sci-chemistry/ccpn: Add latest python patches

Package-Manager: portage-2.2.0_alpha187/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

3 files changed, 187 insertions, 15 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index e414f28af653..070b14085eef 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/ccpn
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.109 2013/07/05 15:21:52 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.110 2013/07/09 07:22:10 jlec Exp $
+
+*ccpn-2.3.0_p130709 (09 Jul 2013)
+
+  09 Jul 2013; Justin Lecher <jlec@gentoo.org> +ccpn-2.3.0_p130709.ebuild:
+  Add latest python patches
 
 *ccpn-2.3.0_p130705 (05 Jul 2013)
 *ccpn-2.2.2_p130705 (05 Jul 2013)
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 0f526aa3db9b..f55445c412de 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -39,22 +39,23 @@ EBUILD ccpn-2.2.2_p130530.ebuild 4649 SHA256 71865dc944175d9c8d89841b4f6901f2285
 EBUILD ccpn-2.2.2_p130618.ebuild 4649 SHA256 b207878c8186f25add8b44b09e0565c0659a72d55a683ba542d09184c6cc108b SHA512 5fb2620d6b12e4a94ead6158538634c5a842b097dcfedaaf570135adcdfb2d5119539c8306abd5ef43293385cf1aacfdc6e8de7e2963ed4c25ccaa727dac4945 WHIRLPOOL ac4561982960cf8d02d864112b97b00ce6af4c0b6a1190a08330a9effab7b41629d1681bdc0bf090faf3d6266549a17e9790b86b4e749b3718717b676197c2eb
 EBUILD ccpn-2.2.2_p130705.ebuild 4649 SHA256 1b3a3af9673c488457fc4b62074178c04c6aa67ef7db4bf1be13c628e8103a06 SHA512 e763f62dc24f181831ca87e301b889e2308a2d3ab34aea5934978cf509a3bc8387c68055d4f18ddc4cebb3d149e0ff0d3650d3dd80d616b551906a5568fdf405 WHIRLPOOL 3d41deb0023bdda918f3745c10f107d787388c88b68e98ee224fcb840029700b01405b2d3185a24c87f695b9dac071c9894376b053cbf961cd3db28190e9a171
 EBUILD ccpn-2.3.0_p130705.ebuild 4717 SHA256 3791c502fab4c7dffd98eb18b41ae7642f687e2763ae9496dfe9927964bb8a03 SHA512 2b1a73869bb1bfd79522432395e3cefbde8fd5e6158d9a87ee8f5977beadefe1feffcd4256888a66baa4b41458a6e327b9ac935dad60779a51fc3d4c04a24d39 WHIRLPOOL 52e733e610056e39a04fe75f6d2baafaf07048044f329408dad336561b60286dbb2b3d84191ee306bea57011d8bffa1b5e43d2b9b5c11570e9565cf3acd97b5e
-MISC ChangeLog 21295 SHA256 ad9d5532774e662caed9f2ea3e69fda0eda8b709345377737e5d31bb680597f7 SHA512 44c4852ede99d600f5c81203379c3d5c381c789abad44c48b6795e37cf2a46d75ec9e7d9e3b04a6c114dc6af45304b0218772ec809e0fed206756b6ffc58f68f WHIRLPOOL 17ae5d5f1d3b0dd179aac883673cc0ac8056d64860412c476ca83eefe0a069d43abadf8f0b8de245a3066073c22696b5f5eccbd657e7da6bac38b8b32356028d
+EBUILD ccpn-2.3.0_p130709.ebuild 4717 SHA256 a6d50c3708a40d6dd9c513fa0f54b431166ddda300c7f2a0c4992a8f1968549f SHA512 97f2a5b2b43fc7973968bca51d53efa4c6756e868037947271da3f707106dfe93c36e1ac665b0cc49e0dcf010654d2fdaad6626ae9c0f96cee68d09e4c2203f9 WHIRLPOOL 3b1eafb4a19964b81874f2569fc24239cb4095e4a9d7a718917148e57906deb578a0fa6ce160bc351f4ae54acb655c0556e605ac3cbb7f9c2bcd90665670a1c3
+MISC ChangeLog 21434 SHA256 3c8fa62d9bdc8c15bdb06915e625176b729842d1a703e3c6480251649390fb6d SHA512 95e1c00a36601dfaba3a72b2e6f2b9d5fc720f36e290c16a8785a323ef64ad4bb033f4acf63a5e0f86645f7bdb2fe585004218dec469a84a75579b28af6e300c WHIRLPOOL f2ae7e29fe7abd72526a6f26263dbf2cad3ec1921b331c091d1281523a9f6320be0f45beb14850ef89c0a280896e0beeeaa5f638f7d5d580c3d3161b87ad10c9
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
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diff --git a/sci-chemistry/ccpn/ccpn-2.3.0_p130709.ebuild b/sci-chemistry/ccpn/ccpn-2.3.0_p130709.ebuild
new file mode 100644
index 000000000000..91575733e1e9
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.3.0_p130709.ebuild
@@ -0,0 +1,166 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.3.0_p130709.ebuild,v 1.1 2013/07/09 07:22:10 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_5,2_6,2_7} )
+PYTHON_REQ_USE="ssl,tk"
+
+inherit eutils flag-o-matic multilib portability python-single-r1 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"
+HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
+SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}r2.tar.gz -> analysis${MY_PV}.tar.gz"
+[[ -n ${PATCHSET} ]] \
+	&& SRC_URI+=" http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+opengl"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+	${PYTHON_DEPS}
+	dev-lang/tk[threads]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-tcltk/tix
+	=sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}]
+	sci-biology/psipred
+	x11-libs/libXext
+	x11-libs/libX11
+	opengl? (
+		media-libs/freeglut
+		dev-python/pyglet[${PYTHON_USEDEP}] )"
+DEPEND="${RDEPEND}"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2)
+
+src_prepare() {
+	[[ -n ${PATCHSET} ]] && \
+		epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
+
+	epatch "${FILESDIR}"/${MY_PV}-parallel.patch
+
+	append-lfs-flags
+
+	sed \
+		-e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
+		-e "s:weights_s:weights:g" \
+		-i python/ccpnmr/analysis/wrappers/Psipred.py || die
+
+	local tk_ver
+	local myconf
+
+	tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
+
+	if use opengl; then
+		GLUT_NEED_INIT="-DNEED_GLUT_INIT"
+		IGNORE_GL_FLAG=""
+		GL_FLAG="-DUSE_GL_TRUE"
+		GL_DIR="${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 ${CPPFLAGS} ${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|^\(TK_LIB =\).*|\1 -ltk|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 -l${EPYTHON}|g" \
+		c/environment_default.txt > c/environment.txt || die
+
+	sed \
+		-e 's:ln -s:cp -f:g' \
+		-i $(find python -name linkSharedObjs) || die
+}
+
+src_compile() {
+	emake -C c all
+	emake -C c links
+}
+
+src_install() {
+	local libdir
+	local tkver
+	local _wrapper
+
+	find . -name "*.pyc" -type f -delete || die
+
+	libdir=$(get_libdir)
+	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
+
+	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr"
+	for wrapper in ${_wrapper}; do
+		sed \
+			-e "s|gentoo_sitedir|$(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|${EPYTHON}|g" \
+			-e "s|gentoousr|${EPREFIX}/usr|g" \
+			-e "s|//|/|g" \
+			"${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
+		dobin "${T}"/${wrapper}
+	done
+
+	local in_path=$(python_get_sitedir)/${PN}
+	local files
+	local pydocs
+
+	pydocs="$(find python -name doc -type d)"
+	rm -rf ${pydocs} || die
+
+	for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
+	sed \
+		-e 's|#from __future__|from __future__|g' \
+		-i ${i} || die
+	done
+
+	dodir ${in_path#${EPREFIX}}/c
+
+	ebegin "Installing main files"
+		python_moduleinto ${PN}
+		python_domodule python
+	eend
+
+	ebegin "Adjusting permissions"
+	for _file in $(find "${ED}" -type f -name "*so"); do
+		chmod 755 ${_file}
+	done
+	eend
+	python_optimize
+}