sci-chemistry/ccpn: Todays python patches

(Portage version: 2.2.0_alpha149/cvs/Linux x86_64, signed Manifest commit with key 70EB7916)

7 files changed, 25 insertions, 743 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 7f52a849ce96..c0dc7ce3b597 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 1.99 2012/11/25 09:16:31 jlec Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.100 2013/01/10 17:41:33 jlec Exp $
+
+*ccpn-2.2.2_p130110 (10 Jan 2013)
+
+  10 Jan 2013; Justin Lecher <jlec@gentoo.org> -ccpn-2.2.2_p120829.ebuild,
+  -ccpn-2.2.2_p120912.ebuild, -ccpn-2.2.2_p121012.ebuild,
+  -ccpn-2.2.2_p121112.ebuild, -ccpn-2.2.2_p121119.ebuild,
+  +ccpn-2.2.2_p130110.ebuild, metadata.xml:
+  Todays python patches
 
 *ccpn-2.2.2_p121125 (25 Nov 2012)
 
diff --git a/sci-chemistry/ccpn/ccpn-2.2.2_p120912.ebuild b/sci-chemistry/ccpn/ccpn-2.2.2_p120912.ebuild
deleted file mode 100644
index 95938b6ad10a..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.2.2_p120912.ebuild
+++ /dev/null
@@ -1,180 +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-2.2.2_p120912.ebuild,v 1.1 2012/09/12 11:26:07 jlec Exp $
-
-EAPI=4
-
-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
-	dev-tcltk/tix
-	=sci-libs/ccpn-data-"${MY_MAJOR}"*
-	sci-biology/psipred
-	x11-libs/libXext
-	x11-libs/libX11
-	opengl? (
-		media-libs/freeglut
-		dev-python/pyglet )"
-# We need to fix this
-#		sci-chemistry/mdd
-DEPEND="${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
-	python_pkg_setup
-}
-
-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 || die
-
-	sed \
-		-e 's:ln -s:cp -f:g' \
-		-i $(find python -name linkSharedObjs) || die
-}
-
-src_compile() {
-	emake -C c all
-	emake -C c links
-}
-
-src_install() {
-	local libdir
-	local tkver
-	local _wrapper
-
-	find . -name "*.pyc" -type f -delete
-
-	libdir=$(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${tkver}|g" \
-			-e "s|gentoopython|$(PYTHON -a)|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}/c
-
-	ebegin "Installing main files"
-		doins -r python
-	eend
-
-	ebegin "Adjusting permissions"
-
-	for _file in $(find "${ED}" -type f -name "*so"); do
-		chmod 755 ${_file}
-	done
-	eend
-}
-
-pkg_postinst() {
-	python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
-	python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.2.2_p121012.ebuild b/sci-chemistry/ccpn/ccpn-2.2.2_p121012.ebuild
deleted file mode 100644
index cd38f77e1eb1..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.2.2_p121012.ebuild
+++ /dev/null
@@ -1,180 +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-2.2.2_p121012.ebuild,v 1.1 2012/10/12 16:24:44 jlec Exp $
-
-EAPI=4
-
-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
-	dev-tcltk/tix
-	=sci-libs/ccpn-data-"${MY_MAJOR}"*
-	sci-biology/psipred
-	x11-libs/libXext
-	x11-libs/libX11
-	opengl? (
-		media-libs/freeglut
-		dev-python/pyglet )"
-# We need to fix this
-#		sci-chemistry/mdd
-DEPEND="${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
-	python_pkg_setup
-}
-
-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 || die
-
-	sed \
-		-e 's:ln -s:cp -f:g' \
-		-i $(find python -name linkSharedObjs) || die
-}
-
-src_compile() {
-	emake -C c all
-	emake -C c links
-}
-
-src_install() {
-	local libdir
-	local tkver
-	local _wrapper
-
-	find . -name "*.pyc" -type f -delete
-
-	libdir=$(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${tkver}|g" \
-			-e "s|gentoopython|$(PYTHON -a)|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}/c
-
-	ebegin "Installing main files"
-		doins -r python
-	eend
-
-	ebegin "Adjusting permissions"
-
-	for _file in $(find "${ED}" -type f -name "*so"); do
-		chmod 755 ${_file}
-	done
-	eend
-}
-
-pkg_postinst() {
-	python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
-	python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.2.2_p121112.ebuild b/sci-chemistry/ccpn/ccpn-2.2.2_p121112.ebuild
deleted file mode 100644
index 86faca1b84bd..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.2.2_p121112.ebuild
+++ /dev/null
@@ -1,180 +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-2.2.2_p121112.ebuild,v 1.1 2012/11/12 08:00:21 jlec Exp $
-
-EAPI=4
-
-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
-	dev-tcltk/tix
-	=sci-libs/ccpn-data-"${MY_MAJOR}"*
-	sci-biology/psipred
-	x11-libs/libXext
-	x11-libs/libX11
-	opengl? (
-		media-libs/freeglut
-		dev-python/pyglet )"
-# We need to fix this
-#		sci-chemistry/mdd
-DEPEND="${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
-	python_pkg_setup
-}
-
-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 || die
-
-	sed \
-		-e 's:ln -s:cp -f:g' \
-		-i $(find python -name linkSharedObjs) || die
-}
-
-src_compile() {
-	emake -C c all
-	emake -C c links
-}
-
-src_install() {
-	local libdir
-	local tkver
-	local _wrapper
-
-	find . -name "*.pyc" -type f -delete
-
-	libdir=$(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${tkver}|g" \
-			-e "s|gentoopython|$(PYTHON -a)|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}/c
-
-	ebegin "Installing main files"
-		doins -r python
-	eend
-
-	ebegin "Adjusting permissions"
-
-	for _file in $(find "${ED}" -type f -name "*so"); do
-		chmod 755 ${_file}
-	done
-	eend
-}
-
-pkg_postinst() {
-	python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
-	python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.2.2_p121119.ebuild b/sci-chemistry/ccpn/ccpn-2.2.2_p121119.ebuild
deleted file mode 100644
index 3cff7cc2486f..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.2.2_p121119.ebuild
+++ /dev/null
@@ -1,180 +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-2.2.2_p121119.ebuild,v 1.1 2012/11/19 09:47:21 jlec Exp $
-
-EAPI=4
-
-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
-	dev-tcltk/tix
-	=sci-libs/ccpn-data-"${MY_MAJOR}"*
-	sci-biology/psipred
-	x11-libs/libXext
-	x11-libs/libX11
-	opengl? (
-		media-libs/freeglut
-		dev-python/pyglet )"
-# We need to fix this
-#		sci-chemistry/mdd
-DEPEND="${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
-	python_pkg_setup
-}
-
-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 || die
-
-	sed \
-		-e 's:ln -s:cp -f:g' \
-		-i $(find python -name linkSharedObjs) || die
-}
-
-src_compile() {
-	emake -C c all
-	emake -C c links
-}
-
-src_install() {
-	local libdir
-	local tkver
-	local _wrapper
-
-	find . -name "*.pyc" -type f -delete
-
-	libdir=$(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${tkver}|g" \
-			-e "s|gentoopython|$(PYTHON -a)|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}/c
-
-	ebegin "Installing main files"
-		doins -r python
-	eend
-
-	ebegin "Adjusting permissions"
-
-	for _file in $(find "${ED}" -type f -name "*so"); do
-		chmod 755 ${_file}
-	done
-	eend
-}
-
-pkg_postinst() {
-	python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
-	python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.2.2_p120829.ebuild b/sci-chemistry/ccpn/ccpn-2.2.2_p130110.ebuild
index bf86ba66284f..71c969df6198 100644
--- a/sci-chemistry/ccpn/ccpn-2.2.2_p120829.ebuild
+++ b/sci-chemistry/ccpn/ccpn-2.2.2_p130110.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2012 Gentoo Foundation
+# 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_p120829.ebuild,v 1.1 2012/08/29 06:24:14 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.2_p130110.ebuild,v 1.1 2013/01/10 17:41:33 jlec Exp $
 
