster-1.50-r1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 DESCRIPTION="Clustering software for microarray analysis"
 HOMEPAGE="http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm#ctv"
@@ -13,9 +13,12 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="X"
 
-DEPEND="X? ( x11-libs/motif )"
+DEPEND="X? ( x11-libs/motif:0= )"
 RDEPEND="
-	X? ( x11-misc/xdg-utils app-text/mupdf )"
+	X? (
+		x11-misc/xdg-utils
+		app-text/mupdf
+	)"
 
 RESTRICT="fetch"
 
@@ -42,7 +45,7 @@ src_configure() {
 src_install() {
 	default
 
-	mv "${ED}"/usr/bin/cluster{,3}
+	mv "${ED}"/usr/bin/cluster{,3} || die
 
 	insinto /usr/share/doc/${P}/examples
 	doins example/example.c example/README
diff --git a/sci-biology/cluster/cluster-1.50.ebuild b/sci-biology/cluster/cluster-1.50.ebuild
deleted file mode 100644
index 09f75522e..000000000
--- a/sci-biology/cluster/cluster-1.50.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-DESCRIPTION="Clustering software for microarray analysis"
-HOMEPAGE="http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm#ctv"
-SRC_URI="${P}.tar.gz"
-
-LICENSE="Eisen"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="X"
-
-DEPEND="X? ( x11-libs/motif )"
-RDEPEND="
-	!>=media-gfx/graphviz-2.28.0
-	X? ( x11-misc/xdg-utils app-text/mupdf )"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	einfo "Please obtain ${P}.tar.gz from ${HOMEPAGE} and place it in ${DISTDIR}"
-}
-
-src_prepare() {
-	sed -i \
-		-e 's:^docdir = .*$:docdir = @docdir@:' \
-		-e 's:^htmldir = .*$:htmldir = @htmldir@:' \
-		-e 's:^imagedir = .*$:imagedir = @htmldir@/images:' \
-		-e 's:^fileformatdir = .*$:fileformatdir = @docdir@:' \
-		X11/Makefile.in || die "sed failed"
-}
-
-src_configure() {
-	econf \
-		$(use_with X x) \
-		--docdir="/usr/share/doc/${P}" \
-		--htmldir="/usr/share/doc/${P}/html"
-}
-
-src_install() {
-	default
-
-	insinto /usr/share/doc/${P}/examples
-	doins example/example.c example/README
-	insinto /usr/share/doc/${PR}
-	doins doc/cluster.pdf
-}
diff --git a/sci-biology/clview/clview-0.1.ebuild b/sci-biology/clview/clview-0.1.ebuild
index c8f81244c..1e897bf2d 100644
--- a/sci-biology/clview/clview-0.1.ebuild
+++ b/sci-biology/clview/clview-0.1.ebuild
@@ -100,7 +100,7 @@ src_prepare() {
 
 src_compile(){
 	cd "${S}"/clview || die
-	emake
+	default
 }
 
 src_install() {
diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild
index 409111c84..b814b4689 100644
--- a/sci-biology/consed/consed-29.ebuild
+++ b/sci-biology/consed/consed-29.ebuild
@@ -54,7 +54,7 @@ src_prepare() {
 
 src_compile() {
 	einfo "consed does not compile with sys-devel/gcc-4.6:* or newer (but 4.4.7 works)"
-	emake
+	default
 	emake -C misc/mktrace
 	emake -C misc/phd2fasta
 	(cd misc/454; $(tc-getCC) ${CFLAGS} ${LDFLAGS} sff2scf.c -o sff2scf) || die
@@ -84,7 +84,7 @@ src_install() {
 	sed \
 		-e 's#/wt1/gordon/genome#/usr/bin#' \
 		-i "${ED}"/usr/bin/fastq2Phrap.perl || die
-	dodoc README.txt *_announcement.txt || die
+	dodoc README.txt *_announcement.txt
 }
 
 pkg_postinst() {
diff --git a/sci-biology/edena/edena-3.131028.ebuild b/sci-biology/edena/edena-3.131028.ebuild
index 073297787..408b8757a 100644
--- a/sci-biology/edena/edena-3.131028.ebuild
+++ b/sci-biology/edena/edena-3.131028.ebuild
@@ -26,7 +26,7 @@ src_prepare(){
 
 src_compile(){
 	cd src
-	emake
+	default
 }
 
 src_install(){
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 0c17e4875..b30b96691 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
+#	default
 #}
 
 src_install(){
diff --git a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
index b40e0e04b..a37262174 100644
--- a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
+++ b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=5
 
-DESCRIPTION="genome annotation tool: view, modify, and store annotation for prokaryotic and eukaryotic genomes."
+DESCRIPTION="genome annotation tool: view, modify, and store annotation for prokaryotic and eukaryotic genomes"
 HOMEPAGE="http://manatee.sourceforge.net/jcvi/downloads.shtml"
 SRC_URI="http://downloads.sourceforge.net/project/manatee/manatee/manatee-2.4.3/manatee-2.4.3.tgz"
 
@@ -49,5 +49,5 @@ src_configure(){
 }
 
 src_compile(){
-	emake
+	default
 }
diff --git a/sci-biology/mgblast/mgblast-0.1.ebuild b/sci-biology/mgblast/mgblast-0.1.ebuild
index 9292f31bf..0a95c2e09 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"
+	default
 }
 
 src_install(){
diff --git a/sci-biology/minced/minced-9999.ebuild b/sci-biology/minced/minced-9999.ebuild
index 8d629e18e..e4aa81fdc 100644
--- a/sci-biology/minced/minced-9999.ebuild
+++ b/sci-biology/minced/minced-9999.ebuild
@@ -19,7 +19,7 @@ DEPEND=">=virtual/jdk-1.7"
 RDEPEND=">=virtual/jre-1.7"
 
 src_compile(){
-	emake
+	default
 }
 
 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
index 9f0bb27fc..734e32d77 120000..100644
--- a/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild
+++ b/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild
@@ -1 +1,156 @@
-ngs_backbone-9999.ebuild
-\ No newline at end of file
+# 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 hardened@g.o.
+# * 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/nrcl/nrcl-110625.ebuild b/sci-biology/nrcl/nrcl-110625.ebuild
index fc81122dc..788a51813 100644
--- a/sci-biology/nrcl/nrcl-110625.ebuild
+++ b/sci-biology/nrcl/nrcl-110625.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit eutils toolchain-funcs
 
diff --git a/sci-biology/pileup/pileup-0.6.ebuild b/sci-biology/pileup/pileup-0.6.ebuild
index 433c1d764..aaa8a56b5 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"
+	default
 
 	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"
+		default
 	done
 }
 
diff --git a/sci-biology/pvmsx/pvmsx-0.1.ebuild b/sci-biology/pvmsx/pvmsx-0.1.ebuild
index f018aef1d..57e3b945e 100644
--- a/sci-biology/pvmsx/pvmsx-0.1.ebuild
+++ b/sci-biology/pvmsx/pvmsx-0.1.ebuild
@@ -35,7 +35,7 @@ src_prepare() {
 }
 
 src_compile() {
-	emake
+	default
 }
 
 src_install() {
diff --git a/sci-biology/samstat/samstat-20130708.ebuild b/sci-biology/samstat/samstat-20130708.ebuild
index 217230893..61c41352b 100644
--- a/sci-biology/samstat/samstat-20130708.ebuild
+++ b/sci-biology/samstat/samstat-20130708.ebuild
@@ -21,7 +21,7 @@ RDEPEND="${DEPEND}"
 S="${WORKDIR}"/"${PN}"/src
 
 src_compile(){
-	emake
+	default
 }
 
 src_install(){
diff --git a/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild b/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild
index f6358fe90..5e57eb5dd 100644
--- a/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild
+++ b/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild
@@ -4,12 +4,16 @@
 
 EAPI=5
 
-S="${WORKDIR}"
+PYTHON_COMPAT=( python2_7 )
+
+inherit python-r1
 
 DESCRIPTION="Combine FASTA contigs from a de novo assembly into scaffolds using a reference assembly"
-HOMEPAGE="http://sourceforge.net/projects/scaffold-b
+HOMEPAGE="
+	http://sourceforge.net/projects/scaffold-b
 	http://edwards.sdsu.edu/scaffold_builder"
-SRC_URI="http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2.1.zip
+SRC_URI="
+	http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2.1.zip
 	http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2_help.doc
 	http://downloads.sourceforge.net/project/scaffold-b/Manual_v2.1.pdf"
 
@@ -19,17 +23,19 @@ SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""
 
-DEPEND=""
-RDEPEND="${DEPEND}
-	sci-biology/mummer
-	dev-lang/python"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}
+	sci-biology/mummer"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"
 
 src_install(){
 	echo "#! /usr/bin/env python" > scaffold_builder.pyy || die
 	cat scaffold_builder.py >> scaffold_builder.pyy || die
 	mv scaffold_builder.pyy scaffold_builder.py || die
-	dobin scaffold_builder.py
+	python_foreach_impl python_doscript scaffold_builder.py
 	dodoc "${DISTDIR}"/scaffold_builder_v2_help.doc
-	cp -p "${DISTDIR}"/Manual_v2.1.pdf scaffold_builder.pdf || die
-	dodoc scaffold_builder.pdf
+	newdoc "${DISTDIR}"/Manual_v2.1.pdf scaffold_builder.pdf
 }
diff --git a/sci-biology/sff_dump/sff_dump-1.04.ebuild b/sci-biology/sff_dump/sff_dump-1.04.ebuild
index a04c22902..59069cb73 100644
--- a/sci-biology/sff_dump/sff_dump-1.04.ebuild
+++ b/sci-biology/sff_dump/sff_dump-1.04.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit toolchain-funcs
 
diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild
index 047ee2158..a2d4897ee 100644
--- a/sci-biology/sga/sga-9999.ebuild
+++ b/sci-biology/sga/sga-9999.ebuild
@@ -31,7 +31,7 @@ src_configure(){
 
 src_compile(){
 	cd src || die
-	emake
+	default
 }
 
 src_install(){
diff --git a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild b/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
index d12fbcc23..b29b5d8c8 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
@@ -55,7 +55,7 @@ src_compile(){
 	emake OUTDIR="${WORKDIR}"/objdir out
 	emake dynamic
 	emake release
-	emake
+	default
 }
 
 src_install(){
@@ -80,7 +80,7 @@ src_install(){
 
 	# install the main libs and the ncbi/vdb-copy.kfg file
 	insinto /usr/lib/ncbi
-	doins "${OBJDIR}"/lib/ncbi/* || die
+	doins "${OBJDIR}"/lib/ncbi/*
 
 	# zap the subdirectory so that copying below does not fail
 	rm -rf "${OBJDIR}"/lib/ncbi || die
diff --git a/sci-biology/tablet-bin/tablet-bin-1.14.10.21.ebuild b/sci-biology/tablet-bin/tablet-bin-1.14.10.21.ebuild
index 29c308f51..ae4e970b5 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.14.10.21.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.14.10.21.ebuild
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
 
 inherit java-pkg-2 python-r1
 
-DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
+DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
 HOMEPAGE="http://ics.hutton.ac.uk/tablet/"
 SRC_URI="
 	x86? ( http://bioinf.hutton.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators _).sh -> ${P}.sh )
diff --git a/sci-biology/tablet/tablet-1.14.04.10.ebuild b/sci-biology/tablet/tablet-1.14.04.10.ebuild
index a170f5471..d8aa02c19 120000..100644
--- a/sci-biology/tablet/tablet-1.14.04.10.ebuild
+++ b/sci-biology/tablet/tablet-1.14.04.10.ebuild
@@ -1 +1,49 @@
-tablet-9999.ebuild
-\ No newline at end of file
+# 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-biology/tclust/tclust-110625.ebuild b/sci-biology/tclust/tclust-110625.ebuild
index 03f4253a1..f76cca140 100644
--- a/sci-biology/tclust/tclust-110625.ebuild
+++ b/sci-biology/tclust/tclust-110625.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit eutils toolchain-funcs
 
diff --git a/sci-biology/trf/trf-4.07b.ebuild b/sci-biology/trf/trf-4.07b.ebuild
index 7003e6373..4d0416a31 100644
--- a/sci-biology/trf/trf-4.07b.ebuild
+++ b/sci-biology/trf/trf-4.07b.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit eutils
 
@@ -10,7 +10,8 @@ MY_P="${PN}404"
 
 DESCRIPTION="Tandem Repeats Finder"
 HOMEPAGE="http://tandem.bu.edu/trf/trf.html"
-SRC_URI="http://tandem.bu.edu/trf/downloads/${MY_P}.linux
+SRC_URI="
+	http://tandem.bu.edu/trf/downloads/${MY_P}.linux
 	http://tandem.bu.edu/trf/trf.unix.help.html
 	http://tandem.bu.edu/trf/trf.definitions.html
 	http://tandem.bu.edu/trf/trf.whatnew.html"
@@ -37,7 +38,8 @@ src_install() {
 	#	doexe trf400.linuxgtk.exe || die
 	#	make_desktop_entry /opt/${PN}/trf400.linuxgtk.exe "Tandem Repeats Finder" || die
 	#fi
-	dodoc "${DISTDIR}/"trf.unix.help.html
-	dodoc "${DISTDIR}/"trf.definitions.html
-	dodoc "${DISTDIR}/"trf.whatnew.html
+	dodoc \
+		"${DISTDIR}/"trf.unix.help.html \
+		"${DISTDIR}/"trf.definitions.html \
+		"${DISTDIR}/"trf.whatnew.html
 }
diff --git a/sci-chemistry/NMRdyn/NMRdyn-3.2.5.ebuild b/sci-chemistry/NMRdyn/NMRdyn-3.2.5.ebuild
index 8b6445f4d..bac742185 100644
--- a/sci-chemistry/NMRdyn/NMRdyn-3.2.5.ebuild
+++ b/sci-chemistry/NMRdyn/NMRdyn-3.2.5.ebuild
@@ -68,7 +68,7 @@ src_compile() {
 
 	if use qt4; then
 		cd src/NMRdynGUI || die
-		emake
+		default
 	fi
 }
 
diff --git a/sci-chemistry/concoord/concoord-2.1.ebuild b/sci-chemistry/concoord/concoord-2.1.ebuild
index d1bbb5a41..8ec96b90b 100644
--- a/sci-chemistry/concoord/concoord-2.1.ebuild
+++ b/sci-chemistry/concoord/concoord-2.1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 DESCRIPTION="Method to generate protein conformations around a known structure based on geometric restrictions"
 HOMEPAGE="http://www.mpibpc.mpg.de/groups/de_groot/concoord/concoord.html"
diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index c76273d94..a63dd8bc8 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -106,6 +106,10 @@ src_unpack() {
 
 src_prepare() {
 	sed \
+		-e '/export LD_LIBRARY/s:^:#:g' \
+		-i src/coot.in || die
+
+	sed \
 		-e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
 		-i configure.ac || die
 
diff --git a/sci-chemistry/drawxtl/drawxtl-45.ebuild b/sci-chemistry/drawxtl/drawxtl-45.ebuild
index 873394dfe..258522239 100644
--- a/sci-chemistry/drawxtl/drawxtl-45.ebuild
+++ b/sci-chemistry/drawxtl/drawxtl-45.ebuild
@@ -44,11 +44,11 @@ src_compile() {
 	mkdir exe || die "mkdir failed"
 	cd source/${MY_P} || die
 	emake clean
-	emake
+	default
 
 	if use fltk; then
 		cd "${S}"/source/DRAWshell${PV} || die
-		emake
+		default
 	fi
 }
 
