sci-chemistry/ccpn: Todays python patches

Package-Manager: portage-2.2.11-r1/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 bd25bf86a2c3..2e984788b9e7 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 1.143 2014/07/07 07:00:12 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.144 2014/08/12 08:27:13 jlec Exp $
+
+*ccpn-2.4.0_p140812 (12 Aug 2014)
+
+  12 Aug 2014; Justin Lecher <jlec@gentoo.org> +ccpn-2.4.0_p140812.ebuild:
+  Todays python patches
 
 *ccpn-2.4.0_p140707 (07 Jul 2014)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 7a8fb25ce71e..759a7c90aa6a 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -27,6 +27,7 @@ DIST ccpn-update-2.4.0-140526.patch.xz 4960 SHA256 0de68fa0492a87d2aac381d663057
 DIST ccpn-update-2.4.0-140605.patch.xz 5712 SHA256 5b8b6c0d1adf2af0115735a714502f1279d902d03be758a2f3d787a8bc92deeb SHA512 20bf8c9186a532c74d9253329a0604ec6a86f87e7ee84bea22cf38b8a29b10312c82cdc24820d76c64cd3d7c7d221e84421846895b9e3eb40e3b9a8d0c363d95 WHIRLPOOL 7e2be8bf5f84d53ab705c2c1b2c689a7bf3d478979fd4d4c09ad5ba2e8663937cf14ae410ded90b505c7b7bf7bff8689bf009d7235d17d2ff8e11632fa5bf2ca
 DIST ccpn-update-2.4.0-140614.patch.xz 6628 SHA256 7775cb0c552566808d0fcbe5eefbf5bd4f321358e9420d99973baf68388e12e9 SHA512 320c2174f961bf423fd1c2e83be54757aab3a60b5e2fd72e66aa5a128e3373ee06ca17667f94e8f3c82971ec3a3dd4dd4d66c67cd634900dd9bf0645e702fd79 WHIRLPOOL e24b48372595a8502abd51f11ae5f8a1c35a4d27d539b404c9b5384271d1368ee33dcba840495fd3a57017b63c865aaebb37bd1dbec1ef510041596d0872ce62
 DIST ccpn-update-2.4.0-140707.patch.xz 7200 SHA256 e5e1e7c3e0e1399684f15410b80c56c876031ba634a40a12088090b45802ff2d SHA512 ad96137f961d357f4be1d77bd6459dfcd2a2874706c29f122eb56c65d14c7000926499dec53bc587230d685198182dace537763c9fc05f3eaf8bd427cd5a8e1b WHIRLPOOL 29771118ac135159ccd5440268f7548fcc9057d4f8c494d860b991af4b024ebe391dc083c100911bf49d028d2e26cfaa5c7ac6aea4969d91be5050bc5d4ac301
+DIST ccpn-update-2.4.0-140812.patch.xz 9548 SHA256 3293db9e68c302d3386598da4c0274427254a07bf70c6da1967b35300e8ec84b SHA512 51bf51463486c4b079e2c04471203cfca8b046409cc404c9a885517afd29348dbf359348c579e21048af42020d4f04ce13cdb346d0d93863eac6f668f1c9a5a3 WHIRLPOOL c1dd2393975b95c65b6afc04014882329049689f309bacc70db269c1c4f18d83d0e7aeda739f57b5df0c4b0e51225314f93e8d73a1eefb4c27bd645c75d83bda
 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
@@ -35,24 +36,25 @@ EBUILD ccpn-2.4.0_p140526.ebuild 4698 SHA256 911532c276294dd31aee4c246ca6b0c9e7d
