[sci-chemistry/gromacs] Version bump

(Portage version: 2.2_rc81_p9/cvs/Linux x86_64)

2 files changed, 59 insertions, 90 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 2fbfdf73e98c..11c65c54f066 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.58 2010/09/11 19:29:31 klausman Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.59 2010/09/14 12:59:31 alexxy Exp $
+
+*gromacs-4.5.1 (14 Sep 2010)
+
+  14 Sep 2010; Alexey Shvetsov <alexxy@gentoo.org> -gromacs-4.0.7-r3.ebuild,
+  +gromacs-4.5.1.ebuild:
+  Version bump. Now it can use ffambber. And threads. Many thanks to
+  Christoph Junghans
 
   11 Sep 2010; Tobias Klausmann <klausman@gentoo.org>
   gromacs-4.0.7-r4.ebuild:
diff --git a/sci-chemistry/gromacs/gromacs-4.0.7-r3.ebuild b/sci-chemistry/gromacs/gromacs-4.5.1.ebuild
index bb8ceb91a518..d065c2194dee 100644
--- a/sci-chemistry/gromacs/gromacs-4.0.7-r3.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.1.ebuild
@@ -1,27 +1,27 @@
 # Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.7-r3.ebuild,v 1.2 2010/07/17 12:40:20 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.1.ebuild,v 1.1 2010/09/14 12:59:31 alexxy Exp $
 
 EAPI="3"
 
 LIBTOOLIZE="true"
 TEST_PV="4.0.4"
+MANUAL_PV="4.5"
 
-inherit autotools bash-completion eutils fortran multilib
+inherit autotools bash-completion eutils fortran multilib toolchain-funcs
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
 SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
-		mirror://gentoo/${P}_upstream2010-06-08.patch.gz
 		test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )
-		ffamber? ( http://ffamber.cnsm.csulb.edu/ffamber_v4.0-doc.tar.gz )"
+		doc? (
+		http://www.gromacs.org/@api/deki/files/126/=gromacs_manual-${MANUAL_PV}.pdf -> gromacs-${MANUAL_PV}.pdf )"
 
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X blas dmalloc doc -double-precision ffamber +fftw fkernels +gsl lapack
-mpi +single-precision static static-libs test +xml zsh-completion"
+IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
+mpi +single-precision static static-libs test +threads +xml zsh-completion"
 
 DEPEND="app-shells/tcsh
 	X? ( x11-libs/libX11
@@ -39,36 +39,38 @@ RDEPEND="${DEPEND}"
 
 RESTRICT="test"
 
-src_prepare() {
+QA_EXECSTACK="usr/lib/libgmx.so.*
+	usr/lib/libgmx_d.so.*"
 
-	epatch "${WORKDIR}/${P}_upstream2010-06-08.patch"
-	sed -e '/AC_INIT/s/4\.0\.7/&-2010-06-08/' -i configure.ac \
-		|| die "Failed to change version in configure.ac"
-	epatch "${FILESDIR}/${PN}-4.0.9999-docdir.patch"
-	epatch "${FILESDIR}/${PN}-4.0.9999-ccache.patch"
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
+use static && QA_EXECSTACK="$QA_EXECSTACK usr/bin/*"
 
-	# Fix a sandbox violation that occurs when re-emerging with mpi.
-	sed "/libdir=\"\$(libdir)\"/ a\	temp_libdir=\"${ED}usr/$( get_libdir )\" ; \\\\" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed -e "s:\$\$libdir:\$temp_libdir:" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
+pkg_setup() {
+	if use fkernels; then
+		FORTRAN="g77 gfortran ifc"
+		fortran_pkg_setup
+	else
+		FORTRANC=""
+	fi
+}
 
-	sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${ED}usr/$( get_libdir )\" ; \\\\" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
+src_prepare() {
 
-	sed -e "s:\$\$libdir:\$\$temp_libdir:" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
+	( use single-precision || use double-precision ) || \
+		die "Nothing to compile, enable single-precision and/or double-precision"
 
