Add todays Python patches

Package-Manager: portage-2.2.8-r1/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

3 files changed, 188 insertions, 15 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 202d300e33a3..9136a07a8452 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/ccpn
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.130 2014/01/20 10:38:50 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.131 2014/01/31 09:07:59 jlec Exp $
+
+*ccpn-2.3.1_p140131 (31 Jan 2014)
+
+  31 Jan 2014; Justin Lecher <jlec@gentoo.org> +ccpn-2.3.1_p140131.ebuild:
+  Add todays Python patches
 
 *ccpn-2.3.1_p140120 (20 Jan 2014)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 685ad49fc27c..a9c0b39176dd 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -25,28 +25,30 @@ DIST ccpn-update-2.3.1-131119.patch.xz 9908 SHA256 c6098bed0078773a5a1adb91ed5c0
 DIST ccpn-update-2.3.1-131125.patch.xz 10160 SHA256 a386e70114b61de2957eccbfdd39f099606f82d0081949923cc68493e69df8d5 SHA512 20457e5b16d834f6c4d086b0fd6ebdd1b23756c170be6dd67766e153e6ed33fe4511a5f718ca99e6f44fc99eed00f90c3f34dc67c14047f89cefcbc100acbdd0 WHIRLPOOL 5d2f072a2ea2f4510172d633cad5de753401b536ff12e3dbe20a5df78feeb414c8457b3965744bb14f8f44fa586c099c095e0acf016aa4f7da47ec1883af250b
 DIST ccpn-update-2.3.1-131127.patch.xz 10488 SHA256 513252fc6376d89e6bbbb1da1206cf0044513c896c8ea01af8262fcfcdb5a4df SHA512 ac4115d48cc0c8d707978216732fe1f29a0b4e8b9900f029707f483a16fb1b5f1e7055bf33d828455babe52afff13485d32de4729bebc567ffa2d19575ecad80 WHIRLPOOL f05d2149f16c6decc93d30ad55a2f1232e913cefc2fa6f1d6bde42534f0695fe68f3a245164b4408f063a1297df5e01add60e01cd9a77528a5833da7c0d78c91
 DIST ccpn-update-2.3.1-140120.patch.xz 11404 SHA256 b01310884ccf27450d767b63e2f49516f6005259bbf859747b26b95371038f62 SHA512 51c23407c7e5018434f84ade50681156f2d59e6b9e83195967959ccf83bef25406ab0438b3f241de0a00ee923c24e93616c3893e78f4dde82c80e43475de18c5 WHIRLPOOL 8063fb5c78e1e6527f37f82d297414d74edeef78daeff19676648b192a6b30684df5e8afd81d1f1fec2268b4fbbeeae5cb54c27f7ad4f100aee450a218822267
+DIST ccpn-update-2.3.1-140131.patch.xz 12588 SHA256 5776d4b22d07c18356b6c61f068648198110fee8fb930908c6a6aab5824ba716 SHA512 0707be8279052f338c537dd57c42c18d9214db32a9007d068f50f522cd9c3ff20cdbda4616f5675f43c05d33b5b701e878e9aea8511a10a80240a2f76e6e0448 WHIRLPOOL 35b981ad9fa13857c149ba23a3503ab5eb43729eade0b1527c54db95aaa0bd2ceeaebfafd80d3640b487c335f8446372cdb31a919b0aedf799885b062af49044
 EBUILD ccpn-2.1.3.1_p100806.ebuild 5181 SHA256 c3ba268461da63ea23ee7f621a8e4837a368eb3e4c85bcc5245250fb6b377b58 SHA512 701ea90a13dc44e5bf1ea17c0f69adea56b1c14788ab79c67fa4b9726cae532998717515568045aec9bb4e1dd4c352227130115d90c50bf07e7fd132cdee385d WHIRLPOOL 898a618f95b254785739e6fab20af333cb3a44bff12cd6840d1b111f1588a60e48055e8af7ca88457173452f6acba86ebd3bada96390211bc4cd063fe4160fd5
 EBUILD ccpn-2.3.1.ebuild 4707 SHA256 b97f41d2321679a416127920c8457e2e019dd98ad79a3e563677c7f2d0f66735 SHA512 54a181c71e47659bc448845c2043f04358dec626162a8c72f392ba91833cb8cbabfc524da5239060531c5d4ca0b3f8d1c81a9a102e14d5014bf57e27e50aede7 WHIRLPOOL 1fe18f4b7349e96ed46648a29aa774fc8ccb6be3880b0f5558914d908bd080462152f3f6d461e961ccbace7d4f4ba6deb36770fa7304d796e6f359c202f5856f
 EBUILD ccpn-2.3.1_p131119.ebuild 4712 SHA256 304c3c6a3748eaa478d98b3af95668cef50262c5f6c7a872dbace8c828bca594 SHA512 678ea73d436550565828f682cf90382ed7f3fd166f9daea8643998781099a561899e7b6db5a53b691950f0c67440caabf3b087608db9532c17db2ac02e277c0c WHIRLPOOL 5f19462b456bae09a6983351c894735dd5c58f244154c8b30a54bda1d564d9728cb13fe779d47b46d2bbedb4a27fd7d575f73613fdcb10484b694ba6117e3d60
