Today's python patches

Package-Manager: portage-2.2.0_alpha89/cvs/Linux x86_64

7 files changed, 455 insertions, 15 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 52351934cb27..fc0fe42ef64c 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/ccpn
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.79 2012/01/09 12:42:11 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.80 2012/03/04 09:18:53 jlec Exp $
+
+*ccpn-2.2.1_p120304 (04 Mar 2012)
+*ccpn-2.1.5_p120304 (04 Mar 2012)
+
+  04 Mar 2012; Justin Lecher <jlec@gentoo.org> ccpn-2.1.3.1_p100806.ebuild,
+  ccpn-2.1.5_p120109.ebuild, +ccpn-2.1.5_p120304.ebuild,
+  ccpn-2.2.1_p120109.ebuild, +ccpn-2.2.1_p120304.ebuild:
+  Today's python patches
 
 *ccpn-2.2.1_p120109 (09 Jan 2012)
 *ccpn-2.1.5_p120109 (09 Jan 2012)
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 96cb90a171e5..e45f8e1ee318 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -23,25 +23,29 @@ DIST ccpn-update-2.1.5-111213.patch.xz 104892 RMD160 d2a83a0b809a91f8f8422a24c11
 DIST ccpn-update-2.1.5-111220.patch.xz 105472 RMD160 f8c358e7bc7757a4f645a2f26fa38e0159e5bc2f SHA1 21721845d3f0df77c548a3e5774ed5a82f3d12df SHA256 a4d8d4982c8bf63031cd11cbe67121a598b97f1c490862c363555bf9c2f11140
 DIST ccpn-update-2.1.5-111221.patch.xz 105424 RMD160 70f3b43b0ef4a827cb43f4673ca426deacff13d5 SHA1 6a240d2db8afe9166c8965207ac6701859089fba SHA256 fa9385c46b2aa535917b68de1c9ac0a0dcf0e4a3b2362ec75274fe8374289ca6
 DIST ccpn-update-2.1.5-120109.patch.xz 105508 RMD160 a485389af341270598a134a37e061674b935b60b SHA1 b0b3159ab01eda8d93971172bf9b62a588604d30 SHA256 024d65a1e2d82815db891ef920c10442366413d9aeefe7dd6d0d17d7bdbb37ba
+DIST ccpn-update-2.1.5-120304.patch.xz 105824 RMD160 8130a7de0f67fd85b434ff7edfe1821f1c73d1db SHA1 9344d675f42611518e9538c733b3435c19d58bce SHA256 f86b36e05f07d7e8674b8642c6a4d230f85431f1a2d98a369660784e80b4a469
 DIST ccpn-update-2.2.1-111213.patch.xz 81520 RMD160 55038a1272f8e01ce54fefdba081ee51ec5d4f36 SHA1 0bbd8c029a98b282002d8b5385a85355722de323 SHA256 807cef8e8b2822e178d50695c7e234ea8c243264a4711610f6a95e30e1b40d12
 DIST ccpn-update-2.2.1-111220.patch.xz 82840 RMD160 c0fb328ad93d7f07e1f0d45215d7686204315f91 SHA1 7b2ef76c62e85fcb4c5c95be053a9e281bc3d59d SHA256 f8942568e4f859da71e5a38b279355222882de19328501a0297bcddefef75c9f