-	use fkernels && epatch "${FILESDIR}/${PN}-4.0.9999-configure-gfortran.patch"
+	if use mpi && use threads; then
+		elog "mdrun uses only threads OR mpi, and gromacs favours the"
+		elog "use of mpi over threads, so a mpi-version of mdrun will"
+		elog "be compiled. If you want to run mdrun on shared memory"
+		elog "machines only, you can safely disable mpi"
+	fi
 
+	if use static; then
+		use X && die "You cannot compile a static version with X support, disable X or static"
+		use xml && die "You cannot compile a static version with xml support
+		(see bug #306479), disable xml or static"
+	fi
+	epatch_user
 	eautoreconf
 	GMX_DIRS=""
 	use single-precision && GMX_DIRS+=" single"
@@ -111,8 +113,7 @@ src_configure() {
 	if use fkernels; then
 		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
 		ewarn "I hope, you know what are you doing..."
-		FORTRAN="g77 gfortran ifc"
-		myconf="${myconf} --enable-fortran" && fortran_pkg_setup
+		myconf="${myconf} --enable-fortran"
 	else
 		myconf="${myconf} --disable-fortran"
 	fi
@@ -132,9 +133,9 @@ src_configure() {
 	# by default its better to have dynamicaly linked binaries
 	if use static; then
 		#gmx build static libs by default
-		myconf="${myconf} $(use_enable static all-static)"
+		myconf="${myconf} --disable-shared $(use_enable static all-static)"
 	else
-		myconf="${myconf} --enable-shared $(use_enable static-libs static)"
+		myconf="${myconf} --disable-all-static --enable-shared $(use_enable static-libs static)"
 	fi
 
 	myconf="--datadir="${EPREFIX}"/usr/share \
@@ -146,6 +147,7 @@ src_configure() {
 			$(use_with gsl) \
 			$(use_with X x) \
 			$(use_with xml) \
+			$(use_enable threads) \
 			${myconf}"
 
 	#if we build single and double - double is suffixed
@@ -182,10 +184,10 @@ src_configure() {
 		einfo "Configuring for ${x} precision"
 		cd "${S}-${x}"
 		local p=myconf${x}
-		ECONF_SOURCE="${S}" econf ${!p} --disable-mpi
+		ECONF_SOURCE="${S}" econf ${!p} --disable-mpi CC="$(tc-getCC)" F77="${FORTRANC}"
 		use mpi || continue
 		cd "${S}-${x}_mpi"
-		ECONF_SOURCE="${S}" econf ${!p} --enable-mpi
+		ECONF_SOURCE="${S}" econf ${!p} --enable-mpi CC="$(tc-getCC)" F77="${FORTRANC}"
 	done
 }
 
@@ -213,10 +215,10 @@ src_test() {
 src_install() {
 	for x in ${GMX_DIRS}; do
 		cd "${S}-${x}"
-		emake DESTDIR="${ED}" install || die "emake install for ${x} failed"
+		emake DESTDIR="${D}" install || die "emake install for ${x} failed"
 		use mpi || continue
 		cd "${S}-${x}_mpi"
-		emake DESTDIR="${ED}" install-mdrun || die "emake install-mdrun for ${x} failed"
+		emake DESTDIR="${D}" install-mdrun || die "emake install-mdrun for ${x} failed"
 	done
 
 	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
@@ -228,59 +230,19 @@ src_install() {
 		insinto /usr/share/zsh/site-functions
 		newins "${ED}"/usr/bin/completion.zsh _${PN}
 	fi
-	rm -r "${ED}"/usr/bin/completion.*
+	rm -f "${ED}"/usr/bin/completion.*
+
+	# Fix typos in a couple of files.
+	sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
+		|| die "Failed to fixup demo script."
 
