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

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  [sci-chemistry/gromacs] switch to cmake
  media-gfx/librecad: version bump to 1.0.0rc1

7 files changed, 108 insertions, 76 deletions

diff --git a/media-gfx/librecad/ChangeLog b/media-gfx/librecad/ChangeLog
index dbaf87f6c..d3f14cf38 100644
--- a/media-gfx/librecad/ChangeLog
+++ b/media-gfx/librecad/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header$
 
+  19 Jun 2011; Dongxu Li <dongxuli2011@gmail.com> +librecad-1.0.0_rc1.ebuild:
+  Version bump to 1.0.0rc1
+
   09 Jun 2011; Dongxu Li <dongxuli2011@gmail.com> +librecad-1.0.0_beta5.ebuild:
   added tagged version 1.0.0beta5
 
diff --git a/media-gfx/librecad/Manifest b/media-gfx/librecad/Manifest
index b28d89239..2f9712b75 100644
--- a/media-gfx/librecad/Manifest
+++ b/media-gfx/librecad/Manifest
@@ -1,4 +1,5 @@
 EBUILD librecad-1.0.0_beta5.ebuild 1026 RMD160 51fcc8a3ea196ebecea814a02cc01eca466e4ed7 SHA1 cb8e1c7f825daacb19fcd40401f4c41690ca4df3 SHA256 dfa8d18c0e22447719eb425a4ae6387c0feb6773f53ad75bbb93813d4caf7f61
+EBUILD librecad-1.0.0_rc1.ebuild 1022 RMD160 175edc46aea2596ca7e167ccee430b2f996d271f SHA1 9199f5b30b7dc35fb2c71d823d2b05f703f54ca9 SHA256 f597851f8e8de0074cea56ecd91ec651a561a91073f628108220d86c2db0b04d
 EBUILD librecad-9999.ebuild 996 RMD160 d9ce7fa7f930871a46f7e0f59f6ea0743a6b4261 SHA1 65afe6bae17430931f2c36bd5f2c95eaaf62a2ff SHA256 9042a2a97a40b4ed23c4a9649c263600988a1f660e6a84854f0198ceb2f0de04
-MISC ChangeLog 478 RMD160 0b3a74f5b4bc5cba8bf6d8b5db0a4364c2ca3dbd SHA1 7c25225e00f2195724979643314874245757a6df SHA256 2eec70764f6409ef93c4efb58849f8248773c6fd40bd77313420e0628f02fd8b
+MISC ChangeLog 584 RMD160 7103b24bbd8dabeeec2b534f64a7063cf597bbae SHA1 6875333492013523dc39548efef316d9a2a67816 SHA256 1225506066f48b259f0fac94515877c725d443725d0575a5292501212e327dc6
 MISC metadata.xml 450 RMD160 62a6501cecfe47078279b48be9b1c658d40e59f9 SHA1 c4ea83204f0d636b89b362f43aa2f5f487b9d9c7 SHA256 891d496161866e9f329036a1a953bd667d7be70de7cb1da41eadbb4be21c7df8
diff --git a/media-gfx/librecad/librecad-1.0.0_rc1.ebuild b/media-gfx/librecad/librecad-1.0.0_rc1.ebuild
new file mode 100644
index 000000000..241a8bc66
--- /dev/null
+++ b/media-gfx/librecad/librecad-1.0.0_rc1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="3"
+inherit qt4-r2 git-2
+
+DESCRIPTION="An generic 2D CAD program"
+HOMEPAGE="http://www.librecad.org/"
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug doc"
+
+EGIT_REPO_URI="https://github.com/LibreCAD/LibreCAD.git"
+EGIT_COMMIT="${PV/_rc/rc}"
+
+RDEPEND="x11-libs/qt-gui[qt3support]"
+DEPEND="${RDEPEND}
+	x11-libs/qt-assistant:4
+	x11-libs/qt-qt3support:4
+"
+
+src_prepare()
+{
+# patch to solve an issue caused by gcc-4.6, by mickele, archlinux
+	sed -e "s|LiteralMask<Value_t, n>::mask;|LiteralMask<Value_t, static_cast<unsigned int>(n)>::mask;|" \
+	-e "s|SimpleSpaceMask<n>::mask;|SimpleSpaceMask<static_cast<unsigned int>(n)>::mask;|" \
+	-i fparser/fparser.cc
+}
+
+src_install()
+{
+	dobin unix/librecad
+	insinto /usr/share/"${PN}"
+	doins -r unix/resources/*
+	if use doc ; then
+	dohtml -r support/doc/*
+	fi
+	doicon res/main/"${PN}".png
+	make_desktop_entry "${PN}" LibreCAD "${PN}.png" Graphics
+}
diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 0aeec1bab..e6f868f5e 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  19 Jun 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+  metadata.xml:
+  autotools is broken
+
   10 Apr 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.0.9999.ebuild:
   remove 4.0.* (EOM)
 