diff --git a/sci-chemistry/gamess/Manifest b/sci-chemistry/gamess/Manifest
index 5652eca6f..bfb7e0159 100644
--- a/sci-chemistry/gamess/Manifest
+++ b/sci-chemistry/gamess/Manifest
@@ -1,3 +1,2 @@
-DIST gamess-20120501.1.tar.gz 26927811 SHA256 7e31bce09bd3f3468b8eeb847d6dfeeca478b3b8b6377cbe019abbf594f5acc7 SHA512 0adbfeaa629f2959f6ea116282d9c87cf1924af74fcb4ce4f2d66ffa8c45eecfbeb895ebe670320fc7c228ba3d037cbd17620906ad4f83b00f8531ee135ee5c5 WHIRLPOOL c3615aa9149cf4c88b98ceff0d8c92fcead291f1229992596f665194a8c8af3ec5d719f24fa7aae0f49122f06996c54331d277f811dee62f67623e4174e57df1
 DIST gamess-20130501.1.tar.gz 29013211 SHA256 315e6fa8f1947d8419b6f1adccf3fc7dd47b581fce107d304b7b99ef0cb15498 SHA512 56623e60762d554318111fd86c352a11393a7fa89cc0861aff7a2c68c687a953de60a4fc78f9860ec99223dd48c2cf6aa930a46a3f1c9cb019e893d871870023 WHIRLPOOL e67da7190613aeae085eea364ae3bbcc556e905e27900345cb75287eec0ea8107e0821826cb606ebb0d4f8f60ebdc264863bfa90954f846b55469c76372c1292
 DIST tinker.tar.Z 1902051 SHA256 7c52454ade7dd81d1b70a7e7722eda3672c644a3ba67ab444824a0212b4a7a8c SHA512 10f5012b6d9e32a3d6646c8d79ccc2a16f2d4322e974755e45605519bf478d36f09497457c7731c264c49ccd0c679b0fd0449d5910b4e1cfa499c7304cd28f6d WHIRLPOOL 4e81b02173f048890ec177f302818cc7664b5733c94db111c86ee6eecc830a83cc54a82797d162a2f26274be88cf786139aba096c8836e4ddd86bb0126f0908f
diff --git a/sci-chemistry/gamess/files/gamess-20120501.1.gentoo.patch b/sci-chemistry/gamess/files/gamess-20120501.1.gentoo.patch
deleted file mode 100644
index 423ed63d0..000000000
--- a/sci-chemistry/gamess/files/gamess-20120501.1.gentoo.patch
+++ /dev/null
@@ -1,271 +0,0 @@
-diff -urN gamess.orig/comp gamess/comp
---- gamess.orig/comp	2012-05-28 12:21:34.887403398 +0300
-+++ gamess/comp	2012-05-28 13:45:38.415079520 +0300
-@@ -1486,7 +1486,7 @@
- #   g77 does not support FORTRAN logical units above 99, or 128 bit math.
- #
-    case g77:
--   set OPT = '-O2'
-+   set gentoo-OPT = '-O2'
-    if ($MODULE == ormas1) set OPT='-O2 -fno-move-all-movables' # RH9, g77 3.3
-    if ($MODULE == zheev)  set OPT='-O0'  # defensive compiling
-    if (($MODULE == qeigen) || ($MODULE == int2c)) then
-@@ -1516,7 +1516,7 @@
- #      -std=legacy  suppresses warnings about use of f77 constructs.
- #
-    case gfortran:
--   set OPT='-O2'
-+   set gentoo-OPT='-O2'
-    if ($MODULE == zheev)  set OPT='-O0'  # defensive compiling
-    if ($MODULE == pcmcv2) set OPT='-O1'  # EFP+CPCM, ala Francois, v4.1.2
-    if (($MODULE == qeigen) || ($MODULE == int2c)) then
-@@ -1542,7 +1542,7 @@
- #    optimizations in 32 bit mode, as a function of the ifort version.
- #
-    case ifort:
--   set OPT = '-O3'
-+   set gentoo-OPT = '-O2'
-    if ($MODULE == delocl) set OPT='-O0'  # from Cheol
-    if ($MODULE == prpamm) set OPT='-O0'  # for exam13
-    if ($MODULE == zheev)  set OPT='-O0'
-@@ -1661,13 +1661,14 @@
- #           -finit-real=<zero|inf|-inf|nan>  could be interesting debug opt
- #           -fno-automatic forces static storage of all local variables
- #           -fno-whole-file suppresses argument's data type checking
--      set OPT='-O2'
-+      set gentoo-OPT='-O2'
-+      set extraflags=''
-       if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS"
-       if ($GMS_GFORTRAN_VERNO == 4.6) then
-          if ($MODULE == tddgrd) set OPT='-O0'   # this issue seen in 4.6.1
-       endif
-       if ($MODULE == zheev)  set OPT='-O0'  # defensive compiling
- #        as of 4.6 tested in late 2011, gfortran can do q.p.!
-       switch ($GMS_GFORTRAN_VERNO)
-          case 4.0:
-          case 4.1:
-@@ -1675,7 +1676,6 @@
-          case 4.3:
-          case 4.4:
-          case 4.5:
--            set extraflags=''
-             if (($MODULE == qeigen) || ($MODULE == int2c)) then
-                mv -f $MODULE.f $MODULE.junk
-                sed -e "s/Q-/D-/g" \
-@@ -1687,6 +1687,11 @@
-          case 4.6:
-             set extraflags='-fno-whole-file'
-             breaksw
-+         case 4.7:
-+            if ($MODULE == fmoio) set OPT='-O2'  # exam37
-+            if ($MODULE == tddgrd) set OPT='-O0' # exam41
-+            if ($MODULE == dcscf) set OPT='-O0'  # exam44
-+            breaksw
-          default:
-             echo Unrecognized gfortran version
-             exit 4
-@@ -1713,7 +1718,7 @@
- #     -WB means warn but don't fail on out-of-bounds array references
- #     -ftz flushes underflow results to zero
- #
--      set OPT = '-O2'
-+      set gentoo-OPT = '-O2'
-       if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS"
- #       alas, I'm so tired of hearing about so many versions failing to
- #       diagonalize, that this time critical code is run w/o optimization.
-@@ -1882,7 +1887,7 @@
-       unset echo
-       breaksw
-    case gfortran:
--      set OPT='-O2'
-+      set gentoo-OPT='-O2'
-       if ($MODULE == zheev)  set OPT='-O0'  # defensive compiling
-       if (($MODULE == qeigen) || ($MODULE == int2c)) then
-          mv -f $MODULE.f $MODULE.junk
-diff -urN gamess.orig/compall gamess/compall
---- gamess.orig/compall	2011-05-17 22:53:33.000000000 +0200
-+++ gamess/compall	2011-10-11 12:13:30.041087251 +0200
-@@ -84,12 +84,11 @@
-    endif
- endif
- if ($TARGET == linux32)      set extraflags='-DLINUX32'
--if ($TARGET == linux64)      then
-+if ($TARGET == linux64) then
-+	set chip=`uname -m`
- #      Ubuntu uses the non-standard -m flag, its -p replies "unknown"
--                         set chip=`uname -p`
--   if ($chip == unknown) set chip=`uname -m`
--   if ($chip == x86_64) set extraflags='-DLINUX64 -m64'
--   if ($chip == ia64)   set extraflags='-DLINUX64'  # this always 64 bits
-+   	if ($chip == x86_64) set extraflags='-DLINUX64 -m64'
-+   	if ($chip == ia64)   set extraflags='-DLINUX64'  # this always 64 bits
- endif
- if ($TARGET == mac32)        set extraflags='-DLINUX32'
- if ($TARGET == mac64)    set extraflags='-DLINUX64 -m64 -I/usr/include/malloc'
-diff -urN gamess.orig/ddi/compddi gamess/ddi/compddi
---- gamess.orig/ddi/compddi	2011-02-15 21:31:30.000000000 +0100
-+++ gamess/ddi/compddi	2011-10-11 12:23:45.513796580 +0200
-@@ -634,7 +634,7 @@
- 
-      set FORTRAN=$GMS_FORTRAN   # might be g77, gfortran, ifort, pgf77, f2c
- 
--     set CC = 'gcc'
-+     set gentoo-CC = 'gcc'
-      set CFLAGS = "-DLINUX -O3 -fstrict-aliasing -I./"
-      set CLIBS  = "-lpthread"
- 
-@@ -687,7 +687,7 @@
-                              set ARCH='-m64'
-      if (`uname -p` == ia64) set ARCH=''
- 
--     set CC = 'gcc'
-+     set gentoo-CC = 'gcc'
-      set CFLAGS = "-DLINUX $ARCH -O3 -fstrict-aliasing -I./"
-      set CLIBS  = "-lpthread"
- 
-diff -urN gamess.orig/ddi/kickoff/ddikick.c gamess/ddi/kickoff/ddikick.c
---- gamess.orig/ddi/kickoff/ddikick.c	2008-05-06 12:16:12.000000000 +0200
-+++ gamess/ddi/kickoff/ddikick.c	2011-10-11 12:25:11.862714681 +0200
-@@ -105,7 +105,7 @@
-           remoteshell = argv[++i];
-        } else {
-           if((remoteshell = getenv("DDI_RSH")) == NULL) {
--              remoteshell = (char *) strdup("rsh");
-+              remoteshell = (char *) strdup("ssh");
-           }
-        }
- 
-diff -urN gamess.orig/lked gamess/lked
---- gamess.orig/lked	2011-08-11 17:41:02.000000000 +0200
-+++ gamess/lked	2011-10-11 12:26:38.564634821 +0200
-@@ -53,7 +53,7 @@
- #
- #   3. optional Nuclear-Electronic Orbital method, using NEO code
- #
--set NEO=false
-+set NEO=true
- #
- #   4. optional Nvidia/CUDA code, for closed shell SCF Fock construction 
- #         see ~/gamess/libcchem/aaa.readme.1st for more information
-@@ -356,17 +356,17 @@
-    switch ($GMS_FORTRAN)
-      case g77:
-         set LDR='g77'
--        set LDOPTS=' '  # add '-Wl,-M' to see load map
-+        set gentoo-LDOPTS=' '  # add '-Wl,-M' to see load map
-         set FORTLIBS=' '
-         breaksw
-      case gfortran:
-         set LDR='gfortran'
--        set LDOPTS=' '
-+        set gentoo-LDOPTS=' '
-         set FORTLIBS=' '
-         breaksw
-      case ifort:
-         set LDR='ifort'
--        set LDOPTS=' '  # add '-Wl,-M' to see load map
-+        set gentoo-LDOPTS=' '  # add '-Wl,-M' to see load map
-         set FORTLIBS='-Vaxlib'
-         breaksw
-      case pgf77:
-@@ -376,7 +376,7 @@
-         breaksw
-      case f2c:
-         set LDR='gcc'
--        set LDOPTS=' '
-+        set gentoo-LDOPTS=' '
-         set FORTLIBS='-lf2c -lm'
-         breaksw
-      default:
-@@ -427,12 +427,7 @@
-       #     Otherwise, attempt a link against shared object libs.
-       #     See the 64 bit Atlas below for a way to fix the linker's
-       #     not being able to locate -lf77blas, if that happens.
--      if (-e $GMS_MATHLIB_PATH/libf77blas.a) then
--         set MATHLIBS="$GMS_MATHLIB_PATH/libf77blas.a"
--         set MATHLIBS="$MATHLIBS $GMS_MATHLIB_PATH/libatlas.a"
--      else
--         set MATHLIBS="-L$GMS_MATHLIB_PATH -lf77blas -latlas"
--      endif
-+      set MATHLIBS=`${PKG_CONFIG} --libs blas`
-       set BLAS=' '
-       breaksw
- 
-@@ -466,12 +461,12 @@
-    switch ($GMS_FORTRAN)
-       case gfortran:
-          set LDR='gfortran'
--         set LDOPTS=' '
-+         set gentoo-LDOPTS=' '
-          set FORTLIBS=' '
-          breaksw
-       case ifort:
-          set LDR='ifort'
--         set LDOPTS='-i8'  # -Wl,-M generates a load map
-+         set gentoo-LDOPTS=' '  # -Wl,-M generates a load map
- #            this auxiliary library seems to have disappeared in ifort 10
-          set FORTLIBS=' '
-          if($GMS_IFORT_VERNO < 10) set FORTLIBS='-Vaxlib'
-@@ -556,12 +551,7 @@
-       #          ln -s liblapack_atlas.so.3.0 liblapack.so
-       #          ln -s liblapack.so.3.0       liblapack.so
-       #     It is strange the RPM's don't do these soft links for us.
--      if (-e $GMS_MATHLIB_PATH/libf77blas.a) then
--         set MATHLIBS="$GMS_MATHLIB_PATH/libf77blas.a"
--         set MATHLIBS="$MATHLIBS $GMS_MATHLIB_PATH/libatlas.a"
--      else
--         set MATHLIBS="-L$GMS_MATHLIB_PATH -lf77blas -latlas"
--      endif
-+      set MATHLIBS=`${PKG_CONFIG} --libs blas`
-       set BLAS=' '
-       breaksw
- 
-diff -urN gamess.orig/runall gamess/runall
---- gamess.orig/runall	2012-05-28 13:58:18.589671828 +0300
-+++ gamess/runall	2012-05-28 14:00:57.635712103 +0300
-@@ -46,7 +46,7 @@
-      xgms -v $VERNO -q $QUEUE -l exam$NUM.log exam$NUM
-      sleep 2
-   else
--     ./rungms exam$NUM $VERNO 1  >&  exam$NUM.log
-+     rungms exam$NUM $VERNO 1  >&  exam$NUM.log
-   endif
-   @ i++
- end
-diff -urN gamess.orig/rungms gamess/rungms
---- gamess.orig/rungms	2012-05-28 14:03:08.390784789 +0300
-+++ gamess/rungms	2012-05-28 14:18:12.424545548 +0300
-@@ -57,9 +57,9 @@
- #       See also a very old LoadLeveler "ll-gms" for some IBM systems.
- #
- set TARGET=sockets
--set SCR=/scr/$USER
--set USERSCR=~$USER/scr
--set GMSPATH=/u1/mike/gamess
-+set SCR=`pwd`
-+set USERSCR=`pwd`
-+set GMSPATH=/usr/bin
- #
- set JOB=$1      # name of the input file xxx.inp, give only the xxx part
- set VERNO=$2    # revision number of the executable created by 'lked' step
-@@ -1033,7 +1033,7 @@
- #   in the case of GDDI runs, we save the first PUNCH file only.
- #   If something goes wrong, the .F06.00x, .F07.00x, ... from the
- #   other groups are potentially interesting to look at.
--if ($GDDIjob == true) cp $SCR/$JOB.F07 ~/scr/$JOB.dat
-+if ($GDDIjob == true) cp $SCR/$JOB.F07 $SCR/$JOB.dat
- #
- #   Clean up the master's scratch directory.
- #
-diff -urN gamess.orig/rungms gamess/rungms
---- gamess.orig/gms-files.csh	2012-05-28 17:14:57.137387985 +0300
-+++ gamess/gms-files.csh	2012-05-28 17:15:31.828413312 +0300
-@@ -28,7 +28,7 @@
- #     to see all the file definitions (one is just below).
- #
- #---quiet---set echo
--setenv AUXDATA $GMSPATH/auxdata
-+setenv AUXDATA /usr/share/gamess
- setenv  EXTBAS /dev/null
- setenv  NUCBAS /dev/null
- setenv  POSBAS /dev/null
diff --git a/sci-chemistry/gamess/gamess-20120501.1.ebuild b/sci-chemistry/gamess/gamess-20120501.1.ebuild
deleted file mode 100644
index 9ef138b73..000000000
--- a/sci-chemistry/gamess/gamess-20120501.1.ebuild
+++ /dev/null
@@ -1,338 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="4"
-
-inherit eutils fortran-2 flag-o-matic pax-utils toolchain-funcs
-
-DESCRIPTION="A powerful quantum chemistry package"
-LICENSE="gamess"
-HOMEPAGE="http://www.msg.chem.iastate.edu/GAMESS/GAMESS.html"
-SRC_URI="
-		${P}.tar.gz
-		qmmm-tinker? ( tinker.tar.Z )"
-
-SLOT="0"
-# NOTE: PLEASE do not stabilize gamess. It does not make sense
-# since the tarball has fetch restrictions and upstream only
-# provides the latest version. In other words: As soon as a
-# new version comes out the stable version will be useless since
-# users can not get at the tarball any more.
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE="mpi neo pax_kernel qmmm-tinker"
-
-CDEPEND="
-	app-shells/tcsh
-	mpi? ( virtual/mpi )
-	virtual/blas"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig"
-RDEPEND="${CDEPEND}
-	net-misc/openssh"
-
-S="${WORKDIR}/${PN}"
-
-RESTRICT="fetch"
-
-GAMESS_DOWNLOAD="http://www.msg.ameslab.gov/GAMESS/License_Agreement.html"
-GAMESS_VERSION="1 MAY 2012 (R1)"
-
-pkg_nofetch() {
-	echo
-	elog "Please download ${PN}-current.tar.gz from"
-	elog "${GAMESS_DOWNLOAD}."
-	elog "Be sure to select the version ${GAMESS_VERSION} tarball!!"
-	elog "Then move the tarball to"
-	elog "${DISTDIR}/${P}.tar.gz"
-	if use qmmm-tinker ; then
-		elog "Also download http://www.msg.ameslab.gov/GAMESS/tinker.tar.Z"
-		elog "and place tinker.tar.Z to ${DISTDIR}"
-	fi
-	echo
-}
-
-get_fcomp() {
-	case $(tc-getFC) in
-		*gfortran* )
-			FCOMP="gfortran" ;;
-		ifort )
-			FCOMP="ifc" ;;
-		* )
-			FCOMP=$(tc-getFC) ;;
-	esac
-}
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	get_fcomp
-	# currently amd64 is only supported with gfortran
-	if [[ "${ARCH}" == "amd64" ]] && [[ ${FCOMP} != *gfortran* ]];
-		then die "You will need gfortran to compile gamess on amd64"
-	fi
-
-	# note about qmmm-tinker
-	if use qmmm-tinker; then
-			einfo "By default MM subsistem is restricted to 1000 atoms"
-			einfo "if you want larger MM subsystems then you should set"
-			einfo "QMMM_GAMESS_MAXMM variable to needed value in your make.conf"
-			einfo "By default maximum number of atom classes types and size of"
-			einfo "hessian are restricted to 250, 500 and 1000000 respectively"
-			einfo "If you want larger sizes set:"
-			einfo "QMMM_GAMESS_MAXCLASS"
-			einfo "QMMM_GAMESS_MAXCTYP"
-			einfo "QMMM_GAMESS_MAXHESS"
-			einfo "in your make.conf"
-	fi
-
-	#note about mpi
-	if use mpi; then
-		ewarn ""
-		ewarn "You should adjust rungms script for your mpi implentation"
-		ewarn "because deafult one will not work"
-		ewarn ""
-	fi
-}
-
-src_unpack() {
-	unpack ${A}
-
-	if use qmmm-tinker; then
-		mv tinker gamess/ || die "failed to move tinker directory"
-	fi
-}
-
-src_prepare() {
-	tc-export PKG_CONFIG
-	# apply LINUX-arch patches to gamess makesfiles
-	epatch "${FILESDIR}/${P}.gentoo.patch"
-	# select arch
-	# NOTE: please leave lked alone; it should be good as is!!
-	cd "${S}"
-	local active_arch;
-	if [[ "${ARCH}" == "amd64" ]]; then
-		active_arch="linux64";
-	else
-		active_arch="linux32";
-	fi
-
-	# for hardened-gcc let't turn off ssp, since it breakes
-	# a few routines
-	if use pax_kernel && [[ ${FCOMP} == g77 ]]; then
-		FFLAGS="${FFLAGS} -fno-stack-protector-all"
-	fi
-
-	# Enable mpi stuff
-	if use mpi; then
-		sed -e "s:set COMM = sockets:set COMM = mpi:g" \
-			-i ddi/compddi || die "Enabling mpi build failed"
-		sed -e "s:MPI_INCLUDE_PATH = ' ':MPI_INCLUDE_PATH =	'-I/usr/include ':g" \
-			-i ddi/compddi || die "Enabling mpi build failed"
-		sed -e "s:MSG_LIBRARIES='../ddi/libddi.a -lpthread':MSG_LIBRARIES='../ddi/libddi.a -lmpi -lpthread':g" \
-			-i lked || die "Enabling mpi build failed"
-	fi
-
-	# enable NEO
-	if use neo; then
-		sed -e "s:NEO=false:NEO=true:" -i compall lked || \
-			die "Failed to enable NEO code"
-	else
-		sed -e "s:NEO=true:NEO=false:" -i compall lked || \
-			die "Failed to disable NEO code"
-	fi
-	# enable GAMESS-qmmm
-	if use qmmm-tinker; then
-		epatch "${FILESDIR}/${PN}-qmmm-tinker-fix-idate.patch"
-		sed -e "s:TINKER=false:TINKER=true:" -i compall lked || \
-			die "Failed to enable TINKER code"
-		if [ "x$QMMM_GAMESS_MAXMM" == "x" ]; then
-			einfo "No QMMM_GAMESS_MAXMM set. Using default value = 1000"
-		else
-			einfo "Setting QMMM_GAMESS_MAXMM to $QMMM_GAMESS_MAXMM"
-			sed -e "s:maxatm=1000:maxatm=$QMMM_GAMESS_MAXMM:g" \
-			 -i tinker/sizes.i \
-			 || die "Setting QMMM_GAMESS_MAXMM failed"
-			sed -e "s:MAXATM=1000:MAXATM=$QMMM_GAMESS_MAXMM:g" \
-			 -i source/inputb.src \
-			 || die "Setting QMMM_GAMESS_MAXMM failed"
-		fi
-		if [ "x$QMMM_GAMESS_MAXCLASS" == "x" ]; then
-			einfo "No QMMM_GAMESS_MAXMM set. Using default value = 250"
-		else
-			sed -e "s:maxclass=250:maxclass=$QMMM_GAMESS_MAXCLASS:g" \
-				-i tinker/sizes.i \
-				|| die "Setting QMMM_GAMESS_MAXCLASS failed"
-		fi
-		if [ "x$QMMM_GAMESS_MAXCTYP" == "x" ]; then
-			einfo "No QMMM_GAMESS_MAXCTYP set. Using default value = 500"
-		else
-			sed -e "s:maxtyp=500:maxtyp=$QMMM_GAMESS_MAXCTYP:g" \
-				-i tinker/sizes.i \
-				|| die "Setting QMMM_GAMESS_MAXCTYP failed"
-		fi
-		if [ "x$QMMM_GAMESS_MAXHESS" == "x" ]; then
-			einfo "No QMMM_GAMESS_MAXHESS set. Usingdefault value = 1000000"
-		else
-			sed -e "s:maxhess=1000000:maxhess=$QMMM_GAMESS_MAXHESS:g" \
-				-i tinker/sizes.i \
-				|| die "Setting QMMM_GAMESS_MAXHESS failed"
-		fi
-	fi
-	# greate proper activate sourcefile
-	cp "./tools/actvte.code" "./tools/actvte.f" || \
-		die "Failed to create actvte.f"
-	sed -e "s/^\*UNX/    /" -i "./tools/actvte.f" || \
-		die "Failed to perform UNX substitutions in actvte.f"
-
-	# fix GAMESS' compall script to use proper CC
-	sed -e "s|\$CCOMP -c \$extraflags source/zunix.c|$(tc-getCC) -c \$extraflags source/zunix.c|" \
-		-i compall || die "Failed setting up compall script"
-
-	# insert proper FFLAGS into GAMESS' comp makefile
-	# in case we're using ifc let's strip all the gcc
-	# specific stuff
-	if [[ ${FCOMP} == "ifort" ]]; then
-		sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS} -quiet'/" \
-			-i comp || die "Failed setting up comp script"
-	elif ! use x86; then
-		sed -e "s/-malign-double //" \
-			-e "s/gentoo-OPT='-O2'/OPT='${FFLAGS}'/" \
-			-i comp || die "Failed setting up comp script"
-	else
-		sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS}'/" \
-			-i comp || die "Failed setting up comp script"
-	fi
-
-	# fix up GAMESS' linker script;
-	sed -e "s/gentoo-LDOPTS=' '/LDOPTS='${LDFLAGS}'/" \
-		-i lked || die "Failed setting up lked script"
-	# fix up GAMESS' ddi TCP/IP socket build
-	sed -e "s/gentoo-CC = 'gcc'/CC = '$(tc-getCC)'/" \
-		-i ddi/compddi || die "Failed setting up compddi script"
-	# Creating install.info
-	cat > install.info <<-EOF
-	#!/bin/csh
-	setenv GMS_PATH $WORKDIR/gamess
-	setenv GMS_BUILD_DIR $WORKDIR/gamess
-	setenv GMS_TARGET $active_arch
-	setenv GMS_FORTRAN $FCOMP
-	setenv GMS_GFORTRAN_VERNO 4.7
-	setenv GMS_MATHLIB atlas
-	setenv GMS_MATHLIB_PATH  /usr/$(get_libdir)/atlas
-	setenv GMS_DDI_COMM sockets
-	EOF
-
-}
-
-src_compile() {
-	# build actvte
-	cd "${S}"/tools
-	${FCOMP} -o actvte.x actvte.f || \
-		die "Failed to compile actvte.x"
-
-	# for hardened (PAX) users and ifc we need to turn
-	# MPROTECT off
-	if [[ ${FCOMP} == "ifort" ]] && use pax_kernel; then
-		pax-mark -PemRxS actvte.x
-	fi
-
-	# build gamess
-	cd "${S}"
-	./compall || die "compall failed"
-
-	# build the ddi TCP/IP socket stuff
-	cd ${S}/"ddi"
-	./compddi || die "compddi failed"
-
-	# finally, link it all together
-	cd "${S}"
-	./lked || die "lked failed"
-
-	# for hardened (PAX) users and ifc we need to turn
-	# MPROTECT off
-	if [[ ${FCOMP} == "ifort" ]] && use pax_kernel; then
-		pax-mark -PemRxS ${PN}.00.x
-	fi
-}
-
-src_install() {
-	# the executables
-	dobin ${PN}.00.x rungms gms-files.csh \
-		|| die "Failed installing binaries"
-	if use !mpi; then
-		dobin ddi/ddikick.x \
-			|| die "Failed installing binaries"
-	fi
-
-	# the docs
-	dodoc *.DOC qmnuc/*.DOC || die "Failed installing docs"
-
-	# install ericftm
-	insinto /usr/share/${PN}
-	doins auxdata/ericfmt.dat || die "Failed installing ericfmt.dat"
-
-	# install mcpdata
-	insinto /usr/share/${PN}/MCP
-	doins auxdata/MCP/* || die "Failed installing MCP"
-
-	# install BASES
-	insinto /usr/share/${PN}/BASES
-	doins auxdata/BASES/* || die "Failed installing BASES"
-
-	# install QUANPOL
-	insinto /usr/share/${PN}/QUANPOL
-	doins auxdata/QUANPOL/* || die "Failed installing QUANPOL"
-
-	# install tinker params in case of qmmm
-	if use qmmm-tinker ; then
-			dodoc tinker/simomm.doc || die "Failed installing docs"
-			insinto /usr/share/${PN}
-			doins -r tinker/params51 || die "Failed to install Tinker params"
-	fi
-
-	# install the tests the user should run, and
-	# fix up the runscript; also grab a copy of rungms
-	# so the user is ready to run the tests
-	insinto /usr/share/${PN}/tests
-	insopts -m0644
-	doins -r tests/* || die "Failed installing tests"
-	insopts -m0744
-	doins runall || die "Failed installing tests"
-	#doins tools/checktst/checktst tools/checktst/chkabs || \
-	#	die "Failed to install main test checker"
-	#doins tools/checktst/exam* || \
-	#	die "Failed to install individual test files"
-
-	insinto /usr/share/${PN}/neotests
-	insopts -m0644
-	doins -r qmnuc/neotests/* || die "Failed to install NEO tests"
-}
-
-pkg_postinst() {
-	echo
-	einfo "Before you use GAMESS for any serious work you HAVE"
-	einfo "to run the supplied test files located in"
-	einfo "/usr/share/gamess/tests and check them thoroughly."
-	einfo "Otherwise all scientific publications resulting from"
-	einfo "your GAMESS runs should be immediately rejected :)"
-	einfo "To do so copy the content of /usr/share/gamess/tests"
-	einfo "to some temporary location and execute './runall'. "
-	einfo "Then run the checktst script in the same directory to"
-	einfo "validate the tests."
-	einfo "Please consult TEST.DOC and the other docs!"
-
-	if [[ ${FCOMP} == "ifort" ]]; then
-		echo
-		ewarn "IMPORTANT NOTE: We STRONGLY recommend to stay away"
-		ewarn "from ifc-9.0 for now and use the ifc-8.1 series of"
-		ewarn "compilers UNLESS you can run through ALL of the "
-		ewarn "test cases (see above) successfully."
-	fi
-
-	echo
-	einfo "If you want to run on more than a single CPU"
-	einfo "you will have to acquaint yourself with the way GAMESS"
-	einfo "does multiprocessor runs and adjust rungms according to"
-	einfo "your target network architecture."
-	echo
-}
diff --git a/sci-chemistry/gamess/gamess-20130501.1.ebuild b/sci-chemistry/gamess/gamess-20130501.1.ebuild
index c7158c9e4..8cc04fb64 100644
--- a/sci-chemistry/gamess/gamess-20130501.1.ebuild
+++ b/sci-chemistry/gamess/gamess-20130501.1.ebuild
@@ -1,19 +1,19 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI="5"
+EAPI=5
 