 EBUILD ccpn-2.3.1_p131125.ebuild 4712 SHA256 4b138cb7a05107ae9feeb6a2827fba1f385d32c0c822b49c779d7accc6546b92 SHA512 55f68c3eb94b7de0c70122e834c7a7506b9ea1a2eefc77c747bfe5576817d0f7c6371918f210b18722a13dde46ec7284335eb13631026987b42e9ffd51f29ed1 WHIRLPOOL 3305402cae34b506ce0917456928b905772773943cbb0fd6540c539ae78e784d6111d982e4c16ed87b81293851ff36cab52caea67e24cb316a92c3c7febc3ba9
 EBUILD ccpn-2.3.1_p131127.ebuild 4712 SHA256 341087325444fd25568d06905b467f33748d66b3e9f31943251cf40bfa657122 SHA512 3b3dfe6ecc4a117b64e4168ae6131186e6a205b5f1ff29561db0fb0bea9cd775259b86e93df59fdd715ab92b7acd03b98441f2a9ae8ce0a029fb09dc92f0d993 WHIRLPOOL 04e36b31ca326a0f1e6983e0714c560a9d60fd0470341742da51aaa4e131e2f7b6726d8f8ceb89ad8ba43d464376a9684609b85df588481eef474f7b8fdfe957
 EBUILD ccpn-2.3.1_p140120.ebuild 4712 SHA256 1bb42d83a252cdd6b9ad8289f8e22467cab4382984a807fc7b12ba1532a2f6a9 SHA512 999a0daf88c62d4118b0c71ebb020f462a018878c3e1981bb4df3275e352b5f8c3e294f02644d8035c4943fe63ba0150af1542d6df16656bc1aaee59add48a9e WHIRLPOOL 8b49fa1654d8d3ede51ed83ce7b21069da41a6094e803d2cda9a0cd37d3acbb8331777031a9dbdfebf9dc57fcc130267c89890dc6beff2156f82abde0b37b8f5
-MISC ChangeLog 25110 SHA256 0ea8dcf1aeb4940a31dc57f113a5251f52f68413b3f5ef63fdf0cc232faaa906 SHA512 27942759c9ddc35086c4bbe2000f1f49c02526bb2379173e4bcf4b0bc00623c3656fdd3038994d873555300d0289be5540bac126eebe1c8ca209f7e54ebeb433 WHIRLPOOL a008f7cb693ea197eab0dd6c7448b817ecf9d62571339f29c56464d8d287171f1a34307070a53ded894142ed15324fb274afcb2551b39316f94ab4eb7940f7d7
+EBUILD ccpn-2.3.1_p140131.ebuild 4712 SHA256 7116645e806da4e0354e9973092af6a127dec00dd9e12f866aa80d8792958f1b SHA512 05b9c34328b972eabcde46173c24001610a7bceadf4feb016b525fc24c45460e6e3129e53e66c4090a77c837b38751acc1e59bc6df9f530584c0035be5f952c8 WHIRLPOOL cb2705bb3ef871e093034ebf0af6b08bc990c094a59da2de440de4a33234e47709eb6fd0719211ac2f1de173ceb4941966bd884f430603f6bdb4a0930220b4bc
+MISC ChangeLog 25249 SHA256 6143ef26dc1c7d79b6d7f18f5890abdfa56530ec4c38ad829f5dcf2a890e7b85 SHA512 680fb94ecdf41a646c7794e4129eccf84ab7677c8455d83953eabb0734fa12b5ebc14fe1df9132324565a9a31f4abf389011501d16bb5cb8b9f0934cdffd0dcf WHIRLPOOL 91af27de7df5a20a0e7342a0f18a2f3fcf3cfb9bcc145769eaff5191c6cc8de498d81b1b08e45da0655aff8a440fb0c1d99f60e11973978297104630c667f25a
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
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diff --git a/sci-chemistry/ccpn/ccpn-2.3.1_p140131.ebuild b/sci-chemistry/ccpn/ccpn-2.3.1_p140131.ebuild
new file mode 100644
index 000000000000..c57dcbcb0602
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.3.1_p140131.ebuild
@@ -0,0 +1,166 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.3.1_p140131.ebuild,v 1.1 2014/01/31 09:07:59 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{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"
+[[ -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 "${FILESDIR}"/talosn.patch
+
+	append-lfs-flags
+
+	sed \
+		-e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
+		-e "s:weights_s:weights:g" \
+		-i python/ccpnmr/analysis/wrappers/Psipred.py || die
+
+	local tk_ver
+	local myconf
+
+	tk_ver="$(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
+}