sci-chemistry/ccpn: Fix for new python eclasses

Package-Manager: portage-2.2.0_alpha166/cvs/Linux x86_64
Manifest-Sign-Key: 0x8009D6F070EB7916

3 files changed, 174 insertions, 5 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 7a386d44b019..3c6a363efc3f 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 1.103 2013/03/18 12:36:30 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.104 2013/03/21 10:26:49 jlec Exp $
+
+*ccpn-2.2.2_p130318-r1 (21 Mar 2013)
+
+  21 Mar 2013; Justin Lecher <jlec@gentoo.org> +ccpn-2.2.2_p130318-r1.ebuild:
+  Fix for new python eclasses
 
 *ccpn-2.2.2_p130318 (18 Mar 2013)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 0fb11304d99f..1e4edd3c20d8 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -28,13 +28,14 @@ EBUILD ccpn-2.2.2_p121125.ebuild 4612 SHA256 08a4b0682c049a6301138ea6f24d665edb0
 EBUILD ccpn-2.2.2_p130110.ebuild 4649 SHA256 53125900943ea89ba3d3483de29a240a0e7282098af869a04bc926c34f3bf51f SHA512 8406a93562897aadfefd03e098b393af5fb29f9bfde8e5727b73ceb6cbe004b73cfd97b61e942189d9fba717761b20cc4914e5c9d858f36bbdbdeea1369490e7 WHIRLPOOL 112e9cab77898ef9246b127d5ef8529948cfaf91157a25bbe39899560af8340f8e5cbd1e2a3935dae083a9291f0d569d3cc5b7588dc2029f3342ecbe5590cb0f
 EBUILD ccpn-2.2.2_p130116.ebuild 4649 SHA256 b1832e30ba4cf40a79a8781f0e84c49f35245ea36a42e7ca5adf2019bcacfdca SHA512 52fe7e59bb3a801ac30f0fb1d503622a0d6e18357fec14a73c9b83d05fdbac33d594e636ab5e72df6eea15dc796ab90c113d0715f1dc06d3ecebfcfcf9fc186e WHIRLPOOL 617306f09808d9bdad288990ffc3da5cacfcae8bfa8c07dbde20c879d9e5308a4d7d9d64afb217be0ef46801d22230a2b8a6152b461332b94448a01f813e4ffd
 EBUILD ccpn-2.2.2_p130213.ebuild 4649 SHA256 bf5b16abe8e4a864b6b8629634464cc026aaf80b45361ca85adb774f1f282d2f SHA512 2fbe3dfe634a43bfa543af91cf7778f178ed5725ad034cbf815c202de6a781b0cf2448efe6e99ff721872c168fa1d1efed784112bf3085d7f1174fc3d2e013db WHIRLPOOL 9c83b89f53e34fc65b169c22686f472b6f2adf92feaa965608b7b725fc7d2507866c7fe32f09100a76d58d0c53e47ef61534612c933199017203a72213642a07
+EBUILD ccpn-2.2.2_p130318-r1.ebuild 4618 SHA256 6464363677d66e8b7f6aa2ec372d90bd7c7d73a2cd9d8c2bb24fcf9df13a926b SHA512 bf465963c0f3a21dcccca4bcc9a2aaae81b52e9ddce7edc4c1d76e1bc648bcd4f6693a1ea374a3eed7ec2a19d1227de45950bb1225d683e8e4d9f7d5de203cf0 WHIRLPOOL c10aaef5b76253033fd7fc9d734b28c240ef4daa24c29b2a6c110f0153c67907f1ceb997d1c000dd6419c03c4aab608bb1d853213f2c22dc61faabb87c94e78d
 EBUILD ccpn-2.2.2_p130318.ebuild 4574 SHA256 cb82394e883319e956dcd49de1c924f3d1c7abac65a155711cf40081087b43f9 SHA512 af77c2e6c0059f9f474fbececa819b13018391a04397adc53ebe07ab77227f0ae4b65054794aecc94a59284d9f7e4c6f5bb9bf89da7e552dab47f0ad41dfbbe5 WHIRLPOOL 08e14c30d250a8229c6ab163479f82836756b28c6d104d6fa9c6ec12a00545a7ac8ba6033087b932f4c8f70489144fe22f2ce8e0fe9620f00d7ce8f9b00684e6
-MISC ChangeLog 20367 SHA256 fdcc47e21d1715d5562f9ac615ec47ba548e595df98aa1215ff1043cc5fd7887 SHA512 d86f775350f6903c42506369e6edc7f2f559f797498287a5450af0704f934e365b12a3107cb5248dc68cbbc2c57ec8d2bef89cbdc8b2b5ededba1401066fbf4d WHIRLPOOL 546ac45b31f3dbad40df69855f26a0c0cef774eee753dce298aa7a8acebb0bb6953f627743f12bb45c3fec9484337ef31bd4b694a8fb29e548cf8b8dc1285d44
+MISC ChangeLog 20514 SHA256 1135f37080001c10ed93c7ee4f56f20012dd4997cd440a61ead7cd90a8c605a2 SHA512 bae62c618933976caf5e38f4584d74d50a4e1321b666b3389cc709e7eef7a1741b81f2ea6f9a3589e329af2b43c71ea4b18a78d32d986a984cc2aef5fa48e562 WHIRLPOOL 9ea4f6987e4ce6d182adfead9d6d2660c91042a71bb20c15fd2aae9046000a22380f4bedb52c0e766d79ae0970469d57c6f6dd7dacc02153e9531a744cf90674
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
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diff --git a/sci-chemistry/ccpn/ccpn-2.2.2_p130318-r1.ebuild b/sci-chemistry/ccpn/ccpn-2.2.2_p130318-r1.ebuild
new file mode 100644
index 000000000000..ec6217dc8271
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.2.2_p130318-r1.ebuild
@@ -0,0 +1,163 @@
+# 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-2.2.2_p130318-r1.ebuild,v 1.1 2013/03/21 10:26:49 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_5,2_6,2_7} )
+PYTHON_REQ_USE="ssl tk"
+
+inherit eutils 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}-${PATCHSET}.patch.xz"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+opengl"
+
+RDEPEND="
+	dev-lang/tk[threads]
+	dev-python/numpy[${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 ${PV})
+
+src_prepare() {
+	[[ -n ${PATCHSET} ]] && \
+		epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
+
+	epatch "${FILESDIR}"/${MY_PV}-parallel.patch
+
+	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 ${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
+
+	insinto ${in_path}
+
+	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
+}