 DIST ccpn-update-2.2.1-111221.patch.xz 82988 RMD160 e1ce373080f97411d9b00a269d8ed29ab8a4db0e SHA1 fe68eccce53bbbc7cfd69d398381cf3b28303c2d SHA256 6482ac0a90b34e4fbb6944a2f158d8743f6a23d7b28193b28fe7517044e27a76
 DIST ccpn-update-2.2.1-120109.patch.xz 85304 RMD160 3f2662f16f8c52b8c3813a0a45ad12f26bb8ba3c SHA1 267686361c0ee730d132beede957591428cd7016 SHA256 2997ae03541267e75577f4df317c6a9b69a282723271a6689265a9c2309c5769
-EBUILD ccpn-2.1.3.1_p100806.ebuild 5188 RMD160 b66825e37b79a5f6ec6635b9f3236d1cda2da672 SHA1 458f516ffad25d9283b21c9dfb8e50c6323f4264 SHA256 ff57abefefd3bb128a3f96bf039cbaa5ed97350f6b41fdbdd4b4365ff9e68e51
+DIST ccpn-update-2.2.1-120304.patch.xz 87980 RMD160 9d37afcd85557bb5385bb48dacb6f1f873a9ab0b SHA1 232365cc75aaa9d3114bf4b88968ad6af8fdbd6f SHA256 5fa751589394f709b0c65a965ac8f2a3bdab35a670c250bd4f2998acfac41153
+EBUILD ccpn-2.1.3.1_p100806.ebuild 5184 RMD160 777155a635a5d23d0e5eaa99fdb568ec36cfc722 SHA1 4ebd6e84c0e832264c726a42203d65b4a4065189 SHA256 255563ee932f4feee3cc3e1332dbd18be844efb78f2f8f10df9b1dd0894295e5
 EBUILD ccpn-2.1.5_p111213.ebuild 5773 RMD160 4fc120d9e6c5ecfd375a3df14a7b8b9afdebb3b5 SHA1 30bb2d2e22087ac6c93434863f1347db50f2514f SHA256 46de0ddcfd2fcb196dfb9ceb07c74c25ff3c8f4655b55f5e4b2f1d90a3787641
 EBUILD ccpn-2.1.5_p111220.ebuild 5773 RMD160 726f13ab2aa4532df15cbdc5a96b15293e53791e SHA1 5038f1c70ee0979181278ad3bbc9cdafff54d81c SHA256 7c21ffd5368b3a1c46ee838be8b970c6f7af371ea1048a253eca9c4c73af40c8
 EBUILD ccpn-2.1.5_p111221.ebuild 5773 RMD160 466f12257ec67eb942856702439f3f3b980618e7 SHA1 c7b160431d76ec2d619d4af84c24daf29a7594af SHA256 64429004d43a013ddeaad65e5aa7e6df9aafb1a5ff05455864f8ed88918bc5de
-EBUILD ccpn-2.1.5_p120109.ebuild 5773 RMD160 e382dac6b717b686f0f3d602ef5a1ca37835196e SHA1 57259c9f366f8f30fd2778491387d0235eff1269 SHA256 13a02a66fd2823d55529f6ccfde31e8523e211f62d892a93af262ff37e29313f
+EBUILD ccpn-2.1.5_p120109.ebuild 5769 RMD160 d7a3d287b84e8fb2bd050d2717b74fe18c958055 SHA1 b5a3ef87df31599384b70cda31161340a872d64e SHA256 31c757860eb49d605b4b5aba8f9efb1cca6816254063945bf5761d4b15f45c2d
+EBUILD ccpn-2.1.5_p120304.ebuild 5769 RMD160 9b07f11458044c944d7b92e959f789798b06151b SHA1 24080423a18afe5aec8d2038625fd74f47ffcd32 SHA256 5381372ac0673711691c726625b1db2960caf301399d345373e20128c0152df0