 inherit eutils fortran-2 flag-o-matic pax-utils toolchain-funcs
 
 DESCRIPTION="A powerful quantum chemistry package"
-LICENSE="gamess"
 HOMEPAGE="http://www.msg.chem.iastate.edu/GAMESS/GAMESS.html"
 SRC_URI="
-		${P}.tar.gz
-		qmmm-tinker? ( tinker.tar.Z )"
+	${P}.tar.gz
+	qmmm-tinker? ( tinker.tar.Z )"
 
 SLOT="0"
+LICENSE="gamess"
 # NOTE: PLEASE do not stabilize gamess. It does not make sense
 # since the tarball has fetch restrictions and upstream only
 # provides the latest version. In other words: As soon as a
@@ -265,29 +265,29 @@ src_install() {
 	fi
 
 	# the docs
-	dodoc *.DOC qmnuc/*.DOC || die "Failed installing docs"
+	dodoc *.DOC qmnuc/*.DOC
 
 	# install ericftm
 	insinto /usr/share/${PN}
-	doins auxdata/ericfmt.dat || die "Failed installing ericfmt.dat"
+	doins auxdata/ericfmt.dat
 
 	# install mcpdata
 	insinto /usr/share/${PN}/MCP
-	doins auxdata/MCP/* || die "Failed installing MCP"
+	doins auxdata/MCP/*
 
 	# install BASES
 	insinto /usr/share/${PN}/BASES
-	doins auxdata/BASES/* || die "Failed installing BASES"
+	doins auxdata/BASES/*
 
 	# install QUANPOL
 	insinto /usr/share/${PN}/QUANPOL
-	doins auxdata/QUANPOL/* || die "Failed installing QUANPOL"
+	doins auxdata/QUANPOL/*
 
 	# install tinker params in case of qmmm
 	if use qmmm-tinker ; then
-			dodoc tinker/simomm.doc || die "Failed installing docs"
+			dodoc tinker/simomm.doc
 			insinto /usr/share/${PN}
-			doins -r tinker/params51 || die "Failed to install Tinker params"
+			doins -r tinker/params51
 	fi
 
 	# install the tests the user should run, and
@@ -295,9 +295,9 @@ src_install() {
 	# so the user is ready to run the tests
 	insinto /usr/share/${PN}/tests
 	insopts -m0644
-	doins -r tests/* || die "Failed installing tests"
+	doins -r tests/*
 	insopts -m0744
-	doins runall || die "Failed installing tests"
+	doins runall
 	#doins tools/checktst/checktst tools/checktst/chkabs || \
 	#	die "Failed to install main test checker"
 	#doins tools/checktst/exam* || \
@@ -305,7 +305,7 @@ src_install() {
 
 	insinto /usr/share/${PN}/neotests
 	insopts -m0644
-	doins -r qmnuc/neotests/* || die "Failed to install NEO tests"
+	doins -r qmnuc/neotests/*
 }
 
 pkg_postinst() {
diff --git a/sci-chemistry/jligand/jligand-1.0.40.ebuild b/sci-chemistry/jligand/jligand-1.0.40.ebuild
index 655ca7501..5d25e5bce 100644
--- a/sci-chemistry/jligand/jligand-1.0.40.ebuild
+++ b/sci-chemistry/jligand/jligand-1.0.40.ebuild
@@ -24,7 +24,7 @@ S="${WORKDIR}"/${MY_PN}.${PV}
 
 src_compile() {
 	sed 's:makefile::g' -i Makefile || die
-	emake
+	default
 }
 
 src_install() {
diff --git a/sci-chemistry/ligplot+/ligplot+-1.4.ebuild b/sci-chemistry/ligplot+/ligplot+-1.4.ebuild
index ac0288b5b..923141b1f 100644
--- a/sci-chemistry/ligplot+/ligplot+-1.4.ebuild
+++ b/sci-chemistry/ligplot+/ligplot+-1.4.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit java-pkg-2
 
@@ -15,7 +15,7 @@ LICENSE="ligplot+"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
-RDEPEND="virtual/jre"
+RDEPEND="virtual/jre:*"
 DEPEND=""
 
 RESTRICT="fetch"
@@ -25,10 +25,10 @@ S="${WORKDIR}"/LigPlus
 QA_PREBUILT="opt/${PN}/.*"
 
 pkg_nofetch() {
-	einfo "Please visit"
-	einfo "http://www.ebi.ac.uk/thornton-srv/software/LigPlus/applicence.html"
-	einfo "download ${A}"
-	einfo "and save in ${DISTDIR}"
+	elog "Please visit"
+	elog "http://www.ebi.ac.uk/thornton-srv/software/LigPlus/applicence.html"
+	elog "download ${A}"
+	elog "and save in ${DISTDIR}"
 }
 
 src_prepare() {
diff --git a/sci-chemistry/simpson/simpson-3.0.1.ebuild b/sci-chemistry/simpson/simpson-3.0.1.ebuild
index 152d943d3..9fa692637 100644
--- a/sci-chemistry/simpson/simpson-3.0.1.ebuild
+++ b/sci-chemistry/simpson/simpson-3.0.1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit eutils prefix toolchain-funcs
 
@@ -21,7 +21,7 @@ RDEPEND="
 	virtual/cblas
 	virtual/lapack
 	gtk? ( x11-libs/gtk+:1 )
-	tk? ( dev-lang/tk )"
+	tk? ( dev-lang/tk:0= )"
 DEPEND="${RDEPEND}
 	virtual/pkgconfig"
 
@@ -30,8 +30,9 @@ S="${WORKDIR}"/${PN}-source-${PV}
 src_prepare() {
 	tc-export PKG_CONFIG
 	edos2unix Makefile
-	epatch "${FILESDIR}"/${PV}-gentoo.patch
-	epatch "${FILESDIR}"/${PV}-type.patch
+	epatch \
+		"${FILESDIR}"/${PV}-gentoo.patch \
+		"${FILESDIR}"/${PV}-type.patch
 	eprefixify Makefile
 }
 
diff --git a/sci-chemistry/simpson/simpson-3.1.0.ebuild b/sci-chemistry/simpson/simpson-3.1.0.ebuild
index 129f47dc0..520ce7d48 100644
--- a/sci-chemistry/simpson/simpson-3.1.0.ebuild
+++ b/sci-chemistry/simpson/simpson-3.1.0.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit eutils prefix toolchain-funcs
 
@@ -21,7 +21,7 @@ RDEPEND="
 	virtual/cblas
 	virtual/lapack
 	gtk? ( x11-libs/gtk+:1 )
-	tk? ( dev-lang/tk )"
+	tk? ( dev-lang/tk:0= )"
 DEPEND="${RDEPEND}
 	virtual/pkgconfig"
 
@@ -30,8 +30,9 @@ S="${WORKDIR}"/${PN}-source-${PV}
 src_prepare() {
 	tc-export PKG_CONFIG
 	edos2unix Makefile
-	epatch "${FILESDIR}"/${PV}-gentoo.patch
-	epatch "${FILESDIR}"/3.0.1-type.patch
+	epatch \
+		"${FILESDIR}"/${PV}-gentoo.patch \
+		"${FILESDIR}"/3.0.1-type.patch
 	eprefixify Makefile
 }
 
diff --git a/sci-chemistry/simpson/simpson-3.1.2.ebuild b/sci-chemistry/simpson/simpson-3.1.2.ebuild
index 129f47dc0..520ce7d48 100644
--- a/sci-chemistry/simpson/simpson-3.1.2.ebuild
+++ b/sci-chemistry/simpson/simpson-3.1.2.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit eutils prefix toolchain-funcs
 
@@ -21,7 +21,7 @@ RDEPEND="
 	virtual/cblas
 	virtual/lapack
 	gtk? ( x11-libs/gtk+:1 )
-	tk? ( dev-lang/tk )"
+	tk? ( dev-lang/tk:0= )"
 DEPEND="${RDEPEND}
 	virtual/pkgconfig"
 
@@ -30,8 +30,9 @@ S="${WORKDIR}"/${PN}-source-${PV}
 src_prepare() {
 	tc-export PKG_CONFIG
 	edos2unix Makefile
-	epatch "${FILESDIR}"/${PV}-gentoo.patch
-	epatch "${FILESDIR}"/3.0.1-type.patch
+	epatch \
+		"${FILESDIR}"/${PV}-gentoo.patch \
+		"${FILESDIR}"/3.0.1-type.patch
 	eprefixify Makefile
 }
 
diff --git a/sci-chemistry/usf-tools/usf-tools-9999.ebuild b/sci-chemistry/usf-tools/usf-tools-9999.ebuild
index 3685887eb..2b3b5fa6f 100644
--- a/sci-chemistry/usf-tools/usf-tools-9999.ebuild
+++ b/sci-chemistry/usf-tools/usf-tools-9999.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 AUTOTOOLS_AUTORECONF=y
 
@@ -22,8 +22,8 @@ KEYWORDS=""
 IUSE="static-libs"
 
 RDEPEND="
-	sci-libs/ccp4-libs
-	sci-libs/mmdb"
+	sci-libs/libccp4
+	sci-libs/mmdb:0"
 DEPEND="${RDEPEND}"
 
 S="${WORKDIR}"/usf_export
diff --git a/sci-chemistry/votca-csg/ChangeLog b/sci-chemistry/votca-csg/ChangeLog
index 1c1eb1dca..827dd5d87 100644
--- a/sci-chemistry/votca-csg/ChangeLog
+++ b/sci-chemistry/votca-csg/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  24 Sep 2015; Christoph Junghans <ottxor@gentoo.org> votca-csg-9999.ebuild:
+  sci-chemistry/votca-csg: sync with gx86
+
   12 Feb 2015; Christoph Junghans <ottxor@gentoo.org> votca-csg-9999.ebuild:
   added support of hdf5, clean up
 
diff --git a/sci-chemistry/votca-csg/votca-csg-9999.ebuild b/sci-chemistry/votca-csg/votca-csg-9999.ebuild
index 7f7a214ac..668702c9c 100644
--- a/sci-chemistry/votca-csg/votca-csg-9999.ebuild
+++ b/sci-chemistry/votca-csg/votca-csg-9999.ebuild
@@ -11,14 +11,14 @@ inherit bash-completion-r1 cmake-utils multilib
 IUSE="doc examples extras +gromacs hdf5"
 PDEPEND="extras? ( =sci-chemistry/${PN}apps-${PV} )"
 if [ "${PV}" != "9999" ]; then
-	SRC_URI="http://downloads.votca.googlecode.com/hg/${P}.tar.gz
-		doc? ( http://downloads.votca.googlecode.com/hg/${PN}-manual-${PV}.pdf )
-		examples? (	http://downloads.votca.googlecode.com/hg/${PN}-tutorials-${PV}.tar.gz )"
+	SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz
+		doc? ( https://github.com/${PN/-//}-manual/releases/download/v1.3_rc1/${PN}-manual-${PV}.pdf )
+		examples? (	https://github.com/${PN/-//}-tutorials/archive/v${PV}.tar.gz -> ${PN}-tutorials-${PV}.tar.gz )"
 	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos"
+	S="${WORKDIR}/${P#votca-}"
 else
-	SRC_URI=""
-	inherit mercurial
-	EHG_REPO_URI="https://code.google.com/p/votca.csg/"
+	inherit git-r3
+	EGIT_REPO_URI="git://github.com/${PN/-//}.git https://github.com/${PN/-//}.git"
 	KEYWORDS=""
 fi
 
@@ -45,21 +45,25 @@ DEPEND="${RDEPEND}
 	>=app-text/txt2tags-2.5
 	virtual/pkgconfig"
 
-DOCS=( README NOTICE )
+DOCS=( README.md NOTICE CHANGELOG.md )
 
 src_unpack() {
 	if [[ ${PV} != *9999 ]]; then
 		default
 	else
-		mercurial_src_unpack
-		use doc && mercurial_fetch \
-			https://code.google.com/p/votca.csg-manual/ \
-			votca.csg-manual \
-			"${WORKDIR}/${PN}-manual"
-		use examples && mercurial_fetch \
-			https://code.google.com/p/votca.csg-tutorials/ \
-			votca.csg-tutorials \
-			"${WORKDIR}/${PN}-tutorials"
+		git-r3_src_unpack
+		if use doc; then
+			EGIT_REPO_URI="git://github.com/${PN/-//}-manual.git https://github.com/${PN/-//}-manual.git"
+			EGIT_BRANCH="master"
+			EGIT_CHECKOUT_DIR="${WORKDIR}/${PN}-manual"\
+				git-r3_src_unpack
+		fi
+		if use examples; then
+			EGIT_REPO_URI="git://github.com/${PN/-//}-tutorials.git https://github.com/${PN/-//}-tutorials.git"
+			EGIT_BRANCH="master"
+			EGIT_CHECKOUT_DIR="${WORKDIR}/${PN#votca-}-tutorials"\
+				git-r3_src_unpack
+		fi
 	fi
 }
 
@@ -96,7 +100,8 @@ src_install() {
 	if use examples; then
 		insinto "/usr/share/doc/${PF}/tutorials"
 		docompress -x "/usr/share/doc/${PF}/tutorials"
-		doins -r "${WORKDIR}/${PN}"-tutorials*/*
+		rm -rf "${WORKDIR}/${PN#votca-}"-tutorials*/CMake*
+		doins -r "${WORKDIR}/${PN#votca-}"-tutorials*/*
 	fi
 }
 
diff --git a/sci-chemistry/votca-csgapps/ChangeLog b/sci-chemistry/votca-csgapps/ChangeLog
index 7cb472731..7afcaa534 100644
--- a/sci-chemistry/votca-csgapps/ChangeLog
+++ b/sci-chemistry/votca-csgapps/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for sci-chemistry/votca-csgapps
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  24 Sep 2015; Christoph Junghans <ottxor@gentoo.org> votca-csgapps-9999.ebuild:
+  sci-chemistry/votca-csgapps: sync with gx86
+
   01 Sep 2014; Christoph Junghans <ottxor@gentoo.org> votca-csgapps-9999.ebuild:
   sync with gx86
 
diff --git a/sci-chemistry/votca-csgapps/votca-csgapps-9999.ebuild b/sci-chemistry/votca-csgapps/votca-csgapps-9999.ebuild
index 98ee4214c..efa51d45c 100644
--- a/sci-chemistry/votca-csgapps/votca-csgapps-9999.ebuild
+++ b/sci-chemistry/votca-csgapps/votca-csgapps-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -9,11 +9,12 @@ CMAKE_MAKEFILE_GENERATOR="ninja"
 inherit cmake-utils
 
 if [ "${PV}" != "9999" ]; then
-	SRC_URI="http://downloads.votca.googlecode.com/hg/${PF}.tar.gz"
+	SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos"
+	S="${WORKDIR}/${P#votca-}"
 else
-	inherit mercurial
-	EHG_REPO_URI="https://code.google.com/p/votca.csgapps/"
+	inherit git-r3
+	EGIT_REPO_URI="git://github.com/${PN/-//}.git https://github.com/${PN/-//}.git"
 	KEYWORDS=""
 fi
 
diff --git a/sci-electronics/stage/stage-2.0.3.ebuild b/sci-electronics/stage/stage-2.0.3.ebuild
index 5a7163354..42cd186d7 100644
--- a/sci-electronics/stage/stage-2.0.3.ebuild
+++ b/sci-electronics/stage/stage-2.0.3.ebuild
@@ -6,7 +6,7 @@ EAPI=5
 
 inherit autotools eutils
 
-DESCRIPTION="2D multiple-robot simulator."
+DESCRIPTION="2D multiple-robot simulator"
 HOMEPAGE="http://playerstage.sourceforge.net/index.php?src=stage"
 SRC_URI="mirror://sourceforge/playerstage/stage-${PV}.tar.bz2"
 
@@ -37,7 +37,7 @@ src_configure() {
 }
 
 src_compile() {
-	emake
+	default
 
 	if use doc; then
 		pushd docsrc
@@ -49,7 +49,7 @@ src_compile() {
 }
 
 src_install() {
-	emake DESTDIR="${D}" install
+	default
 
 	if use doc; then
 		pushd docsrc
diff --git a/sci-geosciences/pydap/pydap-3.1.1.ebuild b/sci-geosciences/pydap/pydap-3.1.1.ebuild
index e536d403f..3666f82e7 100644
--- a/sci-geosciences/pydap/pydap-3.1.1.ebuild
+++ b/sci-geosciences/pydap/pydap-3.1.1.ebuild
@@ -12,7 +12,7 @@ MY_PN=${PN/pydap/Pydap}
 MY_P=${P/pydap/Pydap}
 MY_P=${MY_P/_rc/.rc.}
 
