sci-chemistry/ccpn: Todays python patches

Package-Manager: portage-2.2.10/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 6ee0b5dab9f8..bb9822c61b0e 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 1.139 2014/05/13 11:15:25 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.140 2014/05/26 13:12:50 jlec Exp $
+
+*ccpn-2.4.0_p140526 (26 May 2014)
+
+  26 May 2014; Justin Lecher <jlec@gentoo.org> +ccpn-2.4.0_p140526.ebuild:
+  Todays python patches
 
 *ccpn-2.4.0_p140513 (13 May 2014)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 3fe1b5a511ff..1bcce39d42a9 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -23,28 +23,30 @@ DIST analysis2.4.0.tar.gz 36047222 SHA256 efde9f398bb62cb79e32cfe3118fe2af4ff6c5
 DIST ccpn-update-2.3.1-140425.patch.xz 19020 SHA256 38cc7100d46966cb07fbb8c032248064191da3e015de4332878e8992f6acc9e6 SHA512 071e1a0c4f589a76a6878cb5636516304c3eb9d929924ed1d03c1838cb1d894cc330cc5c6c0b222a71e24513e212f469a69fc3e746ea82e34eb669292d7ce52e WHIRLPOOL 72d6850734e0e4f64fb63b1790ecd942b03b03c3e4682c1bc6248b3ee1f12bf014534a2f37ca31914b4a1be87ad8ef8a160364aa5dd0e1b3e5bfe47f3a83b8f3
 DIST ccpn-update-2.4.0-140425.patch.xz 1096 SHA256 ea1325b4b4ce6e03f004686f0b75243c0b354c72b7431f3611c59f8b288afd8d SHA512 8c1d3df4210f02e8fbb07caabab740c115769457296ae62903f5401ca875b006e355b99dcda32f9606c93c84b0e0cee07acff53fc953bc77918597b58f826e0f WHIRLPOOL 594ed27fc74ef56473af76de164a2c3e30f63ffd677ebcd17d3c36f724961afbb2952212a1140cd1aaf7ba6bd5d9ba960c70ec95808f97a5b94a641b51cc8653
 DIST ccpn-update-2.4.0-140513.patch.xz 4112 SHA256 fbee8e6fc4c2b8617027050ff02eee5ef37a8608b5f8ee36f692100018f69f24 SHA512 ae6c659e65612eba1ec23740a6d8e504ab1fc3404899a10eeca98bfed8b691037116029dba6a02f83ff90a45d782dd0b629f2b933b8bd264d52ded460475b14d WHIRLPOOL 8a0c7ddf84a035bb92f8c9c058ca34b18815f298ad15f2da6c781e954b7d3d53f46166f09541ca89b7dd90fdf99d4a717384bb06be19f39bd5d610e1ecc64689
+DIST ccpn-update-2.4.0-140526.patch.xz 4960 SHA256 0de68fa0492a87d2aac381d6630575b863a349414118b775f52f63c11553ee94 SHA512 6f8146d6a86319c3771571c9af010d1155ea3a8033716889b006cd2a8f004d75a455254a70bda5aee4f43790b498014b25311806f6e7663d0f1c9f924a909791 WHIRLPOOL 9241d6e8f1651eb87bcf951594ae21fa9e528c9185308ada9c3030577769e93ee35df0193df4e385910e34915eab522b7a3d176f73af45cc0c3aab3fefc448c2
 EBUILD ccpn-2.3.1_p140425.ebuild 4703 SHA256 8bdc74da4c23ab1c25147abd87ef87a8567bdf21a15a511d1ee966f09ef2c6c3 SHA512 a22af894d808cb5ca19190fb9dfdfe21e47b3626e2b18eebc1946fca28bbd463fb1bd4fca0a2b2ff57558ec2f004798c58253ccc7740f18174df258d07499ef8 WHIRLPOOL abc9ac85b431e2acc5ec8bf760ff52ae77c60df8e72dab823cb83c0040f895b6234b28b7e63ca854422bd311cf17079cacf03e702d3cc6e5907bcd13080b2208