 	cd "${S}"
 	dodoc AUTHORS INSTALL README
-	use doc && dodoc "${DISTDIR}/manual-4.0.pdf"
-
-	if use ffamber; then
-		use doc && dodoc "${WORKDIR}/ffamber_v4.0/README/pdfs/*.pdf"
-		# prepare vdwradii.dat
-		cat >>"${ED}"/usr/share/gromacs/top/vdwradii.dat <<-EOF
-			SOL  MW    0
-			SOL  LP    0
-		EOF
-		# regenerate aminoacids.dat
-		cat "${WORKDIR}"/ffamber_v4.0/aminoacids*.dat \
-		"${ED}"/usr/share/gromacs/top/aminoacids.dat \
-		| awk '{print $1}' | sort -u | tail -n+4 | wc -l \
-		>> "${ED}"/usr/share/gromacs/top/aminoacids.dat.new
-		cat "${WORKDIR}"/ffamber_v4.0/aminoacids*.dat \
-		"${ED}"/usr/share/gromacs/top/aminoacids.dat \
-		| awk '{print $1}' | sort -u | tail -n+4 \
-		>> "${ED}"/usr/share/gromacs/top/aminoacids.dat.new
-		mv -f "${ED}"/usr/share/gromacs/top/aminoacids.dat.new \
-		"${ED}"/usr/share/gromacs/top/aminoacids.dat
-		# copy ff files
-		for x in ffamber94 ffamber96 ffamber99 ffamber99p ffamber99sb \
-				ffamberGS ffamberGSs ffamber03 ; do
-			einfo "Adding ${x} to gromacs"
-			cp "${WORKDIR}"/ffamber_v4.0/${x}/* "${ED}"/usr/share/gromacs/top
-		done
-		# copy suplementary files
-		cp "${WORKDIR}"/ffamber_v4.0/*.gro "${ED}"/usr/share/gromacs/top
-		cp "${WORKDIR}"/ffamber_v4.0/*.itp "${ED}"/usr/share/gromacs/top
-		# actualy add records to FF.dat
-		cat >>"${ED}"/usr/share/gromacs/top/FF.dat.new <<-EOF
-			ffamber94   AMBER94 Cornell protein/nucleic forcefield
-			ffamber96   AMBER96 Kollman protein/nucleic forcefield
-			ffamberGS   AMBER-GS Garcia &  Sanbonmatsu forcefield
-			ffamberGSs  AMBER-GSs Nymeyer &  Garcia forcefield
-			ffamber99   AMBER99 Wang protein/nucleic acid forcefield
-			ffamber99p  AMBER99p protein/nucleic forcefield
-			ffamber99sb AMBER99sb Hornak protein/nucleic forcefield
-			ffamber03   AMBER03 Duan protein/nucleic forcefield
-		EOF
-		cat "${ED}"/usr/share/gromacs/top/FF.dat \
-			"${ED}"/usr/share/gromacs/top/FF.dat.new \
-			| tail -n+2 > "${ED}"/usr/share/gromacs/top/FF.dat.new2
-		cat "${ED}"/usr/share/gromacs/top/FF.dat.new2 | wc -l > \
-			"${ED}"/usr/share/gromacs/top/FF.dat
-		cat "${ED}"/usr/share/gromacs/top/FF.dat.new2 >> \
-			"${ED}"/usr/share/gromacs/top/FF.dat
-		rm -f "${ED}"/usr/share/gromacs/top/FF.dat.new*
+	if use doc; then
+		dodoc "${DISTDIR}/manual-${MANUAL_PV}.pdf"
+		dohtml -r "${ED}usr/share/gromacs/html/"
 	fi
+	rm -rf "${ED}usr/share/gromacs/html/"
 }
 
 pkg_postinst() {
@@ -292,7 +254,7 @@ pkg_postinst() {
 	elog
 	bash-completion_pkg_postinst
 	elog
-	elog $(luck)
+	elog $(g_luck)
 	elog "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
 	elog
 }