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

7 files changed, 13 insertions, 330 deletions

diff --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog
index c3f4e3d01..a57ab4c07 100644
--- a/sci-physics/abinit/ChangeLog
+++ b/sci-physics/abinit/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*abinit-6.12.3-r2 (19 Jun 2012)
+
+  19 Jun 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
+  -abinit-6.12.3-r1.ebuild, +abinit-6.12.3-r2.ebuild:
+  Reflect the split of the fortran interface out of sci-libs/netcdf
+
   22 May 2012; Justin Lecher <jlec@gentoo.org> abinit-6.12.3-r1.ebuild,
   metadata.xml:
   Add missing eutils.eclass
diff --git a/sci-physics/abinit/Manifest b/sci-physics/abinit/Manifest
index 692c589e7..6392e02a1 100644
--- a/sci-physics/abinit/Manifest
+++ b/sci-physics/abinit/Manifest
@@ -1 +1 @@
-DIST abinit-6.12.3.tar.gz 58483889 SHA256 243a3832e258d12998d9d188141cfedeabdbfee9867c1951d7f27b8230dec5e9 SHA512 a14764c7c031890ea9cb64dd8fb439959fae4b50d59985bd2e9d9c12a06f71f92491c015c64c7273b4089cd57934a699f3d4c3c2f377032cbd655aa887241a65 WHIRLPOOL caa5e8159fac7353ee87663f195419acee57246f1a3015941368ed026c3a15a07cf135dbf57fc8a81f0cdd24c042af1ccc1c63e3e20a73042d3462530bd5b904
+DIST abinit-6.12.3.tar.gz 58483889 RMD160 d2a1009af7eaafa9d4df99aa6e98e35faa644931 SHA1 ab7bca747639902d586155cb5d335595e3b2b1dc SHA256 243a3832e258d12998d9d188141cfedeabdbfee9867c1951d7f27b8230dec5e9 SHA512 a14764c7c031890ea9cb64dd8fb439959fae4b50d59985bd2e9d9c12a06f71f92491c015c64c7273b4089cd57934a699f3d4c3c2f377032cbd655aa887241a65 WHIRLPOOL caa5e8159fac7353ee87663f195419acee57246f1a3015941368ed026c3a15a07cf135dbf57fc8a81f0cdd24c042af1ccc1c63e3e20a73042d3462530bd5b904
diff --git a/sci-physics/abinit/abinit-6.12.3-r1.ebuild b/sci-physics/abinit/abinit-6.12.3-r2.ebuild
index fc22cebc3..a5c883145 100644
--- a/sci-physics/abinit/abinit-6.12.3-r1.ebuild
+++ b/sci-physics/abinit/abinit-6.12.3-r2.ebuild
@@ -16,15 +16,17 @@ KEYWORDS="~amd64 ~x86"
 IUSE="cuda cuda-double -debug +etsf_io +fftw +fftw-threads +fox gsl gui +hdf5 libabinit mpi +netcdf python -test +threads -vdwxc"
 
 RDEPEND="~sci-libs/bigdft-1.6_pre1
-	sci-libs/etsf_io
 	=sci-libs/libxc-1*[fortran]
 	sci-physics/atompaw[libxc]
 	etsf_io? ( sci-libs/etsf_io )
 	fox? ( >=sci-libs/fox-4.1.2-r1[sax] )
 	netcdf? (
-		sci-libs/netcdf[fortran]
+		|| (
+			sci-libs/netcdf[fortran]
+			sci-libs/netcdf-fortran
+			)
 		hdf5? (
-			  sci-libs/netcdf[fortran,hdf5]
+			  sci-libs/netcdf[hdf5]
 			  )
 		)
 	hdf5? ( sci-libs/hdf5[fortran] )
diff --git a/sci-physics/elk/Manifest b/sci-physics/elk/Manifest
index 88dada474..b0fce503e 100644
--- a/sci-physics/elk/Manifest
+++ b/sci-physics/elk/Manifest
@@ -1,3 +1 @@
-DIST elk-1.3.15.tgz 1834503 SHA256 6e35d1c3830aeea0fe8016e25efa9debddf0e4bd90fe910520a35608a2f81fcf SHA512 ab18c78616447abdba7f82215cf4f10ff26eb052e47693266246b60225a436d21f877f5b97f3e62c0a91d2fd267c9e017568e8d5a80e488835d279d40494cf1e WHIRLPOOL fc528cd6e4ca0ddf42996f126aaf7cbcfd65bcc284faa9c0eb84cfcfae1055f20c83aea8dc5bfefeacb4a29755980f5881ec2fecc8fabb648727780c4b1cea93
-DIST elk-1.4.18.tgz 1855415 SHA256 14df155a254f0d0b24ffa98a3a25130e1d55f652f87f1f20781bb45169a20281 SHA512 5bcae5903aa6880fa43000f43e2f6aa5789d20107e0dd004104821ae39e663d6e1172441c3b69ed214fde0b6786450be16800116c0905288afc6fe644c8190a2 WHIRLPOOL dddb8b8eca84484bb1d8906ba2ccb53659509f7624b7b602758857c81a3f7e81c0f8b17037c1dd760c5bfdec47e57e92d88fda956bd1c2feb3b41bb42812925f