 EBUILD ccpn-2.2.1_p111213.ebuild 5788 RMD160 49f50c489d3eee93f80e1548c66fe2acf1131e20 SHA1 fe36614826a38746d32f32071f8583744fa263fd SHA256 2f25c2e6e348f37d95bc89dc36137303def1c66a02ff1603eedb8c32f61867e4
 EBUILD ccpn-2.2.1_p111220.ebuild 5788 RMD160 abb85d91207669ef94be18d38b4e9efc5dca135b SHA1 e07108a62c4867be2d4538a0ecf09bf5ac4dd968 SHA256 37885cacf0a4e97d05201b18949b87889c5e5965f04434399a2e52b24d30cf98
 EBUILD ccpn-2.2.1_p111221.ebuild 5788 RMD160 e722eaef088dbe8f273190fed6331157ab57c553 SHA1 97328118dcde05d92d7d5410f61a8c2b9b5badc5 SHA256 72216a2ec437f6cafa02eb435fffcf97bc274c5d6009f303a3eb214bd08badf5
-EBUILD ccpn-2.2.1_p120109.ebuild 5788 RMD160 2497c798c7de97c708b7835810623a0384d1e218 SHA1 233aa1787b5dfa4e39fe7bd330d38255e77be5cb SHA256 bd873ee86eff68721575836e60a989e966ace314dd34dd07dd3ece180b899239
-MISC ChangeLog 16170 RMD160 ade7204956f1edd0a9e1990cf71f194b9e93b019 SHA1 b38a208282c65b6f7aab5c8867fdf845fe74d6e3 SHA256 1afcaa694756d306bb7c967050ed859ccfdeea97c44d33c8e29cd54e88d2ac85
+EBUILD ccpn-2.2.1_p120109.ebuild 5784 RMD160 c6279bd8aab43037353347299c139da99c4d4bda SHA1 7cd2a6425cc8fd62396891874f16e1bfa7f33010 SHA256 b4b08ff9094119e5bd50066f72d41927bd3bbe840c0985f49c585501925ba593
+EBUILD ccpn-2.2.1_p120304.ebuild 5784 RMD160 e4278559ae4129bf56c73b7df807d73898910322 SHA1 c3e8b18e7a42c7e4d9e786e580ed40ae73b96710 SHA256 387882b2a69b312bfe9d7edaaf8a2dc399e1d3d16f62e3b250d91207e64c3f72
+MISC ChangeLog 16455 RMD160 8f55d4c31ab61d3171977692951efa465644b32a SHA1 ce11f27aef0cd91c2d5ba997eac00ecf9c73d396 SHA256 8b34994ce18407c55221ef78bc279eb4d94765b7086690150bb06ad11b4dfa19
 MISC metadata.xml 322 RMD160 9fd5fba7405b689fc39a089d81ffdaa9f961b514 SHA1 0c31132b25fca04cff97ef11fdc11940f90c77d0 SHA256 7468ba4c27b879e7ed5f82274f5837e51f1f389673a33b9e26e1756a6b0783df
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diff --git a/sci-chemistry/ccpn/ccpn-2.1.3.1_p100806.ebuild b/sci-chemistry/ccpn/ccpn-2.1.3.1_p100806.ebuild
index c81ae201d6a7..6c16fb6a5480 100644
--- a/sci-chemistry/ccpn/ccpn-2.1.3.1_p100806.ebuild
+++ b/sci-chemistry/ccpn/ccpn-2.1.3.1_p100806.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.3.1_p100806.ebuild,v 1.4 2011/06/29 05:51:28 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.3.1_p100806.ebuild,v 1.5 2012/03/04 09:18:53 jlec Exp $
 
