Version Bump

Package-Manager: portage-2.2.0_alpha12/cvs/Linux x86_64

3 files changed, 235 insertions, 6 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index e7372d1efc11..c02cae06c988 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,11 @@
 # 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 1.47 2010/12/05 15:12:38 jlec Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.48 2011/01/04 07:48:47 jlec Exp $
+
+*ccpn-2.1.5_p110103 (04 Jan 2011)
+
+  04 Jan 2011; Justin Lecher <jlec@gentoo.org> +ccpn-2.1.5_p110103.ebuild:
+  Version Bump
 
 *ccpn-2.1.5_p101201 (05 Dec 2010)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index bf87231149d0..be41afe3eff0 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -18,15 +18,17 @@ DIST analysis2.1.5.tar.gz 20338459 RMD160 b0706c859c1ee4da2ab80ee41534197268f73d
 DIST ccpn-update-100806.patch.bz2 187965 RMD160 3297162fe3314aa405ee58737ce45cda084834e5 SHA1 338423d9f36da3fb10dc9d9a3b8aeb932ae3bfd0 SHA256 5cea7899edb96237a6674f04a1beee6ad7b309e12964ea8b25d9ea6ff752d0d4
 DIST ccpn-update-101114.patch.bz2 43432 RMD160 d3a1725737e1d722de5ef172674400569bcad45f SHA1 bde020a3fe2ded176d05e4c611fdfbe67050c96d SHA256 5f92721c928afad0022b56fc9c9b78979b31735e457d92aa6ce8b261b64d73d6
 DIST ccpn-update-101201.patch.bz2 45897 RMD160 d7ff94e8239e871c7595b5f760e013317b62173d SHA1 193e9790ed2e1fad5587550e4ea890ad5a33ca3d SHA256 b0466d5d408f3f9e752d4581eeddedd1ea244e2cd4f29b42f7c321a065628844
+DIST ccpn-update-110103.patch.bz2 46865 RMD160 798b3f6630eca9a8a3bd5ad37327ba13bab63086 SHA1 da0f1e1049a8f7842491f0504a9085f43508afe1 SHA256 5e530489aac522a1aad71a52a12d75b0d4d92291e6e08c23b0a39f9abc743ecc
 EBUILD ccpn-2.1.3.1_p100806.ebuild 5190 RMD160 c1dd4e2443ab5cf8386627a9feba25be6e61b715 SHA1 0d9700191a04c6ed5f106e2712b010d499315827 SHA256 ed26ef362193f91d4726fd49a1c4b19c1f975c3847b0616ada2e64ce7a90ffa5
 EBUILD ccpn-2.1.5_p101114.ebuild 6080 RMD160 5392e66597c374b3487aa406357246c8acb3f739 SHA1 57d6f4523e4834bd4cfe935f9631f09eb4b71bf0 SHA256 3703ebc2c47b20ed0778d4aa996cf51681ea17467ba1870941a8a06a2c251728
 EBUILD ccpn-2.1.5_p101201.ebuild 6080 RMD160 7ad3203f685880b8c6e9148dd106e834db178fc5 SHA1 7accc62831ca664c82c3146eed3d50d6ffa8f72a SHA256 f1e750fb720a6b12f6250cdbc8cee95c6ba5127b3de47f979ec43c2108cc4e74
-MISC ChangeLog 8055 RMD160 84f1641822d01db260dddaba155a98127061b3eb SHA1 301b90bd72d76fdc53a36ef49866c7bc30909810 SHA256 5a23e4c5074b6042738e24dde3a228861f768c110d1a29dff0e4889a1732dc4d
+EBUILD ccpn-2.1.5_p110103.ebuild 6080 RMD160 03569f3cd15142a8535b0c57da09dae0618a9f2e SHA1 3a10d64edf64902aa3e60aa903763688cf92c045 SHA256 38008afd20d46e4156772052773b4914eeef6745c0e7bfa58cefc320180c01ee
+MISC ChangeLog 8181 RMD160 406113ff6e70e1803ebe4426a83929288a6fbe07 SHA1 69dcb5795b93618eb883fcf32c142b7e296e7221 SHA256 1caa9578dc0ca66672b501462359ca556bfdb5a390e911b5168be87d944bcb07
 MISC metadata.xml 317 RMD160 6e56ad407f163d80504468f6fedcfb35fc31db00 SHA1 30b72b0612b1f91712537d24e3a2407eec50e1dd SHA256 1fb093ab05124dcd078fc93a4aa6f787f5829066e100ed98da8ecf65cece63fb
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diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p110103.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p110103.ebuild
new file mode 100644
index 000000000000..47da78d38fe7
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.1.5_p110103.ebuild
@@ -0,0 +1,222 @@
+# Copyright 1999-2011 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_p110103.ebuild,v 1.1 2011/01/04 07:48:47 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
+	opengl? (
+		media-libs/freeglut
+		dev-python/pyglet )"
+# We need to fix this
+#		sci-chemistry/mdd
+DEPEND="${RDEPEND}"
+PDEPEND="
+	extendnmr? (
+		sci-chemistry/aria
+		sci-chemistry/prodecomp )"
+
+RESTRICT="mirror"
+S="${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$(python_get_version):g" \
+			c/environment_default.txt > c/environment.txt
+	}
+	python_execute_function -s preparation
+}
+
+src_compile() {
+	building() {
+		emake -C c all links
+	}
+	python_execute_function -s building
+}
+
+src_install() {
+	local libdir
+	local tkver
+	local _wrapper
+
+	find . -name "*.pyc" -type d -delete
+
+	libdir=$(get_libdir)
+	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
+
+	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara"
+	use extendnmr && _wrapper="${_wrapper} extendNmr"
+	for wrapper in ${_wrapper}; do
+		sed \
+			-e "s:gentoo_sitedir:${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}
+}