-DIST elk-1.4.5.tgz 1851444 SHA256 84c4e19da2d76e25f0395343aa6e7ecf883a9a870d7b1c5256336e220d1fbb9e SHA512 8fdecd8e11a3b53e8a891963d005d753cc06ce3c5a27cfe581f2d64edbdc620551d3a91ce31be31f50fce60beb402562662b215e64ae93e4dbf507910c31e7be WHIRLPOOL 6b463d09e1e5e75e8a08cc9224a57d93927ce1998653872ace73f1bf9bcf3f9a826eaea284319bdb85f19da16523430ff62496171a4b497103f8bc45d00e2391
+DIST elk-1.4.22.tgz 1866287 RMD160 6af2454eab5af8c97447529db013fbfe41f016fb SHA1 71c9b7cb1ddd5ab2eb7d83e1922a7aa0c2e0ddf8 SHA256 bc8b70d42924c77c9328418bd133285fe2caa4a8b14df4016eecff647ca15ec0 SHA512 7c512ac6738d883fe1c76964c8bd44ef34269f58f4c8d97ee63949949391ef1040dc41cf0c2626492f6c94649b696d7b67eef8292011dc75c312a3c4b3c21da6 WHIRLPOOL 392804fc8bc3ce03208f9689ffafb84d4a61b343d80c09d787adcd23f25ab824dd0d6477bbad41ae2e61ab0acc9cba2f965d6c576fd7d69bb976fd29770e4a1d
diff --git a/sci-physics/elk/elk-1.3.15.ebuild b/sci-physics/elk/elk-1.3.15.ebuild
deleted file mode 100644
index ac1b4f0e6..000000000
--- a/sci-physics/elk/elk-1.3.15.ebuild
+++ /dev/null
@@ -1,104 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="3"
-
-inherit eutils fortran-2 multilib toolchain-funcs
-
-DESCRIPTION="All-electron full-potential linearised augmented-plane wave (FP-LAPW) code with advanced features."
-HOMEPAGE="http://elk.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tgz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="-debug lapack libxc mpi openmp test"
-
-RDEPEND="lapack? ( virtual/blas
-		virtual/lapack )
-	libxc? ( =sci-libs/libxc-1*[fortran] )
-	mpi? ( virtual/mpi )"
-DEPEND="${RDEPEND}
-	dev-util/pkgconfig"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	if use openmp; then
-		tc-has-openmp || \
-		die "Please select an openmp capable compiler like gcc[openmp]"
-	fi
-}
-
-src_prepare() {
-	if use libxc; then
-		sed -i -e's/^\(SRC_libxc =\)/#\1/' "${S}/src/Makefile"
-	fi
-	if use mpi; then
-		sed -i -e's/^\(SRC_mpi =\)/#\1/' "${S}/src/Makefile"
-	fi
-}
-
-src_configure() {
-	if use mpi; then
-		MY_FC="mpif90"
-		MY_CC="mpicc"
-		MY_CXX="mpic++"
-	else
-		MY_FC="$(tc-getFC)"
-		MY_CC="$(tc-getCC)"
-		MY_CXX="$(tc-getCXX)"
-	fi
-	if use openmp; then
-		MY_FC="${MY_FC} -fopenmp"
-		MY_CC="${MY_CC} -fopenmp"
-		MY_CXX="${MY_CXX} -fopenmp"
-	fi
-	MY_FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O3 -funroll-loops -ffast-math}}"
-	MY_FCFLAGS="${MY_FCFLAGS} -I/usr/include -I/usr/$(get_libdir)/finclude"
-	MY_CFLAGS="${CFLAGS:- -O3 -funroll-loops -ffast-math}"
-	MY_CXXFLAGS="${CXXFLAGS:- ${CFLAGS:- -O3 -funroll-loops -ffast-math}}"
-	echo "MAKE = make" > make.inc
-	echo "F90 = $MY_FC" >> make.inc
-	echo "F90_OPTS = $MY_FCFLAGS" >> make.inc
-	echo "F77 = $MY_FC" >> make.inc
-	echo "F77_OPTS = $MY_FCFLAGS" >> make.inc
-	echo "CC = ${MY_CC}" >> make.inc
-	echo "CXX = ${MY_CXX}" >> make.inc
-	echo "CFLAGS = ${MY_CFLAGS}" >> make.inc
-	echo "CXXFLAGS = ${MY_CXXFLAGS}" >> make.inc
-	echo "LD = $(tc-getLD)" >> make.inc
-	echo "AR = ar" >> make.inc
-	echo "LIB_SYS = " >> make.inc
-	if use lapack; then
-		echo "LIB_LPK = $(pkg-config --libs lapack)" >> make.inc
-	else
-		echo "LIB_LPK = lapack.a blas.a" >> make.inc
-	fi
-	echo "LIB_FFT = fftlib.a" >> make.inc
-	if use libxc; then
-		echo "LIB_XC = -L/usr/$(get_libdir) -lxc" >> make.inc
-		echo "SRC_libxc = libxc_funcs.f90 libxc.f90 libxcifc.f90" >>make.inc
-	fi
-}
-
-src_compile() {
-	emake -j1 || die "make failed"
-}
-
-src_test() {
-	emake test
-}
-
-src_install() {
-	dobin src/elk src/eos/eos src/spacegroup/spacegroup utilities/elk-bands
-	dodoc README
-	for doc in docs/*; do