-DESCRIPTION="Data Access Protocol client and server."
+DESCRIPTION="Data Access Protocol client and server"
 HOMEPAGE="http://pydap.org"
 SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
 
diff --git a/sci-geosciences/pydap/pydap-3.1.ebuild b/sci-geosciences/pydap/pydap-3.1.ebuild
index e536d403f..3666f82e7 100644
--- a/sci-geosciences/pydap/pydap-3.1.ebuild
+++ b/sci-geosciences/pydap/pydap-3.1.ebuild
@@ -12,7 +12,7 @@ MY_PN=${PN/pydap/Pydap}
 MY_P=${P/pydap/Pydap}
 MY_P=${MY_P/_rc/.rc.}
 
-DESCRIPTION="Data Access Protocol client and server."
+DESCRIPTION="Data Access Protocol client and server"
 HOMEPAGE="http://pydap.org"
 SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
 
diff --git a/sci-geosciences/pydap_handlers_hdf5/pydap_handlers_hdf5-0.1.7.ebuild b/sci-geosciences/pydap_handlers_hdf5/pydap_handlers_hdf5-0.1.7.ebuild
index 9264aa49c..eb83be2b2 100644
--- a/sci-geosciences/pydap_handlers_hdf5/pydap_handlers_hdf5-0.1.7.ebuild
+++ b/sci-geosciences/pydap_handlers_hdf5/pydap_handlers_hdf5-0.1.7.ebuild
@@ -11,7 +11,7 @@ inherit distutils-r1
 MY_PN=${PN//_/.}
 MY_P=${P//_/.}
 
-DESCRIPTION="HDF5 file handler for Pydap Data Access Protocol server."
+DESCRIPTION="HDF5 file handler for Pydap Data Access Protocol server"
 HOMEPAGE="http://pydap.org/"
 SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
 
diff --git a/sci-geosciences/pydap_handlers_nca/pydap_handlers_nca-0.1.3.ebuild b/sci-geosciences/pydap_handlers_nca/pydap_handlers_nca-0.1.3.ebuild
index e8fc04166..a8b0cda68 100644
--- a/sci-geosciences/pydap_handlers_nca/pydap_handlers_nca-0.1.3.ebuild
+++ b/sci-geosciences/pydap_handlers_nca/pydap_handlers_nca-0.1.3.ebuild
@@ -11,7 +11,7 @@ inherit distutils-r1
 MY_PN=${PN//_/.}
 MY_P=${P//_/.}
 
-DESCRIPTION="Aggregated NetCDF handler for Pydap Data Access Protocol server."
+DESCRIPTION="Aggregated NetCDF handler for Pydap Data Access Protocol server"
 HOMEPAGE="http://pydap.org/"
 SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
 
diff --git a/sci-geosciences/pydap_handlers_netcdf/pydap_handlers_netcdf-0.6.4.ebuild b/sci-geosciences/pydap_handlers_netcdf/pydap_handlers_netcdf-0.6.4.ebuild
index 969ceebee..33a08dcfa 100644
--- a/sci-geosciences/pydap_handlers_netcdf/pydap_handlers_netcdf-0.6.4.ebuild
+++ b/sci-geosciences/pydap_handlers_netcdf/pydap_handlers_netcdf-0.6.4.ebuild
@@ -11,7 +11,7 @@ inherit distutils-r1
 MY_PN=${PN//_/.}
 MY_P=${P//_/.}
 
-DESCRIPTION="NetCDF handler for Pydap Data Access Protocol server."
+DESCRIPTION="NetCDF handler for Pydap Data Access Protocol server"
 HOMEPAGE="http://pydap.org/"
 SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
 
diff --git a/sci-geosciences/pydap_handlers_proxy/pydap_handlers_proxy-0.1.1.ebuild b/sci-geosciences/pydap_handlers_proxy/pydap_handlers_proxy-0.1.1.ebuild
index b1216881b..33919eefd 100644
--- a/sci-geosciences/pydap_handlers_proxy/pydap_handlers_proxy-0.1.1.ebuild
+++ b/sci-geosciences/pydap_handlers_proxy/pydap_handlers_proxy-0.1.1.ebuild
@@ -11,7 +11,7 @@ inherit distutils-r1
 MY_PN=${PN//_/.}
 MY_P=${P//_/.}
 
-DESCRIPTION="Proxy handler for Pydap server that can serve data from other web sites."
+DESCRIPTION="Proxy handler for Pydap server that can serve data from other web sites"
 HOMEPAGE="http://pydap.org/handlers.html#cdms"
 SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
 
diff --git a/sci-libs/Cgraph/Cgraph-2.04.ebuild b/sci-libs/Cgraph/Cgraph-2.04.ebuild
index 6df2ac05e..09e5a1650 100644
--- a/sci-libs/Cgraph/Cgraph-2.04.ebuild
+++ b/sci-libs/Cgraph/Cgraph-2.04.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit eutils flag-o-matic multilib
 
diff --git a/sci-libs/Cgraph/metadata.xml b/sci-libs/Cgraph/metadata.xml
index b229aec85..d369d068f 100644
--- a/sci-libs/Cgraph/metadata.xml
+++ b/sci-libs/Cgraph/metadata.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci</herd>
+	<herd>sci</herd>
 </pkgmetadata>
diff --git a/sci-libs/arrayfire/arrayfire-3.1.1-r2.ebuild b/sci-libs/arrayfire/arrayfire-3.1.1-r2.ebuild
index 929f4e22d..e1810f19f 100644
--- a/sci-libs/arrayfire/arrayfire-3.1.1-r2.ebuild
+++ b/sci-libs/arrayfire/arrayfire-3.1.1-r2.ebuild
@@ -8,7 +8,7 @@ inherit cmake-utils multilib
 
 GTEST_PV="1.7.0"
 
-DESCRIPTION="A general purpose GPU library."
+DESCRIPTION="A general purpose GPU library"
 HOMEPAGE="http://www.arrayfire.com/"
 SRC_URI="http://arrayfire.com/arrayfire_source/${PN}-full-${PV}.tar.bz2 -> ${P}.tar.bz2
 test? ( https://googletest.googlecode.com/files/gtest-${GTEST_PV}.zip )"
diff --git a/sci-libs/arrayfire/arrayfire-9999.ebuild b/sci-libs/arrayfire/arrayfire-9999.ebuild
index 593dc5160..511aee3e1 100644
--- a/sci-libs/arrayfire/arrayfire-9999.ebuild
+++ b/sci-libs/arrayfire/arrayfire-9999.ebuild
@@ -8,7 +8,7 @@ inherit cmake-utils git-r3
 
 GTEST_PV="1.7.0"
 
-DESCRIPTION="A general purpose GPU library."
+DESCRIPTION="A general purpose GPU library"
 HOMEPAGE="http://www.arrayfire.com/"
 EGIT_REPO_URI="https://github.com/${PN}/${PN}.git git://github.com/${PN}/${PN}.git"
 SRC_URI="test? ( https://googletest.googlecode.com/files/gtest-${GTEST_PV}.zip )"
diff --git a/sci-libs/asl/asl-0.1.5.ebuild b/sci-libs/asl/asl-0.1.5.ebuild
index 2176c62f8..3163a5d82 120000..100644
--- a/sci-libs/asl/asl-0.1.5.ebuild
+++ b/sci-libs/asl/asl-0.1.5.ebuild
@@ -1 +1,48 @@
-asl-9999.ebuild
-\ No newline at end of file
+# 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
index 28324bd7a..4b9d2eaf7 120000..100644
--- a/sci-libs/blas-reference/blas-reference-20131116-r1.ebuild
+++ b/sci-libs/blas-reference/blas-reference-20131116-r1.ebuild
@@ -1 +1,118 @@
-blas-reference-99999999.ebuild
-\ No newline at end of file
+# 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 ${profname}.pc
+		fi
+	}
+	multibuild_foreach_variant fortran-int64_multilib_multibuild_wrapper my_src_install
+}
diff --git a/sci-libs/cblas-reference/cblas-reference-20110218-r1.ebuild b/sci-libs/cblas-reference/cblas-reference-20110218-r1.ebuild
index ad42bf234..9e7e1f391 100644
--- a/sci-libs/cblas-reference/cblas-reference-20110218-r1.ebuild
+++ b/sci-libs/cblas-reference/cblas-reference-20110218-r1.ebuild
@@ -106,7 +106,7 @@ src_test() {
 		local profname=$(fortran-int64_get_profname)
 		local libname="${profname//-/_}"
 		cd testing || die
-		emake
+		default
 		emake run
 	}
 	multibuild_foreach_variant run_in_build_dir fortran-int64_multilib_multibuild_wrapper my_src_test
diff --git a/sci-libs/cblas-reference/cblas-reference-20110218.ebuild b/sci-libs/cblas-reference/cblas-reference-20110218.ebuild
index bd1ea4ae6..c2c9b6f1f 100644
--- a/sci-libs/cblas-reference/cblas-reference-20110218.ebuild
+++ b/sci-libs/cblas-reference/cblas-reference-20110218.ebuild
@@ -81,7 +81,7 @@ src_compile() {
 
 src_test() {
 	cd testing || die
-	emake
+	default
 	emake run
 }
 
diff --git a/sci-libs/cgnstools/cgnstools-2.5.4-r1.ebuild b/sci-libs/cgnstools/cgnstools-2.5.4-r1.ebuild
index 4382192d1..96c51bea4 100644
--- a/sci-libs/cgnstools/cgnstools-2.5.4-r1.ebuild
+++ b/sci-libs/cgnstools/cgnstools-2.5.4-r1.ebuild
@@ -8,7 +8,7 @@ inherit eutils multilib versionator
 
 MY_P="${PN}-$(replace_all_version_separators '-')"
 
-DESCRIPTION="The CFD General Notation System (CGNS) tools."
+DESCRIPTION="The CFD General Notation System (CGNS) tools"
 HOMEPAGE="http://www.cgns.org/"
 SRC_URI="mirror://sourceforge/cgns/${MY_P}.tar.gz"
 
diff --git a/sci-libs/fdlibm/fdlibm-5.3.ebuild b/sci-libs/fdlibm/fdlibm-5.3.ebuild
index de3eb2cac..e63c3d11c 100644
--- a/sci-libs/fdlibm/fdlibm-5.3.ebuild
+++ b/sci-libs/fdlibm/fdlibm-5.3.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit toolchain-funcs flag-o-matic versionator multilib
 
@@ -15,9 +15,6 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="static-libs"
 
-RDEPEND=""
-DEPEND="${RDEPEND}"
-
 static_to_shared() {
 	local libstatic=${1}; shift
 	local libname=$(basename ${libstatic%.a})
@@ -36,27 +33,26 @@ static_to_shared() {
 			-Wl,--whole-archive ${libstatic} -Wl,--no-whole-archive \
 			"$@" -o ${libdir}/${soname} || die "${soname} failed"
 		[[ $(get_version_component_count) -gt 1 ]] && \
-			ln -s ${soname} ${libdir}/${libname}$(get_libname $(get_major_version))
-		ln -s ${soname} ${libdir}/${libname}$(get_libname)
+			ln -s ${soname} ${libdir}/${libname}$(get_libname $(get_major_version)) || die
+		ln -s ${soname} ${libdir}/${libname}$(get_libname) || die
 	fi
 }
 
 src_compile() {
 	append-cflags -D_IEEE_LIBM
 	emake CFLAGS="${CFLAGS} -fPIC" CC=$(tc-getCC)
-	mv libm.a lib${PN}.a
+	mv libm.a lib${PN}.a || die
 	static_to_shared lib${PN}.a
 	if use static-libs; then
-		rm -f *.o
+		rm -f *.o || die
 		emake CFLAGS="${CFLAGS}" CC=$(tc-getCC)
-		mv libm.a lib${PN}.a
+		mv libm.a lib${PN}.a || die
 	fi
 }
 
 src_install() {
 	dolib.so lib${PN}$(get_libname)*
 	use static-libs && dolib.a lib${PN}.a
-	insinto /usr/include
-	doins fdlibm.h
+	doheader fdlibm.h
 	dodoc readme
 }
diff --git a/sci-libs/fdlibm/metadata.xml b/sci-libs/fdlibm/metadata.xml
index b07eef8ab..d1e81f301 100644
--- a/sci-libs/fdlibm/metadata.xml
+++ b/sci-libs/fdlibm/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci</herd>
-<longdescription lang="en">
+  <herd>sci</herd>
+  <longdescription lang="en">
   FDLIBM (Freely Distributable LIBM) is a C math library 
   for machines that support IEEE 754 floating-point arithmetic. 
   In this release, only double precision is supported.
diff --git a/sci-libs/fgsl/Manifest b/sci-libs/fgsl/Manifest
index a255872f4..1fd6ac931 100644
--- a/sci-libs/fgsl/Manifest
+++ b/sci-libs/fgsl/Manifest
@@ -1,2 +1 @@
-DIST fgsl-0.9.3.tar.gz 293761 SHA256 ba6c7d95ea73ea81435b6960fa9dc1e6e11d2da7fa145117111352d873c71ce9 SHA512 6cba7f3b50f43d66deb27791cc5e59aaa41305797246469f48e5060693830987d7397c6b7088ae7918e9576190015d4b11ea2ffca34196becffd8a7d1a8dec2a WHIRLPOOL 4ed970f10e8b96205ff68658552dcea9c8b1b77acdbc80de31b5e46d563e28b3cfa9b4125861e913716a25cf4eb97fa2fc59fd3be148bb23ea95e691cfd7ea41
 DIST fgsl-0.9.4.tar.gz 999825 SHA256 f589283f5b9df5df9ef39b108114df2ed740109fabb8956fe98eaaac20924ba7 SHA512 45186a17d2b7e46968a29e99cbb1c7bb4cb22c14b322337e0166ee2e05e6bd63f709d6da566c30e7b350231dff268e65908e542288bdec7ca88ff1cb505eae3e WHIRLPOOL 3c6e2c1221b1e5f8aeee83b78951c2d777550401c41c416d4dd911e946b6f03fd4f2ede6df7c123f59ada9477e3c6cd05b202d2f0e8c121cedf250001610deb8
diff --git a/sci-libs/fgsl/fgsl-0.9.3.ebuild b/sci-libs/fgsl/fgsl-0.9.3.ebuild
deleted file mode 100644
index 3140d3116..000000000
--- a/sci-libs/fgsl/fgsl-0.9.3.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils fortran-2 multilib toolchain-funcs
-
-DESCRIPTION="A Fortran interface to the GNU Scientific Library"
-HOMEPAGE="http://www.lrz.de/services/software/mathematik/gsl/fortran/"
-SRC_URI="http://www.lrz.de/services/software/mathematik/gsl/fortran/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="static-libs"
-
-RDEPEND=">=sci-libs/gsl-1.14"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-#TODO: make docs
-
-FORTRAN_STANDARD=90
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-sharedlibs.patch
-	if use amd64; then
-		ln -s interface/integer_ilp64.finc integer.finc || die
-	elif use x86; then
-		ln -s interface/integer_ilp32.finc integer.finc || die
-	else
-		die "Don't know who you are"
-	fi
-
-	cat <<- EOF > "${S}/make.inc"
-		F90 = $(tc-getFC)
-		CC = $(tc-getCC)
-		GSL_LIB = $($(tc-getPKG_CONFIG) --libs gsl)
-		GSL_INC = $($(tc-getPKG_CONFIG) --cflags gsl)
-		PREFIX = /usr
-		ARFLAGS = -csrv
-		FPP = -cpp
-		LIB = $(get_libdir)
-	EOF
-
-	use static-libs && echo "STATIC_LIBS = yes" >> "${S}/make.inc"
-}
-
-src_configure() {
-	return
-}
-
-src_install() {
-	dodoc NEWS README
-	ln -s lib${PN}.so.0.0.0 lib${PN}.so.0 || die
-	ln -s lib${PN}.so.0.0.0 lib${PN}.so || die
-	dolib.so lib${PN}.so*
-	insinto /usr/include
-	doins ${PN}.mod
-	if use static-libs ; then
-		newlib.a lib${PN}_$(tc-getFC).a lib${PN}.a
-	fi
-}
diff --git a/sci-libs/fgsl/fgsl-0.9.4.ebuild b/sci-libs/fgsl/fgsl-0.9.4.ebuild
index 9f9c180a4..35d325dea 100644
--- a/sci-libs/fgsl/fgsl-0.9.4.ebuild
+++ b/sci-libs/fgsl/fgsl-0.9.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -55,9 +55,7 @@ src_install() {
 	ln -s lib${PN}.so.0.0.0 lib${PN}.so.0 || die
 	ln -s lib${PN}.so.0.0.0 lib${PN}.so || die
 	dolib.so lib${PN}.so*
-	insinto /usr/include
-	doins ${PN}.mod
-	if use static-libs ; then
+	doheader ${PN}.mod
+	use static-libs && \
 		newlib.a lib${PN}_$(tc-getFC).a lib${PN}.a
-	fi
 }
diff --git a/sci-libs/fox/fox-4.1.2-r2.ebuild b/sci-libs/fox/fox-4.1.2-r2.ebuild
index 928deff37..38b52fa63 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() {
@@ -60,10 +60,10 @@ 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"
-	dodoc README.FoX.txt || die "dodoc failed"
+	emake -j1 DESTDIR="${D}" install
+	dodoc README.FoX.txt
 	if use doc; then
 		dodoc Changelog
-		dohtml -r DoX/ || die "installing the HTML docs failed"
+		dohtml -r DoX/
 	fi
 }
diff --git a/sci-libs/framewave/framewave-1.3.1.ebuild b/sci-libs/framewave/framewave-1.3.1.ebuild
index 7a673c487..43a5bef29 100644
--- a/sci-libs/framewave/framewave-1.3.1.ebuild
+++ b/sci-libs/framewave/framewave-1.3.1.ebuild
@@ -4,6 +4,8 @@
 
 EAPI=5
 
+inherit scons-utils
+
 MY_P="FRAMEWAVE_${PV}_SRC"
 
 DESCRIPTION="A collection of popular image and signal processing routines"
@@ -31,7 +33,7 @@ src_compile() {
 	local bits="32"
 	use amd64 && bits="64"
 
