Version bump, keyworded for amd64-linux and x86-linux

Package-Manager: portage-2.2_rc62/cvs/Linux x86_64

5 files changed, 271 insertions, 5 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 66df50a5de3b..de61ed403acd 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/ccpn
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.5 2010/02/16 21:40:19 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.6 2010/02/17 20:59:19 jlec Exp $
+
+*ccpn-2.1.3 (17 Feb 2010)
+
+  17 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  +files/2.1.3-dynamics.patch, +ccpn-2.1.3.ebuild,
+  +files/2.1.3-parallel.patch:
+  Version bump, keyworded for amd64-linux and x86-linux
 
 *ccpn-2.1.2.1_p100216 (16 Feb 2010)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 416a3cd4d15b..29ea69307458 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -2,6 +2,8 @@
 Hash: SHA1
 
 AUX 2.1.2_1-parallel.patch 490 RMD160 73b6c601950c9c83f8f3d3dd204db23ab9a60567 SHA1 676774362a3b5a2ecd2083cac09d3f73b38aeab0 SHA256 60f1b33d80545b97e32f8cbd5c01cd67824b9d3adf12cf2adceb197850d01d24
+AUX 2.1.3-dynamics.patch 1271 RMD160 3ce267fbe9b2f68bc9ae6936b74ba74b5976c966 SHA1 8a0a7b0c669ffc8b42982d97ecce22f537e4850f SHA256 f3bcc43c6334d89abf054d6031e74bd3e14b1e421d712ea68e10bee1cd77b27b
+AUX 2.1.3-parallel.patch 1158 RMD160 b9135a8f529374310e9a521fc1ac3c5bb96d3443 SHA1 fc94deb1d4978493abaef33178888f7d2d12076f SHA256 a7e5a741a98236d753fe32a28cd341583c9f9c08997bcf4924f4ff7f033e0f6a
 AUX analysis 290 RMD160 0615c926527a59cbcafd2084680bd491f55c6295 SHA1 03ed24715a97f96857026ca018c141ad3e685301 SHA256 ce472f49720fe6ed1f217c519ad66eb5921e64e0d4d002683dc516846b99c30d
 AUX dangle 286 RMD160 b0e6b5162b8940f129debfd006fba635b6d250e9 SHA1 d83cf9ee0940ff3d7c62270d8a79384b4e49f7af SHA256 3913f3ea1638638b76997ce02320bde74d279b3391d177e11d11678bfee9da08
 AUX dataShifter 289 RMD160 dde8a9f9effc6ef682cfad550a12b0e98585c8ec SHA1 0ccde2b8aeecdfe5b30c7b953e9cc49f61de3631 SHA256 27daf72a001b8114b7b133a0fb0c284f334a45026f1c1afcd29e46efc794f16d
@@ -9,18 +11,20 @@ AUX eci 274 RMD160 a940e822e64242500ec3aa656f41d908724a3ba2 SHA1 018cd59152dbfb5
 AUX formatConverter 293 RMD160 a2229663a5d682e17af8a6cb5f927f66ce59bea6 SHA1 fcd45ab7019911756194457bef1889b4320f00f5 SHA256 e0a4c8303185813084b3f2077e8909cd72593f1d0043443d7ba5f21901f81d2a
 AUX pipe2azara 297 RMD160 0cd01c0cf629710ff4b4267d9449b0b1f3d586e1 SHA1 16566033682903504d77f4acaa93a6625557087e SHA256 e34774b668732c3f4fb764e6c83cc938da3fb514cf5a58bb820827304dc80979
 DIST analysis2.1.2_1.tar.gz 19227793 RMD160 f633a8338e3fbb9d8ad77c9482d63191419b0885 SHA1 f711a424da22c84295610483a6cc481d2d2161e9 SHA256 e7eda0b50c357a2b62633c473da4621ccdc48c747c59d8ccb495d57e846308fa
+DIST analysis2.1.3.tar.gz 18917835 RMD160 068fed988cb20d899266680f7dd7af2ca1ae2b46 SHA1 51d54036775cc271251c9deaf112903296db19e6 SHA256 6e614d0ab7d4ccaed9d5e0401f25a821c81def4bda28e1426f4112c521031e47