-		dodoc $doc
-	done
-	insinto /usr/share/${P}
-	doins -r species
-	doins -r utilities
-	doins -r examples
-	doins -r tests
-}
diff --git a/sci-physics/elk/elk-1.4.18.ebuild b/sci-physics/elk/elk-1.4.18.ebuild
deleted file mode 100644
index 27b3f3af5..000000000
--- a/sci-physics/elk/elk-1.4.18.ebuild
+++ /dev/null
@@ -1,115 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="4"
-
-inherit eutils fortran-2 multilib toolchain-funcs
-
-DESCRIPTION="All-electron full-potential linearised augmented-plane wave (FP-LAPW) code with advanced features."
-HOMEPAGE="http://elk.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tgz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="-debug lapack libxc mpi openmp perl test"
-
-RDEPEND="lapack? ( virtual/blas
-		virtual/lapack )
-	libxc? ( =sci-libs/libxc-1*[fortran] )
-	mpi? ( virtual/mpi )"
-DEPEND="${RDEPEND}
-	perl? ( dev-lang/perl )
-	dev-util/pkgconfig"
-
-DOCS=( README  )
-
-FORTRAN_STANDARD=90
-
-pkg_setup() {
-	# fortran-2.eclass does not handle mpi wrappers
-	if use mpi; then
-		export FC="mpif90"
-		export F77="mpif77"
-		export CC="mpicc"
-		export CXX="mpic++"
-	else
-		tc-export FC F77 CC CXX
-	fi
-
-	if use openmp; then
-		FORTRAN_NEED_OPENMP=1
-	fi
-
-	fortran-2_pkg_setup
-
-	if use openmp; then
-		export FC="${FC} -fopenmp"
-		export F77="${F77} -fopenmp"
-		export CC="${CC} -fopenmp"
-		export CXX="${CXX} -fopenmp"
-	fi
-}
-
-src_prepare() {
-	if use libxc; then
-		sed -i -e's/^\(SRC_libxc =\)/#\1/' "${S}/src/Makefile"
-	fi
-	if use mpi; then
-		sed -i -e's/^\(SRC_mpi =\)/#\1/' "${S}/src/Makefile"
-	fi
-}
-
-src_configure() {
-	FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O3 -funroll-loops -ffast-math}}"
-	FCFLAGS="${FCFLAGS} -I/usr/include -I/usr/$(get_libdir)/finclude"
-	CFLAGS="${CFLAGS:- -O3 -funroll-loops -ffast-math}"
-	CXXFLAGS="${CXXFLAGS:- ${CFLAGS}}"
-	export FCFLAGS CFLAGS CXXFLAGS
-	echo "MAKE = make" > make.inc
-	echo "F90 = $FC" >> make.inc
-	echo "F90_OPTS = $FCFLAGS" >> make.inc
-	echo "F77 = $FC" >> make.inc
-	echo "F77_OPTS = $FCFLAGS" >> make.inc
-	echo "CC = ${CC}" >> make.inc
-	echo "CXX = ${CXX}" >> make.inc
-	echo "CFLAGS = ${CFLAGS}" >> make.inc
-	echo "CXXFLAGS = ${CXXFLAGS}" >> make.inc
-	echo "LD = $(tc-getLD)" >> make.inc
-	echo "AR = ar" >> make.inc
-	echo "LIB_SYS = " >> make.inc
-	if use lapack; then
-		echo "LIB_LPK = $(pkg-config --libs lapack)" >> make.inc
-	else
-		echo "LIB_LPK = lapack.a blas.a" >> make.inc
-	fi
-	echo "LIB_FFT = fftlib.a" >> make.inc
-	if use libxc; then
-		echo "LIB_XC = -L/usr/$(get_libdir) -lxc" >> make.inc
-		echo "SRC_libxc = libxc_funcs.f90 libxc.f90 libxcifc.f90" >>make.inc
-	fi
-}
-
-src_compile() {
-	emake -j1 || die "make failed"
-}
-
-src_test() {
-	emake test
-}
-
-src_install() {
-	dobin src/elk src/protex src/eos/eos src/spacegroup/spacegroup
-	dobin utilities/elk-bands
-	use perl && dobin utilities/xps_exc.pl utilities/se.pl
-	dodoc README
-	for doc in docs/*; do
-		dodoc $doc
-	done
-	insinto /usr/share/${P}
-	doins -r species
-	doins -r utilities
-	doins -r examples
-	doins -r tests
-}
diff --git a/sci-physics/elk/elk-1.4.5.ebuild b/sci-physics/elk/elk-1.4.5.ebuild
deleted file mode 100644
index ac1b4f0e6..000000000
--- a/sci-physics/elk/elk-1.4.5.ebuild
+++ /dev/null
@@ -1,104 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="3"
-
-inherit eutils fortran-2 multilib toolchain-funcs
-
-DESCRIPTION="All-electron full-potential linearised augmented-plane wave (FP-LAPW) code with advanced features."
