Version Bump and add support for extendNMR

Package-Manager: portage-2.2_rc98/cvs/Linux x86_64

4 files changed, 234 insertions, 6 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 96cd6f2119eb..37a86016fea8 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,12 @@
 # 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 1.41 2010/10/13 07:40:31 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.42 2010/10/20 07:04:45 jlec Exp $
+
+*ccpn-2.1.5_p101020 (20 Oct 2010)
+
+  20 Oct 2010; Justin Lecher <jlec@gentoo.org> +ccpn-2.1.5_p101020.ebuild,
+  metadata.xml:
+  Version Bump and add support for extendNMR
 
 *ccpn-2.1.5_p101013 (13 Oct 2010)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 6febc730e7cd..8712f96c8123 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -20,17 +20,19 @@ DIST ccpn-update-100921.patch.bz2 17693 RMD160 a1c2de812ce524969b9148d5e0f6e0c5c
 DIST ccpn-update-100924.patch.bz2 20846 RMD160 e914a04322bad3d1eaefd5250ff70c10e7d50dbb SHA1 765e4e8590b471152f6acdbe0f088df5e2bbd541 SHA256 762a95cdb410c8b08dd4d4d17f76595549e890031c7f8bf379ab78d5850228f8
 DIST ccpn-update-100927.patch.bz2 20853 RMD160 e6b8c606504a7607c01487ba992353951d94681d SHA1 5dd5648286575abf39e34d054d54f552615b88bb SHA256 831295d28f827636b2ad9620556190f58ffcb607b373147c3715c80a9a292cce
 DIST ccpn-update-101013.patch.bz2 36926 RMD160 d1cd280599cd66ee0729f1bcb47b3a4647c0d83c SHA1 9a63a95c2b2281084ac9e98edba28c1e9ff1bdf1 SHA256 288ec2995ea7d49c3a477be57f509f9cd32719b2a10ab50745069a321f8f5c88
+DIST ccpn-update-101020.patch.bz2 37643 RMD160 2ebdef4783f420589026870bc319c33c4b210953 SHA1 4b114192862b461822907732620dfbefc82f985f SHA256 893f49a264af9335a3bcf11b4165f66a62f36adf052c75eacdf78c3a4e7a8ce8
 EBUILD ccpn-2.1.3.1_p100806.ebuild 5190 RMD160 c1dd4e2443ab5cf8386627a9feba25be6e61b715 SHA1 0d9700191a04c6ed5f106e2712b010d499315827 SHA256 ed26ef362193f91d4726fd49a1c4b19c1f975c3847b0616ada2e64ce7a90ffa5
 EBUILD ccpn-2.1.5_p100921-r2.ebuild 5815 RMD160 83a020277c866ae39a093a1745cf5b7f4cb38b44 SHA1 10d4161af742915be2715c23d3be4756a5ec4152 SHA256 c1b15892c449205a8bf94a544481d86059ecd9352db2e454790abd90214b2df1
 EBUILD ccpn-2.1.5_p100924.ebuild 5812 RMD160 19790f131cc251e4fc637ca3cb78ab8797488625 SHA1 b7f322f97dfdea15b553a00e6fb1db13a120d553 SHA256 89c2201e7fa61902d7db063ce499a85e1aab1b6f87451e0568eb6024401561c0
 EBUILD ccpn-2.1.5_p100927.ebuild 5871 RMD160 3b636e724225f9749b3469dddf2259bea5299566 SHA1 0d378b29421a4668fa430cacc16285ae63e2762d SHA256 d4df7a1404a685d59339db2d0a300994664e204a309ca1002351d019c8101d9f
 EBUILD ccpn-2.1.5_p101013.ebuild 5871 RMD160 4b09dca2f1831086d1c244a2ed7e0e3408b75218 SHA1 24a5408a535bd09af7681bf19ef748ddf6eb5d3d SHA256 adea7d4adefea50c2b4d1024eb7b289942afd2574eb506ea3fb32c6107f977e2
-MISC ChangeLog 6975 RMD160 4fa62c222f2ba5aef518b41b6bdb2cdb95a4403f SHA1 7208f44652f8ce50bbf7bf94c3ad9972bd3c3c6f SHA256 830e9b6629e0f2fa2b214fa1505721d47889ae24823c59ba86a328bf275f90f5
-MISC metadata.xml 226 RMD160 0355d90bd8d1c106a19b136045ebdf970a0a2485 SHA1 1db0b2a470657641079d6613829df49a5c043ed6 SHA256 094a3ac740c81b9afbff3c855ba93cc20a593cad2392f6f4404715608a836fa1
+EBUILD ccpn-2.1.5_p101020.ebuild 5987 RMD160 d30032f094aa48f91602c9faf0bf5f3f993d4c3a SHA1 d10dac38e6a66ff605be4b5a6620d46b9f86a41a SHA256 b389e10458b72258c9128ea5cc8423044bf974ecba618fae6afe507dde64283f
+MISC ChangeLog 7147 RMD160 6761ee8e8fdaa87e1abb3c7e509e2a320a2eda41 SHA1 3f0f9482ebb580d802827c5e10db03de82a0c6d3 SHA256 e591d6f9c4004c61a5bf74b6aa6692461afcefae8c4c4e98958d26d2517b0636
+MISC metadata.xml 317 RMD160 6e56ad407f163d80504468f6fedcfb35fc31db00 SHA1 30b72b0612b1f91712537d24e3a2407eec50e1dd SHA256 1fb093ab05124dcd078fc93a4aa6f787f5829066e100ed98da8ecf65cece63fb
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diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p101020.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p101020.ebuild
new file mode 100644
index 000000000000..b66bddaf7837
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.1.5_p101020.ebuild
@@ -0,0 +1,217 @@
+# 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-2.1.5_p101020.ebuild,v 1.1 2010/10/20 07:04:45 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2:2.5"
+SUPPORT_PYTHON_ABIS="1"
+PYTHON_USE_WITH="ssl tk"
+RESTRICT_PYTHON_ABIS="2.4 3.*"
