version bump

Package-Manager: portage-2.2.0_alpha149/cvs/Linux x86_64
Manifest-Sign-Key: 0xC2000586

4 files changed, 33 insertions, 39 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 1e26308fc329..3b92ed0c2520 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.113 2012/12/08 22:15:02 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.114 2012/12/22 19:41:32 ottxor Exp $
+
+*gromacs-4.6_beta3 (22 Dec 2012)
+
+  22 Dec 2012; Christoph Junghans <ottxor@gentoo.org> +gromacs-4.6_beta3.ebuild,
+  -gromacs-4.6_beta2.ebuild, metadata.xml:
+  version bump
 
   08 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.5-r1.ebuild,
   gromacs-4.6_beta2.ebuild:
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 7dc44233be6f..91b3cc0571c2 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -7,21 +7,21 @@ DIST 0001-Make-stack-non-executable-for-GAS-assembly.patch.gz 3569527 SHA256 17a
 DIST 0002-Make-stack-non-executable-for-ATT-assembly.patch.gz 3868244 SHA256 af12b3632aaf4e3d0c49ce99e0a4ed5de61c40d293bc592b70f89e08738f2581 SHA512 321d70aaf2c0bc7f9b22155029b0ac8a65c585a92f3473ce3eed3e39d9609f67d3dd28029f04a7d007dc03be9820c1e694ee76630557a6eb0bc875c4302edb8a WHIRLPOOL 47519f2e0a8aa3658841c32b18e8696f32b691236d9378c8ee57668c1762e21b781d24bcdcd903bb1ece66b3667215843610354f88e8647952bb81afb33951d4
 DIST gmxtest-4.0.4.tgz 14845017 SHA256 6a7f787f4bb7cbecb688115ff0854a5ffd2ef33487d7bce4b031e63848b6f361 SHA512 f8165ef1d7e2ed69db0a069a1c85fc5fa440d66e96aa54b474392a6331d2327b60f76b8dceb02f9233ce06eb6b7a4e7c448fc71f666e244efa571cf94f1e86ec WHIRLPOOL dbb122736a588deb7931204b29142dd3d9b074691e94341b04dcad2cdf428eb0aae739aa37ef6f61d1dcd6fb96ddcc1292e76f267694f3c18ee67d17352bfd9b
 DIST gromacs-4.5.5.tar.gz 10398178 SHA256 e0605e4810b0d552a8761fef5540c545beeaf85893f4a6e21df9905a33f871ba SHA512 8af0b81261a6b08c461275bccc4e72d23efd664ed5af12e3579956b5822ab6c6eea2ccbfbfe6ea1f4b30403a3c1367f52638e281cd1d7bc49e9220332c3e2b8c WHIRLPOOL 021a07171c3301184c48d31e2ad2068ce54b7746b9b0f9086d34796ddcfe750006e6f23bc0d8c52942fb491bd047411d7f5f21aaa9d7eb8ab9b7485fcb587f8c
-DIST gromacs-4.6-beta2.tar.gz 10224320 SHA256 6456a79c7322ddfdaf78f0d81350841ef0d738936059f032611c4688b1e71bf8 SHA512 f669180342be95bbf34b4b5fc4a47ce1fdeee13199a64552154ee5d3b61ccf645618f59f1498e45da19ddadcf0e21505b96b55d9e5fb5a3c49ef36a3144996d0 WHIRLPOOL e93f8486065d61023ccb2ae74ea7aea7e91e33c0edf819f37dd8b3ed1c7eeb72aeb4192aa3af43ad333e1a2c6443d0c45ac5b7b1955b4e54f71f31e6649d06ee
+DIST gromacs-4.6-beta3.tar.gz 10238128 SHA256 4ec708c0def71435d513fba01fe0d71f0cb8da71639a42cb9da8bf9e3985cae4 SHA512 862835e6c9fcdfd432d0205558279c775ccbd3fe5a1092728e2a0991a603bc74944ac4ab29fef0552aa4f17d945d1e74f87021533c42bf63d4c07dfcce73b427 WHIRLPOOL ecf080eafaa381ae9b80755a9389bd85e6b93d557e31aedbc385a5c0b32223e081220f44693ac9f5b50d502a908d6203101fd9290bafa190769f1a36ea64fcc2
 DIST gromacs-manual-4.5.4.pdf 2463242 SHA256 dc14504a7072b61e7aa576c48f04df03356824f3a9d9e744dfaf51529ab46252 SHA512 957995333163f6f28568a18d5423a75dc6c315215692da94d0916f09b6221e2a875c5ff4b05385ad6604bd8ae38f0cb61c740cd734c76b360aa4b598cd2c3380 WHIRLPOOL 07077d81ea89bc02207e45e56c77a668375a7284bf6f4a3cc7fe637f1f53ce4ab687c722f13f208cdd2c056b9d766ebfcbe5ea9579ce7649ec9e088371e7db8d
 DIST gromacs-manual-4.6-beta1.pdf 5527287 SHA256 788a424720b149d905d236d3c792d72c3f5af1c054f6ef19192bd12f44fe1fb9 SHA512 5a76aa847a865bfa8ca77bbad67eec18e8328c3db8af411a609a7039f48bcc1973ac6af0201c78f1428ed05040102cbe96638399413520bb1f1c1013031662c6 WHIRLPOOL 1c189bc1cc1da42bcb7332c45c13789ca822e57dbbff6452be7328163a95ed29b678a201250018a214a95e23fb43258d7cc6a58bdde88afcdf718db0c80cf45a
 EBUILD gromacs-4.5.5-r1.ebuild 7808 SHA256 ffedeea7d72e555a7ee13232b252c536d917ea9f428558386e72ccc010779b01 SHA512 1c21a6b55611c7aff88bf67a5519e5926cb9277bba44db36eebdf4e22f9fcc733a157ae2e2643123f1e38f998fd8d1524a5440b20de5c041d832567e12976497 WHIRLPOOL 7a2664e943bbd2eac9e095a37946794a32f843ec90dcc3c05209a77c454a17c61ea19ed5105bd81ccc1014f500ac434f4a2e73802decbbed0041a298f1c7dc54
-EBUILD gromacs-4.6_beta2.ebuild 7172 SHA256 b7d8ada1ba29a54aacab731200e6b68ef9f1c8db4bd08dbddc20637f47b93e14 SHA512 32381a341dce7ec21468d2b3aa25a23cf8075d4b537130af791fc65ffb4824c3fd752ef62ea9deb9684022990d345cec43754abb1c9fb243b0fc882dc93c1d78 WHIRLPOOL 1150a3f0a4609675fb07939882ea81f51a86f7c8503739c302ce533d173e5eca3212897cf685e047112fa7f7a53a52845b3a8656d15247d2b08b0f4206dc4551
-MISC ChangeLog 19019 SHA256 a5bbc0c28ed659bdb0fa13b58f3a35630c1b057e5b0d50eb7c15253d810176b7 SHA512 18e8b7f4862c081048f09166c0b2c8208794db534733141f7d0a36de21a4621dbca621718b637b65ea777d097c22fab0dbc6ae0f7c99eb1a8311c3e82fdc0bfb WHIRLPOOL f19efaed84155616eadd6ddfd45a07b0c822b695b4234bc841a09e6194cf88240da0a26ac19a9e48b29ad4b47fd1bb4c8cd141f0c7fac8c3de0af403c4237823
-MISC metadata.xml 1011 SHA256 86b258212de20c0346564d9e1705da78bf98c38b3a167417754f980734f12c20 SHA512 b824647ab78588b7312fb8b1cff5931e65940b0027b9f1edc7a258dfb981b8dd2cd88757d2b479d99cb150dd51dc3c93cc888b85aaa238403519dd28fed586e3 WHIRLPOOL 8cd1dc1682ad266ff47d5bf0770cf60649e30ce40e8fd2a072cf040efc6db99374242a5d0d1ea5eb24c5f68a4f04d1d946883d8d88741036256e0ba10d80da12
+EBUILD gromacs-4.6_beta3.ebuild 6867 SHA256 309333a6d7ed257106d0256fd2ecedb1dd4ce30818be710f9817b427060c8aa4 SHA512 991009e41ae2808ecaac8b97792b3442ad281e7ada702c8e97182da646943287830f35fec4272bfe32e92299da1a4b454f7b388c15dcb9717c0b8441713ee8fc WHIRLPOOL f702d3a97108e2fd0963ce015249d1a18260d3fb8ef85050f482760a2897530907749d1e41c486058a0b6f78dc9437de22abbc0861d45389f30d016c733040e3
+MISC ChangeLog 19193 SHA256 91b9e0d852dea688f27d461c844b924e8a673a957960b2abbc2324482f824002 SHA512 b26792ccde3355c2d07cd196eeafae9ca0d8b8467341c718a7f6159240c5fba48e1bb92a3d47169701b54b81c541899b324f9d7eed46e95a778dc77808dc82cc WHIRLPOOL a436a41a4d93c98926b1a06a6151e189cf42acf14b2dcda97472290b22262f7651e30cdabd44a4aa3e13870fcf35d669c24c74a38d3222fbae40640f2f343b13
+MISC metadata.xml 1025 SHA256 06243b817d8d4f9c3c391da58acb870fb1a4fb52627723968b15c975dfe57647 SHA512 7c1a532274bd74d186fdd6db7bccb7542f1642e75ed648277fb4ec89f83d5dc8706d135d973435ded6fc9826263860c0b536b306d60b97b6275e0bc4c78b6f8d WHIRLPOOL 5b4337a167d29a5e741449de7763526b382309c3b59d4de8d76e352f5460dfd08acae364cbdea042d9a1e8d452e56fac4ab8cad39cbcb403faff9b5586a8ddf3
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diff --git a/sci-chemistry/gromacs/gromacs-4.6_beta2.ebuild b/sci-chemistry/gromacs/gromacs-4.6_beta3.ebuild
index 478742a691ff..746dba40ba5b 100644
--- a/sci-chemistry/gromacs/gromacs-4.6_beta2.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6_beta3.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6_beta2.ebuild,v 1.2 2012/12/08 22:15:02 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6_beta3.ebuild,v 1.1 2012/12/22 19:41:32 ottxor Exp $
 