-HOMEPAGE="http://elk.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tgz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="-debug lapack libxc mpi openmp test"
-
-RDEPEND="lapack? ( virtual/blas
-		virtual/lapack )
-	libxc? ( =sci-libs/libxc-1*[fortran] )
-	mpi? ( virtual/mpi )"
-DEPEND="${RDEPEND}
-	dev-util/pkgconfig"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	if use openmp; then
-		tc-has-openmp || \
-		die "Please select an openmp capable compiler like gcc[openmp]"
-	fi
-}
-
-src_prepare() {
-	if use libxc; then
-		sed -i -e's/^\(SRC_libxc =\)/#\1/' "${S}/src/Makefile"
-	fi
-	if use mpi; then
-		sed -i -e's/^\(SRC_mpi =\)/#\1/' "${S}/src/Makefile"
-	fi
-}
-
-src_configure() {
-	if use mpi; then
-		MY_FC="mpif90"
-		MY_CC="mpicc"
-		MY_CXX="mpic++"
-	else
-		MY_FC="$(tc-getFC)"
-		MY_CC="$(tc-getCC)"
-		MY_CXX="$(tc-getCXX)"
-	fi
-	if use openmp; then
-		MY_FC="${MY_FC} -fopenmp"
-		MY_CC="${MY_CC} -fopenmp"
-		MY_CXX="${MY_CXX} -fopenmp"
-	fi
-	MY_FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O3 -funroll-loops -ffast-math}}"
-	MY_FCFLAGS="${MY_FCFLAGS} -I/usr/include -I/usr/$(get_libdir)/finclude"
-	MY_CFLAGS="${CFLAGS:- -O3 -funroll-loops -ffast-math}"
-	MY_CXXFLAGS="${CXXFLAGS:- ${CFLAGS:- -O3 -funroll-loops -ffast-math}}"
-	echo "MAKE = make" > make.inc
-	echo "F90 = $MY_FC" >> make.inc
-	echo "F90_OPTS = $MY_FCFLAGS" >> make.inc
-	echo "F77 = $MY_FC" >> make.inc
-	echo "F77_OPTS = $MY_FCFLAGS" >> make.inc
-	echo "CC = ${MY_CC}" >> make.inc
-	echo "CXX = ${MY_CXX}" >> make.inc
-	echo "CFLAGS = ${MY_CFLAGS}" >> make.inc
-	echo "CXXFLAGS = ${MY_CXXFLAGS}" >> make.inc
-	echo "LD = $(tc-getLD)" >> make.inc
-	echo "AR = ar" >> make.inc
-	echo "LIB_SYS = " >> make.inc
-	if use lapack; then
-		echo "LIB_LPK = $(pkg-config --libs lapack)" >> make.inc
-	else
-		echo "LIB_LPK = lapack.a blas.a" >> make.inc
-	fi
-	echo "LIB_FFT = fftlib.a" >> make.inc
-	if use libxc; then
-		echo "LIB_XC = -L/usr/$(get_libdir) -lxc" >> make.inc
-		echo "SRC_libxc = libxc_funcs.f90 libxc.f90 libxcifc.f90" >>make.inc
-	fi
-}
-
-src_compile() {
-	emake -j1 || die "make failed"
-}
-
-src_test() {
-	emake test
-}
-
-src_install() {
-	dobin src/elk src/eos/eos src/spacegroup/spacegroup utilities/elk-bands
-	dodoc README
-	for doc in docs/*; do
-		dodoc $doc
-	done
-	insinto /usr/share/${P}
-	doins -r species
-	doins -r utilities
-	doins -r examples
-	doins -r tests
-}