 DIST ccpn-update-100204.patch.bz2 24401 RMD160 ec5f52845640706f87b7c04d83c6fb85140fd621 SHA1 f654efbaa66b26a596e77992ece2d8c9b2d41a27 SHA256 1888ad1857772a6adc79ec6d5e936e656cb2010532fa8b4ee7527a9938d5afb0
 DIST ccpn-update-100213.patch.bz2 35100 RMD160 9f4d415e91e8d227d62796098008e72f5010390b SHA1 5f5411d800c52b1b7d27dbf1ef712f48fa2b3145 SHA256 d652ae3b012ff4258b883077b2b4f27182f0220871840eef22a037f9ff3b9e8e
 DIST ccpn-update-100216.patch.bz2 37914 RMD160 92d2845f9a21a5ddc9fd71cf56928b61f497530c SHA1 de61701435675d10165826cf4cd590dca336cbb2 SHA256 13e062188e953ea62e779b7d89004ce103db61daf228cf6b9f7d3c77f39947fc
 EBUILD ccpn-2.1.2.1_p100204.ebuild 4886 RMD160 d16d658dca152c535626cafcf3604f1dab89120c SHA1 4c8c843a2d294692f07290df2b45d5992d54f03e SHA256 2a7897fdfd70577b11fd6066d383873bbf1d239029dc7a71eafb1b870c780067
 EBUILD ccpn-2.1.2.1_p100213.ebuild 4886 RMD160 8a13c927894e056377a5160766f0caad176f81a9 SHA1 73c731ae0b9c25114f44e667ee5e78650bfae21b SHA256 254fca3522a6a3020470eda87ba3e3b7907a56cdecd0077a0017659df1260aef
 EBUILD ccpn-2.1.2.1_p100216.ebuild 4886 RMD160 d8e6a014c77a7ce40c40ae46416c2d5c15c14b09 SHA1 8e47f0a495d720eda820f94baca5b1088b26b4a8 SHA256 5478960144f864ebdcd57048084d54bfa6c0d59350223ab9404715fb36bdabd4
-MISC ChangeLog 1091 RMD160 ae040b333619235a054e1f951536cdd250428db2 SHA1 d867fd990a968b6853fe11892001e5a07ce4ddf5 SHA256 5e246b9cfe436f7c2515b03d2f75efa2f33a18cf3ccd8a9e5ee619a113c49ebf
+EBUILD ccpn-2.1.3.ebuild 4981 RMD160 9404d1d8ee7c1638f024b9ea1b0de703510fcd64 SHA1 f2f1fd6496af93b8dc59affa6e9ed8188b8bcc84 SHA256 2411dbdc3631aa2606d6a6780fefaa02f6c1d66626b0321c7567136e769ae47c
+MISC ChangeLog 1311 RMD160 b4f001e1f92c9c671895c36e62f4770444fcb4d8 SHA1 4ab2192b53d43f4285c139394182b173af8045a6 SHA256 e3ca694b48e261fb59da2b129a43741ea7ea71911a9f769275245b9e06d16d94
 MISC metadata.xml 226 RMD160 0355d90bd8d1c106a19b136045ebdf970a0a2485 SHA1 1db0b2a470657641079d6613829df49a5c043ed6 SHA256 094a3ac740c81b9afbff3c855ba93cc20a593cad2392f6f4404715608a836fa1
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.14 (GNU/Linux)
 
-iEYEARECAAYFAkt7EMgACgkQgAnW8HDreRbmggCgmKp8rsuxJagR/Y2M5ITv4fa5
-LwoAoLlTaPsvt8bAs+NflVB1VWuCRlOC
-=CEeY
+iEYEARECAAYFAkt8WKwACgkQgAnW8HDreRbwjQCggkn/5qbyWOX4A+Si4fWDQfS7
+T/AAoMiC2GYnv3ShZOrDdi/DHjfs8SB7
+=d6Fz
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/ccpn/ccpn-2.1.3.ebuild b/sci-chemistry/ccpn/ccpn-2.1.3.ebuild
new file mode 100644
index 000000000000..8c47384cbf35
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.1.3.ebuild
@@ -0,0 +1,181 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.3.ebuild,v 1.1 2010/02/17 20:59:19 jlec Exp $
+
+EAPI="3"
+PYTHON_DEPEND="2:2.5"
+SUPPORT_PYTHON_ABIS="1"
+PYTHON_USE_WITH="ssl tk"
+
+inherit eutils portability python toolchain-funcs versionator
+