-	scons \
+	escons \
 		CCFLAGS="${CFLAGS}" bitness="${bits}" variant="release" \
 		libtype="shared" ${MAKEOPTS}|| die "make failed"
 }
@@ -42,6 +44,5 @@ src_install() {
 
 	dolib.so Framewave/build/bin/release_shared_${bits}/*.so*
 
-	insinto /usr/include
-	doins Framewave/build/include/*
+	doheader Framewave/build/include/*
 }
diff --git a/sci-libs/itk/itk-4.4.2-r1.ebuild b/sci-libs/itk/itk-4.4.2-r1.ebuild
index 54c0e4189..518c455c7 100644
--- a/sci-libs/itk/itk-4.4.2-r1.ebuild
+++ b/sci-libs/itk/itk-4.4.2-r1.ebuild
@@ -129,7 +129,7 @@ src_install() {
 		rm -f *.md5 || die "Failed to remove superfluous hashes"
 		einfo "Installing API docs. This may take some time."
 		insinto "/usr/share/doc/${PF}/api-docs"
-		doins -r ./* || die "Failed to install docs"
+		doins -r ./*
 	fi
 
 	doenvd "${T}"/40${PN}
diff --git a/sci-libs/lapack-reference/lapack-reference-3.4.2.ebuild b/sci-libs/lapack-reference/lapack-reference-3.4.2.ebuild
index 0d81fdd39..e81c5a2fc 120000..100644
--- a/sci-libs/lapack-reference/lapack-reference-3.4.2.ebuild
+++ b/sci-libs/lapack-reference/lapack-reference-3.4.2.ebuild
@@ -1 +1,139 @@
-lapack-reference-9999.ebuild
-\ No newline at end of file
+# 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
index 0d81fdd39..e81c5a2fc 120000..100644
--- a/sci-libs/lapack-reference/lapack-reference-3.5.0.ebuild
+++ b/sci-libs/lapack-reference/lapack-reference-3.5.0.ebuild
@@ -1 +1,139 @@
-lapack-reference-9999.ebuild
-\ No newline at end of file
+# 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
index 19f551af7..2c53640b8 120000..100644
--- a/sci-libs/lapacke-reference/lapacke-reference-3.4.2.ebuild
+++ b/sci-libs/lapacke-reference/lapacke-reference-3.4.2.ebuild
@@ -1 +1,103 @@
-lapacke-reference-9999.ebuild
-\ No newline at end of file
+# 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
index 19f551af7..2c53640b8 120000..100644
--- a/sci-libs/lapacke-reference/lapacke-reference-3.5.0.ebuild
+++ b/sci-libs/lapacke-reference/lapacke-reference-3.5.0.ebuild
@@ -1 +1,103 @@
-lapacke-reference-9999.ebuild
-\ No newline at end of file
+# 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
index 2541d9df3..a922f6b41 120000..100644
--- a/sci-libs/libsc/libsc-1.1.ebuild
+++ b/sci-libs/libsc/libsc-1.1.ebuild
@@ -1 +1,71 @@
-libsc-1.0.ebuild
-\ No newline at end of file
+# 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/mpiblacs/mpiblacs-1.1-r1.ebuild b/sci-libs/mpiblacs/mpiblacs-1.1-r1.ebuild
index fb6f4adba..a6a4639a7 100644
--- a/sci-libs/mpiblacs/mpiblacs-1.1-r1.ebuild
+++ b/sci-libs/mpiblacs/mpiblacs-1.1-r1.ebuild
@@ -116,7 +116,7 @@ src_install() {
 		Requires: blas
 	EOF
 	insinto /usr/$(get_libdir)/pkgconfig
-	doins ${PN}.pc || die
+	doins ${PN}.pc
 	alternatives_for blacs ${PN} 0 \
 		/usr/$(get_libdir)/pkgconfig/blacs.pc ${PN}.pc
 	popd > /dev/null
diff --git a/sci-libs/omalloc/metadata.xml b/sci-libs/omalloc/metadata.xml
index 884f5b57e..198ffa14f 100644
--- a/sci-libs/omalloc/metadata.xml
+++ b/sci-libs/omalloc/metadata.xml
@@ -1,12 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci</herd>
-<maintainer>
-<email>tom111@gmx.de</email>
-<name>Thomas Kahle</name>
-</maintainer>
-<longdescription lang="en">
+	<herd>sci</herd>
+	<maintainer>
+		<email>tom111@gmx.de</email>
+		<name>Thomas Kahle</name>
+	</maintainer>
+	<longdescription lang="en">
 omalloc is the memory management of Singular
 </longdescription>
 </pkgmetadata>
diff --git a/sci-libs/omalloc/omalloc-0.9.6.ebuild b/sci-libs/omalloc/omalloc-0.9.6.ebuild
index ff067a157..b03291a06 100644
--- a/sci-libs/omalloc/omalloc-0.9.6.ebuild
+++ b/sci-libs/omalloc/omalloc-0.9.6.ebuild
@@ -18,13 +18,10 @@ SRC_URI="${SRC_COM}/Singular-3-1-1-2.tar.gz"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~ppc ~x86"
-IUSE="debug"
+IUSE=""
 
 S=${WORKDIR}/Singular-3-1-1/omalloc
 
-# Until tarballs are mirrored:
-RESTRICT="mirror"
-
 pkg_setup() {
 	tc-export CC CXX
 }
@@ -39,11 +36,5 @@ src_configure() {
 }
 
 src_test () {
-	if use debug; then
-		emake check
-	fi
-}
-
-src_install () {
-	emake DESTDIR="${D}" install
+	emake check
 }
diff --git a/sci-libs/openblas/openblas-0.2.12.ebuild b/sci-libs/openblas/openblas-0.2.12.ebuild
index 2381753b7..91736c817 120000..100644
--- a/sci-libs/openblas/openblas-0.2.12.ebuild
+++ b/sci-libs/openblas/openblas-0.2.12.ebuild
@@ -1 +1,227 @@
-openblas-9999.ebuild
-\ No newline at end of file
+# 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
index 2381753b7..91736c817 120000..100644
--- a/sci-libs/openblas/openblas-0.2.14.ebuild
+++ b/sci-libs/openblas/openblas-0.2.14.ebuild
@@ -1 +1,227 @@
-openblas-9999.ebuild
-\ No newline at end of file
+# 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/openlibm/openlibm-9999.ebuild b/sci-libs/openlibm/openlibm-9999.ebuild
index 864627b80..a088a7f69 100644
--- a/sci-libs/openlibm/openlibm-9999.ebuild
+++ b/sci-libs/openlibm/openlibm-9999.ebuild
@@ -28,7 +28,7 @@ src_compile() {
 }
 
 src_test() {
-	emake
+	default
 }
 
 src_install() {
diff --git a/sci-libs/p4est/p4est-1.1.ebuild b/sci-libs/p4est/p4est-1.1.ebuild
index 89804b22a..e686b86aa 120000..100644
--- a/sci-libs/p4est/p4est-1.1.ebuild
+++ b/sci-libs/p4est/p4est-1.1.ebuild
@@ -1 +1,99 @@
-p4est-1.0.ebuild
-\ No newline at end of file
+# 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-libs/pg2plplot/pg2plplot-0.2.0.ebuild b/sci-libs/pg2plplot/pg2plplot-0.2.0.ebuild
index ad018dd6a..1606c7558 100644
--- a/sci-libs/pg2plplot/pg2plplot-0.2.0.ebuild
+++ b/sci-libs/pg2plplot/pg2plplot-0.2.0.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit cmake-utils fortran-2
 
@@ -15,14 +15,13 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="X png postscript static-libs"
 
-DEPEND="virtual/fortran
-		sci-libs/plplot[fortran]"
+DEPEND="sci-libs/plplot[fortran]"
 
 # If USE="png" or "postscript", ensure PLplot has USE="cairo":
 RDEPEND="${DEPEND}
-		 sci-libs/plplot[fortran,X?]
-		 png? ( sci-libs/plplot[cairo] )
-		 postscript? ( sci-libs/plplot[cairo] )"
+	 sci-libs/plplot[fortran,X?]
+	 png? ( sci-libs/plplot[cairo] )
+	 postscript? ( sci-libs/plplot[cairo] )"
 
 src_configure() {
 	local mycmakeargs=(
diff --git a/sci-libs/pg2plplot/pg2plplot-0.3.1.ebuild b/sci-libs/pg2plplot/pg2plplot-0.3.1.ebuild
index 6a5cb331e..953ea72ed 100644
--- a/sci-libs/pg2plplot/pg2plplot-0.3.1.ebuild
+++ b/sci-libs/pg2plplot/pg2plplot-0.3.1.ebuild
@@ -1,9 +1,11 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
 EAPI=5
 
+FORTRAN_STANDARD=90
+
 inherit cmake-utils fortran-2
 
 DESCRIPTION="Assist the transition from PGPlot to PLplot in Fortran programs"
@@ -15,8 +17,7 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="X png postscript static-libs"
 
-DEPEND="virtual/fortran
-	sci-libs/plplot[fortran]"
+DEPEND="sci-libs/plplot[fortran]"
 
 # If USE="png" or "postscript", ensure PLplot has USE="cairo":
 RDEPEND="${DEPEND}
@@ -25,7 +26,6 @@ RDEPEND="${DEPEND}
 	postscript? ( sci-libs/plplot[cairo] )"
 
 DOCS=( CHANGELOG README VERSION )
-FORTRAN_STANDARD=90
 
 src_prepare() {
 	sed -i -e "s:/usr:${EPREFIX}/usr:g" CMake/CMakeLocations.cmake || die
diff --git a/sci-libs/spglib/spglib-1.6.0.ebuild b/sci-libs/spglib/spglib-1.6.0.ebuild
index 554e3942a..e21553a46 100644
--- a/sci-libs/spglib/spglib-1.6.0.ebuild
+++ b/sci-libs/spglib/spglib-1.6.0.ebuild
@@ -30,5 +30,5 @@ src_configure() {
 }
 
 src_compile() {
-	emake
+	default
 }
diff --git a/sci-libs/tmglib/tmglib-3.4.2.ebuild b/sci-libs/tmglib/tmglib-3.4.2.ebuild
index 9c74ec1c3..9d98070a0 100644
--- a/sci-libs/tmglib/tmglib-3.4.2.ebuild
+++ b/sci-libs/tmglib/tmglib-3.4.2.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit cmake-utils fortran-2
 
diff --git a/sci-libs/votca-tools/ChangeLog b/sci-libs/votca-tools/ChangeLog
index 3fef99a59..c5ce2378a 100644
--- a/sci-libs/votca-tools/ChangeLog
+++ b/sci-libs/votca-tools/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for sci-libs/votca-tools
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  24 Sep 2015; Christoph Junghans <ottxor@gentoo.org> votca-tools-9999.ebuild:
+  sci-libs/votca-tools: sync with gx86
+
   13 Nov 2014; Christoph Junghans <ottxor@gentoo.org> votca-tools-9999.ebuild:
   deps on boost:=
 
diff --git a/sci-libs/votca-tools/votca-tools-9999.ebuild b/sci-libs/votca-tools/votca-tools-9999.ebuild
index e724f4ef6..4dae0bfce 100644
--- a/sci-libs/votca-tools/votca-tools-9999.ebuild
+++ b/sci-libs/votca-tools/votca-tools-9999.ebuild
@@ -9,12 +9,12 @@ CMAKE_MAKEFILE_GENERATOR="ninja"
 inherit cmake-utils eutils multilib
 
 if [ "${PV}" != "9999" ]; then
-	SRC_URI="http://downloads.votca.googlecode.com/hg/${P}_pristine.tar.gz"
+	SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos"
+	S="${WORKDIR}/${P#votca-}"
 else
-	SRC_URI=""
-	inherit mercurial
-	EHG_REPO_URI="https://code.google.com/p/votca.tools/"
+	inherit git-r3
+	EGIT_REPO_URI="git://github.com/${PN/-//}.git https://github.com/${PN/-//}.git"
 	KEYWORDS=""
 fi
 
diff --git a/sci-libs/wannier90/metadata.xml b/sci-libs/wannier90/metadata.xml
index b229aec85..d369d068f 100644
--- a/sci-libs/wannier90/metadata.xml
+++ b/sci-libs/wannier90/metadata.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci</herd>
+	<herd>sci</herd>
 </pkgmetadata>
diff --git a/sci-libs/wannier90/wannier90-1.2-r3.ebuild b/sci-libs/wannier90/wannier90-1.2-r3.ebuild
index c21d63907..08621ac99 100644
--- a/sci-libs/wannier90/wannier90-1.2-r3.ebuild
+++ b/sci-libs/wannier90/wannier90-1.2-r3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -13,7 +13,7 @@ SRC_URI="http://wannier.org/code/${P}.tar.gz"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="doc examples perl test"
+IUSE="doc examples perl static-libs test"
 
 RDEPEND="
 	virtual/blas
@@ -52,7 +52,7 @@ src_compile() {
 
 src_test() {
 	einfo "Compare the 'Standard' and 'Current' outputs of this test."
-	pushd tests
+	cd tests
 	emake test
 	cat wantest.log
 }
@@ -60,9 +60,8 @@ src_test() {
 src_install() {
 	dobin wannier90.x
 	use perl && dobin utility/kmesh.pl
-	dolib.a libwannier.a
-	insinto /usr/include
-	doins src/*.mod
+	use static-libs && dolib.a libwannier.a
+	doheader src/*.mod
 	if use examples; then
 		insinto /usr/share/${PN}
 		doins -r examples
diff --git a/sci-libs/wannier90/wannier90-2.0.0.ebuild b/sci-libs/wannier90/wannier90-2.0.0.ebuild
index 6d6cff0c4..66fde81ec 100644
--- a/sci-libs/wannier90/wannier90-2.0.0.ebuild
+++ b/sci-libs/wannier90/wannier90-2.0.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -13,7 +13,7 @@ SRC_URI="http://wannier.org/code/${P}.tar.gz"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="doc examples perl test"
+IUSE="doc examples perl static-libs test"
 
 RDEPEND="
 	virtual/blas
@@ -45,7 +45,7 @@ src_compile() {
 
 src_test() {
 	einfo "Compare the 'Standard' and 'Current' outputs of this test."
-	pushd tests
+	cd tests
 	emake test
 	cat wantest.log
 }
@@ -53,9 +53,8 @@ src_test() {
 src_install() {
 	dobin wannier90.x
 	use perl && dobin utility/kmesh.pl
-	dolib.a libwannier.a
-	insinto /usr/include
-	doins src/obj/*.mod
+	use static-libs && dolib.a libwannier.a
+	doheader src/obj/*.mod
 	if use examples; then
 		insinto /usr/share/${PN}
 		doins -r examples
diff --git a/sci-libs/wannier90/wannier90-2.0.1.ebuild b/sci-libs/wannier90/wannier90-2.0.1.ebuild
index e58bf47e0..cd0e03249 100644
--- a/sci-libs/wannier90/wannier90-2.0.1.ebuild
+++ b/sci-libs/wannier90/wannier90-2.0.1.ebuild
@@ -13,7 +13,7 @@ SRC_URI="http://wannier.org/code/${P}.tar.gz"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="doc examples perl test"
+IUSE="doc examples perl static-libs test"
 
 RDEPEND="
 	virtual/blas
@@ -46,7 +46,7 @@ src_compile() {
 
 src_test() {
 	einfo "Compare the 'Standard' and 'Current' outputs of this test."
-	pushd tests
+	cd tests
 	emake test
 	cat wantest.log
 }
@@ -54,9 +54,8 @@ src_test() {
 src_install() {
 	dobin wannier90.x
 	use perl && dobin utility/kmesh.pl
-	dolib.a libwannier.a
-	insinto /usr/include
-	doins src/obj/*.mod
+	use static-libs && dolib.a libwannier.a
+	doheader src/obj/*.mod
 	if use examples; then
 		insinto /usr/share/${PN}
 		doins -r examples
diff --git a/sci-mathematics/aribas/aribas-1.63.ebuild b/sci-mathematics/aribas/aribas-1.63.ebuild
index 1a4dc489f..337c70399 100644
--- a/sci-mathematics/aribas/aribas-1.63.ebuild
+++ b/sci-mathematics/aribas/aribas-1.63.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit elisp-common versionator
 
@@ -15,8 +15,8 @@ SLOT="0"
 KEYWORDS="~x86"
 IUSE="doc emacs examples"
 
-DEPEND="emacs? ( virtual/emacs )"
-RDEPEND="${DEPEND}"
+RDEPEND="emacs? ( virtual/emacs )"
+DEPEND="${RDEPEND}"
 
 SITEFILE=64${PN}-gentoo.el
 CH_PV=$(delete_all_version_separators)
@@ -24,8 +24,8 @@ CH_PV=$(delete_all_version_separators)
 src_prepare() {
 	# Linux x86 assembly piece
 	if use x86; then
-		mv LINUX/arito386.S .
-		mv LINUX/Makefile.linux Makefile
+		mv LINUX/arito386.S . || die
+		mv LINUX/Makefile.linux Makefile || die
 	fi
 
 	# removing strip
@@ -33,7 +33,7 @@ src_prepare() {
 }
 
 src_compile() {
-	cd src
+	cd src || die
 	if use x86; then
 		emake CFLAGS="-DLiNUX -DPROTO ${CFLAGS}"
 	else
@@ -41,8 +41,8 @@ src_compile() {
 	fi
 
 	if use emacs; then
-		cd EL
-		elisp-compile *.el || die "elisp-compile failed"
+		cd EL || doe
+		elisp-compile *.el
 	fi
 }
 
@@ -61,8 +61,8 @@ src_install() {
 	fi
 
 	if use emacs; then
-		cd src/EL
-		elisp-install ${PN} *.el *.elc die "elisp-install failed"
+		cd src/EL || die
+		elisp-install ${PN} *.el *.elc
 		elisp-site-file-install "${FILESDIR}"/${SITEFILE}
 		newdoc EL/README README.emacs
 	fi
diff --git a/sci-mathematics/cadabra/cadabra-1.39.ebuild b/sci-mathematics/cadabra/cadabra-1.39.ebuild
index ce3603b33..0e19badf1 100644
--- a/sci-mathematics/cadabra/cadabra-1.39.ebuild
+++ b/sci-mathematics/cadabra/cadabra-1.39.ebuild
@@ -51,7 +51,7 @@ src_compile() {
 
 	if use doc; then
 		cd "${S}/doc" || die
-		emake
+		default
 		cd doxygen/latex || die
 		emake pdf
 	fi
diff --git a/sci-mathematics/htk/htk-3.4.1.ebuild b/sci-mathematics/htk/htk-3.4.1.ebuild
index 99d9adcdd..650f0ce14 100644
--- a/sci-mathematics/htk/htk-3.4.1.ebuild
+++ b/sci-mathematics/htk/htk-3.4.1.ebuild
@@ -1,40 +1,38 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI="4"
+EAPI=5
 
 inherit eutils
 
 DESCRIPTION="Toolkit for building and manipulating hidden Markov models"
 HOMEPAGE="http://htk.eng.cam.ac.uk/"
-SRC_URI="http://htk.eng.cam.ac.uk/ftp/software/HTK-3.4.1.tar.gz -> HTK-3.4.1.tar.gz
-	hdecode? ( http://htk.eng.cam.ac.uk/ftp/software/hdecode/HDecode-3.4.1.tar.gz
-		-> HDecode-3.4.1.tar.gz )"
+SRC_URI="
+	http://htk.eng.cam.ac.uk/ftp/software/HTK-3.4.1.tar.gz -> HTK-3.4.1.tar.gz
+	hdecode? (
+		http://htk.eng.cam.ac.uk/ftp/software/hdecode/HDecode-3.4.1.tar.gz -> HDecode-3.4.1.tar.gz
+	)"
 HDECODE_HOME="http://htk.eng.cam.ac.uk/extensions/index.shtml"
 
-LICENSE="HTKCambridge
-	hdecode? ( HDecodeCambridge )"
+LICENSE="HTKCambridge hdecode? ( HDecodeCambridge )"
 SLOT="0"
 KEYWORDS="~amd64"
 IUSE="-hlmtools -hslab -htkbook -hdecode"
 
-DEPEND=""
-RDEPEND="${DEPEND}"
-
 RESTRICT="fetch"
 
-S=""${WORKDIR}/${PN}""
+S="${WORKDIR}/${PN}"
 
 pkg_nofetch() {
-	einfo "Please download"
-	einfo "  - HTK-3.4.1.tar.gz"
-	einfo "from ${HOMEPAGE}"
+	elog "Please download"
+	elog "  - HTK-3.4.1.tar.gz"
+	elog "from ${HOMEPAGE}"
 	if use hdecode; then
-		einfo "  - HDecode-3.4.1.tar.gz"
-		einfo "from ${HDECODE_HOME}"
+		elog "  - HDecode-3.4.1.tar.gz"
+		elog "from ${HDECODE_HOME}"
 	fi
-	einfo "and place them in ${DISTDIR}"
+	elog "and place them in ${DISTDIR}"
 }
 
 src_prepare() {
@@ -42,7 +40,8 @@ src_prepare() {
 }
 
 src_configure() {
-	econf $(use_enable hlmtools) \
+	econf \
+		$(use_enable hlmtools) \
 		$(use_enable hslab) \
 		$(use_enable htkbook) \
 		$(use_enable hdecode)
@@ -50,12 +49,8 @@ src_configure() {
 
 src_compile() {
 	if use hlmtools || use hdecode; then
-		emake -j1 || die "Cannot compile"
+		emake -j1
 	else
-		emake
+		default
 	fi
 }
-
-src_install() {
-	emake DESTDIR="${D}" install
-}
diff --git a/sci-mathematics/htk/metadata.xml b/sci-mathematics/htk/metadata.xml
index f1118955f..8cf13cc05 100644
--- a/sci-mathematics/htk/metadata.xml
+++ b/sci-mathematics/htk/metadata.xml
@@ -7,7 +7,7 @@
 		<name>Pedro Batista</name>
 	</maintainer>
 	<longdescription>The Hidden Markov Model Toolkit (HTK) is a portable toolkit for building and manipulating hidden Markov models</longdescription>
-		<use>
+	<use>
 		<flag name="hlmtools">Install the tools for manipulation of language models</flag>
 		<flag name="hdecode">Install HDecode, a large vocabulary word recogniser</flag>
 		<flag name="htkbook">Build the HTK documentation (HTK Book)</flag>
diff --git a/sci-mathematics/kash-bin/kash-bin-3.ebuild b/sci-mathematics/kash-bin/kash-bin-3.ebuild
index fe9b686db..7bbd92cc6 100644
--- a/sci-mathematics/kash-bin/kash-bin-3.ebuild
+++ b/sci-mathematics/kash-bin/kash-bin-3.ebuild
@@ -1,29 +1,22 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 # inherit eutils
 
