sci-chemistry/ccpn: Todays python patches

Package-Manager: portage-2.2.0_alpha125/cvs/Linux x86_64

3 files changed, 192 insertions, 5 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index f0a18c04d384..d9f306683470 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 1.93 2012/08/29 06:24:14 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.94 2012/09/12 11:26:07 jlec Exp $
+
+*ccpn-2.2.2_p120912 (12 Sep 2012)
+
+  12 Sep 2012; Justin Lecher <jlec@gentoo.org> +ccpn-2.2.2_p120912.ebuild:
+  Todays python patches
 
 *ccpn-2.2.2_p120829 (29 Aug 2012)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 712757d387bc..16c6a529f423 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -30,6 +30,7 @@ DIST ccpn-update-2.2.2-120809.patch.xz 45296 SHA256 b0fa50a3f6fc9acbd45f2a11b002
 DIST ccpn-update-2.2.2-120812.patch.xz 45836 SHA256 81071c680018250e3ab4e2a279b121a5e073a77e7d6a75a0a8fe1521177d83ca SHA512 b98a537334c142ad8dd9b4f0e77177a08c17208e60c2ae4b29cc4022c3ed044c7a09428b1109c9e8468db6204e23346344cbcfd241dcde49368e3bc3f8d98141 WHIRLPOOL ab68ca3204e2b95e53ffc2440e15639976c9a9e63b7774b0bf2b95e218929a97d31750622a533fe5a965155363318c0a42faa8b66892f21ed849cf0d41682180
 DIST ccpn-update-2.2.2-120826.patch.xz 47148 SHA256 89bd0c49f47340375adba1c5bed08da0575d44480d4ed70327f2d8fe0ec66fb3 SHA512 eec0133ef318ca0f3c3b0bddd54561a750cfe4f55eb5915248e921bf452c93791a9ef9203e9de03001eae9dff028187a637ce2cf0f147ff5f064bead784f911e WHIRLPOOL ab8f1768a58e6dbbed0b01940944d2a04bfa415550a731ec2e6b7e698eb52968043d6bfd60a714bd33b9c3a191990736612bce5fb672f882015a1f785f193cdc
 DIST ccpn-update-2.2.2-120829.patch.xz 47500 SHA256 0ec4cd5103f4cd5d6dcddbfd1ee904ac443f0af99c6083ebdaf1a18377f139b3 SHA512 4c59299ad240c58c576634c47b777fb58c0c762d987415c1a919ff7d8634b6602a55abafd600396faab5e6669c45a47ee5a05f0e2c90b87c4787330055fb734a WHIRLPOOL 5ada41db62bece7a05f304c55f742aad0003be486900b040f16cf6dd36bc2d08595296c05a058cab3f505132dfe17fa7c2a80db3f396a3b1526055d169d8bcde
+DIST ccpn-update-2.2.2-120912.patch.xz 48644 SHA256 96d0287900a586439b49cc8f763864e0cb9765a0823b343a3345af3a46d35b99 SHA512 ad7f3f943c94352d2618dda1ccf483507690225c66fc41cdebd5185dfadc776e7dbd1978cae4c31e8fd6bfc7023ab8154fa733be47b3a44f414cba2e636577d3 WHIRLPOOL 6e87d9c090b2ea58a6e011bb8dda8d5728ad4b9edd0e7544111cea539c9fba3909b8e244d50312f28989c7ef895c4b816f3d9fb57acd6880a020c601454cccc6
 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
@@ -43,13 +44,14 @@ EBUILD ccpn-2.2.2_p120809-r1.ebuild 4802 SHA256 bccdcdd8e479f2310b794188028402cc
