sci-chemistry/ccpn: Version Bump

Package-Manager: portage-2.2.14_rc1/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

3 files changed, 189 insertions, 16 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 763b34e85fbc..9bf0de92d2d6 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 1.147 2014/09/25 07:03:55 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.148 2014/10/06 07:23:45 jlec Exp $
+
+*ccpn-2.4.1 (06 Oct 2014)
+
+  06 Oct 2014; Justin Lecher <jlec@gentoo.org> +ccpn-2.4.1.ebuild:
+  Version Bump
 
 *ccpn-2.4.0_p140925 (25 Sep 2014)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 94a9f9b9b115..0d3dd4044273 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -20,6 +20,7 @@ AUX talosn.patch 1358 SHA256 55e4e412158b851f040ac25d93b8b1a42ffa6354c26327cb880
 AUX xeasy2azara 324 SHA256 89945dae1c7bd78aefdd19c81c79571a13aaa149d6c50e12cc0ecd075930ed4c SHA512 de31df36c259fa58483c6a0e24bfa6ece3a86db5d556c5c99f610c7c2ff659742fcf319ef387538cc5a74444bf4be8ffff96da7ee819ac583e2605f4f90a5806 WHIRLPOOL 6a40d21fa7cef520de86f04282b5e26e3a8809c7a8caed8e19a0758419039358e1b1f33a53f956bc77a10cddda703cce8f21584d8e9e3648fccca3a486ab9be8
 DIST analysis2.3.1r2.tar.gz 21683215 SHA256 a9e47a24d84f7b8261c6c23a8607af5a6ba2f2db9e161a7f873794c1ba8663ef SHA512 96bf75d1e958340d83836348f5a3045e5b2632913c66d9d74272140085800ea096f1ae53eadfb5bc0eba76804f1864553e82a517d637bdc3bace71b0c1c785ee WHIRLPOOL 2d1e55a4d8e62decc649a885d767dc5a2bdec701447a97ef8bc5e15ddde8c6add5fb0606c0cdd5871bbb9af74c163a13a28207b3e254fb41ba56293c88d6bc85
 DIST analysis2.4.0.tar.gz 36047222 SHA256 efde9f398bb62cb79e32cfe3118fe2af4ff6c56e5a9068bee654b3aa00f20ae1 SHA512 2f9c5abd401675796d64c620f6142b484084c54af98e0a4800b2bea81de447d711d594ccf773f86ef6631f0482fe0a0ad2881da713d6e022e0704f8dea8d65d9 WHIRLPOOL 922aaf0b464966d91286e1e96757cdf66238373f5c358623657f552012473cea4196622274dbbc8455b60df3580132497c6e9de2f3d9c2f539fb4ad8684dbf96
+DIST analysis2.4.1.tar.gz 36088236 SHA256 1cb089dcc739e8536d938a68536f556094f5d728907b251fe337758ba5bef106 SHA512 db44468c360d51815614fe0055505001c0a7a722f980c2c049c00524672bdfd4a507134ce1d68b29ebf622ffe94e0c9bb9685fea5b3441790b997a64f78c0dc1 WHIRLPOOL b53fc0438a878a8f8ce0244f5c1ce9edb616665149a699364e3bcd38c5db548c22b80ef67b4183ad5321b71b69a3b85aecc7d912893bba947700003a411651ac
 DIST ccpn-update-2.3.1-140425.patch.xz 19020 SHA256 38cc7100d46966cb07fbb8c032248064191da3e015de4332878e8992f6acc9e6 SHA512 071e1a0c4f589a76a6878cb5636516304c3eb9d929924ed1d03c1838cb1d894cc330cc5c6c0b222a71e24513e212f469a69fc3e746ea82e34eb669292d7ce52e WHIRLPOOL 72d6850734e0e4f64fb63b1790ecd942b03b03c3e4682c1bc6248b3ee1f12bf014534a2f37ca31914b4a1be87ad8ef8a160364aa5dd0e1b3e5bfe47f3a83b8f3
 DIST ccpn-update-2.4.0-140915.patch.xz 11956 SHA256 bce6fe96adf75aafe5d902fd1e5a598cb1e7073f3dc6eb667489beb7095d3bd2 SHA512 76e8a46c98d4e8d93bdbadbecfcd7cec4f7e6ce2b2e1fff7334e6bfdefa33ddf8755f8f00c5abb114438cf3ebc1598c15dca6f8c2cafd86a9a6dcd65746ad23d WHIRLPOOL 22d9a79aae70de1b14962d1c1a958204dfcaa9a33a0020d5c1a012478b4f4d2ed9f7f0b3ca4f963c0ebce5de1a798d6ad7c3057faf4a3b167f7bbe52e05fdb04
 DIST ccpn-update-2.4.0-140917.patch.xz 12092 SHA256 24d872303bf2ef0ce8fcdca4bc1cf63c7b9036ccd8b46813cfc8b1766482b737 SHA512 5c6dec8253358e6a12adb1473e99b88202c7cce2952ac8d5e9e2ee56df3a83a69ef7d8b3d28244462386aa2a5c7537c084a04b0366de9c5225ba7de29d17e950 WHIRLPOOL ae07cae5d7be20460709a24b4ac6bb50debd1eee1a70b03e98e94f2038122bc7b723ba81ea0377a1fc7e995f3e00d036a3dc91b417e38f42b766deed001e4c4c
