sci-chemistry/ccpn: Todays python patches

Package-Manager: portage-2.2.0_alpha137/cvs/Linux x86_64

3 files changed, 200 insertions, 2 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 65c44220327f..19c4efd586c4 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 1.95 2012/09/20 13:48:45 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.96 2012/10/12 16:24:44 jlec Exp $
+
+*ccpn-2.2.2_p121012 (12 Oct 2012)
+
+  12 Oct 2012; Justin Lecher <jlec@gentoo.org> +ccpn-2.2.2_p121012.ebuild:
+  Todays python patches
 
   20 Sep 2012; Justin Lecher <jlec@gentoo.org> -ccpn-2.2.1_p120109.ebuild,
   -ccpn-2.2.1_p120304.ebuild, -ccpn-2.2.2.ebuild, -ccpn-2.2.2_p120403.ebuild,
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index d26ef869f492..ddff2e1563b6 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -1,3 +1,6 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA256
+
 AUX 2.1.3_1-dynamics.patch 825 SHA256 53577b6f9621a707b1b5d676d57ed16f3963f3172598d944b823133908226edb SHA512 56d89056a2916cf7c5a90084b151a46a39a456ad84c1d9d4042bfa1bd236b576e3f3232a2e34c0adbeff77a4f954d73b1565e0df701a29a0eca1e0a654728e74 WHIRLPOOL 084bdee6ca240491db0a718e23529887c3b4341217a036be4f87e3172cdb01db364ff4adc6a63d66aa146c605e05891d2d1c879cf0576084c5662e016314b74e
 AUX 2.1.3_1-impl-dec.patch 2818 SHA256 f175a1b4a9cc4f1636bf36928883d37a266af830234aa3d7676f4fe4f7f1ddd8 SHA512 11d54abe5578424c601f97e28f7af613284b789ad977c6b1f4e737116828ad0eee3183f65ba20e609065d602028a3cc59ebd6fe232d0c06133b0dcaea5f3dbea WHIRLPOOL 597d03fab86dcd61991a256a06644df0edb3edbbcbc6b916b8b3dd6808f5809a473383facabd46bf1ac343a9d75f9c49cac36c1a1a8cc60974f66b43237634fe
 AUX 2.1.3_1-parallel.patch 577 SHA256 7e650ef2fa1ff0626349affdf1bc9578fe1da3b8cee7dd9125d33a2164978b69 SHA512 c8a94fd6622dfdd90dc2f40ce2aea3440a1cb2c56e4143339675995e8cf29dfb73e4e501117db1e1f6c6cbcb62d49dd52a4c239680c2c4db6145f9bbbb2486af WHIRLPOOL f943d5bcef2ae2cdf969b15e03a50c5cb3cd640c6e7400657c78b2120aa0bf7847c93bc652dfc0510bee11b9c2d1a8cff9e8deb8946bf07be6055a6259458943
@@ -17,8 +20,18 @@ DIST analysis2.2.2.tar.gz 21044504 SHA256 8e46d12b8fb7763d282933e14ddfa9ce197954
 DIST ccpn-update-100806.patch.bz2 187965 SHA256 5cea7899edb96237a6674f04a1beee6ad7b309e12964ea8b25d9ea6ff752d0d4 SHA512 ab145f14137955bcb4dcc4d242eb718a806152bf3376e4cc9ff5e8186ed54812051ad07de1c9d2316ce3379c8c74db4af36f714aa3291ea7a1d11d4f432df06f WHIRLPOOL 2a0cbf62aca74e22fc0e00a0a91c3c185c10fb07277ba30791511565a2fa645b123a8c5164389eb9fb5a2d1f591e26c6416c46038acceefa2f1ecf347b631a66
 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
+DIST ccpn-update-2.2.2-121012.patch.xz 155460 SHA256 7a5441049fe0f002ee84cfce853043b350ade73c0c564901964db59ec13bb5fe SHA512 86d8bd03cde0a81542cde451c9ab759971c9ea30a1ada0e2961370640d1c139fa8e050e102969d7dd59c2d4664c87da6ccaae1af803a48c0d2ff6c52fb49d295 WHIRLPOOL 7acaeeee4eda9f6d16b630c898244683d40e1809bb0457ce68f26e1ac8c8b691ef227dc873b9f60e53b6c077d2b602f682a782121aa5c9f004e35d9460181016
 EBUILD ccpn-2.1.3.1_p100806.ebuild 5181 SHA256 c3ba268461da63ea23ee7f621a8e4837a368eb3e4c85bcc5245250fb6b377b58 SHA512 701ea90a13dc44e5bf1ea17c0f69adea56b1c14788ab79c67fa4b9726cae532998717515568045aec9bb4e1dd4c352227130115d90c50bf07e7fd132cdee385d WHIRLPOOL 898a618f95b254785739e6fab20af333cb3a44bff12cd6840d1b111f1588a60e48055e8af7ca88457173452f6acba86ebd3bada96390211bc4cd063fe4160fd5
 EBUILD ccpn-2.2.2_p120829.ebuild 4799 SHA256 6930082cd40aad6f0503c4e02e21b377f4e3411264007a5b72b77ad107616843 SHA512 4b1e894a6650fa0ecbd9c6acc8811fd9317cffb1eebe40e8364394bd8d979c55956fafd1c67a8bc2349bd1b78b8dd3f3539f112b8de29cb6bcebdfe13887a699 WHIRLPOOL dae24e4ba14c8846c8413236b88261ecc2cd3ab00dae680bc5cc8cee6a1f1333a7bb40cdc069c9a2bf1687dca284f8a68e66aef58e237be5fdb86328f2dd0125
 EBUILD ccpn-2.2.2_p120912.ebuild 4799 SHA256 e2d429881107e93973f2dd87982cbf2aff65bfc4d7def242931854f4d8199a74 SHA512 dc0e6b64d01164a68896701a9f9880206dccf067752865bfbd01afb6f5ceb3cb2603f41b96f275a65a6249f31af1306bcba77890cb773e15c6cb0000a967ce69 WHIRLPOOL fab86d5cc8e204ede0d3af451d736bce90fbfb52ce384ceb6c925fc97f41938590ea2b82f260ea3a07d6636b4e507528b9fa4de0a2ff9fdbefac763c42bf0f9e
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+EBUILD ccpn-2.2.2_p121012.ebuild 4799 SHA256 8d50143deb47c2fe91a82d373f5d9f17ce16f12aa5ba1fa9ad616cfee2510a52 SHA512 865d37b28ec93eabf7cac2a9f61bd3561bec3df194b1f87850477891853f17f1dfeec8c95cbea3a2a8b8fea43d46b70d286583c2543c44f89c7c368123b1164f WHIRLPOOL dc8794af8523f643a333169bd3f349c44cc1ff001c71d61e75fca18394a16f279aef035aeb50ac0ce6de2f9f72bc2b2087c4c346524e95bbaa90552e2a5f6683
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diff --git a/sci-chemistry/ccpn/ccpn-2.2.2_p121012.ebuild b/sci-chemistry/ccpn/ccpn-2.2.2_p121012.ebuild
new file mode 100644
index 000000000000..cd38f77e1eb1
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.2.2_p121012.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_p121012.ebuild,v 1.1 2012/10/12 16:24:44 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}
+}