[sci-chemistry/gromacs] Version bump

Package-Manager: portage-2.2_rc81_p9/cvs/Linux x86_64

3 files changed, 83 insertions, 92 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/Manifest b/sci-chemistry/gromacs/Manifest
index b0deb767e8fa..bb7ddcceb5d8 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,3 +1,6 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA256
+
 AUX gromacs-4.0.4-configure-gfortran.patch 731 RMD160 1ccea4fafd6837461114fc36bc31db4f9390fc08 SHA1 0ec79e9ab691cbae5f116adaa3245ef0b123a598 SHA256 5b902eac127bc84e188224fbfe0182ab3fa3b03c200325ada9cd628bb913b479
 AUX gromacs-4.0.4-sparc-cyclecounter.patch 492 RMD160 0edd643a6dc11820e9785561f03047795044311f SHA1 66c0339c308b3d661def0e184311be510e804c3b SHA256 01565b45b73b32d8d6f83bf1fdf750de4215b24935d992c81191a52d01eb6bed
 AUX gromacs-4.0.9999-ccache.patch 678 RMD160 043d0e207e04a275fe00a3bd2b28f8dc0dfd4b7f SHA1 08bc5ac8bc0b28f68e1ede994d49616dd920af5d SHA256 ca477d54351c418f1d39dda29373a1426c9403ec0d2f21c28fc7568227d47632
@@ -9,10 +12,29 @@ DIST gromacs-4.0.4.tar.gz 8443779 RMD160 f90327814170c26a43d99fe7587357a46989fde
 DIST gromacs-4.0.5.tar.gz 8465397 RMD160 4c2344629307f3a3daa11b986153d65883a44783 SHA1 9969aae6f77e2216add22a7b29805c4de8df649f SHA256 436b7a2a1ba3637eb07e30d676d78962008373a28fd17a3d889fa5816ca30339
 DIST gromacs-4.0.7.tar.gz 8404518 RMD160 4fa8e5c90f549ef627a98a907a166676692a4c4b SHA1 8519bef2fa989fb487d54612b0a2d0228f228b30 SHA256 048f8ece2829f01d99f7e04e1d6e8f88d3a32273192274f2e9fcf71f41f212c1
 DIST gromacs-4.0.7_upstream2010-06-08.patch.gz 11876 RMD160 d65c9cf0386319953113ac1a5dc548768a745345 SHA1 823a72c4126d789ae38921bd46743414d4f391c1 SHA256 91d3eee79a0ec20df506e59bab789fe15428b4323548af5f97ccbae506036879
+DIST gromacs-4.5.1.tar.gz 10304547 RMD160 116ca5bc4644d1460086cfb2097961abd11db63b SHA1 cbe52c3ec613fe8b652cd24b86c4fdf31b58c71b SHA256 768a02ee995f950b442dc131c25c1b946f1907d2286fd3fa3eb7fa967ed8efb0
+DIST gromacs-4.5.pdf 2445884 RMD160 65548f56a71697128ab44cae59d5b7997c86fbdb SHA1 1a6ff8fb56873eccfa03b104770a136e0befe298 SHA256 028cb5b150185157a7d93849c0c1f8e442c41c942932ffbf0530ef1774e66449
 DIST manual-4.0.pdf 2135100 RMD160 b963642f8e1433f11328c3d0c4b1645c9de506da SHA1 8ae951ee15b2a7dc626331fce36511bc8766144c SHA256 646f810477eee2d710de6019c52056550413d0ba77baf9680195c835ddafe80a
 EBUILD gromacs-4.0.4.ebuild 6918 RMD160 d31ffadfe240147555b227c36456d81c35f5f5dc SHA1 52b59952c4fb4861ed6bbe2f48ba4c3443b07cd4 SHA256 078f3942a1b5bf671326be97dacb22f37783c082c154bf193e28e18c4e314d3e
 EBUILD gromacs-4.0.5.ebuild 6762 RMD160 c9945b966f14d1aa3fab96928a8c1269f2d0b4fb SHA1 535119ceb458903fd294f21959df4338eafd475d SHA256 dc76914d616ac4f750e9073601f1fc9cd30ab6f7b15a01152b95ef625a755c3b
-EBUILD gromacs-4.0.7-r3.ebuild 9540 RMD160 b7c43616491ec6279aca067a51a3fc5aed54ec29 SHA1 5e90f2bccd73a2028774bf616443d5126f9e8f42 SHA256 3334fbb93e15796ed1e39671dfee967b110bc20cca515cb3581ae789fe4caebd
 EBUILD gromacs-4.0.7-r4.ebuild 10002 RMD160 75c73eb0cdb1b6864c05240dad42ff0b8a8be612 SHA1 c5574abb0300832cf85f83c0707d6df14ac0e480 SHA256 e14c9d1378f8a9b43282f4c5b2f23d0b4c0bef551e22b6e8c6fa97d8a789b6e3
-MISC ChangeLog 11370 RMD160 e341c0beebf25d325ee56c2418567d90ac655552 SHA1 34b879291f0aec40cd8fd4a4019bac14207f01cf SHA256 056c701a90c713a7c8be74bd405e3ace03e8a78e4554f5f98ad8897634ac6cfd
+EBUILD gromacs-4.5.1.ebuild 7575 RMD160 686727c7c26b20a2068417b0dbe284b2bf771e7f SHA1 582f88829a46789b41738876a0874ad63fd8a343 SHA256 ba6dab49699bc8ee494c9f26b517cc9aa45a70916a2a46f38a93eb57ac8c95e9
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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
 }