sci-chemistry/ccpn: Cleaned old, add latest python patches

(Portage version: 2.2.0_alpha99/cvs/Linux x86_64)

10 files changed, 36 insertions, 1596 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 15d7869a79fe..e34b7e51bff8 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,16 @@
 # 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 1.81 2012/04/03 14:45:33 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.82 2012/04/03 17:24:27 jlec Exp $
+
+*ccpn-2.2.2_p120403 (03 Apr 2012)
+
+  03 Apr 2012; Justin Lecher <jlec@gentoo.org> -files/2.1.5-parallel.patch,
+  -ccpn-2.1.5_p111213.ebuild, -ccpn-2.1.5_p111220.ebuild,
+  -ccpn-2.1.5_p111221.ebuild, -ccpn-2.1.5_p120109.ebuild,
+  -ccpn-2.1.5_p120304.ebuild, -ccpn-2.2.1_p111213.ebuild,
+  -ccpn-2.2.1_p111220.ebuild, -ccpn-2.2.1_p111221.ebuild,
+  +ccpn-2.2.2_p120403.ebuild:
+  Cleaned old, add latest python patches
 
 *ccpn-2.2.2 (03 Apr 2012)
 
diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p111213.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p111213.ebuild
deleted file mode 100644
index 7c1269cadc79..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.1.5_p111213.ebuild
+++ /dev/null
@@ -1,214 +0,0 @@
-# Copyright 1999-2011 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_p111213.ebuild,v 1.1 2011/12/13 08:33:36 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.bio.cam.ac.uk/ccpn/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-2.1.5_p111220.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p111220.ebuild
deleted file mode 100644
index 1ae1679ac13f..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.1.5_p111220.ebuild
+++ /dev/null
@@ -1,214 +0,0 @@
-# Copyright 1999-2011 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_p111220.ebuild,v 1.1 2011/12/20 08:39:39 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.bio.cam.ac.uk/ccpn/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-2.1.5_p111221.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p111221.ebuild
deleted file mode 100644
index 260983cbe464..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.1.5_p111221.ebuild
+++ /dev/null
@@ -1,214 +0,0 @@
-# Copyright 1999-2011 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_p111221.ebuild,v 1.1 2011/12/21 13:46:42 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.bio.cam.ac.uk/ccpn/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-2.1.5_p120109.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p120109.ebuild
deleted file mode 100644
index b35f479c46d2..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.1.5_p120109.ebuild
+++ /dev/null
@@ -1,214 +0,0 @@
-# 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 1.2 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_p111213.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p111213.ebuild
deleted file mode 100644
index b004c24dc7a2..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.2.1_p111213.ebuild
+++ /dev/null
@@ -1,214 +0,0 @@
-# Copyright 1999-2011 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_p111213.ebuild,v 1.1 2011/12/13 08:33:36 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.bio.cam.ac.uk/ccpn/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}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p111220.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p111220.ebuild
deleted file mode 100644
index e1600d68538f..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.2.1_p111220.ebuild
+++ /dev/null
@@ -1,214 +0,0 @@
-# Copyright 1999-2011 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_p111220.ebuild,v 1.1 2011/12/20 08:39:39 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.bio.cam.ac.uk/ccpn/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}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p111221.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p111221.ebuild
deleted file mode 100644
index a7fddbd45dd4..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.2.1_p111221.ebuild
+++ /dev/null
@@ -1,214 +0,0 @@
-# Copyright 1999-2011 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_p111221.ebuild,v 1.1 2011/12/21 13:46:42 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.bio.cam.ac.uk/ccpn/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}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p120304.ebuild b/sci-chemistry/ccpn/ccpn-2.2.2_p120403.ebuild
index bc83d5014b0e..4e92b9943ea6 100644
--- a/sci-chemistry/ccpn/ccpn-2.1.5_p120304.ebuild
+++ b/sci-chemistry/ccpn/ccpn-2.2.2_p120403.ebuild
@@ -1,8 +1,8 @@
 # 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 $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.2_p120403.ebuild,v 1.1 2012/04/03 17:24:27 jlec Exp $
 
-EAPI="3"
+EAPI=4
 
 PYTHON_DEPEND="2:2.5"
 PYTHON_USE_WITH="ssl tk"
@@ -15,9 +15,9 @@ 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"
+HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
 