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 5cfe6fb63..86aaaf454 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -3,18 +3,18 @@ Hash: SHA1
 
 DIST gmxtest-4.0.4.tgz 14845017 RMD160 c7c583415438bdef4c9996da9064254e9460cf16 SHA1 998179aa2bfbc4f80514f10ed774762f85c854c3 SHA256 6a7f787f4bb7cbecb688115ff0854a5ffd2ef33487d7bce4b031e63848b6f361
 DIST gromacs-manual-4.5.4.pdf 2463242 RMD160 309a1d9bc5f4821076d53f668c36f1c6bfc1714f SHA1 58c0261308212af29fa0c4f4a6d1b81da6d84766 SHA256 dc14504a7072b61e7aa576c48f04df03356824f3a9d9e744dfaf51529ab46252
-EBUILD gromacs-4.5.9999.ebuild 7545 RMD160 69969f6ad0593b4fadfe45aa1df24a82d75536f3 SHA1 55f40f07cd3affa411c7169ac2ca83b8421295f3 SHA256 435eb79316f5d61a5c116e0ba122efa7ef6950684b9c37ea6506c517cdbeef7f
+EBUILD gromacs-4.5.9999.ebuild 7092 RMD160 3cab367d6b5f94d9a217b7a2dc649518d329876c SHA1 5c13305d1805ac8e1986718a3a53638a71852b2c SHA256 947f1846f90f0ce7b0757c585cdd129f33fef792f002f154b94c07091e07ccb6
 EBUILD gromacs-9999.ebuild 6949 RMD160 9faa82a67668cfb24d18a1f5cb219367f145ec5e SHA1 546217bdd0a13e0f2f3ad61fb24cb7834241a7e3 SHA256 124feeb94b1d44e6c80f8b15b2d8ffe8f2ffe04ddeedbf540b9fe44b46a997c9
-MISC ChangeLog 8191 RMD160 8ed43c9efd0bf0c3696b525530b9b1064b97520d SHA1 37f9aab566e89cbcebf071570a519f4bc045192f SHA256 cd8f5e6acbaf4c251e4b605a0893455ce4d2cc0182af1dd0e7d3280849f14f3c
-MISC metadata.xml 621 RMD160 7875bd7f4880d1f08123d4457e98df4421c259ea SHA1 fee39a7fd465f3c4944be645ce622353c1ab5480 SHA256 ce14ff9ec55fd9c34c2ca75d796cff3fb443a1c5e94204089d58a7fff0598ef1
+MISC ChangeLog 8309 RMD160 e9f8f099957de0d6153034a927bd2b3d17e52f69 SHA1 337e2cab8f4d9f98595990cb1d2581c84b6c1fbf SHA256 88413af68d9e1b0e3aeb104136dcae6dfcba0cad069636f62fa7bfae586e306b
+MISC metadata.xml 564 RMD160 86538191a78eecb3e5264a0ec2c140bcd934fe5b SHA1 9d558b6a973ebf97af5610d120a95952c0856c38 SHA256 84d4035296101b9d443eb9eca49b4698cea484e0c3b840c73d006d1278961813
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.17 (GNU/Linux)
 