+#PATCHSET="${PV##*_p}"
+MY_PN="${PN}mr"
+MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
+
+DESCRIPTION="The Collaborative Computing Project for NMR"
+SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
+	[[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI}	http://dev.gentooexperimental.org/~jlec/distfiles/ccpn-update-${PATCHSET}.patch.bz2"
+HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+opengl"
+
+RDEPEND="
+	dev-lang/tk
+	dev-python/numpy
+	dev-tcltk/tix
+	opengl? ( virtual/glut )"
+DEPEND="${RDEPEND}"
+RESTRICT_PYTHON_ABIS="2.4 3.*"
+
+RESTRICT="mirror"
+S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
+
+src_prepare() {
+	[[ -n ${PATCHSET} ]] && \
+		epatch "${WORKDIR}"/ccpn-update-${PATCHSET}.patch
+
+	epatch "${FILESDIR}"/${MY_PV}-parallel.patch
+	epatch "${FILESDIR}"/${MY_PV}-dynamics.patch
+
+	local tk_ver
+	local myconf
+
+	tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
+
+	if use opengl; then
+		GLUT_NEED_INIT="-DNEED_GLUT_INIT"
+		IGNORE_GL_FLAG=""
+		GL_FLAG="-DUSE_GL_FALSE"
+		GL_DIR="${EPREFIX}/usr"
+		GL_LIB="-lglut -lGLU -lGL"
+		GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
+		GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
+
+	else
+		IGNORE_GL_FLAG="-DIGNORE_GL"
+		GL_FLAG="-DUSE_GL_FALSE"
+	fi
+
+	GLUT_NOT_IN_GL=""
+	GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
+
+	python_copy_sources --no-link
+
+	preparation() {
+		sed \
+			-e "s:/usr:${EPREFIX}/usr:g" \
+			-e "s:^\(CC =\).*:\1 $(tc-getCC):g" \
+			-e "s:^\(OPT_FLAG =\).*:\1 ${CFLAGS}:g" \
+			-e "s:^\(LINK_FLAGS =.*\):\1 ${LDFLAGS}:g" \
+			-e "s:^\(IGNORE_GL_FLAG =\).*:\1 ${IGNORE_GL_FLAG}:g" \
+			-e "s:^\(GL_FLAG =\).*:\1 ${GL_FLAG}:g" \
+			-e "s:^\(GLUT_NEED_INIT =\).*:\1 ${GLUT_NEED_INIT}:g" \
+			-e "s:^\(GLUT_NOT_IN_GL =\).*:\1:g" \
+			-e "s:^\(X11_LIB_FLAGS =\).*:\1 -L${EPREFIX}/usr/$(get_libdir):g" \
+			-e "s:^\(TCL_LIB_FLAGS =\).*:\1 -L${EPREFIX}/usr/$(get_libdir):g" \
+			-e "s:^\(TK_LIB_FLAGS =\).*:\1 -L${EPREFIX}/usr/$(get_libdir):g" \
+			-e "s:^\(PYTHON_INCLUDE_FLAGS =\).*:\1 -I\$(PYTHON_DIR)/include/python$(python_get_version):g" \
+			-e "s:^\(PYTHON_LIB =\).*:\1 -lpython$(python_get_version):g" \
+			-e "s:^\(GL_LIB_FLAGS =\).*:\1 -L${EPREFIX}/usr/$(get_libdir):g" \
+			c/environment_default.txt > c/environment.txt
+	}
+	python_execute_function -s preparation
+}
+
+src_compile() {
+	building() {
+		emake -C c all links
+	}
+	python_execute_function -s building
+}
+
+src_install() {
+	local libdir
+	local tkver
+
+	libdir=$(get_libdir)
+	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
+
+	for wrapper in analysis dangle dataShifter eci formatConverter pipe2azara; do
+		sed -e "s:gentoo_sitedir:${EPREFIX}/$(python_get_sitedir -f):g" \
+		    -e "s:gentoolibdir:${EPREFIX}/usr/${libdir}:g" \
+			-e "s:gentootk:${EPREFIX}/usr/${libdir}/tk${tkver}:g" \