 EBUILD ccpn-2.4.0_p140605.ebuild 4698 SHA256 9f437e27eec31b215326c1671ceb1988b7e752e31d462eb19ff0f673d4b2b4b8 SHA512 c5343f975e99b4c395b106c64abc24b3abe94d413bee2a7511ef94b487649d9254e2eebd877aeab13470016e2f44ddfa84183744834d3b2ce858871b9b5f3a99 WHIRLPOOL 0036ff06e70d79d9eb4951386c35e905b71f1bdd9b712d6337944b4b45da00619cdaea5931d727ef9e9f29001d0e884694a26d762377f6929396fa9d17baf7bd
 EBUILD ccpn-2.4.0_p140614.ebuild 4692 SHA256 4491c66d8fa7d477b409d7c984120b01c5823cf2d28a35dcfcbd8751271688a7 SHA512 03f5e790d78373b57dc0bdb8dded8cf376d4663140803143efb178e02d4cd5c93001b633cb43b11be541e08060d0c8fb2ebece9daad69d37d3cd622c31c9d620 WHIRLPOOL 5316f5310e45b6241ea46704372740695d763c03e86390f1c6fd68b89caa56b5efe8f88317776bb6e0895a85f6f5bb172a6b4312f310c7cef8aea293b7a93d82
 EBUILD ccpn-2.4.0_p140707.ebuild 4692 SHA256 66fabf46c6f1ee374886422e66cb11c43a8d08c5f1425ae42c6b6a2beb917fc6 SHA512 b4334be0ceecad999e7f792a84760970ad900870783dad413f708bfed6355b1631c507503b0eb4c75d3136850bc75afa4894da90eb0dc0ca99dfefdb2d4e2a07 WHIRLPOOL 65b260fa675c8230faa62192f2246775ba78e232d481a8b347d44054ed34e2208be519592b1422b1fe7a3b1de8e2a0d68a7bacc6ddfebf81a0edb08d345e0f6d
-MISC ChangeLog 27352 SHA256 56d602c77bf3dec373f1610e1dc2d22dbe86e09e5552d6f3cc5de680ffaecaf7 SHA512 5cf02c80922433d8d62cf40f4c38a59f32004857b73ea0264dc6cba0c7f9e608978871146dcbdac2c3aab5e80d6a7bbaeba8b98f1be59d2d3ff9c834621905ac WHIRLPOOL 8e29579004802f1dbeeb21ddb0e504dfbf877eca363d497810b4c55687e14106c2a04b9c84dd3cdff5a34ce4947fecebf17b7cb6f888099675ff6d022ae6b87f
+EBUILD ccpn-2.4.0_p140812.ebuild 4692 SHA256 de194baa937a47a04d1d70fbfc23c6133bc8653aca93f99cc781a0f8acfd0a2e SHA512 07aaf75d010ec11513de2614ee74dca616cdd015d1378d189542abc19793f5fc91ffa00b73d007d3856622d3da116db424d56fe7fbd45395c1a8a62f987918f7 WHIRLPOOL 08b649f7ce2a6f5d437a268c8e029d02890aea72e1d38c6da6ab45f0232ab5ac2b91dcc568ec8f92481b3be34b60e256ed3176fa582c9261db8d02ba9318e3c2
+MISC ChangeLog 27487 SHA256 b01512f140d7767a98d3228d61ba3424bba3a33c259c62fe90c5fed5fe741b32 SHA512 2acf38d2bc926820e5c0fbb96d98d49f62dd980dfd3b8d0553b478eaee4e5f305ec9b745a797b730181836c5bee85a398309143fcbe1975c81d8d1eb8dd11103 WHIRLPOOL b510fe2839c3dad4ea89f80b6dc10cb28700833b7f3ff93982d488df19bda8368201d51cfd2c8e01355ff6f712347534c05fb2edd4ef2901d5e6bc2ad7eaa851
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
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diff --git a/sci-chemistry/ccpn/ccpn-2.4.0_p140812.ebuild b/sci-chemistry/ccpn/ccpn-2.4.0_p140812.ebuild
new file mode 100644
index 000000000000..4485ea1da04e
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.4.0_p140812.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_p140812.ebuild,v 1.1 2014/08/12 08:27:13 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
+}