 EBUILD ccpn-2.2.2_p120812.ebuild 4799 SHA256 5d12d6a86f9d695c257d3665f7933d2a8ee3065363ecc05854f83ba33d6a9018 SHA512 bb8506aceb25cf0131a08e482c594d9333a054bebf91e2334268ea99c124f83b6b4f8c0fbd81a82eb315c1429527b903c291dddec7df8105aff8149b19eaf435 WHIRLPOOL 4fc777f362c838e0c7ecec4f538efce7740c55d36ccb888761cb4869fb68442ee45431e49138b49aa151b80af2588e3b38ca7a9c2034f1c509fad69bea0db5cc
 EBUILD ccpn-2.2.2_p120826.ebuild 4799 SHA256 ed120c939f731fa3eb7b2dba15ca18977c8a41658f10e0b2f464b2d6f37e4476 SHA512 8001b4b7623d6666b9bbed243d3dea4d7c739eebe89d40ebfa6d1baa27257bd71e54d642f60d2924dbe32539cf544c3486d54c6e416d965a75ea8b7dead21ca4 WHIRLPOOL 4ef33c97240c334744a3c8d2239592dbd4268b9affc9d4d71e6dab6cd6cff06735f2da4f0820b1620b4616e360318c81ee92854236cc146c2d49b4d2f26cc060
 EBUILD ccpn-2.2.2_p120829.ebuild 4799 SHA256 6930082cd40aad6f0503c4e02e21b377f4e3411264007a5b72b77ad107616843 SHA512 4b1e894a6650fa0ecbd9c6acc8811fd9317cffb1eebe40e8364394bd8d979c55956fafd1c67a8bc2349bd1b78b8dd3f3539f112b8de29cb6bcebdfe13887a699 WHIRLPOOL dae24e4ba14c8846c8413236b88261ecc2cd3ab00dae680bc5cc8cee6a1f1333a7bb40cdc069c9a2bf1687dca284f8a68e66aef58e237be5fdb86328f2dd0125
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+EBUILD ccpn-2.2.2_p120912.ebuild 4799 SHA256 e2d429881107e93973f2dd87982cbf2aff65bfc4d7def242931854f4d8199a74 SHA512 dc0e6b64d01164a68896701a9f9880206dccf067752865bfbd01afb6f5ceb3cb2603f41b96f275a65a6249f31af1306bcba77890cb773e15c6cb0000a967ce69 WHIRLPOOL fab86d5cc8e204ede0d3af451d736bce90fbfb52ce384ceb6c925fc97f41938590ea2b82f260ea3a07d6636b4e507528b9fa4de0a2ff9fdbefac763c42bf0f9e
+MISC ChangeLog 18589 SHA256 65fc4d84a5b14d772a1e983eaee601e3c9ca3508640d3a96ca6a8ede5b098e66 SHA512 0cc5b79537e5a03134205e2cfdacaca96bb492f445d0b888bcaef6e1946d0bb9566cbe735543cc205c27b075742c65650d89a230c96c471be5d6461f9f540fe1 WHIRLPOOL 61dd8384693c142709f76d2b503bc8020e58c2c750752103b7bfc6da8fb9e2f0468a4286ec87ac0a48154f1f0232568debf93c97242b6080cc7996eea43a884f
 MISC metadata.xml 322 SHA256 7468ba4c27b879e7ed5f82274f5837e51f1f389673a33b9e26e1756a6b0783df SHA512 01933ddaa7b2ab20fd0c07ba6725c162dc9e0512275c91ff657732a69135f1ca7cb3ce39002b4e386aedf27fca26c086f80d31bd8a0821b696c9b99f59c140a4 WHIRLPOOL 1bd202323ff47b3fb34ca4cc6c89567b69a480d38abbcf1a140cbf8f316ebad8b7f95b4525ac261174e1b94555644cdb791dc532398b8f2fbf3cce74283d8ef8
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diff --git a/sci-chemistry/ccpn/ccpn-2.2.2_p120912.ebuild b/sci-chemistry/ccpn/ccpn-2.2.2_p120912.ebuild
new file mode 100644
index 000000000000..95938b6ad10a
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.2.2_p120912.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_p120912.ebuild,v 1.1 2012/09/12 11:26:07 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}
+}