+			-e "s:gentootcl:${EPREFIX}/usr/${libdir}/tclk${tkver}:g" \
+			-e "s:gentoopython:${EPREFIX}/usr/bin/python:g" \
+		    "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
+		dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
+	done
+
+	installation() {
+		local in_path
+		local files
+
+		in_path=$(python_get_sitedir)/${PN}
+
+		for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
+			sed \
+				-e 's:#from __future__:from __future__:g' \
+				-i ${i}
+		done
+
+		insinto ${in_path}
+
+		dodir ${in_path}/c
+
+		ebegin "Installing main files"
+		doins -r data model python || die "main files installation failed"
+		eend
+
+		dohtml -r doc/* || die
+		dosym ../../../../share/doc/${PF}/html ${in_path}/doc || die
+
+		einfo "Adjusting permissions"
+
+		files="ccpnmr/c/ContourFile.so
+			ccpnmr/c/ContourLevels.so
+			ccpnmr/c/ContourStyle.so
+			ccpnmr/c/PeakList.so
+			ccpnmr/c/SliceFile.so
+			ccpnmr/c/WinPeakList.so
+			ccpnmr/c/AtomCoordList.so
+			ccpnmr/c/AtomCoord.so
+			ccpnmr/c/Bacus.so
+			ccpnmr/c/CloudUtil.so
+			ccpnmr/c/DistConstraintList.so
+			ccpnmr/c/DistConstraint.so
+			ccpnmr/c/DistForce.so
+			ccpnmr/c/Dynamics.so
+			ccpnmr/c/Midge.so
+			ccp/c/StructAtom.so
+			ccp/c/StructBond.so
+			ccp/c/StructStructure.so
+			ccp/c/StructUtil.so
+			memops/c/BlockFile.so
+			memops/c/FitMethod.so
+			memops/c/GlHandler.so
+			memops/c/MemCache.so
+			memops/c/PdfHandler.so
+			memops/c/PsHandler.so
+			memops/c/ShapeFile.so
+			memops/c/StoreFile.so
+			memops/c/StoreHandler.so
+			memops/c/TkHandler.so"
+
+		for FILE in ${files}; do
+			fperms 755 ${in_path}/python/${FILE}
+		done
+	}
+	python_execute_function -s installation
+}
+
+pkg_postinst() {
+	python_mod_optimize ${PN}
+}
+
+pkg_postrm() {
+	python_mod_cleanup ${PN}
+}
diff --git a/sci-chemistry/ccpn/files/2.1.3-dynamics.patch b/sci-chemistry/ccpn/files/2.1.3-dynamics.patch
new file mode 100644
index 000000000000..89c36d4d3e8f
--- /dev/null
+++ b/sci-chemistry/ccpn/files/2.1.3-dynamics.patch
@@ -0,0 +1,22 @@
+diff --git a/ccpnmr2.1/python/ccpnmr/c/linkSharedObjs b/ccpnmr2.1/python/ccpnmr/c/linkSharedObjs
+index 8f56168..093bbe8 100755
+--- a/ccpnmr2.1/python/ccpnmr/c/linkSharedObjs
++++ b/ccpnmr2.1/python/ccpnmr/c/linkSharedObjs
+@@ -5,7 +5,6 @@ ln -s ../../../c/ccpnmr/analysis/ContourFile.so ContourFile.so
+ ln -s ../../../c/ccpnmr/analysis/ContourLevels.so ContourLevels.so
+ ln -s ../../../c/ccpnmr/analysis/ContourStyle.so ContourStyle.so
+ ln -s ../../../c/ccpnmr/analysis/PeakCluster.so PeakCluster.so
+-ln -s ../../../c/ccpnmr/analysis/PeakClusterList.so PeakClusterList.so
+ ln -s ../../../c/ccpnmr/analysis/PeakList.so PeakList.so
+ ln -s ../../../c/ccpnmr/analysis/SliceFile.so SliceFile.so
+ ln -s ../../../c/ccpnmr/analysis/WinPeakList.so WinPeakList.so
+@@ -18,9 +17,3 @@ ln -s ../../../c/ccpnmr/clouds/DistForce.so .