 EAPI=5
 
@@ -12,7 +12,7 @@ CMAKE_MIN_VERSION="2.8.5-r2"
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
+inherit bash-completion-r1 cmake-utils eutils multilib toolchain-funcs
 
 SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
 
@@ -23,14 +23,14 @@ if [[ $PV = *9999* ]]; then
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="release-4-6"
 	inherit git-2
-	PDEPEND="doc? ( ~app-doc/gromacs-manual-${PV} )"
+	PDEPEND="doc? ( ~app-doc/${PN}-manual-${PV} )"
 else
 	S="${WORKDIR}/${P//_/-}"
 	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P//_/-}.tar.gz
-		doc? (  ftp://ftp.gromacs.org/pub/manual/gromacs-manual-${MANUAL_PV}.pdf )"
+		doc? (  ftp://ftp.gromacs.org/pub/manual/${PN}-manual-${MANUAL_PV}.pdf )"
 fi
 
-ACCE_IUSE="fkernels power6 sse2 sse41 avx128fma avx256"
+ACCE_IUSE="sse2 sse41 avx128fma avx256"
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
@@ -38,8 +38,7 @@ HOMEPAGE="http://www.gromacs.org/"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE="X blas cuda doc -double-precision +fftw gsl lapack
-mpi openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
+IUSE="X blas cuda doc -double-precision +fftw gsl lapack mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -50,7 +49,6 @@ CDEPEND="
 	blas? ( virtual/blas )
 	cuda? ( dev-util/nvidia-cuda-toolkit )
 	fftw? ( sci-libs/fftw:3.0 )
-	fkernels? ( !threads? ( !sse2? ( virtual/fortran ) ) )
 	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
 	mpi? ( virtual/mpi )
@@ -69,22 +67,11 @@ pkg_pretend() {
 		die "Please switch to an openmp compatible compiler"
 }
 
-pkg_setup() {
+src_prepare() {
 	#notes/todos
 	# -on apple: there is framework support
 	# -mkl support
-	# -there are power6 kernels
-	if use fkernels; then
-		if use threads; then
-			ewarn "Fortran kernels and threads do not work together, disabling"
-			ewarn "fortran kernels"
-		else
-			fortran-2_pkg_setup
-		fi
-	fi
-}
 
-src_prepare() {
 	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
 	epatch_user
 
@@ -106,8 +93,6 @@ src_configure() {
 
 	#go from slowest to fastest acceleration
 	local acce="None"
-	use fkernels && use !threads && acce="Fortran"
-	use power6 && acce="Power6"
 	use sse2 && acce="SSE2"
 	use sse41 && acce="SSE4.1"
 	use avx128fma && acce="AVX_128_FMA"
@@ -124,6 +109,7 @@ src_configure() {
 		$(cmake-utils_use gsl GMX_GSL)
 		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
 		$(cmake-utils_use openmp GMX_OPENMP)
+		$(cmake-utils_use !offensive GMX_NO_QUOTES)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_ACCELERATION="$acce"
 		-DGMXLIB="$(get_libdir)"
@@ -221,7 +207,7 @@ src_install() {
 			ls -1 "${ED}"/usr/bin | sed -e '/_d$/d' > "${T}"/programs.list
 			doins "${T}"/programs.list
 		else
-			dodoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf"
+			dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf"
 		fi
 	fi
 	rm -rf "${ED}usr/share/gromacs/html/"
@@ -232,9 +218,11 @@ pkg_postinst() {
 	einfo  "Please read and cite:"
 	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
 	einfo  "http://dx.doi.org/10.1021/ct700301q"
-	einfo
-	einfo  $(g_luck)
-	einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
+	if use offensive; then
+		einfo
+		einfo  $(g_luck)
+		einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
+	fi
 	einfo
 	elog  "Gromacs can use sci-chemistry/vmd to read additional file formats"
 }
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 41931c0c7a95..24ddf421224b 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -15,7 +15,7 @@
 		<flag name="sse41">Enable sse4.1 acceleration</flag>
 		<flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
 		<flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
+		<flag name="offensive">Enable gromacs partly offensive quotes</flag>
 		<flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag>
-		<flag name="power6">Enable Power6 optimizations</flag>
 	</use>
 </pkgmetadata>