sci-chemistry/ccpn: Todays python patches

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 3ac67a82b078..2002e30eb793 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 1.150 2014/10/08 07:29:07 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.151 2014/10/20 10:44:36 jlec Exp $
+
+*ccpn-2.4.1_p141020 (20 Oct 2014)
+
+  20 Oct 2014; Justin Lecher <jlec@gentoo.org> +ccpn-2.4.1_p141020.ebuild:
+  Todays python patches
 
   08 Oct 2014; Justin Lecher <jlec@gentoo.org> ccpn-2.4.1_p141008.ebuild:
   Uncomment variable
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index b9e63a5772d6..b1c2b78a1d7a 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -26,30 +26,32 @@ DIST ccpn-update-2.4.0-140915.patch.xz 11956 SHA256 bce6fe96adf75aafe5d902fd1e5a
 DIST ccpn-update-2.4.0-140917.patch.xz 12092 SHA256 24d872303bf2ef0ce8fcdca4bc1cf63c7b9036ccd8b46813cfc8b1766482b737 SHA512 5c6dec8253358e6a12adb1473e99b88202c7cce2952ac8d5e9e2ee56df3a83a69ef7d8b3d28244462386aa2a5c7537c084a04b0366de9c5225ba7de29d17e950 WHIRLPOOL ae07cae5d7be20460709a24b4ac6bb50debd1eee1a70b03e98e94f2038122bc7b723ba81ea0377a1fc7e995f3e00d036a3dc91b417e38f42b766deed001e4c4c
 DIST ccpn-update-2.4.0-140925.patch.xz 13400 SHA256 018f70ad72088d9535711d4b72c7363fc93a195274863ff13ae792284f12eaaf SHA512 30af27fc9e8b9cd435e0ee7315fee135afb0196b710a3dae7d2db84792b39253e23d0cadb7790255c2615b7be70c1f3db2e5844ad55d17153146e05d41a64f23 WHIRLPOOL 07c13bc0ffdb55c3508fbedb047208dfd87a30c056feb66b7772dab50e5d71c00658a6b8acc5f8b9c78463589acc85080fa887818bfcbf7aac52f22ba7cd1580
 DIST ccpn-update-2.4.1-141008.patch.xz 960 SHA256 e838cfe46b4897939fbcb631225adc88bf1076fe5376e2a62fee155ef5227bd0 SHA512 85ebd8c2929a15c840b4eb18998a73074547bd538e064b89992bc2f1d2c203265d5808d513d2bee93d0c6560f52e0656b8f4fcc3b6d9192298fd607696872a15 WHIRLPOOL 20285e14e452865c7b17b4763a1d5520b8479d117193495a2bf8f17296df5f9a441eb5d74e4ee2e1ec68951d39a12b29b88d6354f6c4be69fe3def9d42068994
+DIST ccpn-update-2.4.1-141020.patch.xz 1900 SHA256 e01a911ba78d972b471a146dae2c35e0ddb756b0f46959dc8f28733caa4ece2d SHA512 6ab67ed68377f17d11c02cbb635e60814e9bd1e9fe0fdb87b1ad96309e18eb6dceb89dfe734aeb81ec0d6cdc7ae735965aef7d9da67be35ffe85db4d43bddd63 WHIRLPOOL 95edc9f6f5a192a58929fb2d52636e774818f8e10583ab3fa19648b7f97ec9ff72c8ab6a761552efd6c17bd448ab93d6ffde14122d643f11a2e49f37a2d60f59
 EBUILD ccpn-2.3.1_p140425.ebuild 4703 SHA256 8bdc74da4c23ab1c25147abd87ef87a8567bdf21a15a511d1ee966f09ef2c6c3 SHA512 a22af894d808cb5ca19190fb9dfdfe21e47b3626e2b18eebc1946fca28bbd463fb1bd4fca0a2b2ff57558ec2f004798c58253ccc7740f18174df258d07499ef8 WHIRLPOOL abc9ac85b431e2acc5ec8bf760ff52ae77c60df8e72dab823cb83c0040f895b6234b28b7e63ca854422bd311cf17079cacf03e702d3cc6e5907bcd13080b2208
 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
 EBUILD ccpn-2.4.1.ebuild 4685 SHA256 6e4c496453063dee64e64975a5732f6bbbc820bb97dc460691187ad15dc3e935 SHA512 a862d7ea10818bf2f219411019db151255a1e09f8e72c7a37eacbe7220b8640958be43079e995828f055ae62e93d002540de5be8f0cff231bb5ec62dbb0e8a8e WHIRLPOOL 6ed8127f87305e1406aed474089a478423dc0ae6b3c81191d650de680d22aea2112c62ac63c02a76bf219bcad49451477682e3ad187999764bcb02fb105e1e58
 EBUILD ccpn-2.4.1_p141008.ebuild 4692 SHA256 2d54fa5ca4f5edbe071d0576e923152806c45e2e0e231faa53ac0c565d7cc4ed SHA512 dc29488a224a8011af2814e182bee6205d4a27e10398c25593d6883d49265e75889a097561c9ae4a84e23a45f8c1ee57a32e20e18b23602a51ce06363323f63c WHIRLPOOL 078d0ec0d22c38a7481d3ef0e6e02c24839d40687d5fa7a13f03fbcd361c377921c79aaff64d31e4f3618e1569e3988efba1ce7377a3ad7f662d01468983d4a1
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+EBUILD ccpn-2.4.1_p141020.ebuild 4692 SHA256 e5c79ece1d0c4fca0fc3cd1d0ddc0b28c7b37ba8d30deaa415b706ac61841f3a SHA512 1cf610b842a1ca89e16954bbc542679bb815db95c4fb9aed3c3c71b09cd2543508944a74c849d87e9753343516b0b933366c4c6584fc916b7ed0482327a12b22 WHIRLPOOL e32844cef4a2c5587da0c469b5da7ef93bd71190827a98a4589109f14e286695b6f7738ffeaf7df03cfe8a756d60e080dc0c2293a457d987467b553cf324e231
+MISC ChangeLog 28613 SHA256 dedfec51ad7fd41c09c98db568eacd3f139e1019109c724a8301f9757de8d192 SHA512 86981b2c12da25d7843375b63fdf658a300ee2db8d84e64c0d757d41a4fc582b698d4eb47419cb23d366d835d79eb5e7539ed82b0dabfc54e260ac122c1eb44f WHIRLPOOL c778c908836a87ac28cac08468a0e0d52233aa71949bdadc173b3529f4850b01e811076396690ca6f2337d7708a52779e3a2e47c3fcedccc1c6d633bc5b09561
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
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diff --git a/sci-chemistry/ccpn/ccpn-2.4.1_p141020.ebuild b/sci-chemistry/ccpn/ccpn-2.4.1_p141020.ebuild
new file mode 100644
index 000000000000..b9e9e8b2b58b
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.4.1_p141020.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_p141020.ebuild,v 1.1 2014/10/20 10:44:36 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
+}