sci-chemistry/ccpn: Use latest upstream tarball and add latest python patches

Package-Manager: portage-2.2.0_alpha191/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 f30083ab9f1a..30bd6dc14578 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/ccpn
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.111 2013/07/10 09:03:41 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.112 2013/08/01 10:43:28 jlec Exp $
+
+*ccpn-2.3.0_p130801 (01 Aug 2013)
+
+  01 Aug 2013; Justin Lecher <jlec@gentoo.org> +ccpn-2.3.0_p130801.ebuild:
+  Use latest upstream tarball and add latest python patches
 
 *ccpn-2.3.0_p130710 (10 Jul 2013)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index f4c5db828472..87f7f334942b 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -19,6 +19,7 @@ AUX xeasy2azara 324 SHA256 89945dae1c7bd78aefdd19c81c79571a13aaa149d6c50e12cc0ec
 DIST analysis2.1.3_1.tar.gz 18932918 SHA256 bbc1ba5434f896d38b6745c1dc9adc470a78d3be7b879160edcd635a19228b74 SHA512 ee95119a972ada7949d646e0fd634d1828bba7562d7ea3a3be1c2b17d22f194dbd1267716f21ce86fffb3eadec136b0b613705f862747ab7933cb2ad57e063b8 WHIRLPOOL 1fb19a4bc676955eca4168595fad0661054061e18fa6e25e7f4ed5026cf31faba75b7644a8e2e18ece10e9641efc81feaccf580d3c766bda1d5232a346d99133
 DIST analysis2.2.2.tar.gz 21044504 SHA256 8e46d12b8fb7763d282933e14ddfa9ce197954ed9fbfa2333e22602ac841b6e5 SHA512 efe8a82381521dbfb95b12dd553f401f200aee3763f9e739c37a9141a14bf038865b2a860b0353adc532582697b58079034386be42161aecbe231952b8abaac7 WHIRLPOOL c9d7fc936dc25b952e711e8fa439ada5a67e68497b6d4ad034586e604bcbd9d1ff7dd48d1a3baace347fc9bab5c17d2f7852906f921708a16ce8c8eb4a8659b9
 DIST analysis2.3.0.tar.gz 21638757 SHA256 4dc693ed2a11bf8707477b4ef21d53c29a9f10c4540f57b2945b9249206b0b50 SHA512 b51e82329e3ee88f7040a256dd8e40121f1f7bf000b98ea8304861bb29b6f0000b61d4f81f9725df3e56641004679105bfa9b3878c447ddde5acf1fd56d010c5 WHIRLPOOL c0041b2e03d3efb8675c119217a09d4495355ad2242d2f1ccf1cacdd77f0461a5a7139d48ed33e8d72e541013513f93e1cf4742f0e9c127f3006621a987dbbbe
+DIST analysis2.3.0r3.tar.gz 21638769 SHA256 e503b88ffc166f40841dd4b0c1ba2712d2dfeca32df0efd8dbf1906319060549 SHA512 da6e07bb10abed5380b23660c6e0394d8f468b7d62cfe3210172f9462d272e129ba04e618097369898c17744751fec4a69074667ee06945af68f6c21bb2c7ec0 WHIRLPOOL b6e1ed35b008864503b39733ed75f2fff972884ff8488ca721ebdf5f77e1cad618dc6c637e2ef898c07b7d10acd1fa2e895713fdd586263d07dd7b79a2a729fd
 DIST ccpn-update-100806.patch.bz2 187965 SHA256 5cea7899edb96237a6674f04a1beee6ad7b309e12964ea8b25d9ea6ff752d0d4 SHA512 ab145f14137955bcb4dcc4d242eb718a806152bf3376e4cc9ff5e8186ed54812051ad07de1c9d2316ce3379c8c74db4af36f714aa3291ea7a1d11d4f432df06f WHIRLPOOL 2a0cbf62aca74e22fc0e00a0a91c3c185c10fb07277ba30791511565a2fa645b123a8c5164389eb9fb5a2d1f591e26c6416c46038acceefa2f1ecf347b631a66
 DIST ccpn-update-2.2.2-121125.patch.xz 223556 SHA256 996f453d7d6a143715a94b1201bd7b8b9c037f6d0baa342f5c0645d500aa5c79 SHA512 d213e072a63110ec478c3ee64792b01c818d3c9052ae6d7dac903508536f78c432c72d5a4756665045579d72f4f54ef5ac9db1fb02eb5ea3111eaa47e72866b0 WHIRLPOOL c268761e4d9cf4c845964c7c865e20439a9cacd00bc56d89d8558e0f601fc9840d4288307c4a4f47ba6d478eb9da9dacd1e149c657d2e6506ef5e32d6b0b75d1