-iQEcBAEBAgAGBQJNvXifAAoJEOeBhlrCAAWGmlYH/jpIhCKz2jOfzx1IsM2a8dqp
-H/14ASVNLYggbn4majWXozaxre+meWw7qIPcpByGsTUMyrQSNSowVX5HgUl/Yb+C
-f0zRNSOoHdQJAbd96mOC2/9bZr7fr+nJJa6/5Bv/JCSBIyXPTpdtbzn633oA8Hl0
-hcyAkwfkEmMn/OadubsQcoNOZSlmt0dIN7Ov97Y08tEabDuiASWF1nFfcQZlvZ7d
-gTd8A3tKmAKTVXaHsUhve6T5ITr7jgdjQGRjpfNoS6ZI1oRbXm03ljwBEE0B8m+R
-vrozeC2w1HmVKl5s9oRosCVenZkGmlScisMX6t6kHs3B9rzIT+HoImjQkrAy5+0=
-=aHGC
+iQEcBAEBAgAGBQJN/lvHAAoJEOeBhlrCAAWGlpMH/1BLwyI5Ya/2JehWIetD39AN
+tgnn6YOezdysVw+W8/9yPvVULbiXG0X2g/vdAwPa5hKOvzaN2XbxIOWGxhbWEwvw
++Fh0Et0sToNh++6+6/j0PdORSPs0IIvXd3bqbRIPTuSZFLayLyuQpE1HshJifrIz
+HXGIm80gN0QIAI/OJuHzCqXUftwqIfe6qQdXkkZ4fF6zxOosZgrIYXhvCdEPNhoQ
+8gES9tbSENGLJcyeomrt6qrd7P4/DJwgQWL3op/zP9eja8PwzlUwLAfi45ZWFsSh
+re7n32Glnk7NN2kzijd9cxzRcF5dCDOLI0QyVN6wsAEMbiqUppDzFuzc/Hf7Cyo=
+=mV+a
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index 469f60402..f144a3f57 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -4,11 +4,10 @@
 
 EAPI="4"
 
-LIBTOOLIZE="true"
 TEST_PV="4.0.4"
 MANUAL_PV="4.5.4"
 
-inherit autotools-utils bash-completion flag-o-matic multilib toolchain-funcs
+inherit bash-completion cmake-utils eutils multilib toolchain-funcs
 
 SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
 		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
@@ -27,8 +26,8 @@ HOMEPAGE="http://www.gromacs.org/"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
-mpi +single-precision sse2 static-libs test +threads +xml zsh-completion"
+IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
+mpi +single-precision sse2 test +threads xml zsh-completion"
 REQUIRED_USE="fkernels? ( !threads )"
 
 CDEPEND="
@@ -37,7 +36,6 @@ CDEPEND="
 		x11-libs/libSM
 		x11-libs/libICE
 		)
-	dmalloc? ( dev-libs/dmalloc )
 	blas? ( virtual/blas )
 	fftw? ( sci-libs/fftw:3.0 )
 	gsl? ( sci-libs/gsl )
@@ -52,6 +50,9 @@ RDEPEND="${CDEPEND}
 RESTRICT="test"
 
 src_prepare() {
+	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
+	epatch_user
+
 	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"
@@ -59,10 +60,6 @@ src_prepare() {
 		elog "machines only, you can safely disable mpi"
 	fi
 
-	autotools-utils_src_prepare || die
-
-	eautoreconf || die
-
 	GMX_DIRS=""
 	use single-precision && GMX_DIRS+=" float"
 	use double-precision && GMX_DIRS+=" double"
@@ -77,8 +74,12 @@ src_prepare() {
 }
 
 src_configure() {
+	local mycmakeargs_pre=( )
 	#from gromacs configure
-	if ! use fftw; then
+	if use fftw; then
+		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
+	else
+		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
 		ewarn "WARNING: The built-in FFTPACK routines are slow."
 		ewarn "Are you sure you don\'t want to use FFTW?"
 		ewarn "It is free and much faster..."
@@ -119,65 +120,52 @@ src_configure() {
 		elog "libmd with and without mpi support."
 	fi
 