 DESCRIPTION="software package for algebraic number theory"
-
-# Homepage, not used by Portage directly but handy for developer reference
 HOMEPAGE="http://page.math.tu-berlin.de/~kant/kash.html"
-
-# Point to any required sources; these will be automatically downloaded by
-# Portage.
-SRC_URI="ftp://ftp.math.tu-berlin.de/pub/algebra/Kant/Kash_3/KASH3-Linux-i686-2008-07-31.tar.bz2
-ftp://ftp.math.tu-berlin.de/pub/algebra/Kant/Kash_3/KASH3-lib-archindep-2008-07-31.tar.bz2"
+SRC_URI="
+	ftp://ftp.math.tu-berlin.de/pub/algebra/Kant/Kash_3/KASH3-Linux-i686-2008-07-31.tar.bz2
+	ftp://ftp.math.tu-berlin.de/pub/algebra/Kant/Kash_3/KASH3-lib-archindep-2008-07-31.tar.bz2"
 
 LICENSE="kash"
 SLOT="0"
 KEYWORDS="~x86 ~amd64 ~x86-linux ~amd64-linux"
 IUSE=""
 
-DEPEND=""
-RDEPEND=""
-
 MY_P="kash3"
 S="${WORKDIR}/${MY_P}"
 
@@ -31,8 +24,8 @@ S="${WORKDIR}/${MY_P}"
 QA_PREBUILT="opt/${MY_P}/kash3"
 
 src_unpack() {
-	unpack ${A}
-	mkdir "${S}"
+	default
+	mkdir "${S}" && cd "${S}" || die
 	mv KASH3-Linux*/* "${S}" || die
 	mv KASH3-lib*/lib/* "${S}/lib/" || die
 }
@@ -43,12 +36,12 @@ src_unpack() {
 # src_compile() { : }
 #
 src_install() {
-	cat > kash3.sh <<EOF
-#/bin/sh
-/opt/${MY_P}/kash3 -l ${EROOT}opt/${MY_P}/lib
-EOF
+	cat > kash3.sh <<- EOF
+	#!"${EPREFIX}/bin/sh"
+	/opt/${MY_P}/kash3 -l "${EROOT}opt/${MY_P}/lib"
+	EOF
 	chmod 755 kash3.sh
 	dodir /opt/${MY_P}
-	cp -R "${S}/" "${D}"opt/ || die
+	cp -R "${S}/" "${ED}"opt/ || die
 	dosym ../${MY_P}/kash3.sh /opt/bin/kash3
 }
diff --git a/sci-mathematics/kash-bin/metadata.xml b/sci-mathematics/kash-bin/metadata.xml
index 1fab0f287..bd6b678dd 100644
--- a/sci-mathematics/kash-bin/metadata.xml
+++ b/sci-mathematics/kash-bin/metadata.xml
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-mathematics</herd>
-<maintainer>
-  <email>tomka@gentoo.org</email>
-</maintainer>
-<longdescription>
+  <herd>sci-mathematics</herd>
+  <maintainer>
+    <email>tomka@gentoo.org</email>
+  </maintainer>
+  <longdescription>
 KANT is a computer algebra system for sophisticated computations in algebraic
 number fields that has been developed under the project leadership of
 Prof. Dr. M. E. Pohst at Technische Universität Berlin.
diff --git a/sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild b/sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild
index 10e83c7e8..edbb9a990 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"
+	default
 }
 
 src_install() {
diff --git a/sci-mathematics/pff/pff-8.4.ebuild b/sci-mathematics/pff/pff-8.4.ebuild
index 2c221adfd..d6c235a42 100644
--- a/sci-mathematics/pff/pff-8.4.ebuild
+++ b/sci-mathematics/pff/pff-8.4.ebuild
@@ -25,7 +25,7 @@ src_prepare() {
 }
 
 src_compile(){
-	emake
+	default
 }
 
 src_install(){
diff --git a/sci-mathematics/scilab/scilab-5.5.2-r1.ebuild b/sci-mathematics/scilab/scilab-5.5.2-r1.ebuild
index 432ffdd9a..fabaeb04c 100644
--- a/sci-mathematics/scilab/scilab-5.5.2-r1.ebuild
+++ b/sci-mathematics/scilab/scilab-5.5.2-r1.ebuild
@@ -232,7 +232,7 @@ src_configure() {
 
 src_compile() {
 	addpredict /proc/mtrr
-	emake
+	default
 	pax-mark m .libs/scilab-bin
 	use doc && emake doc
 }
diff --git a/sci-mathematics/why3/why3-0.83.ebuild b/sci-mathematics/why3/why3-0.83.ebuild
index 7ff28271f..b07bcc30e 100644
--- a/sci-mathematics/why3/why3-0.83.ebuild
+++ b/sci-mathematics/why3/why3-0.83.ebuild
@@ -40,7 +40,7 @@ src_configure() {
 src_compile() {
 	MAKEOPTS+=" -j1"
 
-	emake
+	default
 	if use doc; then
 		emake doc/manual.pdf
 	fi
diff --git a/sci-mathematics/yorick/yorick-2.1.06.ebuild b/sci-mathematics/yorick/yorick-2.1.06.ebuild
index 0ba5b87ea..e0020b1fb 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-misc/foma/foma-0.9.14_alpha.ebuild b/sci-misc/foma/foma-0.9.14_alpha.ebuild
index 0b62787ce..52fca31fd 100644
--- a/sci-misc/foma/foma-0.9.14_alpha.ebuild
+++ b/sci-misc/foma/foma-0.9.14_alpha.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 MY_P=${P/_alpha/alpha}
 
@@ -17,7 +17,7 @@ IUSE=""
 
 RDEPEND="
 	sys-libs/libtermcap-compat
-	sys-libs/readline"
+	sys-libs/readline:0="
 DEPEND="${RDEPEND}
 	>=sys-devel/bison-2.3
 	>=sys-devel/flex-2.5.35"
@@ -33,7 +33,7 @@ src_prepare() {
 }
 
 src_compile() {
-	emake
+	default
 	emake libfoma
 }
 
diff --git a/sci-misc/foma/foma-0.9.16_alpha.ebuild b/sci-misc/foma/foma-0.9.16_alpha.ebuild
index 3ce7a129a..37700c369 100644
--- a/sci-misc/foma/foma-0.9.16_alpha.ebuild
+++ b/sci-misc/foma/foma-0.9.16_alpha.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 MY_P=${P/_alpha/alpha}
 
@@ -17,7 +17,7 @@ IUSE=""
 
 RDEPEND="
 	sys-libs/libtermcap-compat
-	sys-libs/readline"
+	sys-libs/readline:0="
 DEPEND="${RDEPEND}
 	>=sys-devel/bison-2.3
 	>=sys-devel/flex-2.5.35"
@@ -33,7 +33,7 @@ src_prepare() {
 }
 
 src_compile() {
-	emake
+	default
 	emake libfoma
 }
 
@@ -41,7 +41,6 @@ src_install() {
 	# since install target doesn't have DESTDIR
 	dobin foma flookup cgflookup
 	dolib.so libfoma.so.${PV/_alpha/}
-	insinto /usr/include
-	doins foma.h fomalib.h fomalibconf.h
+	doheader foma.h fomalib.h fomalibconf.h
 	dodoc README README.symbols
 }
diff --git a/sci-misc/hfst/hfst-2.2.ebuild b/sci-misc/hfst/hfst-2.2.ebuild
index be590be46..90a007cc0 100644
--- a/sci-misc/hfst/hfst-2.2.ebuild
+++ b/sci-misc/hfst/hfst-2.2.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 DESCRIPTION="Helsinki Finite State Transducer API and tools"
 HOMEPAGE="http://hfst.sourceforge.net/"
diff --git a/sci-misc/hfst/hfst-3.0.2.ebuild b/sci-misc/hfst/hfst-3.0.2.ebuild
index d58aa7190..7541c764e 100644
--- a/sci-misc/hfst/hfst-3.0.2.ebuild
+++ b/sci-misc/hfst/hfst-3.0.2.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 DESCRIPTION="Helsinki Finite State Transducer API and tools"
 HOMEPAGE="http://hfst.sourceforge.net/"
diff --git a/sci-misc/hfst/hfst-3.3.12.ebuild b/sci-misc/hfst/hfst-3.3.12.ebuild
index a2945ba78..bc2f7c160 100644
--- a/sci-misc/hfst/hfst-3.3.12.ebuild
+++ b/sci-misc/hfst/hfst-3.3.12.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 DESCRIPTION="Helsinki Finite State Transducer API and tools"
 HOMEPAGE="http://hfst.sourceforge.net/"
@@ -18,7 +18,7 @@ RDEPEND="
 	sfst? ( >sci-misc/sfst-1.3 )
 	foma? ( >sci-misc/foma-0.9.13 )
 	xml? ( dev-libs/libxml2 dev-cpp/libxmlpp )
-	glib? ( dev-libs/glib )"
+	glib? ( dev-libs/glib:2 )"
 DEPEND="${RDEPEND}
 	>=sys-devel/flex-2.5.35
 	sys-devel/bison"
diff --git a/sci-misc/kaldi/kaldi-0_p20150709.ebuild b/sci-misc/kaldi/kaldi-0_p20150709.ebuild
index 0ce2b8a8d..ad8c84d36 100644
--- a/sci-misc/kaldi/kaldi-0_p20150709.ebuild
+++ b/sci-misc/kaldi/kaldi-0_p20150709.ebuild
@@ -47,7 +47,7 @@ src_configure() {
 }
 
 src_compile() {
-	emake
+	default
 	use doc && doxygen
 }
 
diff --git a/sci-misc/openfst/openfst-1.3.4.ebuild b/sci-misc/openfst/openfst-1.3.4.ebuild
index 00c5e6b26..fa1cf9fcb 100644
--- a/sci-misc/openfst/openfst-1.3.4.ebuild
+++ b/sci-misc/openfst/openfst-1.3.4.ebuild
@@ -6,7 +6,7 @@ EAPI="5"
 
 inherit eutils flag-o-matic multilib
 
-DESCRIPTION="Finite State Transducer tools by Google et al."
+DESCRIPTION="Finite State Transducer tools by Google et al"
 HOMEPAGE="http://www.openfst.org"
 SRC_URI="http://www.openfst.org/twiki/pub/FST/FstDownload/${P}.tar.gz"
 
diff --git a/sci-misc/openfst/openfst-1.4.1.ebuild b/sci-misc/openfst/openfst-1.4.1.ebuild
index bf31f4feb..499404403 100644
--- a/sci-misc/openfst/openfst-1.4.1.ebuild
+++ b/sci-misc/openfst/openfst-1.4.1.ebuild
@@ -6,7 +6,7 @@ EAPI="5"
 
 inherit eutils
 
-DESCRIPTION="Finite State Transducer tools by Google et al."
+DESCRIPTION="Finite State Transducer tools by Google et al"
 HOMEPAGE="http://www.openfst.org"
 SRC_URI="http://www.openfst.org/twiki/pub/FST/FstDownload/${P}.tar.gz"
 
diff --git a/sci-misc/opennlp-maxent/opennlp-maxent-2.4.0.ebuild b/sci-misc/opennlp-maxent/opennlp-maxent-2.4.0.ebuild
index 65364d122..8d001e296 100644
--- a/sci-misc/opennlp-maxent/opennlp-maxent-2.4.0.ebuild
+++ b/sci-misc/opennlp-maxent/opennlp-maxent-2.4.0.ebuild
@@ -11,7 +11,7 @@ inherit eutils java-pkg-2 java-ant-2
 MY_PN="maxent"
 MY_P="${MY_PN}-${PV}"
 
-DESCRIPTION="Maximum entropy model implementation for opennlp."
+DESCRIPTION="Maximum entropy model implementation for opennlp"
 HOMEPAGE="http://maxent.sf.net/"
 SRC_URI="mirror://sourceforge/maxent/${MY_P}.tgz"
 
diff --git a/sci-misc/sfst/sfst-1.4.2.ebuild b/sci-misc/sfst/sfst-1.4.2.ebuild
index 7d032c399..1215ed3e5 100644
--- a/sci-misc/sfst/sfst-1.4.2.ebuild
+++ b/sci-misc/sfst/sfst-1.4.2.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit elisp eutils
 
@@ -21,12 +21,10 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="emacs vim-syntax"
 
-DEPEND="
-	sys-libs/readline
+RDEPEND="sys-libs/readline:0="
+DEPEND="${RDEPEND}
 	sys-devel/bison
-	sys-devel/flex
-	sys-apps/sed"
-RDEPEND="sys-libs/readline"
+	sys-devel/flex"
 
 S="${WORKDIR}/${MY_PN}"
 
@@ -42,29 +40,29 @@ src_prepare() {
 		-e 's/ldconfig/true/' \
 		-e 's/$(INSTALL_LIBS)/$(INSTALL_DIR) $(DESTDIR)$(PREFIX)\/lib\n\t\0/' \
 		-i "${S}"/src/Makefile || die "sed failed"
-	cd "${S}"
+	cd "${S}" || die
 	if use emacs ; then
-		cp "${DISTDIR}/sfst.el" "${S}"
+		cp "${DISTDIR}/sfst.el" "${S}" || die
 	fi
 	if use vim-syntax ; then
-		mv "${WORKDIR}"/INSTALL "${S}"/INSTALL-vim-syntax
-		mv "${WORKDIR}"/sfst.vim "${S}"/
+		mv "${WORKDIR}"/INSTALL "${S}"/INSTALL-vim-syntax || die
+		mv "${WORKDIR}"/sfst.vim "${S}"/ || die
 	fi
 }
 
 src_compile() {
 	emake -C "${S}/src"
 	if use emacs ; then
-		cd "${S}"
+		cd "${S}" || die
 		elisp_src_compile
 	fi
 }
 
 src_install() {
-	cd "${S}/src"
+	cd "${S}/src" || die
 	# destdir works but prefix fails
 	emake DESTDIR="${D}" install maninstall libinstall
-	cd "${S}"
+	cd "${S}" || die
 	dodoc README
 	insinto /usr/share/doc/${PF}/
 	doins doc/SFST-Manual.pdf doc/SFST-Tutorial.pdf
diff --git a/sci-misc/sfst/sfst-1.4.6g.ebuild b/sci-misc/sfst/sfst-1.4.6g.ebuild
index f7798738e..c59d0cc2e 100644
--- a/sci-misc/sfst/sfst-1.4.6g.ebuild
+++ b/sci-misc/sfst/sfst-1.4.6g.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit elisp-common eutils
 
@@ -21,12 +21,12 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="emacs vim-syntax"
 
-RDEPEND="sys-libs/readline"
+RDEPEND="
+	sys-libs/readline:0=
+	emacs? ( virtual/emacs )"
 DEPEND="${RDEPEND}
 	sys-devel/bison
-	sys-devel/flex
-	sys-apps/sed
-	emacs? ( virtual/emacs )"
+	sys-devel/flex"
 
 S="${WORKDIR}/${MY_PN}"
 
@@ -42,29 +42,29 @@ src_prepare() {
 		-e 's/ldconfig/true/' \
 		-e 's/$(INSTALL_LIBS)/$(INSTALL_DIR) $(DESTDIR)$(PREFIX)\/lib\n\t\0/' \
 		-i "${S}"/src/Makefile || die "sed failed"
-	cd "${S}"
+	cd "${S}" || die
 	if use emacs ; then
-		cp "${DISTDIR}/sfst.el" "${S}"
+		cp "${DISTDIR}/sfst.el" "${S}" || die
 	fi
 	if use vim-syntax ; then
-		mv "${WORKDIR}"/INSTALL "${S}"/INSTALL-vim-syntax
-		mv "${WORKDIR}"/sfst.vim "${S}"/
+		mv "${WORKDIR}"/INSTALL "${S}"/INSTALL-vim-syntax || die
+		mv "${WORKDIR}"/sfst.vim "${S}"/ || die
 	fi
 }
 
 src_compile() {
 	emake -C "${S}/src"
 	if use emacs ; then
-		cd "${S}"
+		cd "${S}" || die
 		elisp-compile *.el || die "could not compile elisp"
 	fi
 }
 
 src_install() {
-	cd "${S}/src"
+	cd "${S}/src" || die
 	# destdir works but prefix fails
 	emake DESTDIR="${D}" install maninstall libinstall
-	cd "${S}"
+	cd "${S}" || die
 	dodoc README
 	insinto /usr/share/doc/${PF}/
 	doins doc/SFST-Manual.pdf doc/SFST-Tutorial.pdf
@@ -78,6 +78,6 @@ src_install() {
 		dodoc INSTALL-vim-syntax
 	fi
 	if use emacs ; then
-		elisp-install ${PN} *.el *.elc || die "could not install elisp"
+		elisp-install ${PN} *.el *.elc
 	fi
 }
diff --git a/sci-physics/abinit/abinit-7.10.4.ebuild b/sci-physics/abinit/abinit-7.10.4.ebuild
index 44625ff30..38ff6820a 100644
--- a/sci-physics/abinit/abinit-7.10.4.ebuild
+++ b/sci-physics/abinit/abinit-7.10.4.ebuild
@@ -351,7 +351,7 @@ src_install() {
 	#autotools-utils_src_install() expanded
 	_check_build_dir
 	pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
-	emake DESTDIR="${D}" install || die "make install failed"
+	default
 
 	use libabinit && dolib libabinit.a
 
@@ -365,7 +365,7 @@ src_install() {
 
 	# XXX: support installing them from builddir as well!!!
 	if [[ ${DOCS} ]]; then
-		dodoc "${DOCS[@]}" || die "dodoc failed"
+		dodoc "${DOCS[@]}"
 	else
 		local f
 		# same list as in PMS
diff --git a/sci-physics/abinit/abinit-7.4.2-r1.ebuild b/sci-physics/abinit/abinit-7.4.2-r1.ebuild
index 783390971..51f7ee7c7 100644
--- a/sci-physics/abinit/abinit-7.4.2-r1.ebuild
+++ b/sci-physics/abinit/abinit-7.4.2-r1.ebuild
@@ -307,7 +307,7 @@ src_install() {
 	#autotools-utils_src_install() expanded
 	_check_build_dir
 	pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
-	emake DESTDIR="${D}" install
+	default
 
 	use libabinit && dolib libabinit.a
 
diff --git a/sci-physics/abinit/abinit-7.6.4-r1.ebuild b/sci-physics/abinit/abinit-7.6.4-r1.ebuild
index ccb875ead..61ba323da 100644
--- a/sci-physics/abinit/abinit-7.6.4-r1.ebuild
+++ b/sci-physics/abinit/abinit-7.6.4-r1.ebuild
@@ -352,7 +352,7 @@ src_install() {
 	#autotools-utils_src_install() expanded
 	_check_build_dir
 	pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
-	emake DESTDIR="${D}" install
+	default
 
 	use libabinit && dolib libabinit.a
 
@@ -366,7 +366,7 @@ src_install() {
 
 	# XXX: support installing them from builddir as well!!!
 	if [[ ${DOCS} ]]; then
-		dodoc "${DOCS[@]}" || die "dodoc failed"
+		dodoc "${DOCS[@]}"
 	else
 		local f
 		# same list as in PMS
diff --git a/sci-physics/fullprof-bin/fullprof-bin-20313.04.ebuild b/sci-physics/fullprof-bin/fullprof-bin-20313.04.ebuild
index 94f0e1705..56b51a74d 100644
--- a/sci-physics/fullprof-bin/fullprof-bin-20313.04.ebuild
+++ b/sci-physics/fullprof-bin/fullprof-bin-20313.04.ebuild
@@ -57,7 +57,7 @@ src_install() {
 			Fps_Icons || die
 	fi
 