 DIST ccpn-update-2.2.2-130110.patch.xz 226800 SHA256 6c0f4d71322e45ef24a15f1e26eb5d4104499fc2391660e575158dc08ae0380a SHA512 2fa7e782ca30402c91793032dc0d4555d9e866ba11b03f8f4b06891c8c80d256f5598bccfc99e9a97ae9b3618b1c24307814de4656087e2c0b40d378df743e47 WHIRLPOOL 5a49c0480328e7b03691a1e63fea339e2a9a29afd845babcce70e57b6e8d6ce21a5cb612d856c22bd3a9033a9ab565b0149e61435bc31ffdf02e247051e29d6d
@@ -41,22 +42,23 @@ EBUILD ccpn-2.2.2_p130705.ebuild 4649 SHA256 1b3a3af9673c488457fc4b62074178c04c6
 EBUILD ccpn-2.3.0_p130705.ebuild 4717 SHA256 3791c502fab4c7dffd98eb18b41ae7642f687e2763ae9496dfe9927964bb8a03 SHA512 2b1a73869bb1bfd79522432395e3cefbde8fd5e6158d9a87ee8f5977beadefe1feffcd4256888a66baa4b41458a6e327b9ac935dad60779a51fc3d4c04a24d39 WHIRLPOOL 52e733e610056e39a04fe75f6d2baafaf07048044f329408dad336561b60286dbb2b3d84191ee306bea57011d8bffa1b5e43d2b9b5c11570e9565cf3acd97b5e
 EBUILD ccpn-2.3.0_p130709.ebuild 4717 SHA256 a6d50c3708a40d6dd9c513fa0f54b431166ddda300c7f2a0c4992a8f1968549f SHA512 97f2a5b2b43fc7973968bca51d53efa4c6756e868037947271da3f707106dfe93c36e1ac665b0cc49e0dcf010654d2fdaad6626ae9c0f96cee68d09e4c2203f9 WHIRLPOOL 3b1eafb4a19964b81874f2569fc24239cb4095e4a9d7a718917148e57906deb578a0fa6ce160bc351f4ae54acb655c0556e605ac3cbb7f9c2bcd90665670a1c3
 EBUILD ccpn-2.3.0_p130710.ebuild 4717 SHA256 b09001eee288136722cc618c24db605abfa2c96f25152a2b77e600421fd94c63 SHA512 1ee3cc63921ba85f50ec2b287a12f925a30da641affcc961b848b501c44539c3b393c51d7f5c461107dd8e9a8e699331a67fbe7a4a2621dc3eede8f9f3bc8975 WHIRLPOOL f653b1bb85689f331b8d201484f7134ae75840f779a7a61699a0a810c5a8e7859a554e30b325008f66e4f1e9bc42eae1563b3fd2289de248b138d34d946224ab
-MISC ChangeLog 21573 SHA256 d5620f045a70c830556263bdfdfcb37b0c7f5bd7a4d54c8f9f791e77cd46ca65 SHA512 a7af74d5acd4beebf912b1e2a9b396f7169a0a9d90a9afb3864c578ea12962737c8c416f44d34bf696249c2bd80b47b2837cee5af1f067b3c7ec00091b0d8887 WHIRLPOOL 9e3890b29d161b11e809abd03c4642b83b70749d29604a5bbca0ae469ee9f037f036aa05cfb1475bdc415df2c7eccfc18904d78a1a02264f7436a64d9c5387e6
+EBUILD ccpn-2.3.0_p130801.ebuild 4690 SHA256 5aa7e80ea1e951d05b66dbf8e41bd19e143aad0704e6eef1b442da081741b94b SHA512 b47c57a93be782a5fdd32c1e0b31c673d83532018ee6878a4f0ed91412fc879e8a43cf08293aa8ecf5d47de14853a8bbb9e2ce7c85cc2ed73d6a1b0ec85464a5 WHIRLPOOL 5ff65334df73dda827254420fc2bba58a457d9d4913e2c4d65e27dc2ba80ed10b2d9f8188615f49c8921069eae9733b68b912114eaa8a72bebf99ba9699ddb64
+MISC ChangeLog 21744 SHA256 a29a9e7b93acc1736c0350e89c97c04ad2f01f49e557015297cff5249cc088ab SHA512 1165f1e74b6f8f95ae23d52401541d89ef905ac376e76abcd258b66ea2707bece29b77945fce153b9a118a393f4b154d9130baebc4cc9c77be6f3715cc336b02 WHIRLPOOL e517333044624940c35219b8f89eb3c40c914309e6953beacf1ff2d4b60ec72cb369543f665ae8a85d5c360fbf0c73ba8571bc29ee3a3f351ac3d63f709cab95
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
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diff --git a/sci-chemistry/ccpn/ccpn-2.3.0_p130801.ebuild b/sci-chemistry/ccpn/ccpn-2.3.0_p130801.ebuild
new file mode 100644
index 000000000000..0f317d6a044f
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.3.0_p130801.ebuild
@@ -0,0 +1,166 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.3.0_p130801.ebuild,v 1.1 2013/08/01 10:43:28 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_5,2_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}r3.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
+
+	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
+}