 EAPI="3"
 PYTHON_DEPEND="2:2.5"
@@ -14,7 +14,7 @@ MY_PN="${PN}mr"
 MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
 
 DESCRIPTION="The Collaborative Computing Project for NMR"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
+SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
 	[[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI}	http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${PATCHSET}.patch.bz2"
 HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
 
diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p120109.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p120109.ebuild
index af75b515c81e..b35f479c46d2 100644
--- a/sci-chemistry/ccpn/ccpn-2.1.5_p120109.ebuild
+++ b/sci-chemistry/ccpn/ccpn-2.1.5_p120109.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p120109.ebuild,v 1.1 2012/01/09 12:42:11 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p120109.ebuild,v 1.2 2012/03/04 09:18:53 jlec Exp $
 
 EAPI="3"
 
@@ -16,7 +16,7 @@ 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.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
+SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
 	[[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI}	http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
 
 SLOT="0"
diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p120304.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p120304.ebuild
new file mode 100644
index 000000000000..bc83d5014b0e
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.1.5_p120304.ebuild
@@ -0,0 +1,214 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p120304.ebuild,v 1.1 2012/03/04 09:18:53 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2:2.5"
+PYTHON_USE_WITH="ssl tk"
+
+inherit eutils portability python 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 ${PATCHSET} ]] && SRC_URI="${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="extendnmr +opengl"
+
+RDEPEND="
+	dev-lang/tk[threads]
+	>=dev-python/numpy-1.4
+	>=dev-tcltk/tix-8.4.3
+	=sci-libs/ccpn-data-"${MY_MAJOR}"*
+	>=sci-libs/ccpn-data-2.1.5_p111011
+	sci-biology/psipred
+	x11-libs/libXext
+	x11-libs/libX11
+	opengl? (
+		media-libs/freeglut
+		dev-python/pyglet )"
+# We need to fix this
+#		sci-chemistry/mdd
+DEPEND="${RDEPEND}"
+PDEPEND="
+	extendnmr? (
+		<=sci-chemistry/aria-2.3.2
+		sci-chemistry/prodecomp )"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
+
+pkg_setup() {
+	python_set_active_version 2
+}
+
+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|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+		-e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
+		-e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
+		c/environment_default.txt > c/environment.txt
+}
+
+src_compile() {
+	emake -C c all links || die
+}
+
+src_install() {
+	local libdir
+	local tkver
+	local _wrapper
+
+	find . -name "*.pyc" -type d -delete
+
+	libdir=$(get_libdir)
+	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
+
+	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara"
+	use extendnmr && _wrapper="${_wrapper} extendNmr"
+	for wrapper in ${_wrapper}; do
+		sed \
+			-e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
+		   -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
+			-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
+			-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
+			-e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
+			-e "s|gentoousr|${EPREFIX}/usr|g" \
+			-e "s|//|/|g" \
+			"${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
+		dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
+	done
+
+	local in_path
+	local files
+	local pydocs
+
+	pydocs="$(find python -name doc -type d)"
+	rm -rf ${pydocs} || die
+
+	in_path=$(python_get_sitedir)/${PN}
+
+	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}/c
+
+	ebegin "Installing main files"
+		doins -r python || die "main files installation failed"
+	eend
+
+	einfo "Adjusting permissions"
+
+	files="
+		cambridge/c/BayesPeakSeparator.so
+		ccp/c/StructUtil.so
+		ccp/c/StructStructure.so
+		ccp/c/StructBond.so
+		ccp/c/StructAtom.so
+		ccpnmr/c/DyAtomCoord.so
+		ccpnmr/c/DyDistConstraint.so
+		ccpnmr/c/DyDistForce.so
+		ccpnmr/c/AtomCoordList.so
+		ccpnmr/c/DyAtomCoordList.so
+		ccpnmr/c/ContourStyle.so
+		ccpnmr/c/ContourLevels.so
+		ccpnmr/c/SliceFile.so
+		ccpnmr/c/PeakCluster.so
+		ccpnmr/c/Dynamics.so
+		ccpnmr/c/Bacus.so
+		ccpnmr/c/Midge.so
+		ccpnmr/c/DyDistConstraintList.so
+		ccpnmr/c/WinPeakList.so
+		ccpnmr/c/PeakList.so
+		ccpnmr/c/DistConstraint.so
+		ccpnmr/c/CloudUtil.so
+		ccpnmr/c/DistForce.so
+		ccpnmr/c/DistConstraintList.so
+		ccpnmr/c/AtomCoord.so
+		ccpnmr/c/DyDynamics.so
+		ccpnmr/c/ContourFile.so
+		memops/c/ShapeFile.so
+		memops/c/BlockFile.so
+		memops/c/PdfHandler.so
+		memops/c/MemCache.so
+		memops/c/FitMethod.so
+		memops/c/PsHandler.so
+		memops/c/GlHandler.so
+		memops/c/StoreFile.so
+		memops/c/StoreHandler.so
+		memops/c/TkHandler.so"
+	for FILE in ${files}; do
+		fperms 755 ${in_path}/python/${FILE}
+	done
+}
+
+pkg_postinst() {
+	python_mod_optimize ${PN}
+}
+
+pkg_postrm() {
+	python_mod_cleanup ${PN}
+}
diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p120109.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p120109.ebuild
index 840639d9880c..0eddec7b5aaf 100644
--- a/sci-chemistry/ccpn/ccpn-2.2.1_p120109.ebuild
+++ b/sci-chemistry/ccpn/ccpn-2.2.1_p120109.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p120109.ebuild,v 1.1 2012/01/09 12:42:11 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p120109.ebuild,v 1.2 2012/03/04 09:18:53 jlec Exp $
 
 EAPI="3"
 
@@ -15,7 +15,7 @@ MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
 MY_MAJOR="$(get_version_component_range 1-3)"
 