+ ln -s ../../../c/ccpnmr/clouds/Dynamics.so .
+ ln -s ../../../c/ccpnmr/clouds/Midge.so .
+ ln -s ../../../c/ccpnmr/clouds/Bacus.so .
+-ln -s ../../../c/ccpnmr/dynamics/DyAtomCoord.so .
+-ln -s ../../../c/ccpnmr/dynamics/DyAtomCoordList.so .
+-ln -s ../../../c/ccpnmr/dynamics/DyDistConstraint.so .
+-ln -s ../../../c/ccpnmr/dynamics/DyDistConstraintList.so .
+-ln -s ../../../c/ccpnmr/dynamics/DyDistForce.so .
+-ln -s ../../../c/ccpnmr/dynamics/DyDynamics.so .
diff --git a/sci-chemistry/ccpn/files/2.1.3-parallel.patch b/sci-chemistry/ccpn/files/2.1.3-parallel.patch
new file mode 100644
index 000000000000..83ee505fa6fc
--- /dev/null
+++ b/sci-chemistry/ccpn/files/2.1.3-parallel.patch
@@ -0,0 +1,52 @@
+diff --git a/ccpnmr2.1/c/Makefile b/ccpnmr2.1/c/Makefile
+index 9fa8500..a99a677 100644
+--- a/ccpnmr2.1/c/Makefile
++++ b/ccpnmr2.1/c/Makefile
+@@ -2,23 +2,20 @@ include environment.txt
+ 
+ all: compile
+ 
+-compile: global structure analysis clouds dynamics
++compile: global structure analysis clouds
+ 
+ global:
+ 	cd memops/global && $(MAKE)
+ 
+-structure:
++structure: global
+ 	cd ccp/structure && $(MAKE)
+ 
+-analysis:
++analysis: global
+ 	cd ccpnmr/analysis && $(MAKE)
+ 
+-clouds:
++clouds: global
+ 	cd ccpnmr/clouds && $(MAKE)
+ 
+-dynamics:
+-	cd ccpnmr/dynamics && $(MAKE)
+-
+ clean: global_clean structure_clean analysis_clean clouds_clean dynamics_clean
+ 
+ global_clean:
+@@ -33,9 +30,6 @@ analysis_clean:
+ clouds_clean:
+ 	cd ccpnmr/clouds && $(MAKE) clean
+ 
+-dynamics_clean:
+-	cd ccpnmr/dynamics && $(MAKE) clean
+-
+ realclean: global_realclean structure_realclean analysis_realclean clouds_realclean dynamics_realclean
+ 
+ global_realclean:
+@@ -50,9 +44,6 @@ analysis_realclean:
+ clouds_realclean:
+ 	cd ccpnmr/clouds && $(MAKE) realclean
+ 
+-dynamics_realclean:
+-	cd ccpnmr/dynamics && $(MAKE) realclean
+-
+ links: memops_links ccp_links ccpnmr_links
+ 
+ memops_links: