sci-chemistry/ccpn: Todays Python Patches

Package-Manager: portage-2.2.0_alpha99/cvs/Linux x86_64

3 files changed, 192 insertions, 5 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index e34b7e51bff8..5167fbb96108 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/ccpn
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.82 2012/04/03 17:24:27 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.83 2012/04/23 08:22:04 jlec Exp $
+
+*ccpn-2.2.2_p120423 (23 Apr 2012)
+
+  23 Apr 2012; Justin Lecher <jlec@gentoo.org> +ccpn-2.2.2_p120423.ebuild:
+  Todays Python Patches
 
 *ccpn-2.2.2_p120403 (03 Apr 2012)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 7f9473386a8f..80ff0ecdf49d 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -22,17 +22,19 @@ DIST ccpn-update-100806.patch.bz2 187965 RMD160 3297162fe3314aa405ee58737ce45cda
 DIST ccpn-update-2.2.1-120109.patch.xz 85304 RMD160 3f2662f16f8c52b8c3813a0a45ad12f26bb8ba3c SHA1 267686361c0ee730d132beede957591428cd7016 SHA256 2997ae03541267e75577f4df317c6a9b69a282723271a6689265a9c2309c5769
 DIST ccpn-update-2.2.1-120304.patch.xz 87980 RMD160 9d37afcd85557bb5385bb48dacb6f1f873a9ab0b SHA1 232365cc75aaa9d3114bf4b88968ad6af8fdbd6f SHA256 5fa751589394f709b0c65a965ac8f2a3bdab35a670c250bd4f2998acfac41153
 DIST ccpn-update-2.2.2-120403.patch.xz 4076 RMD160 87d49d46f7c0d36302d329d4931436261ee1f29d SHA1 89217679fc9ed64b002fdf8d6111949bdbd26b4e SHA256 1c9c01c8d06e430f22f08e073a4657deab28a669a4f682ed57756e73b7e58f49
+DIST ccpn-update-2.2.2-120423.patch.xz 14732 RMD160 b574554bbb7f47bc4c6b532cb5b620d7e31d3246 SHA1 12efe549e29348c0ed25d5325cd1613b6ea22e82 SHA256 61edae84fce89a05eaf92babc700823b9aacb7952ec343a83b961f7850a60190
 EBUILD ccpn-2.1.3.1_p100806.ebuild 5184 RMD160 777155a635a5d23d0e5eaa99fdb568ec36cfc722 SHA1 4ebd6e84c0e832264c726a42203d65b4a4065189 SHA256 255563ee932f4feee3cc3e1332dbd18be844efb78f2f8f10df9b1dd0894295e5
 EBUILD ccpn-2.2.1_p120109.ebuild 5784 RMD160 c6279bd8aab43037353347299c139da99c4d4bda SHA1 7cd2a6425cc8fd62396891874f16e1bfa7f33010 SHA256 b4b08ff9094119e5bd50066f72d41927bd3bbe840c0985f49c585501925ba593
 EBUILD ccpn-2.2.1_p120304.ebuild 5784 RMD160 e4278559ae4129bf56c73b7df807d73898910322 SHA1 c3e8b18e7a42c7e4d9e786e580ed40ae73b96710 SHA256 387882b2a69b312bfe9d7edaaf8a2dc399e1d3d16f62e3b250d91207e64c3f72
 EBUILD ccpn-2.2.2.ebuild 4792 RMD160 66866605d58520d45257e277f9b8a483ccae9fbc SHA1 977794e3110f24e8b63bca12e9f9ca96a632b9fb SHA256 268766d35ac9f38942d7bb5143daeb2e02cde8d72716aaa0c6cf4924642e6145
 EBUILD ccpn-2.2.2_p120403.ebuild 4799 RMD160 a50ffa3b80cb3a146d99a2337c76a693609261dc SHA1 c855594ee418f973bf9db6d45efcde8daee2ff83 SHA256 33104414788b86a93578114d0a14e91d57a4852e3cf4d37547f4ae3124424099
-MISC ChangeLog 17011 RMD160 a763d21ab60e1cfea75fa38b96e7f31733f41134 SHA1 7dc103103307a9fd471158f65a25f5119ac21f9f SHA256 4a826aaf6b5f0db5116c8b9bce60a07bd6886732131bdefaf22b0aa14d812d42
