sci-chemistry/ccpn: Todays python patches

Package-Manager: portage-2.2.0_alpha121/cvs/Linux x86_64

3 files changed, 192 insertions, 5 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index f5c1c26e9f8c..9b8ae8d7c35f 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 1.90 2012/08/09 16:32:10 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.91 2012/08/12 09:19:09 jlec Exp $
+
+*ccpn-2.2.2_p120812 (12 Aug 2012)
+
+  12 Aug 2012; Justin Lecher <jlec@gentoo.org> +ccpn-2.2.2_p120812.ebuild:
+  Todays python patches
 
 *ccpn-2.2.2_p120809-r1 (09 Aug 2012)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 89487e872c07..899096d19e1b 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -27,6 +27,7 @@ DIST ccpn-update-2.2.2-120511.patch.xz 16728 SHA256 01ce6f8fe051921c0b05d4e5cc47
 DIST ccpn-update-2.2.2-120709.patch.xz 36136 SHA256 b51c9517a8bc493402dfa73f8d0a95fa5f3e2e4878a1835ce1c1d305f4b0aa4f SHA512 3ca122ca3201ad9576d6b01900cd298af5e01d8ed42054b5d8e17a75ac77fa965e00bd423d3e32f919b63d8a9157744705bd4265e257d4e5da9f036b3b16e419 WHIRLPOOL dff03e0d7f5f9175b765af700821901e8d2d475149b94b65f3919304bf67ebef823445f262b845127710916e101185fb946c9496578edde7e6770be0437b9587
 DIST ccpn-update-2.2.2-120731.patch.xz 43592 SHA256 73949616d170606b7ebb12d24f409bbef82515fad4fedd1877894944f68fff36 SHA512 7b1163ca7ad7a1fcaa0dc4433b9f3a254429b5df80ae5fb4b7988b23d65351a15a9629970959f8c4bfaf8570d375bf229f9243dc29230c1797b124e95cea9d78 WHIRLPOOL f5b169a776348de9e91c83fa3f2035eecb3d5caea96af2f85945adeba7fa8641e931b404bf0b8c17966a02d92413b091774720811fccc35ed0c7d992e4001cc4
 DIST ccpn-update-2.2.2-120809.patch.xz 45296 SHA256 b0fa50a3f6fc9acbd45f2a11b0020a14817a064cffd8e0d168ad925416265564 SHA512 b0af882d7167b8024822ff195e91618e1a03f0b9368e29ac75ce75e47644e37ce570fccc1fa8f9a6e8c093097691aa4e6e700836641bbdbb059ac2153849c693 WHIRLPOOL 002b6f590a1defb12944d79fa24c2a35502a568b7bde5d162505e0c50b136307795b70ba24a56a80838bf195f69cba609cc7ea9e3b3c716083b94be1ed926c07
+DIST ccpn-update-2.2.2-120812.patch.xz 45836 SHA256 81071c680018250e3ab4e2a279b121a5e073a77e7d6a75a0a8fe1521177d83ca SHA512 b98a537334c142ad8dd9b4f0e77177a08c17208e60c2ae4b29cc4022c3ed044c7a09428b1109c9e8468db6204e23346344cbcfd241dcde49368e3bc3f8d98141 WHIRLPOOL ab68ca3204e2b95e53ffc2440e15639976c9a9e63b7774b0bf2b95e218929a97d31750622a533fe5a965155363318c0a42faa8b66892f21ed849cf0d41682180
 EBUILD ccpn-2.1.3.1_p100806.ebuild 5181 SHA256 c3ba268461da63ea23ee7f621a8e4837a368eb3e4c85bcc5245250fb6b377b58 SHA512 701ea90a13dc44e5bf1ea17c0f69adea56b1c14788ab79c67fa4b9726cae532998717515568045aec9bb4e1dd4c352227130115d90c50bf07e7fd132cdee385d WHIRLPOOL 898a618f95b254785739e6fab20af333cb3a44bff12cd6840d1b111f1588a60e48055e8af7ca88457173452f6acba86ebd3bada96390211bc4cd063fe4160fd5
 EBUILD ccpn-2.2.1_p120109.ebuild 5784 SHA256 b4b08ff9094119e5bd50066f72d41927bd3bbe840c0985f49c585501925ba593 SHA512 37ff9cb372f395cb0497db2bf396e523b7a1ec16f03670425b6f5807a7ab15eae4718fd248af81ef9fdf5c4fbbd4f824d1d9c982c3aa9aefa57ce330b438b559 WHIRLPOOL b3b42229f7d32caffe7f81ddefbdce225438c07c203c67ee1a514e48b923e014166d3fd63601a4d9f2845c4b4aa9b8df98aa65e5c3dfc81ab1f0d7ac501eb6a2
 EBUILD ccpn-2.2.1_p120304.ebuild 5784 SHA256 387882b2a69b312bfe9d7edaaf8a2dc399e1d3d16f62e3b250d91207e64c3f72 SHA512 63596f039c56d69815d9250581dd41c61309a277e67d1ede04b7c4cdf7249af614e5a9f653d013bd2e63d25f54e3f07e9612efde04a39d141c6a202123211b3d WHIRLPOOL 87400bca5581904c5f0e0f43ca3bd375338f46082236128e01b93edc4ce791fe71da8e3c3b625ea7346d824ddfd9f2f57696642abbcaea5f29405e9b99f43b37