 EAPI=4
 
@@ -15,14 +15,15 @@ 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"
+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="extendnmr +opengl"
+IUSE="+opengl"
 
 RDEPEND="
 	dev-lang/tk[threads]
@@ -35,13 +36,7 @@ RDEPEND="
 	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"
 
@@ -102,6 +97,7 @@ src_prepare() {
 		-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${tk_ver}|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 $(python_get_library -l)|g" \
@@ -127,8 +123,7 @@ src_install() {
 	libdir=$(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"
+	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr"
 	for wrapper in ${_wrapper}; do
 		sed \
 			-e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
@@ -164,7 +159,6 @@ src_install() {
 	eend
 
 	ebegin "Adjusting permissions"
-
 	for _file in $(find "${ED}" -type f -name "*so"); do
 		chmod 755 ${_file}
 	done
diff --git a/sci-chemistry/ccpn/metadata.xml b/sci-chemistry/ccpn/metadata.xml
index d65c846daad4..8a82c7657734 100644
--- a/sci-chemistry/ccpn/metadata.xml
+++ b/sci-chemistry/ccpn/metadata.xml
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-chemistry</herd>
-	<maintainer>
-		<email>jlec@gentoo.org</email>
-	</maintainer>
-	<use>
-		<flag name="extendnmr">Install needed packages for extendNMR support</flag>
-	</use>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>jlec@gentoo.org</email>
+  </maintainer>
+  <use>
+    <flag name="extendnmr">Install needed packages for extendNMR support</flag>
+  </use>
 </pkgmetadata>