+
+inherit eutils portability python toolchain-funcs versionator
+
+PATCHSET="${PV##*_p}"
+MY_PN="${PN}mr"
+MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
+MY_MAJOR="$(get_version_component_range 1-3)"
+
+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.gentoo.org/~jlec/distfiles/ccpn-update-${PATCHSET}.patch.bz2"
+HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="extendnmr +opengl"
+
+RDEPEND="
+	dev-lang/tk[threads]
+	>=dev-python/numpy-1.4
+	>=dev-tcltk/tix-8.4.3
+	=sci-libs/ccpn-data-"${MY_MAJOR}"*
+	x11-libs/libXext
+	x11-libs/libX11
+	extendnmr? (
+		sci-chemistry/aria
+		sci-chemistry/prodecomp )
+	opengl? (
+		media-libs/freeglut
+		dev-python/pyglet )"
+# We need to fix this
+#		sci-chemistry/mdd
+DEPEND="${RDEPEND}"
+
+RESTRICT="mirror"
+S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
+
+src_prepare() {
+	[[ -n ${PATCHSET} ]] && \
+		epatch "${WORKDIR}"/ccpn-update-${PATCHSET}.patch
+
+	epatch "${FILESDIR}"/${MY_PV}-parallel.patch
+
+	local tk_ver
+	local myconf
+
+	tk_ver="$(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)"
+
+	rm -rf data model doc license || die
+	python_copy_sources
+
+	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:^\(GL_DIR =\).*:\1 ${GL_DIR}:g" \
+			-e "s:^\(GL_LIB =\).*:\1 ${GL_LIB}:g" \
+			-e "s:^\(GL_LIB_FLAGS =\).*:\1 ${GL_LIB_FLAGS}:g" \
+			-e "s:^\(GL_INCLUDE_FLAGS =\).*:\1 ${GL_INCLUDE_FLAGS}: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$(python_get_version):g" \
+			c/environment_default.txt > c/environment.txt
+	}
+	python_execute_function -s preparation
+}
+
+src_compile() {
+	building() {
+		emake -C c all links
+	}
+	python_execute_function -s building
+}
+
+src_install() {
+	local libdir
+	local tkver
+
+	find . -name "*.pyc" -type d -delete
+
+	libdir=$(get_libdir)
+	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
+
+	for wrapper in analysis dangle dataShifter depositionFileImporter extendNmr eci formatConverter pipe2azara; do
+		sed -e "s:gentoo_sitedir:${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" \
+			-e "s://:/:g" \
+		    "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
+		dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
+	done
+
+	installation() {
+		local in_path
+		local files
+		local pydocs
+
+		pydocs="$(find python -name doc -type d)"
+		rm -rf ${pydocs} || die
+
+		in_path=$(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} || die
+		done
+
+		insinto ${in_path}
+
+		dodir ${in_path}/c
+
+		ebegin "Installing main files"
+			doins -r python || die "main files installation failed"
+		eend
+
+		dosym ../../../..//share/doc/ccpn-data-${MY_MAJOR}/html ${in_path}/doc || die
+		for i in ${pydocs}; do
+			dosym /usr/share/doc/ccpn-data-${MY_MAJOR}/html/${i} ${in_path}/${i}
+		done
+
+		dosym /usr/share/ccpn/data ${in_path}/data
+		dosym /usr/share/ccpn/model ${in_path}/model
+
+		einfo "Adjusting permissions"
+
+		files="
+			cambridge/c/BayesPeakSeparator.so
+			ccp/c/StructUtil.so
+			ccp/c/StructStructure.so
+			ccp/c/StructBond.so
+			ccp/c/StructAtom.so
+			ccpnmr/c/DyAtomCoord.so
+			ccpnmr/c/DyDistConstraint.so
+			ccpnmr/c/DyDistForce.so
+			ccpnmr/c/AtomCoordList.so
+			ccpnmr/c/DyAtomCoordList.so
+			ccpnmr/c/ContourStyle.so
+			ccpnmr/c/ContourLevels.so
+			ccpnmr/c/SliceFile.so
+			ccpnmr/c/PeakCluster.so
+			ccpnmr/c/Dynamics.so
+			ccpnmr/c/Bacus.so
+			ccpnmr/c/Midge.so
+			ccpnmr/c/DyDistConstraintList.so
+			ccpnmr/c/WinPeakList.so
+			ccpnmr/c/PeakList.so
+			ccpnmr/c/DistConstraint.so
+			ccpnmr/c/CloudUtil.so
+			ccpnmr/c/DistForce.so
+			ccpnmr/c/DistConstraintList.so
+			ccpnmr/c/AtomCoord.so
+			ccpnmr/c/DyDynamics.so
+			ccpnmr/c/ContourFile.so
+			memops/c/ShapeFile.so
+			memops/c/BlockFile.so
+			memops/c/PdfHandler.so
+			memops/c/MemCache.so
+			memops/c/FitMethod.so
+			memops/c/PsHandler.so
+			memops/c/GlHandler.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/metadata.xml b/sci-chemistry/ccpn/metadata.xml
index dde7ca88a50f..032b2a83a1fe 100644
--- a/sci-chemistry/ccpn/metadata.xml
+++ b/sci-chemistry/ccpn/metadata.xml
@@ -5,4 +5,7 @@
 <maintainer>
   <email>jlec@gentoo.org</email>
 </maintainer>
+<use>
+  <flag name='extendnmr'>Install needed packages for extendNMR support</flag>
+</use>
 </pkgmetadata>