@@ -37,13 +38,14 @@ EBUILD ccpn-2.2.2_p120511.ebuild 4799 SHA256 02a0cf33a3cf98f798e4f9eea7f4febad9a
 EBUILD ccpn-2.2.2_p120709.ebuild 4799 SHA256 c757f21a728d4321577fcee7f3ee2346d68225aded0415ef5cf19a63f4f78fcc SHA512 7ce0c39f08f071bea1b3f7b84df61155e84d0d902d4ea097fe60e48b96a216976adb1161ebfcfd06089b91004ca5186dd9920a89fd7542fb0857db65b7124f5f WHIRLPOOL 7b3544a39be0826a5a64114e8d3c20816c8bd224fc1be39a726d441f25ffe4ee561340fe4db5612945da34a0c8d0c215cabab663368285b879b42df25f857fbe
 EBUILD ccpn-2.2.2_p120731.ebuild 4799 SHA256 e995094ac244da2cc73f519f6dc736edeba4d17ec863664e404a92c11a324483 SHA512 6861ac7f14559109593e3f166a7128c7c29135f84bdc12df04602181b36402b8446d762883c97f4c48ddc1995bed6cdfbc11ecc05e2bf8763655760ec59666b5 WHIRLPOOL b46af9e9b039fd7d702e113d612169bd38691504ae7a46a98f11281f0de6dcbd00d1c34d3b404a27f180d553a4f0e9b38477bfd1bb8eed4757e4540775d5152b
 EBUILD ccpn-2.2.2_p120809-r1.ebuild 4802 SHA256 bccdcdd8e479f2310b794188028402ccbcf021eb9ae433410dfcb22475d853ed SHA512 b912be59f726fecaa41a90fe1fa7e76dbce1a8651481b3321f9f714dc16c4370c28256bee2d11c0c684d7e34279fefde4d905ba93a58708a119521ca92ad17ec WHIRLPOOL da166beb37382249002f4f108cb2be86e5ae81ab14c9ab34581c18318822e722f7176cbc113ca2779c4c0228c6cf313e5818a3037d24deb8ec9ead0ce90488cf
-MISC ChangeLog 18051 SHA256 857e92f11ec68d7ec7e0ae515d9eb0df004ae9f1b1cf923b9fb694fb57e00dc4 SHA512 de363b505a19e611151ffe1014b7822df3ce805f74d56b38a1020f69df6d327424272168676c130befa379f1558c7725ac001c425075c7a4efaaba504effc686 WHIRLPOOL a481190215c9f23e6e72c4dbb64a3c832b4768756a744f47deb9e7ae16aea07d0a1ef3d96861ec9a0617776d5298f87a4a916e8aa81e3db714285b27c67168a8
+EBUILD ccpn-2.2.2_p120812.ebuild 4799 SHA256 5d12d6a86f9d695c257d3665f7933d2a8ee3065363ecc05854f83ba33d6a9018 SHA512 bb8506aceb25cf0131a08e482c594d9333a054bebf91e2334268ea99c124f83b6b4f8c0fbd81a82eb315c1429527b903c291dddec7df8105aff8149b19eaf435 WHIRLPOOL 4fc777f362c838e0c7ecec4f538efce7740c55d36ccb888761cb4869fb68442ee45431e49138b49aa151b80af2588e3b38ca7a9c2034f1c509fad69bea0db5cc
+MISC ChangeLog 18186 SHA256 ca7fc45a0e48bf46d0e6fed0c8d2e284d58333b6cffef982cd533ecdd0bd9405 SHA512 964828cd3ce5e446c9bf6a95d80347e43c1e51e53aab2ac834d7294560bddd5ab6acfedec5e4daed52ff5a2611c75b99416361246743003cc61234e1f9c70bef WHIRLPOOL 7ef2d91f51ae13313f9ffb73104c7cc56e550b3633344cf424aeab7c085e13e3d7e2fe0c97c7e952a880f541886abacdc41d9a73ecc9fdfb4779d370ba8ee4e9
 MISC metadata.xml 322 SHA256 7468ba4c27b879e7ed5f82274f5837e51f1f389673a33b9e26e1756a6b0783df SHA512 01933ddaa7b2ab20fd0c07ba6725c162dc9e0512275c91ff657732a69135f1ca7cb3ce39002b4e386aedf27fca26c086f80d31bd8a0821b696c9b99f59c140a4 WHIRLPOOL 1bd202323ff47b3fb34ca4cc6c89567b69a480d38abbcf1a140cbf8f316ebad8b7f95b4525ac261174e1b94555644cdb791dc532398b8f2fbf3cce74283d8ef8
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diff --git a/sci-chemistry/ccpn/ccpn-2.2.2_p120812.ebuild b/sci-chemistry/ccpn/ccpn-2.2.2_p120812.ebuild
new file mode 100644
index 000000000000..716c59aa714e
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.2.2_p120812.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_p120812.ebuild,v 1.1 2012/08/12 09:19:09 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}
+}