fix bash completion (bug #526318)

Package-Manager: portage-2.2.8-r2/cvs/Linux x86_64
Manifest-Sign-Key: 0xC2000586

3 files changed, 290 insertions, 15 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 6ce07f6e5a4d..6a137bf00014 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.146 2014/10/02 15:34:59 alexxy Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.147 2014/10/21 19:10:08 ottxor Exp $
+
+*gromacs-5.0.2-r1 (21 Oct 2014)
+
+  21 Oct 2014; Christoph Junghans <ottxor@gentoo.org> +gromacs-5.0.2-r1.ebuild:
+  fix bash completion (bug #526318)
 
 *gromacs-5.0.2 (02 Oct 2014)
 
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 8b3c35ce1614..3bddc443db56 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -20,24 +20,19 @@ EBUILD gromacs-4.6.5.ebuild 9004 SHA256 b6dc5dc03033100defe0ab09e0573a7c83c3042c
 EBUILD gromacs-4.6.6.ebuild 9072 SHA256 0e2f3f1ac07c8db2ac3ac114c1279d988d8e0536e02dc0d6bd0e014a0046cf6f SHA512 37170e342f3f6b6d4927c22fba7453b5e21ee44703d2756cd93ed3eec452b478941c2009351f6683d11063e45a9c195d54e3f5294f278086804e0437f370a84d WHIRLPOOL d7f76dd0c19cf7c0f756bbc08aca24b2d96096575f1cc655adba10c6b655aa90776cef365ba68501f9732727385952cc0fd585cff34f830f1d6e30cf79b671d7
 EBUILD gromacs-4.6.7.ebuild 9072 SHA256 d9d7d1725e104a19e060d327be136874e68e0b3cbf738c92c35f520217b3aa53 SHA512 7df1968b428a6ae098fbcd84ab403dba7adb5803a3eede1d75b8b0293b3da2aa08ed58ec0462fc7eb38a3af2e6b1b5b0a49e41f1e00987dac6228cd51f793bd8 WHIRLPOOL b0bd2c28e57b22a9f810299ae527ba50fbeeae74abe514402e9b2aa0712319d145f5aaa6bd15d104f7c1699ed08c5bc1bf0fe25f3a355ad8e6071d61f23bb851
 EBUILD gromacs-5.0.1.ebuild 7656 SHA256 48da04e5e6589bc82836dea034f93271cc0e6161cfe4774002196d66c56b50dd SHA512 643e3ef402d8a9a33fb3d40186f1562b794e05cfefba4dcacb7bbf90f2e51e1dcd0024f30e93e03069b96998f26d3d8f30e3ca89b8271a7b6f4e0a6798b52b3b WHIRLPOOL 35d53661f53e0127be3d7b1e27e9ec59af25ff34cb61971fc11e78fd287bcba1c4f05357d8d4214e2f132af1ff4d7765bc408acb968288aba1a60e733f592e97
+EBUILD gromacs-5.0.2-r1.ebuild 8304 SHA256 91e9494754edb5e954ae1213adee8b059b4869fe41956fe4a4fb9b2ca47d4b37 SHA512 2bf7b544cc3f9f5bb7ad8b3a5ccf6eda85587563cae1d0736e3f0603c5df538a810051b28d61b6731570d4f64e0e0397d4e4716bae9cc338a75f7b5e5971e6d6 WHIRLPOOL c34275f2741995f590d4ae15a66a69bdac2817d84ed1cfb0aebd786811e54241625b7f5793b1c60f7dbfd417e9b94e7ad7f3ad1b1cf91e458a8488ac59419b6d
 EBUILD gromacs-5.0.2.ebuild 7656 SHA256 4853a6fe94adc48a8b88a3c48ac133490168b3c212b0b2101dfc880872cd69ea SHA512 53e510a1ecae0b65a9c2235585e7188340fcb014078708420f7bad13a48b610b7c173055e8436c62ea3541ecb9dc6d1f1a3bcef560f21658ce36a0afe9aa532d WHIRLPOOL ba9a2a97c822f811da6c502d161b8c93bcd37541bd9dd36402ef2e8ebcbbc02c0c51bfc58fb97059d45d346323219ec08b5e0d96dcf0837d58c0f2decdfae597
 EBUILD gromacs-5.0.ebuild 7781 SHA256 7ce7eef26b173d60e85cbcc87e721465a05983c41033321568d6e9a8604b8830 SHA512 a15b6a8809522c2fc708bf389fb5862882deb1416f30702fe7ab3ba6128c6d4a127fcebc2b097256ee4dd59a5c4165ee43cc886026035cff9b030ff1e4556e52 WHIRLPOOL 888be2a1e032a164d31b8b7aa9e9419ff5c582525a326a1184c35f3cfa1cf0199e4dbd394946b1d12503eeb1ea1216aabed9c9571fdaae72ddd2b13521fc45e5
-MISC ChangeLog 23416 SHA256 fd2d4edd2658b16d32925e37b25f1b664be5dc068d7487e76edefe271ae284fe SHA512 a8458c361c68100c4f57b6c6237ea256d5dc09e01e6f5fa3d5db59fe5f74e1dffe46748f585626020422d5952dc53cc620349cf15b71c3101ec829c3e0dcd126 WHIRLPOOL 1d018152e9c9b2246a21ef1d8c7aefa815be4464c504884399eb8a0cc7489e8ea239c3c104c15085ef0db1e737b124f3825710b56a34969626a343a09fb1c9c5
+MISC ChangeLog 23566 SHA256 a6c2c6e1de8106b6dc713c6c685990a813e007a186891e1fed93964aee3c0fa3 SHA512 abb543d02cae6bbe97d937155f6f843f4349a174753acdf809ee6d7afd4b4e4dea6fc8c7b9122e4e557186283083e1bf67215cc80ed88cf65da87ea02395fcda WHIRLPOOL 21a73b9f170e0c55649094de9ababef06ec515413d7cd071d54f25975088467136c71089d8bda53bd8984670f19443d34003b0f7906b777fff4e487eafbd5011
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diff --git a/sci-chemistry/gromacs/gromacs-5.0.2-r1.ebuild b/sci-chemistry/gromacs/gromacs-5.0.2-r1.ebuild
new file mode 100644
index 000000000000..3353106716c3
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-5.0.2-r1.ebuild
@@ -0,0 +1,275 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.2-r1.ebuild,v 1.1 2014/10/21 19:10:08 ottxor Exp $
+
+EAPI=5
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
+
+if [[ $PV = *9999* ]]; then
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
+		https://gerrit.gromacs.org/gromacs.git
+		git://github.com/gromacs/gromacs.git
+		http://repo.or.cz/r/gromacs.git"
+	EGIT_BRANCH="release-5-0"
+	inherit git-r3
+	KEYWORDS=""
+else
+	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
+		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
+	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+fi
+
+ACCE_IUSE="sse2 sse4_1 avx_128_fma avx_256 avx2_256"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
+# see COPYING for details
+# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
+#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
+LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
+SLOT="0/${PV}"
+IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+
+CDEPEND="
+	X? (
+		x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE
+		)
+	blas? ( virtual/blas )
+	boost? ( >=dev-libs/boost-1.55 )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
+	fftw? ( sci-libs/fftw:3.0 )
+	lapack? ( virtual/lapack )
+	mkl? ( sci-libs/mkl )
+	mpi? ( virtual/mpi )
+	"
+DEPEND="${CDEPEND}
+	virtual/pkgconfig
+	doc? (
+		app-doc/doxygen
+		dev-texlive/texlive-latex
+		dev-texlive/texlive-latexextra
+		media-gfx/imagemagick
+	)"
+RDEPEND="${CDEPEND}"
+
+REQUIRED_USE="
+	|| ( single-precision double-precision )
+	cuda? ( single-precision )
+	mkl? ( !blas !fftw !lapack )"
+
+DOCS=( AUTHORS README )
+
+if [[ ${PV} != *9999 ]]; then
+	S="${WORKDIR}/${PN}-${PV/_/-}"
+fi
+
+pkg_pretend() {
+	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
+	use openmp && ! tc-has-openmp && \
+		die "Please switch to an openmp compatible compiler"
+}
+
+src_unpack() {
+	if [[ ${PV} != *9999 ]]; then
+		default
+	else
+		git-r3_src_unpack
+		if use test; then
+			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
+			EGIT_BRANCH="master" EGIT_COMMIT="master" \
+			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
+				git-r3_src_unpack
+		fi
+	fi
+}
+
+src_prepare() {
+	#notes/todos
+	# -on apple: there is framework support
+
+	cmake-utils_src_prepare
+
+	use cuda && cuda_src_prepare
+
+	GMX_DIRS=""
+	use single-precision && GMX_DIRS+=" float"
+	use double-precision && GMX_DIRS+=" double"
+
+	if use test; then
+		for x in ${GMX_DIRS}; do
+			mkdir -p "${WORKDIR}/${P}_${x}" || die
+			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
+		done
+	fi
+
+	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
+}
+
+src_configure() {
+	local mycmakeargs_pre=( ) extra fft_opts=( )
+
+	#go from slowest to fastest acceleration
+	local acce="None"
+	use sse2 && acce="SSE2"
+	use sse4_1 && acce="SSE4.1"
+	use avx_128_fma && acce="AVX_128_FMA"
+	use avx_256 && acce="AVX_256"
+	use avx2_256 && acee="AVX2_256"
+
+	#to create man pages, build tree binaries are executed (bug #398437)
+	[[ ${CHOST} = *-darwin* ]] && \
+		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
+
+	if use fftw; then
+		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
+	elif use mkl && has_version "=sci-libs/mkl-10*"; then
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
+			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
+		)
+	elif use mkl; then
+		local bits=$(get_libdir)
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
+			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
+		)
+	else
+		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
+	fi
+
+	mycmakeargs_pre+=(
+		"${fft_opts[@]}"
+		$(cmake-utils_use X GMX_X11)
+		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
+		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
+		$(cmake-utils_use openmp GMX_OPENMP)
+		$(cmake-utils_use offensive GMX_COOL_QUOTES)
+		$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
+		$(cmake-utils_use tng GMX_USE_TNG)
+		$(cmake-utils_use doc GMX_BUILD_MANUAL)
+		$(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES)
+		-DGMX_DEFAULT_SUFFIX=off
+		-DGMX_SIMD="$acce"
+		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
+		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
+		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
+		-DBUILD_TESTING=OFF
+		-DGMX_BUILD_UNITTESTS=OFF
+		${extra}
+	)
+
+	for x in ${GMX_DIRS}; do
+		einfo "Configuring for ${x} precision"
+		local suffix=""
+		#if we build single and double - double is suffixed
+		use double-precision && use single-precision && \
+			[[ ${x} = "double" ]] && suffix="_d"
+		local p
+		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+		local cuda=( "-DGMX_GPU=OFF" )
+		[[ ${x} = "float" ]] && use cuda && \
+			cuda=( -DGMX_GPU=ON )
+		mycmakeargs=(
+			${mycmakeargs_pre[@]} ${p}
+			-DGMX_MPI=OFF
+			$(cmake-utils_use threads GMX_THREAD_MPI)
+			"${cuda[@]}"
+			-DGMX_OPENMM=OFF
+			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
+			-DGMX_BINARY_SUFFIX="${suffix}"
+			-DGMX_LIBS_SUFFIX="${suffix}"
+			)
+		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		[[ ${CHOST} != *-darwin* ]] || \
+		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
+		use mpi || continue
+		einfo "Configuring for ${x} precision with mpi"
+		mycmakeargs=(
+			${mycmakeargs_pre[@]} ${p}
+			-DGMX_THREAD_MPI=OFF
+			-DGMX_MPI=ON ${cuda}
+			-DGMX_OPENMM=OFF
+			-DGMX_BUILD_MDRUN_ONLY=ON
+			-DBUILD_SHARED_LIBS=OFF
+			-DGMX_BUILD_MANUAL=OFF
+			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
+			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
+			)
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+		[[ ${CHOST} != *-darwin* ]] || \
+		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
+	done
+}
+
+src_compile() {
+	for x in ${GMX_DIRS}; do
+		einfo "Compiling for ${x} precision"
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_compile
+		# generate bash completion, not 100% necessary for
+		# rel ebuilds as bundled
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_compile completion
+		# not 100% necessary for rel ebuilds as available from website
+		if use doc; then
+			BUILD_DIR="${WORKDIR}/${P}_${x}"\
+				cmake-utils_src_compile manual
+		fi
+		use mpi || continue
+		einfo "Compiling for ${x} precision with mpi"
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+			cmake-utils_src_compile
+	done
+}
+
+src_test() {
+	for x in ${GMX_DIRS}; do
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_make check
+	done
+}
+
+src_install() {
+	for x in ${GMX_DIRS}; do
+		BUILD_DIR="${WORKDIR}/${P}_${x}" \
+			cmake-utils_src_install
+		if use doc; then
+			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
+		fi
+		#release ebuild does this automatically
+		if [[ $PV = *9999* ]]; then
+			cp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash "${ED}/usr/bin" || die
+			echo "complete -o nospace -F _gmx_compl gmx" > "${ED}/usr/bin/gmx-completion-gmx.bash" || die
+		fi
+		use mpi || continue
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+			cmake-utils_src_install
+	done
+	# drop unneeded stuff
+	rm "${ED}"usr/bin/GMXRC* || die
+	#concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs)
+	#little hacckery as some gmx-completion* newlines ,so cat won't work
+	for x in "${ED}"usr/bin/gmx-completion{,?*}.bash ; do
+		echo $(<${x})
+	done > "${T}"/gmx-bashcomp || die
+	newbashcomp "${T}"/gmx-bashcomp gromacs
+	rm "${ED}"usr/bin/gmx-completion{,?*}.bash || die
+
+	readme.gentoo_create_doc
+}
+
+pkg_postinst() {
+	einfo
+	einfo  "Please read and cite:"
+	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
+	einfo  "http://dx.doi.org/10.1021/ct700301q"
+	einfo
+	readme.gentoo_print_elog
+}