-	dodir "${BASEDIR}" || die
+	dodir "${BASEDIR}"
 	# make symlinks
 	for i in * ; do
 		[[ -x $i && ! -d $i ]] && dosym "../fullprof/${i}" /opt/bin/"${i##*/}"
diff --git a/sci-physics/geant-vmc/geant-vmc-4.2.15a.ebuild b/sci-physics/geant-vmc/geant-vmc-4.2.15a.ebuild
index f79c02ccb..c00fbca5e 100644
--- a/sci-physics/geant-vmc/geant-vmc-4.2.15a.ebuild
+++ b/sci-physics/geant-vmc/geant-vmc-4.2.15a.ebuild
@@ -34,7 +34,7 @@ src_compile() {
 	source $(ls -1 "${EROOT}"usr/share/Geant4-*/geant4make/geant4make.sh) || die
 	for d in ${dirs}; do
 		pushd ${d} > /dev/null || die
-		emake
+		default
 		if use doc; then
 			doxygen || die
 		fi
@@ -44,7 +44,7 @@ src_compile() {
 
 src_test() {
 	cd examples || die
-	emake
+	default
 	./run_suite.sh || die
 }
 
diff --git a/sci-physics/genfit/genfit-02.00.00.ebuild b/sci-physics/genfit/genfit-02.00.00.ebuild
index c4f24f2cb..a449b62bc 120000..100644
--- a/sci-physics/genfit/genfit-02.00.00.ebuild
+++ b/sci-physics/genfit/genfit-02.00.00.ebuild
@@ -1 +1,59 @@
-genfit-9999.ebuild
-\ No newline at end of file
+# 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/sci-physics/mc-tester/mc-tester-1.25.0.ebuild b/sci-physics/mc-tester/mc-tester-1.25.0.ebuild
index f19634968..78eff0e66 100644
--- a/sci-physics/mc-tester/mc-tester-1.25.0.ebuild
+++ b/sci-physics/mc-tester/mc-tester-1.25.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -38,8 +38,8 @@ src_configure() {
 }
 
 src_compile() {
-	emake
-	use doc && cd doc && emake
+	default
+	use doc && cd doc && default
 }
 
 src_install() {
diff --git a/sci-physics/mc-tester/metadata.xml b/sci-physics/mc-tester/metadata.xml
index 2edb7b2ba..d5e96a2a9 100644
--- a/sci-physics/mc-tester/metadata.xml
+++ b/sci-physics/mc-tester/metadata.xml
@@ -1,16 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-
-<herd>sci-physics</herd>
-<maintainer>
-  <email>piatlicki@gmail.com</email>
-</maintainer>
-
-<longdescription>
+  <herd>sci-physics</herd>
+  <maintainer>
+    <email>piatlicki@gmail.com</email>
+  </maintainer>
+  <longdescription>
   A universal tool for comparisons of Monte Carlo predictions in High Energy Physics
 </longdescription>
-<use>
-  <flag name="hepmc">Compile <pkg>sci-physics/hepmc</pkg> interface</flag>
-</use>
+  <use>
+    <flag name="hepmc">Compile <pkg>sci-physics/hepmc</pkg> interface</flag>
+  </use>
 </pkgmetadata>
diff --git a/sci-physics/root/metadata.xml b/sci-physics/root/metadata.xml
index 7e1dbd5bc..76b4f49ab 100644
--- a/sci-physics/root/metadata.xml
+++ b/sci-physics/root/metadata.xml
@@ -1,12 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<maintainer>
-  <email>bircoph@gentoo.org</email>
-  <name>Andrew Savchenko</name>
-</maintainer>
-<herd>sci-physics</herd>
-<longdescription lang="en">
+  <maintainer>
+    <email>bircoph@gentoo.org</email>
+    <name>Andrew Savchenko</name>
+  </maintainer>
+  <herd>sci-physics</herd>
+  <longdescription lang="en">
   ROOT Object Oriented Technologies is an object oriented data
   analysis framework written in C++ by the CERN. Widely used in
   high energy physics, but also in other data analysis applications. It
@@ -14,13 +14,13 @@
   statistics, serialization, optimization, linear algebra, graphics,
   GUI toolkit, and a complete visualization framework.
 </longdescription>
-<use>
-  <flag name="fits">Support for images and data from FITS files with <pkg>sci-libs/cfitsio</pkg></flag>
-  <flag name="geocad">Enable ROOT-CAD interface using <pkg>sci-libs/opencascade</pkg></flag>
-  <flag name="http">Enable http server support including but not limited to fastcgi support</flag>
-  <flag name="math">Build all math related libraries plugins, needs <pkg>sci-libs/gsl</pkg> </flag>
-  <flag name="pythia6">Build the interface for <pkg>sci-physics/pythia</pkg> version 6.x </flag>
-  <flag name="pythia8">Build the interface for <pkg>sci-physics/pythia</pkg> version 8.x </flag>
-  <flag name="xrootd">Build the interface for <pkg>net-libs/xrootd</pkg> </flag>
-</use>
+  <use>
+    <flag name="fits">Support for images and data from FITS files with <pkg>sci-libs/cfitsio</pkg></flag>
+    <flag name="geocad">Enable ROOT-CAD interface using <pkg>sci-libs/opencascade</pkg></flag>
+    <flag name="http">Enable http server support including but not limited to fastcgi support</flag>
+    <flag name="math">Build all math related libraries plugins, needs <pkg>sci-libs/gsl</pkg> </flag>
+    <flag name="pythia6">Build the interface for <pkg>sci-physics/pythia</pkg> version 6.x </flag>
+    <flag name="pythia8">Build the interface for <pkg>sci-physics/pythia</pkg> version 8.x </flag>
+    <flag name="xrootd">Build the interface for <pkg>net-libs/xrootd</pkg> </flag>
+  </use>
 </pkgmetadata>
diff --git a/sci-physics/root/root-9999.ebuild b/sci-physics/root/root-9999.ebuild
index 45b50dfc9..91415ffd3 100644
--- a/sci-physics/root/root-9999.ebuild
+++ b/sci-physics/root/root-9999.ebuild
@@ -398,7 +398,7 @@ cleanup_install() {
 }
 
 src_install() {
-	emake DESTDIR="${D}" install
+	default
 	dodoc README.md
 
 	echo "LDPATH=${EPREFIX%/}/usr/$(get_libdir)/root" > 99root
diff --git a/sci-physics/tauola/tauola-1.1.3.ebuild b/sci-physics/tauola/tauola-1.1.3.ebuild
index 28072cec2..6c115a204 100644
--- a/sci-physics/tauola/tauola-1.1.3.ebuild
+++ b/sci-physics/tauola/tauola-1.1.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -47,12 +47,12 @@ src_configure() {
 }
 
 src_compile() {
-	emake
+	default
 	if use doc; then
 		cd "${S}/documentation/doxy_documentation" || die
-		emake
+		default
 		cd "${S}/documentation/latex_documentation" || die
-		emake
+		default
 	fi
 }
 
diff --git a/sci-physics/tauola/tauola-1.1.4.ebuild b/sci-physics/tauola/tauola-1.1.4.ebuild
index c7ad81add..67a62f334 100644
--- a/sci-physics/tauola/tauola-1.1.4.ebuild
+++ b/sci-physics/tauola/tauola-1.1.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -50,9 +50,9 @@ src_compile() {
 	emake -j1
 	if use doc; then
 		cd "${S}/documentation/doxy_documentation" || die
-		emake
+		default
 		cd "${S}/documentation/latex_documentation" || die
-		emake
+		default
 	fi
 }
 
diff --git a/sci-physics/tauola/tauola-1.1.5.ebuild b/sci-physics/tauola/tauola-1.1.5.ebuild
index b3245ba91..48a249100 100644
--- a/sci-physics/tauola/tauola-1.1.5.ebuild
+++ b/sci-physics/tauola/tauola-1.1.5.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -51,9 +51,9 @@ src_compile() {
 	emake -j1
 	if use doc; then
 		cd "${S}/documentation/doxy_documentation" || die
-		emake
+		default
 		cd "${S}/documentation/latex_documentation" || die
-		emake
+		default
 	fi
 }
 
diff --git a/sci-physics/tauola/tauola-9999.ebuild b/sci-physics/tauola/tauola-9999.ebuild
index a10c121ab..4785126b3 100644
--- a/sci-physics/tauola/tauola-9999.ebuild
+++ b/sci-physics/tauola/tauola-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -55,9 +55,9 @@ src_compile() {
 	emake -j1
 	if use doc; then
 		cd "${S}/documentation/doxy_documentation" || die
-		emake
+		default
 		cd "${S}/documentation/latex_documentation" || die
-		emake
+		default
 	fi
 }
 
diff --git a/sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild b/sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild
index ea423fb13..9c63fe4e6 100644
--- a/sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild
+++ b/sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild
@@ -154,7 +154,7 @@ src_compile() {
 }
 
 src_install () {
-	emake DESTDIR="${D}" install
+	default
 
 	dodoc BUGS ChangeLog NEWS PGPKEYS PORTING README*
 	newdoc term/PostScript/README README-ps
diff --git a/sci-visualization/gnuplot/gnuplot-5.1.9999.ebuild b/sci-visualization/gnuplot/gnuplot-5.1.9999.ebuild
index 3d974274a..d7c805a6b 100644
--- a/sci-visualization/gnuplot/gnuplot-5.1.9999.ebuild
+++ b/sci-visualization/gnuplot/gnuplot-5.1.9999.ebuild
@@ -157,7 +157,7 @@ src_compile() {
 }
 
 src_install () {
-	emake DESTDIR="${D}" install
+	default
 
 	dodoc BUGS ChangeLog NEWS PGPKEYS PORTING README*
 	newdoc term/PostScript/README README-ps
diff --git a/sci-visualization/gnuplot/metadata.xml b/sci-visualization/gnuplot/metadata.xml
index cccec8e78..8178349a8 100644
--- a/sci-visualization/gnuplot/metadata.xml
+++ b/sci-visualization/gnuplot/metadata.xml
@@ -16,11 +16,11 @@
   three-dimensional plots in many different formats. It is designed
   primarily for the visual display of scientific data.
 </longdescription>
-<use>
-	<flag name="compat">Enable backwards compatibility with version 4 syntax</flag>
+  <use>
+    <flag name="compat">Enable backwards compatibility with version 4 syntax</flag>
     <flag name="gd">Add support for <pkg>media-libs/gd</pkg>.
     Needed for GIF, JPEG, and PNG image output.</flag>
-<flag name="libcerf">Enable special functions from <pkg>sci-libs/libcerf</pkg></flag>
+    <flag name="libcerf">Enable special functions from <pkg>sci-libs/libcerf</pkg></flag>
     <flag name="bitmap">Enable dot-matrix printers and pbm terminal</flag>
   </use>
   <upstream>
diff --git a/sci-visualization/nodemon/metadata.xml b/sci-visualization/nodemon/metadata.xml
index 7ea4d9797..317855c68 100644
--- a/sci-visualization/nodemon/metadata.xml
+++ b/sci-visualization/nodemon/metadata.xml
@@ -1,17 +1,17 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci</herd>
-<maintainer>
-<email>bryan.d.green@nasa.gov</email>
-<name>Bryan Green</name>
-</maintainer>
-<longdescription>
+	<herd>sci</herd>
+	<maintainer>
+		<email>bryan.d.green@nasa.gov</email>
+		<name>Bryan Green</name>
+	</maintainer>
+	<longdescription>
 NodeMon is a distributed visualization tool for monitoring system resource
 utilization.  It is primarily intended for clusters and large-scale NUMA
 systems.
 </longdescription>
-<use>
-<flag name="pbs">Enable support for the Portable Batch System.</flag>
-</use>
+	<use>
+		<flag name="pbs">Enable support for the Portable Batch System.</flag>
+	</use>
 </pkgmetadata>
diff --git a/sci-visualization/nodemon/nodemon-0.3.5.ebuild b/sci-visualization/nodemon/nodemon-0.3.5.ebuild
index 61adb3879..7c2f56030 100644
--- a/sci-visualization/nodemon/nodemon-0.3.5.ebuild
+++ b/sci-visualization/nodemon/nodemon-0.3.5.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI="4"
+EAPI=5
 
-DESCRIPTION="Distributed visualization tool for monitoring system resource utilization."
+DESCRIPTION="Distributed visualization tool for monitoring system resource utilization"
 HOMEPAGE="http://nodemon.sourceforge.net/"
 SRC_URI="http://downloads.sourceforge.net/nodemon/nodemon-${PV}.tar.gz"
 
@@ -15,7 +15,10 @@ IUSE="gtk pbs"
 
 RDEPEND="
 	>=dev-cpp/growler-arch-0.3.7.1
-	gtk? ( >=x11-libs/gtkglext-1.0 x11-libs/gtk+:2 )"
+	gtk? (
+		>=x11-libs/gtkglext-1.0
+		x11-libs/gtk+:2
+	)"
 DEPEND="${RDEPEND}"
 
 DOCS="README NEWS AUTHORS NOSA ChangeLog"
diff --git a/sci-visualization/v_sim/v_sim-3.6.0.ebuild b/sci-visualization/v_sim/v_sim-3.6.0.ebuild
index 95198f36a..0ad1fb5ea 100644
--- a/sci-visualization/v_sim/v_sim-3.6.0.ebuild
+++ b/sci-visualization/v_sim/v_sim-3.6.0.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI="4"
+EAPI=5
 
 inherit eutils multilib
 
@@ -23,12 +23,11 @@ RDEPEND="
 	x11-libs/gtk+:2
 	dev-libs/glib:2
 	x11-libs/pango
-	media-libs/libpng
+	media-libs/libpng:0=
 	virtual/opengl"
 DEPEND="${RDEPEND}
 	abinit? ( sci-physics/abinit sci-libs/etsf_io )
 	blas? ( virtual/blas )
-	sys-apps/sed
 	netcdf? ( sci-libs/netcdf )
 	openbabel? ( sci-chemistry/openbabel )
 	doc?  ( >=dev-util/gtk-doc-1.4-r1 )"
@@ -47,7 +46,7 @@ src_prepare() {
 
 src_configure() {
 	if use doc ; then
-		gtkdocize
+		gtkdocize || die
 	fi
 	local MY_CONF="--without-etsf-io"
 	use abinit && MY_CONF="--with-etsf-io=/usr --with-etsf-io-include=/usr/lib/finclude --with-etsf-io-libdir=/usr/$(get_libdir)"
@@ -65,10 +64,6 @@ src_compile() {
 	HOME="${S}" emake
 }
 
-src_install() {
-	emake DESTDIR="${D}" install
-}
-
 pkg_postinst() {
 	einfo "Example files are in /usr/share/doc/${PF}/examples"
 	einfo "(even with USE='-doc')"
diff --git a/sys-cluster/blcr/blcr-0.8.4.ebuild b/sys-cluster/blcr/blcr-0.8.4.ebuild
index feaff9b96..8145dd015 100644
--- a/sys-cluster/blcr/blcr-0.8.4.ebuild
+++ b/sys-cluster/blcr/blcr-0.8.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -41,13 +41,13 @@ pkg_setup() {
 src_install() {
 	dodoc README NEWS
 	cd "${S}"/util || die
-	emake DESTDIR="${D}" install
+	default
 	cd "${S}"/libcr || die
-	emake DESTDIR="${D}" install
+	default
 	cd "${S}"/man || die
-	emake DESTDIR="${D}" install
+	default
 	cd "${S}"/include || die
-	emake DESTDIR="${D}" install
+	default
 	linux-mod_src_install
 }
 
diff --git a/sys-cluster/hpl/hpl-2.0-r1.ebuild b/sys-cluster/hpl/hpl-2.0-r1.ebuild
index 1f381dd34..06f6f4c32 100644
--- a/sys-cluster/hpl/hpl-2.0-r1.ebuild
+++ b/sys-cluster/hpl/hpl-2.0-r1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit eutils mpi toolchain-funcs
 
diff --git a/sys-cluster/hpx/hpx-9999.ebuild b/sys-cluster/hpx/hpx-9999.ebuild
index 5b883f4ec..cdff1c638 100644
--- a/sys-cluster/hpx/hpx-9999.ebuild
+++ b/sys-cluster/hpx/hpx-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -41,7 +41,7 @@ RDEPEND="
 DEPEND="${RDEPEND}
 	app-arch/p7zip
 	virtual/pkgconfig
-	test? ( dev-lang/python )
+	test? ( ${PYTHON_DEPS} )
 	doc? ( >=dev-libs/boost-1.56.0-r1[tools] )
 "
 REQUIRED_USE="test? ( ${PYTHON_REQUIRED_USE} )"
diff --git a/sys-cluster/hpx/metadata.xml b/sys-cluster/hpx/metadata.xml
index ea01f2ff7..a0669011b 100644
--- a/sys-cluster/hpx/metadata.xml
+++ b/sys-cluster/hpx/metadata.xml
@@ -1,8 +1,8 @@
-<?xml version='1.0' encoding='UTF-8'?>
+<?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>cluster</herd>
-<longdescription>
+  <herd>cluster</herd>
+  <longdescription>
   HPX (High Performance ParalleX) is a general C++ runtime system
   for parallel and distributed applications of any scale. It is the
   first freely available, open source, feature-complete, modular,
@@ -11,15 +11,15 @@
   currently, Linux based systems, such as SMP nodes and conventional
   clusters.
 </longdescription>
-<maintainer>
-  <email>gentryx@gmx.de</email>
-</maintainer>
-<use>
-  <flag name="jemalloc">Use <pkg>dev-libs/jemalloc</pkg> for memory allocation</flag>
-  <flag name="perftools">Use <pkg>dev-util/google-perftools</pkg> for
+  <maintainer>
+    <email>gentryx@gmx.de</email>
+  </maintainer>
+  <use>
+    <flag name="jemalloc">Use <pkg>dev-libs/jemalloc</pkg> for memory allocation</flag>
+    <flag name="perftools">Use <pkg>dev-util/google-perftools</pkg> for
   memory allocation</flag>
-  <flag name="tbb">Use <pkg>dev-cpp/tbb</pkg> for memory
+    <flag name="tbb">Use <pkg>dev-cpp/tbb</pkg> for memory
   allocation</flag>
-  <flag name="papi">Use <pkg>dev-libs/papi</pkg> for NaCl</flag>
-</use>
+    <flag name="papi">Use <pkg>dev-libs/papi</pkg> for NaCl</flag>
+  </use>
 </pkgmetadata>
diff --git a/sys-cluster/modules/modules-3.2.10.ebuild b/sys-cluster/modules/modules-3.2.10.ebuild
index 962b92887..b8845e765 100644
--- a/sys-cluster/modules/modules-3.2.10.ebuild
+++ b/sys-cluster/modules/modules-3.2.10.ebuild
@@ -6,7 +6,7 @@ EAPI=5
 
 inherit autotools-utils
 
-DESCRIPTION="Dynamic modification of a user's environment via modulefiles."
+DESCRIPTION="Dynamic modification of a user's environment via modulefiles"
 HOMEPAGE="http://modules.sourceforge.net/"
 SRC_URI="http://sourceforge.net/projects/modules/files/Modules/${P%[a-z]}/${P}.tar.bz2/download -> ${P}.tar.bz2"
 
diff --git a/sys-cluster/modules/modules-3.2.9c-r1.ebuild b/sys-cluster/modules/modules-3.2.9c-r1.ebuild
index 962b92887..b8845e765 100644
--- a/sys-cluster/modules/modules-3.2.9c-r1.ebuild
+++ b/sys-cluster/modules/modules-3.2.9c-r1.ebuild
@@ -6,7 +6,7 @@ EAPI=5
 
 inherit autotools-utils
 
-DESCRIPTION="Dynamic modification of a user's environment via modulefiles."
+DESCRIPTION="Dynamic modification of a user's environment via modulefiles"
 HOMEPAGE="http://modules.sourceforge.net/"
 SRC_URI="http://sourceforge.net/projects/modules/files/Modules/${P%[a-z]}/${P}.tar.bz2/download -> ${P}.tar.bz2"
 
diff --git a/sys-cluster/modules/modules-3.2.9c.ebuild b/sys-cluster/modules/modules-3.2.9c.ebuild
index 51640189b..a9a4edada 100644
--- a/sys-cluster/modules/modules-3.2.9c.ebuild
+++ b/sys-cluster/modules/modules-3.2.9c.ebuild
@@ -6,7 +6,7 @@ EAPI=5
 
 inherit autotools-utils
 
-DESCRIPTION="Dynamic modification of a user's environment via modulefiles."
+DESCRIPTION="Dynamic modification of a user's environment via modulefiles"
 HOMEPAGE="http://modules.sourceforge.net/"
 SRC_URI="http://sourceforge.net/projects/modules/files/Modules/${P%[a-z]}/${P}.tar.bz2/download -> ${P}.tar.bz2"
 
diff --git a/sys-cluster/nullmpi/nullmpi-0.7.ebuild b/sys-cluster/nullmpi/nullmpi-0.7.ebuild
index 66ca56078..4bd72036f 100644
--- a/sys-cluster/nullmpi/nullmpi-0.7.ebuild
+++ b/sys-cluster/nullmpi/nullmpi-0.7.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit autotools-utils
 
diff --git a/sys-cluster/openmpi/ChangeLog b/sys-cluster/openmpi/ChangeLog
index 2f2ca0155..689380265 100644
--- a/sys-cluster/openmpi/ChangeLog
+++ b/sys-cluster/openmpi/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+*openmpi-1.10.0 (23 Sep 2015)
+
+  23 Sep 2015; Justin Bronder <jsbronder@gentoo.org> +openmpi-1.10.0.ebuild:
+  sys-cluster/openmpi: bump 1.10.0  bug 561226
+
 *openmpi-1.8.8-r1 (06 Aug 2015)
 