@@ -28,24 +29,25 @@ EBUILD ccpn-2.3.1_p140425.ebuild 4703 SHA256 8bdc74da4c23ab1c25147abd87ef87a8567
 EBUILD ccpn-2.4.0_p140915.ebuild 4692 SHA256 32847b9452cab2d8579eb372548812497425f25715f4597a9c967abdf8ccf687 SHA512 67b2c0c969cf83194435667dfb92719d8b75be049cafa708c124e91a60519ae8b43843278004ecac92dc1035cd8391cd8531f58b82cf1fffe5151d0a4595b340 WHIRLPOOL e5de10a8838cfee05a23e81f1f3f032e23263633b67504afe71ae5a7d06a4097eba4ec32714907380ce17d82619fb8db9e0217b16952e19f0babe19dd3e30c79
 EBUILD ccpn-2.4.0_p140917.ebuild 4692 SHA256 9f4acfd7e56f6f0ccd12037b91bbd7e739e932e4543b8f34214273c0d2954012 SHA512 a7abfe87f100596d9f1c1bb22c43f35833a7f256c153fe2e52d2be4570eecb82b641081b35fd62478800a579ce4a5eb84f917095cd6172665b1d3e6c6db117ec WHIRLPOOL f0bc39c7ffd2b4b74919eec8d4b5bb619c3b45d1fc19f6cc5de6ca762b13189e5067e0e397f0ffe2e13e46ddfa6d18df78e8ef2def28426bdeab479bd9aee075
 EBUILD ccpn-2.4.0_p140925.ebuild 4692 SHA256 e8e61c4b039fd0c5cbafbb66086210098983963e63f64a18cd052826ed7a1ffd SHA512 d7729412ff7513648c09213789cfce19c7f9bf8e8765ea60d55a596c7b7be23d734e82e6039e5e478365b1dc2260ebaa108acab8897cc91c42a00da9c0d567eb WHIRLPOOL 9edde643a2eedb577705c71a8cf20300a5794f3589534753c1bf8e0eae1fd54c078032a4e0f9b4b68e432a79b2083598f8ae5255f9d38c903206442c0b86a8f6
-MISC ChangeLog 28137 SHA256 d38248edba7d948b4ba63f2464108d9ba5733096e7e077743a563a55f8532619 SHA512 41dbc275c876ad1d6991ba64fd2a92dafb591c893d0e4cc7a6ea72eede29e70b7382bf81d13eae1fa171a14f73df13ce819ffc017b53eb7538a76ab4bfa55974 WHIRLPOOL 9d8d0091b8d39ce335eee98de7ac43d81c7e828c882ace790d8f89f9ec659068e2b0a06ea2c46f0806c6dd445c45893e34b080aa3a449af850a80f60a624121f
+EBUILD ccpn-2.4.1.ebuild 4685 SHA256 6e4c496453063dee64e64975a5732f6bbbc820bb97dc460691187ad15dc3e935 SHA512 a862d7ea10818bf2f219411019db151255a1e09f8e72c7a37eacbe7220b8640958be43079e995828f055ae62e93d002540de5be8f0cff231bb5ec62dbb0e8a8e WHIRLPOOL 6ed8127f87305e1406aed474089a478423dc0ae6b3c81191d650de680d22aea2112c62ac63c02a76bf219bcad49451477682e3ad187999764bcb02fb105e1e58
+MISC ChangeLog 28247 SHA256 32361cada0a129883f2eb079ada9e68180e937e118a3519b21b0c828bacffbc9 SHA512 14134bc7d8d33bfcfa49b7259e297a978f45827e0be28412b3be68ca30cb85d1c9bc35e646e9dad6ef61a1f45a205035cbcf01245d848e799703a43d36128791 WHIRLPOOL 3d715cbfc2ac25a240446634428cbd926a27934754deaae1c046c2a2e8c703f379e234d794145df4cc1f91c356a8b8c46d928464eca6504835d1e5e17a542562
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
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diff --git a/sci-chemistry/ccpn/ccpn-2.4.1.ebuild b/sci-chemistry/ccpn/ccpn-2.4.1.ebuild
new file mode 100644
index 000000000000..13bb3cc0d97c
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.4.1.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-2.4.1.ebuild,v 1.1 2014/10/06 07:23:45 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_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}.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 ${PATCHSET} ]] && \
+		EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
+
+	epatch "${FILESDIR}"/2.3.1-parallel.patch
+
+	append-lfs-flags
+
+	sed \
+		-e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
+		-e "s:weights_s:weights:g" \
+		-i python/ccpnmr/analysis/wrappers/Psipred.py || die
+
+	local tk_ver
+	local myconf
+
+	tk_ver="$(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
+}