-	# if we need external blas or lapack
-	use blas && export LIBS+=" $(pkg-config blas --libs)"
-	use lapack && export LIBS+=" $(pkg-config lapack --libs)"
-	local sseflag="x86-64-sse"
-	use x86 && sseflag="ia32-sse"
-
-	#missing flag in autotools (bug #339837)
-	use sse2 && append-flags -msse2
+	#go from slowest to fasterest acceleration
+	local acce="none"
+	use fkernels && acce="fortran"
+	use altivec && acce="altivec"
+	use ia64 && acce="ia64"
+	use sse2 && acce="sse"
+
+	mycmakeargs_pre+=(
+		$(cmake-utils_use X GMX_X11)
+		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
+		$(cmake-utils_use gsl GMX_GSL)
+		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
+		$(cmake-utils_use threads GMX_THREADS)
+		$(cmake-utils_use xml GMX_XML)
+		-DGMX_DEFAULT_SUFFIX=off
+		-DGMX_ACCELERATION="$acce"
+	)
 
 	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"
-		myeconfargs=(
-			--bindir="${EPREFIX}"/usr/bin
-			--docdir="${EPREFIX}"/usr/share/doc/"${PF}"
-			--enable-"${x}"
-			$(use_with dmalloc)
-			$(use_with fftw fft fftw3)
-			$(use_with gsl)
-			$(use_with X x)
-			$(use_with xml)
-			$(use_enable threads)
-			$(use_enable altivec ppc-altivec)
-			$(use_enable ia64 ia64-asm)
-			$(use_with lapack external-lapack)
-			$(use_with blas external-blas)
-			$(use_enable fkernels fortran)
-			--disable-bluegene
-			--disable-la-files
-			--disable-power6
-			--disable-ia32-sse
-			--disable-x86-64-sse
-			$(use_enable sse2 $sseflag)
-		)
-		#disable ia32-sse and x86-64-sse and enable what we really need in last line
-
-		einfo "Configuring for ${x} precision"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			autotools-utils_src_configure --disable-mpi	--program-suffix="${suffix}" \
-			CC="$(tc-getCC)" F77="$(tc-getFC)"
+		local p
+		[ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
+			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
 		use mpi || continue
 		einfo "Configuring for ${x} precision with mpi"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			autotools-utils_src_configure --enable-mpi --program-suffix="_mpi${suffix}" \
-			CC="$(tc-getCC)" F77="$(tc-getFC)"
+		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
+			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
 	done
 }
 
 src_compile() {
 	for x in ${GMX_DIRS}; do
 		einfo "Compiling for ${x} precision"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			autotools-utils_src_compile
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_compile
 		use mpi || continue
 		einfo "Compiling for ${x} precision with mpi"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			autotools-utils_src_compile mdrun
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+			cmake-utils_src_compile mdrun
 	done
 }
 
@@ -193,18 +181,13 @@ src_test() {
 
 src_install() {
 	for x in ${GMX_DIRS}; do
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			autotools-utils_src_install
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" \
+			cmake-utils_src_install
 		use mpi || continue
-		#autotools-utils_src_install does not support args
-		#using autotools-utils_src_compile instead
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			autotools-utils_src_compile install-mdrun DESTDIR="${D}"
-
-		#stolen from autotools-utils_src_install see comment above
-		local args
-		has static-libs ${IUSE//+} && ! use	static-libs || args='none'
-		remove_libtool_files ${args}
+		#cmake-utils_src_install does not support args
+		#using cmake-utils_src_compile instead
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+			cmake-utils_src_make install-mdrun DESTDIR="${D}"
 	done
 
 	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 4aa2d9900..1126439eb 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -7,7 +7,6 @@
 		<name>Christoph Junghans</name>
 	</maintainer>
 	<use>
-		<flag name='dmalloc'>Enable use of Debug Malloc</flag>
 		<flag name='double-precision'>More precise calculations at the expense of speed</flag>
 		<flag name='fkernels'>Enable building of Fortran Kernels for platforms that dont have assembly loops</flag>
 		<flag name='single-precision'>Single precision version of gromacs (default)</flag>