   06 Aug 2015; Justin Bronder <jsbronder@gentoo.org> +openmpi-1.8.8-r1.ebuild,
diff --git a/sys-cluster/openmpi/Manifest b/sys-cluster/openmpi/Manifest
index 77ba3dbf3..216d99b8b 100644
--- a/sys-cluster/openmpi/Manifest
+++ b/sys-cluster/openmpi/Manifest
@@ -1,3 +1,4 @@
+DIST openmpi-1.10.0.tar.bz2 13207009 SHA256 26b432ce8dcbad250a9787402f2c999ecb6c25695b00c9c6ee05a306c78b6490 SHA512 62966f1e8aca162040659d4f774f17b686a19a6eecd272d345eb882a88fcfe00e768316b047bfb6b1653b3d947e355266b702eba5cf0e783f799835d384a4823 WHIRLPOOL fa60102708c10c9dd07ed8d912b7f54be79246db0c6d20774c466cf749eb2b088da8a187be0a6be38fa0eb528314b0a1210ea77911ec09504c3e6cc4d532ac44
 DIST openmpi-1.6.5.tar.bz2 10943881 SHA256 fe37bab89b5ef234e0ac82dc798282c2ab08900bf564a1ec27239d3f1ad1fc85 SHA512 b0ede0264cd9263b8ba59ec51d17ad47b5f20d49d219ca05f7c396d608398d517b2023a46a2535fd6191160d709e4805c4de436dcfee56eda287383bd69f9652 WHIRLPOOL d0288677827c1deba17295ee1b69cd21da294ac314cc49404389b4c286384f9f2f229cae4c4fd62511e7f20abc510998642d6a2edfac3f16f83078f474f8e735
 DIST openmpi-1.7.3.tar.bz2 12479769 SHA256 438d96c178dbf5a1bc92fa1d238a8225d87b64af26ce2a07789faaf312117e45 SHA512 a66d3b1df2a7dc76df4ffa0083919cefb0e7d4133f80bfd5c1c4bf6c5254f2a4773e3c4c9069c39b1467057c406eba3ea892d4a86030b0bd8097d12073af8ef8 WHIRLPOOL 5509f48370f5a00fee68048df5d84824fa63e528df617fc9209840f3077c2c868dbf2c3da964334e7a80c428056a5e2f9a39ddcda9967350e68222444ca918f0
 DIST openmpi-1.8.4.tar.bz2 13488749 SHA256 23158d916e92c80e2924016b746a93913ba7fae9fff51bf68d5c2a0ae39a2f8a SHA512 d4c8ce2bd3359cf2e85958b58ba18b52c9cef6676718eb3d948309b164b2f54544f8f8419ef6881c7a51ba268a876cd56e9b2d340a106a16fa25fb9fc3e4eff9 WHIRLPOOL 793f64ad44c2e3451a269bcb53d747d15a01649978d80f13599596e1bdd6a6011b50fdd60222bbe3a4ebe567a4785b2660e3c1eb09bdba77420581a0062480a2
diff --git a/sys-cluster/openmpi/openmpi-1.10.0.ebuild b/sys-cluster/openmpi/openmpi-1.10.0.ebuild
new file mode 100644
index 000000000..97bdb5c38
--- /dev/null
+++ b/sys-cluster/openmpi/openmpi-1.10.0.ebuild
@@ -0,0 +1,180 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+FORTRAN_NEEDED=fortran
+
+inherit cuda eutils flag-o-matic fortran-2 java-pkg-opt-2 multilib mpi toolchain-funcs versionator
+
+MY_P=${P/-mpi}
+S=${WORKDIR}/${MY_P}
+
+IUSE_OPENMPI_FABRICS="
+	openmpi_fabrics_ofed
+	openmpi_fabrics_knem
+	openmpi_fabrics_psm"
+
+IUSE_OPENMPI_RM="
+	openmpi_rm_pbs
+	openmpi_rm_slurm"
+
+IUSE_OPENMPI_OFED_FEATURES="
+	openmpi_ofed_features_control-hdr-padding
+	openmpi_ofed_features_connectx-xrc
+	openmpi_ofed_features_udcm
+	openmpi_ofed_features_rdmacm
+	openmpi_ofed_features_dynamic-sl
+	openmpi_ofed_features_failover"
+
+DESCRIPTION="A high-performance message passing library (MPI)"
+HOMEPAGE="http://www.open-mpi.org"
+SRC_URI="http://www.open-mpi.org/software/ompi/v$(get_version_component_range 1-2)/downloads/${MY_P}.tar.bz2"
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux"
+IUSE="cma cuda +cxx elibc_FreeBSD fortran heterogeneous ipv6 java mpi-threads numa romio threads vt
+	${IUSE_OPENMPI_FABRICS} ${IUSE_OPENMPI_RM} ${IUSE_OPENMPI_OFED_FEATURES}"
+
+REQUIRED_USE="openmpi_rm_slurm? ( !openmpi_rm_pbs )
+	openmpi_rm_pbs? ( !openmpi_rm_slurm )
+	openmpi_fabrics_psm? ( openmpi_fabrics_ofed )
+	openmpi_ofed_features_control-hdr-padding? ( openmpi_fabrics_ofed )
+	openmpi_ofed_features_connectx-xrc? ( openmpi_fabrics_ofed )
+	openmpi_ofed_features_udcm? ( openmpi_fabrics_ofed )
+	openmpi_ofed_features_rdmacm? ( openmpi_fabrics_ofed )
+	openmpi_ofed_features_dynamic-sl? ( openmpi_fabrics_ofed )
+	openmpi_ofed_features_failover? ( openmpi_fabrics_ofed )"
+
+MPI_UNCLASSED_DEP_STR="
+	vt? (
+		!dev-libs/libotf
+		!app-text/lcdf-typetools
+	)"
+
+CDEPEND="
+	dev-libs/libevent
+	dev-libs/libltdl:0
+	>=sys-apps/hwloc-1.9.1[numa?]
+	sys-libs/zlib
+	cuda? ( dev-util/nvidia-cuda-toolkit )
+	elibc_FreeBSD? ( dev-libs/libexecinfo )
+	openmpi_fabrics_ofed? ( sys-infiniband/ofed:* )
+	openmpi_fabrics_knem? ( sys-cluster/knem )
+	openmpi_fabrics_psm? ( sys-infiniband/infinipath-psm:* )
+	openmpi_rm_pbs? ( sys-cluster/torque )
+	openmpi_rm_slurm? ( sys-cluster/slurm )
+	openmpi_ofed_features_rdmacm? ( sys-infiniband/librdmacm:* )
+	$(mpi_imp_deplist)"
+
+RDEPEND="${CDEPEND}
+	java? ( >=virtual/jre-1.6 )"
+
+DEPEND="${CDEPEND}
+	java? ( >=virtual/jdk-1.6 )"
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	java-pkg-opt-2_pkg_setup
+	MPI_ESELECT_FILE="eselect.mpi.openmpi"
+
+	if use mpi-threads; then
+		echo
+		ewarn "WARNING: use of MPI_THREAD_MULTIPLE is still disabled by"
+		ewarn "default and officially unsupported by upstream."
+		ewarn "You may stop now and set USE=-mpi-threads"
+		echo
+	fi
+
+	echo
+	elog "OpenMPI has an overwhelming count of configuration options."
+	elog "Don't forget the EXTRA_ECONF environment variable can let you"
+	elog "specify configure options if you find them necessary."
+	echo
+}
+
+src_prepare() {
+	# Necessary for scalibility, see
+	# http://www.open-mpi.org/community/lists/users/2008/09/6514.php
+	if use threads; then
+		echo 'oob_tcp_listen_mode = listen_thread' \
+			>> opal/etc/openmpi-mca-params.conf
+	fi
+}
+
+src_configure() {
+	local myconf=(
+		--sysconfdir="${EPREFIX}/etc/${PN}"
+		--enable-pretty-print-stacktrace
+		--enable-orterun-prefix-by-default
+		--with-hwloc="${EPREFIX}/usr"
+		--with-libltdl="${EPREFIX}/usr"
+		)
+
+	if use fortran; then
+		myconf+=(--enable-mpi-fortran=all)
+	else
+		myconf+=(--enable-mpi-fortran=no)
+	fi
+
+	if use java; then
+		# We must always build with the right -source and -target
+		# flags. Passing flags to javac isn't explicitly supported here
+		# but we can cheat by overriding the configure test for javac.
+		export ac_cv_path_JAVAC="$(java-pkg_get-javac) $(java-pkg_javac-args)"
+	fi
+
+	! use vt && myconf+=(--enable-contrib-no-build=vt)
+
+	econf $(mpi_econf_args) "${myconf[@]}" \
+		$(use_enable cxx mpi-cxx) \
+		$(use_with cma) \
+		$(use_with cuda cuda "${EPREFIX}"/opt/cuda) \
+		$(use_enable romio io-romio) \
+		$(use_enable heterogeneous) \
+		$(use_enable ipv6) \
+		$(use_enable java) \
+		$(use_enable java mpi-java) \
+		$(use_enable mpi-threads mpi-thread-multiple) \
+		$(use_with openmpi_fabrics_ofed verbs "${EPREFIX}"/usr) \
+		$(use_with openmpi_fabrics_knem knem "${EPREFIX}"/usr) \
+		$(use_with openmpi_fabrics_psm psm "${EPREFIX}"/usr) \
+		$(use_enable openmpi_ofed_features_control-hdr-padding openib-control-hdr-padding) \
+		$(use_enable openmpi_ofed_features_connectx-xrc openib-connectx-xrc) \
+		$(use_enable openmpi_ofed_features_rdmacm openib-rdmacm) \
+		$(use_enable openmpi_ofed_features_udcm openib-udcm) \
+		$(use_enable openmpi_ofed_features_dynamic-sl openib-dynamic-sl) \
+		$(use_enable openmpi_ofed_features_failover btl-openib-failover) \
+		$(use_with openmpi_rm_pbs tm) \
+		$(use_with openmpi_rm_slurm slurm)
+}
+
+src_install () {
+	default
+
+	# From USE=vt see #359917
+	rm "${ED}"/$(mpi_root)/usr/share/libtool &> /dev/null
+
+	# Avoid collisions with libevent
+	rm -rf "${ED}"/$(mpi_root)/usr/include/event2 &> /dev/null
+
+	# Remove la files, no static libs are installed and we have pkg-config
+	find "${ED}"/$(mpi_root)/usr/$(get_libdir)/ -type f -name '*.la' -delete
+
+	if use java; then
+		local mpi_jar="${ED}"/$(mpi_root)/usr/$(get_libdir)/mpi.jar
+		java-pkg_dojar "${mpi_jar}"
+		# We don't want to install the jar file twice
+		# so let's clean after ourselves.
+		rm "${mpi_jar}" || die
+	fi
+
+	mpi_dodoc README AUTHORS NEWS VERSION
+	mpi_imp_add_eselect
+}
+
+src_test() {
+	# Doesn't work with the default src_test as the dry run (-n) fails.
+	emake -j1 check
+}
diff --git a/sys-cluster/openmpi/openmpi-1.6.5.ebuild b/sys-cluster/openmpi/openmpi-1.6.5.ebuild
index c454e37a6..8314533d3 100644
--- a/sys-cluster/openmpi/openmpi-1.6.5.ebuild
+++ b/sys-cluster/openmpi/openmpi-1.6.5.ebuild
@@ -147,10 +147,10 @@ src_configure() {
 }
 
 src_install () {
-	emake DESTDIR="${D}" install || die "make install failed"
+	default
 	# From USE=vt see #359917
 	rm "${ED}"/$(mpi_root)/usr/share/libtool &> /dev/null
-	mpi_dodoc README AUTHORS NEWS VERSION || die
+	mpi_dodoc README AUTHORS NEWS VERSION
 	mpi_imp_add_eselect
 }
 
@@ -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
 }
diff --git a/sys-cluster/openmpi/openmpi-1.7.3.ebuild b/sys-cluster/openmpi/openmpi-1.7.3.ebuild
index b4cbb26af..61719d3f0 100644
--- a/sys-cluster/openmpi/openmpi-1.7.3.ebuild
+++ b/sys-cluster/openmpi/openmpi-1.7.3.ebuild
@@ -142,12 +142,12 @@ src_configure() {
 }
 
 src_install () {
-	emake DESTDIR="${D}" install
+	default
 	# From USE=vt see #359917
 	rm "${ED}"/$(mpi_root)/usr/share/libtool &> /dev/null
 	# Avoid collisions with libevent
 	rm -rf "${ED}"/$(mpi_root)/usr/include/event2 &> /dev/null
-	mpi_dodoc README AUTHORS NEWS VERSION || die
+	mpi_dodoc README AUTHORS NEWS VERSION
 	mpi_imp_add_eselect
 }
 
diff --git a/sys-cluster/openmpi/openmpi-1.8.4-r99.ebuild b/sys-cluster/openmpi/openmpi-1.8.4-r99.ebuild
index 996f231f7..61d021b41 100644
--- a/sys-cluster/openmpi/openmpi-1.8.4-r99.ebuild
+++ b/sys-cluster/openmpi/openmpi-1.8.4-r99.ebuild
@@ -155,7 +155,7 @@ multilib_src_configure() {
 }
 
 multilib_src_install() {
-	emake DESTDIR="${D}" install
+	default
 
 	# Remove la files, no static libs are installed and we have pkg-config
 	find "${ED}"/usr/$(get_libdir)/ -type f -name '*.la' -delete
@@ -182,7 +182,7 @@ multilib_src_install_all() {
 	# Avoid collisions with libevent
 	rm -rf "${ED}"/usr/include/event2 &> /dev/null
 
-	dodoc README AUTHORS NEWS VERSION || die
+	dodoc README AUTHORS NEWS VERSION
 }
 
 multilib_src_test() {
diff --git a/sys-cluster/openmpi/openmpi-1.8.8.ebuild b/sys-cluster/openmpi/openmpi-1.8.8.ebuild
index 97ae89495..18a734271 100644
--- a/sys-cluster/openmpi/openmpi-1.8.8.ebuild
+++ b/sys-cluster/openmpi/openmpi-1.8.8.ebuild
@@ -151,7 +151,7 @@ src_configure() {
 }
 
 src_install () {
-	emake DESTDIR="${D}" install
+	default
 
 	# From USE=vt see #359917
 	rm "${ED}"/$(mpi_root)/usr/share/libtool &> /dev/null
@@ -170,7 +170,7 @@ src_install () {
 		rm "${mpi_jar}" || die
 	fi
 
-	mpi_dodoc README AUTHORS NEWS VERSION || die
+	mpi_dodoc README AUTHORS NEWS VERSION
 	mpi_imp_add_eselect
 }
 
diff --git a/sys-cluster/ovis/ovis-3.0.1.ebuild b/sys-cluster/ovis/ovis-3.0.1.ebuild
index 26d5ed77d..a080199ab 100644
--- a/sys-cluster/ovis/ovis-3.0.1.ebuild
+++ b/sys-cluster/ovis/ovis-3.0.1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit cmake-utils eutils
 
@@ -20,9 +20,9 @@ RDEPEND="
 	>=dev-libs/boost-1.44
 	dev-libs/libevent
 	>=dev-libs/qjson-0.7.1
-	sys-libs/readline
-	>=dev-qt/qthelp-4.7.4[compat]
-	>=dev-qt/qtgui-4.7.4
+	sys-libs/readline:0=
+	>=dev-qt/qthelp-4.7.4:4=[compat]
+	>=dev-qt/qtgui-4.7.4:4=
 	avahi? ( >=net-dns/avahi-0.6.27 )"
 DEPEND="${RDEPEND}
 	avahi? ( >=net-dns/avahi-0.6.27 )"
diff --git a/sys-devel/gdebugger/gdebugger-6.2.438.ebuild b/sys-devel/gdebugger/gdebugger-6.2.438.ebuild
index f3bd758da..ac6fe767f 100644
--- a/sys-devel/gdebugger/gdebugger-6.2.438.ebuild
+++ b/sys-devel/gdebugger/gdebugger-6.2.438.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit eutils toolchain-funcs versionator
 
@@ -22,7 +22,8 @@ KEYWORDS="~amd64 ~x86"
 IUSE="examples"
 
 DEPEND=""
-RDEPEND="virtual/libstdc++
+RDEPEND="
+	virtual/libstdc++
 	dev-libs/atk
 	dev-libs/glib:2
 	media-libs/fontconfig
diff --git a/www-client/casperjs/ChangeLog b/www-client/casperjs/ChangeLog
new file mode 100644
index 000000000..eec6cb0d5
--- /dev/null
+++ b/www-client/casperjs/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for www-client/casperjs
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Id$
+
+  24 Sep 2015; Sean Vig <sean.v.775@gmail.com> casperjs-1.1_beta3.ebuild:
+  www-client/casjerjs: Fix installation of casperjs executable
+
+*casperjs-1.1_beta3 (02 Sep 2015)
+
+  02 Sep 2015; Sean Vig <sean.v.775@gmail.com> +casperjs-1.1_beta3.ebuild,
+  +metadata.xml:
+  www-client/casperjs: Initial ebuild
diff --git a/www-client/casperjs/Manifest b/www-client/casperjs/Manifest
new file mode 100644
index 000000000..d3943fbcd
--- /dev/null
+++ b/www-client/casperjs/Manifest
@@ -0,0 +1 @@
+DIST casperjs-1.1_beta3.tar.gz 652836 SHA256 bc286424fb52df6cf16cb9b8ef6534ee830bb8ab0b87d2625910d8c1824152dc SHA512 8965ff7edc2728fed6ce18f43cc82f27330134d6442ef1e91e484b472a259461f6c841cbec1c86c773a7ccf0d3cb08be68a5287a868cb88f40ef114fab92b35e WHIRLPOOL bd4e8423c2fb52d30ac381d0ec67650a63edb3df703136a9b3093804d7883fb8510af071ff2ec7071ec88b7a12942f9cdf3193cfa772ef449b1213759adead62
diff --git a/www-client/casperjs/casperjs-1.1_beta3.ebuild b/www-client/casperjs/casperjs-1.1_beta3.ebuild
new file mode 100644
index 000000000..b71ba9727
--- /dev/null
+++ b/www-client/casperjs/casperjs-1.1_beta3.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+MY_PV=${PV/_beta/-beta}
+
+DESCRIPTION="Navigation scripting & testing utility for PhantomJS and SlimerJS"
+HOMEPAGE="http://casperjs.org/"
+SRC_URI="https://github.com/n1k0/${PN}/archive/${MY_PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="<www-client/phantomjs-2.0.0"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${PN}-${MY_PV}"
+
+src_compile() {
+	return
+}
+
+src_install() {
+	insinto /usr/share/${P}/
+	doins -r modules/
+	doins -r tests/
+	doins package.json
+
+	insinto /usr/share/${P}/bin
+	doins bin/bootstrap.js
+	doins bin/usage.txt
+
+	exeinto /usr/share/${P}/bin
+	doexe bin/casperjs
+	dosym ../share/${P}/bin/casperjs /usr/bin/casperjs
+
+	dodoc CHANGELOG.md CONTRIBUTORS.md README.md
+}
diff --git a/www-client/casperjs/metadata.xml b/www-client/casperjs/metadata.xml
new file mode 100644
index 000000000..acad08b5a
--- /dev/null
+++ b/www-client/casperjs/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci</herd>
+  <upstream>
+    <remote-id type="github">n1k0/casperjs</remote-id>
+  </upstream>
+</pkgmetadata>
author	Justin Lecher <jlec@gentoo.org>	2015-09-25 18:22:42 +0200
committer	Justin Lecher <jlec@gentoo.org>	2015-09-25 18:22:42 +0200
commit	e3417554a48f19740c35e981c3a67a341e88d3c1 (patch)
tree	4ea71ccc921da9cce2ebe845418eae33b93c8b59
parent	Add local USE description (diff)
parent	Merge remote-tracking branch 'github/master' (diff)
download	sci-e3417554.tar.gz sci-e3417554.tar.bz2 sci-e3417554.zip