 DESCRIPTION="The Collaborative Computing Project for NMR"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
+SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
 	[[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI}	http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
 HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
 
diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p120304.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p120304.ebuild
new file mode 100644
index 000000000000..a479d2064514
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.2.1_p120304.ebuild
@@ -0,0 +1,214 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p120304.ebuild,v 1.1 2012/03/04 09:18:53 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2:2.5"
+PYTHON_USE_WITH="ssl tk"
+
+inherit eutils portability python 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"
+SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
+	[[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI}	http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
+HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="extendnmr +opengl"
+
+RDEPEND="
+	dev-lang/tk[threads]
+	>=dev-python/numpy-1.4
+	>=dev-tcltk/tix-8.4.3
+	=sci-libs/ccpn-data-"${MY_MAJOR}"*
+	>=sci-libs/ccpn-data-2.2.1_p111011
+	sci-biology/psipred
+	x11-libs/libXext
+	x11-libs/libX11
+	opengl? (
+		media-libs/freeglut
+		dev-python/pyglet )"
+# We need to fix this
+#		sci-chemistry/mdd
+DEPEND="${RDEPEND}"
+PDEPEND="
+	extendnmr? (
+		>=sci-chemistry/aria-2.3.2-r1
+		sci-chemistry/prodecomp )"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
+
+pkg_setup() {
+	python_set_active_version 2
+}
+
+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|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+		-e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
+		-e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
+		c/environment_default.txt > c/environment.txt
+}
+
+src_compile() {
+	emake -C c all links || die
+}
+
+src_install() {
+	local libdir
+	local tkver
+	local _wrapper
+
+	find . -name "*.pyc" -type d -delete
+
+	libdir=$(get_libdir)
+	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
+
+	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara"
+	use extendnmr && _wrapper="${_wrapper} extendNmr"
+	for wrapper in ${_wrapper}; do
+		sed \
+			-e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
+		   -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
+			-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
+			-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
+			-e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
+			-e "s|gentoousr|${EPREFIX}/usr|g" \
+			-e "s|//|/|g" \
+			"${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
+		dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
+	done
+
+	local in_path
+	local files
+	local pydocs
+
+	pydocs="$(find python -name doc -type d)"
+	rm -rf ${pydocs} || die
+
+	in_path=$(python_get_sitedir)/${PN}
+
+	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}/c
+
+	ebegin "Installing main files"
+		doins -r python || die "main files installation failed"
+	eend
+
+	einfo "Adjusting permissions"
+
+	files="
+		cambridge/c/BayesPeakSeparator.so
+		ccp/c/StructUtil.so
+		ccp/c/StructStructure.so
+		ccp/c/StructBond.so
+		ccp/c/StructAtom.so
+		ccpnmr/c/DyAtomCoord.so
+		ccpnmr/c/DyDistConstraint.so
+		ccpnmr/c/DyDistForce.so
+		ccpnmr/c/AtomCoordList.so
+		ccpnmr/c/DyAtomCoordList.so
+		ccpnmr/c/ContourStyle.so
+		ccpnmr/c/ContourLevels.so
+		ccpnmr/c/SliceFile.so
+		ccpnmr/c/PeakCluster.so
+		ccpnmr/c/Dynamics.so
+		ccpnmr/c/Bacus.so
+		ccpnmr/c/Midge.so
+		ccpnmr/c/DyDistConstraintList.so
+		ccpnmr/c/WinPeakList.so
+		ccpnmr/c/PeakList.so
+		ccpnmr/c/DistConstraint.so
+		ccpnmr/c/CloudUtil.so
+		ccpnmr/c/DistForce.so
+		ccpnmr/c/DistConstraintList.so
+		ccpnmr/c/AtomCoord.so
+		ccpnmr/c/DyDynamics.so
+		ccpnmr/c/ContourFile.so
+		memops/c/ShapeFile.so
+		memops/c/BlockFile.so
+		memops/c/PdfHandler.so
+		memops/c/MemCache.so
+		memops/c/FitMethod.so
+		memops/c/PsHandler.so
+		memops/c/GlHandler.so
+		memops/c/StoreFile.so
+		memops/c/StoreHandler.so
+		memops/c/TkHandler.so"
+	for FILE in ${files}; do
+		fperms 755 ${in_path}/python/${FILE}
+	done
+}
+
+pkg_postinst() {
+	python_mod_optimize ${PN}
+}
+
+pkg_postrm() {
+	python_mod_cleanup ${PN}
+}