 SLOT="0"
 LICENSE="|| ( CCPN LGPL-2.1 )"
@@ -26,10 +26,9 @@ IUSE="extendnmr +opengl"
 
 RDEPEND="
 	dev-lang/tk[threads]
-	>=dev-python/numpy-1.4
-	>=dev-tcltk/tix-8.4.3
+	dev-python/numpy
+	dev-tcltk/tix
 	=sci-libs/ccpn-data-"${MY_MAJOR}"*
-	>=sci-libs/ccpn-data-2.1.5_p111011
 	sci-biology/psipred
 	x11-libs/libXext
 	x11-libs/libX11
@@ -41,7 +40,7 @@ RDEPEND="
 DEPEND="${RDEPEND}"
 PDEPEND="
 	extendnmr? (
-		<=sci-chemistry/aria-2.3.2
+		>=sci-chemistry/aria-2.3.2-r1
 		sci-chemistry/prodecomp )"
 
 RESTRICT="mirror"
@@ -50,6 +49,7 @@ S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
 
 pkg_setup() {
 	python_set_active_version 2
+	python_pkg_setup
 }
 
 src_prepare() {
@@ -105,11 +105,16 @@ src_prepare() {
 		-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
+		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 links || die
+	emake -C c all
+	emake -C c links
 }
 
 src_install() {
@@ -117,12 +122,12 @@ src_install() {
 	local tkver
 	local _wrapper
 
-	find . -name "*.pyc" -type d -delete
+	find . -name "*.pyc" -type f -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"
+	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara"
 	use extendnmr && _wrapper="${_wrapper} extendNmr"
 	for wrapper in ${_wrapper}; do
 		sed \
@@ -130,22 +135,20 @@ src_install() {
 		   -e "s|gentoolibdir|${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|gentoopython|$(PYTHON -a)|g" \
 			-e "s|gentoousr|${EPREFIX}/usr|g" \
 			-e "s|//|/|g" \
 			"${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
-		dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
+		dobin "${T}"/${wrapper}
 	done
 
-	local in_path
+	local in_path=$(python_get_sitedir)/${PN}
 	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' \
@@ -157,52 +160,15 @@ src_install() {
 	dodir ${in_path}/c
 
 	ebegin "Installing main files"
-		doins -r python || die "main files installation failed"
+		doins -r python
 	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}
+	ebegin "Adjusting permissions"
+
+	for _file in $(find "${ED}" -type f -name "*so"); do
+		chmod 755 ${_file}
 	done
+	eend
 }
 
 pkg_postinst() {
diff --git a/sci-chemistry/ccpn/files/2.1.5-parallel.patch b/sci-chemistry/ccpn/files/2.1.5-parallel.patch
deleted file mode 100644
index 2bffed78b11d..000000000000
--- a/sci-chemistry/ccpn/files/2.1.5-parallel.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-diff --git a/ccpnmr2.1/c/Makefile b/ccpnmr2.1/c/Makefile
-index 01fb25a..8e8e1fe 100644
---- a/ccpnmr2.1/c/Makefile
-+++ b/ccpnmr2.1/c/Makefile
-@@ -5,22 +5,22 @@ all: compile
- compile: global structure analysis clouds dynamics bayes
- 
- global:
--	cd memops/global && $(MAKE)
-+	$(MAKE) -C memops/global
- 
--structure:
--	cd ccp/structure && $(MAKE)
-+structure: global
-+	$(MAKE) -C ccp/structure
- 
--analysis:
--	cd ccpnmr/analysis && $(MAKE)
-+analysis: global
-+	$(MAKE) -C ccpnmr/analysis
- 
--clouds:
--	cd ccpnmr/clouds && $(MAKE)
-+clouds: global
-+	$(MAKE) -C ccpnmr/clouds
- 
--dynamics:
--	cd ccpnmr/dynamics && $(MAKE)
-+dynamics: global
-+	$(MAKE) -C ccpnmr/dynamics
- 
--bayes:
--	cd other/cambridge/bayes && $(MAKE)
-+bayes: global
-+	$(MAKE) -C other/cambridge/bayes
- 
- clean: global_clean structure_clean analysis_clean clouds_clean dynamics_clean bayes_clean
-