 EBUILD ccpn-2.4.0_p140425-r1.ebuild 4731 SHA256 82ce5d2b9fefeeca1941091b1bae47516ce74b0c472043140d1d9ae5b9e706a6 SHA512 2c9a09894c25f6c74c98db4fa69cf2c37695e10ab3fa91812e2912610f2e2d87d856b7864790832f9ff25e27cb4a2cbfa02f8cf5695c06ccb3d93def042090e6 WHIRLPOOL f1af39c0e5df8d6a301fa17371b045cab9a6dc261973315d3584bd748044fec8edd0199f2d4c07932efaec3328a211708a906281cb7d85f92e5e64bcd21216c9
 EBUILD ccpn-2.4.0_p140425.ebuild 4698 SHA256 b5e2d0fdf255ad588edba56e00aa41e75d24f8f5eb94e9cc20fbf7523ae45ff7 SHA512 ad5c1563d2565634b4add451c581c3cd2790850ab4d2c20d51cd07d0844c725685c5996fef4c5ae06c1cdd16062c853a6ac47eb244a454cc3305c3a78417a93c WHIRLPOOL 1586cc2c05fd004bbe0f9264bbb49568a2eb1e342da44a996cb7aa835cf9040401c2a5226275a1249d13a87a2c05924ca65792309120c1c57066b7724ce5ca99
 EBUILD ccpn-2.4.0_p140513.ebuild 4698 SHA256 579e5a0bab5561da630033be60f5b70cb651b46e3882c0e6f3f016efb2e4ad2a SHA512 56d7c8b64c9b549a48a611df76132235b60d794b7c97be8a5a4a8ecde90577d551a618bc10ad2f88c1778c0f5adefcad3813e88e414a83e4b1cc9663dd1b1f34 WHIRLPOOL 4dda434a2b225fbca03ba82fec0ac19559e174dcefc7815750df28d17cdb76222d5fb7bbcdce82df9b45c98dee24a9ef865538410652c994e6029e615ccd5aac
-MISC ChangeLog 26804 SHA256 5780166d4462de4f6d83bd291628e89916e439209a02c6abea45123d882182cd SHA512 15163b77c430762ee20d325793f9da0340d83096b5bc55b4fb84eee710794cd64fd96c80baf8197f40b1fbadf5d08c5daa6155db26d19953f64540e68e4a120d WHIRLPOOL d37173315e92c1a0413056d76886fdb92e7a3b88b66f7ed5fe9af6d808326e6ea4d9d7e472894e5864064e54865f4b54bd5b9ccdde5e3b98736f0d059e48e8db
+EBUILD ccpn-2.4.0_p140526.ebuild 4698 SHA256 911532c276294dd31aee4c246ca6b0c9e7d5cb900ace5e60a8cb8fbf1d61ef3d SHA512 f03b4fc9414396856136115fe6a8fa50e777ed01b96761e81115d5bbe295ac6845fb14b5c4cb48b51562d658c06124c747eae9ee55266e1ca70c9225496af5cd WHIRLPOOL 8ea6aec1c97a780ac540cf05305041130b9fc72173534a64e43826d49d32a08a1485281506ad0d4afdde1c4bbfbf2734cb26e9fd91f35d91768afb37fe5421d9
+MISC ChangeLog 26939 SHA256 033e7fde75f76d95ac04d3e6ffd64386a6af5d0f39333692cba8206ee90a1b9c SHA512 9981a41ea82bfe32705bccebda278e09fccd808b5a810595b7c10cbadcc1af5d0186629a3738eec4c8049e4475864f9e7a7508594f469995a0c7c3659c17d56d WHIRLPOOL 112cc5b59114564b22cc99d594a454f8a8b13ce74a4facfe2d80266bc2152b21872f43377ce6ccb7d05f7516e130816f462a80e0af34e925dc79d3d7f6024c59
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
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diff --git a/sci-chemistry/ccpn/ccpn-2.4.0_p140526.ebuild b/sci-chemistry/ccpn/ccpn-2.4.0_p140526.ebuild
new file mode 100644
index 000000000000..b88ced067d01
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.4.0_p140526.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-2.4.0_p140526.ebuild,v 1.1 2014/05/26 13:12:50 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}.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
+}