+EBUILD ccpn-2.2.2_p120423.ebuild 4799 RMD160 3a2a3a2ea0dc0a81bb3e5d80f016ae7e1722081d SHA1 ac51d13d13345ab7d40462baf6874e7b5f8fbe1e SHA256 5a9d2bc41515c2b1a05f5938b6719c80b5f4de19c04ae3f92557a332f52fa4c9
+MISC ChangeLog 17146 RMD160 76aa0dd6e2c5ccef6a1244986e817ecf2388e1b6 SHA1 aae13160356335346170c327b1b75b1e7d73e965 SHA256 823ec38c1759ac55a498d618a0d24fe9fce535790a01d0f00115350ff4b4ed85
 MISC metadata.xml 322 RMD160 9fd5fba7405b689fc39a089d81ffdaa9f961b514 SHA1 0c31132b25fca04cff97ef11fdc11940f90c77d0 SHA256 7468ba4c27b879e7ed5f82274f5837e51f1f389673a33b9e26e1756a6b0783df
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diff --git a/sci-chemistry/ccpn/ccpn-2.2.2_p120423.ebuild b/sci-chemistry/ccpn/ccpn-2.2.2_p120423.ebuild
new file mode 100644
index 000000000000..e4acdf7e9351
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.2.2_p120423.ebuild
@@ -0,0 +1,180 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.2_p120423.ebuild,v 1.1 2012/04/23 08:22:04 jlec Exp $
+
+EAPI=4
+
+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-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
+	[[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI}	http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
+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
+	dev-tcltk/tix
+	=sci-libs/ccpn-data-"${MY_MAJOR}"*
+	sci-biology/psipred
+	x11-libs/libXext
+	x11-libs/libX11
+	opengl? (
+		media-libs/freeglut
+		dev-python/pyglet )"
+# We need to fix this
+#		sci-chemistry/mdd
+DEPEND="${RDEPEND}"
+PDEPEND="
+	extendnmr? (
+		>=sci-chemistry/aria-2.3.2-r1
+		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
+	python_pkg_setup
+}
+
+src_prepare() {
+	[[ -n ${PATCHSET} ]] && \
+		epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
+
+	epatch "${FILESDIR}"/${MY_PV}-parallel.patch
+
+	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 ${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${EPREFIX}/$(python_get_includedir)|g" \
+		-e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
+		c/environment_default.txt > c/environment.txt || die
+
+	sed \
+		-e 's:ln -s:cp -f:g' \
+		-i $(find python -name linkSharedObjs) || die
+}
+
+src_compile() {
+	emake -C c all
+	emake -C c links
+}
+
+src_install() {
+	local libdir
+	local tkver
+	local _wrapper
+
+	find . -name "*.pyc" -type f -delete
+
+	libdir=$(get_libdir)
+	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
+
+	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara"
+	use extendnmr && _wrapper="${_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${tkver}|g" \
+			-e "s|gentoopython|$(PYTHON -a)|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
+
+	insinto ${in_path}
+
+	dodir ${in_path}/c
+
+	ebegin "Installing main files"
+		doins -r python
+	eend
+
+	ebegin "Adjusting permissions"
+
+	for _file in $(find "${ED}" -type f -name "*so"); do
+		chmod 755 ${_file}
+	done
+	eend
+}
+
+pkg_postinst() {
+	python_mod_optimize ${PN}
+}
+
+pkg_postrm() {
+	python_mod_cleanup ${PN}
+}