Python patches included from today

Package-Manager: portage-2.2.0_alpha15/cvs/Linux x86_64

3 files changed, 225 insertions, 5 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 12f38e5c18ee..b49a0076442c 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/ccpn
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.49 2011/01/05 19:02:25 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.50 2011/01/13 20:16:05 jlec Exp $
+
+*ccpn-2.1.5_p110113 (13 Jan 2011)
+
+  13 Jan 2011; Justin Lecher <jlec@gentoo.org> +ccpn-2.1.5_p110113.ebuild:
+  Python patches included from today
 
 *ccpn-2.1.5_p110105 (05 Jan 2011)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 1dc917845b9d..62ce9c8e603a 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -17,14 +17,16 @@ DIST analysis2.1.3_1.tar.gz 18932918 RMD160 5f19ea6fe47c2910d16fcba8d1a78f0e1dea
 DIST analysis2.1.5.tar.gz 20338459 RMD160 b0706c859c1ee4da2ab80ee41534197268f73d44 SHA1 70dc5e6b2752d6b7d5c8673fc992ebd0a88e6ad0 SHA256 9f91f1bd56fb73fd24e71d396c96c0f0d31b92287664b6a2e756f6efc630b31b
 DIST ccpn-update-100806.patch.bz2 187965 RMD160 3297162fe3314aa405ee58737ce45cda084834e5 SHA1 338423d9f36da3fb10dc9d9a3b8aeb932ae3bfd0 SHA256 5cea7899edb96237a6674f04a1beee6ad7b309e12964ea8b25d9ea6ff752d0d4
 DIST ccpn-update-110105.patch.bz2 47734 RMD160 0628b1bf5b5e7479abc587efb7a359e91c265b35 SHA1 b9271bb09fc676420b0c517a2a4e13d89ca0d02a SHA256 f107d9ccf6b699a63a95e5cf72950d9e23dcb8bcde17f64246f73694594912fa
+DIST ccpn-update-110113.patch.bz2 53812 RMD160 3d515870a7307de06a292a70adb88e1644ae92b0 SHA1 df05b65192d9e955e059139a12a80e8c32712561 SHA256 e4a87b0404cca92a633f649e81bd473e6d4362740bc8096bf15619a203fee48b
 EBUILD ccpn-2.1.3.1_p100806.ebuild 5190 RMD160 c1dd4e2443ab5cf8386627a9feba25be6e61b715 SHA1 0d9700191a04c6ed5f106e2712b010d499315827 SHA256 ed26ef362193f91d4726fd49a1c4b19c1f975c3847b0616ada2e64ce7a90ffa5
 EBUILD ccpn-2.1.5_p110105.ebuild 5753 RMD160 01bd53830ab36e5665508c31aa4e87b2c7f48f24 SHA1 e8dd3780ba22c4cfe16b5e533f91b16c32a4c73c SHA256 53212dbc19de5e3b03654c1498350dfe6ea6a11a20f379f2fe3aa97cf66e6a22
-MISC ChangeLog 8435 RMD160 0b3f328d06135725fe857ad3ad8e520879b66278 SHA1 96a552bc22fbb1f0562454bab98e45c8debe726a SHA256 b4115f2a37b26df1e1aeb37753f462b3d0f99b999addbac52c8a282e59b96ee1
+EBUILD ccpn-2.1.5_p110113.ebuild 5753 RMD160 b565ba9b7259c8f531bd4643b7a051497a808def SHA1 889e006503849764c0b3044d8190ff41d813645a SHA256 780d36c243c40ea7b31b09bc828a803b103ecbca24ad01cce02588936df7b886
+MISC ChangeLog 8583 RMD160 15a3f9e8fe5dcd071f3c6758703877017ed0140f SHA1 70707cb4952c1a5954b797fdbad8da5d76f605c7 SHA256 c525aeb2a90ba5676a6fc37a2707817ef73161fc7e91eb0b473915ea8bae38c4
 MISC metadata.xml 317 RMD160 6e56ad407f163d80504468f6fedcfb35fc31db00 SHA1 30b72b0612b1f91712537d24e3a2407eec50e1dd SHA256 1fb093ab05124dcd078fc93a4aa6f787f5829066e100ed98da8ecf65cece63fb
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diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p110113.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p110113.ebuild
new file mode 100644
index 000000000000..fb93cfbb133d
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.1.5_p110113.ebuild
@@ -0,0 +1,213 @@
+# 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_p110113.ebuild,v 1.1 2011/01/13 20:16:05 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2:2.5"
+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 _ ${PV%%_p*})"
+MY_MAJOR="$(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})
+
+pkg_setup() {
+	python_set_active_version 2
+}
+
+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
+
+	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_get_includedir):g" \
+		-e "s:^\(PYTHON_LIB =\).*:\1 $(python_get_library -l):g" \
+		c/environment_default.txt > c/environment.txt
+}
+
+src_compile() {
+	emake -C c all links
+}
+
+src_install() {
+	local libdir
+	local tkver
+	local _wrapper
+
+	find . -name "*.pyc" -type d -delete
+
+	libdir=$(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}$(python_get_sitedir):g" \
+		   -e "s:gentoolibdir:${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 ${wrapper}"
+	done
+
+	local in_path
+	local files
+	local pydocs
+
+	pydocs="$(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
+}
+
+pkg_postinst() {
+	python_mod_optimize ${PN}
+}
+
+pkg_postrm() {
+	python_mod_cleanup ${PN}
+}