Todays Python patches, fix for psipred32

(Portage version: 2.2.0_alpha69/cvs/Linux x86_64)

8 files changed, 235 insertions, 7 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index b53d5e7e1b83..8aedca2b990d 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/ccpn
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.72 2011/10/17 15:38:40 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.73 2011/10/19 07:25:58 jlec Exp $
+
+*ccpn-2.2.1_p111019 (19 Oct 2011)
+
+  19 Oct 2011; Justin Lecher <jlec@gentoo.org> +ccpn-2.2.1_p111019.ebuild,
+  ccpn-2.1.5_p110926.ebuild, ccpn-2.2.1_p111017.ebuild,
+  ccpn-2.2.1_p110926.ebuild, ccpn-2.1.5_p111017.ebuild, metadata.xml,
+  ccpn-2.2.1_p111011.ebuild, ccpn-2.1.5_p111011.ebuild:
+  Todays Python patches, fix for psipred32
 
 *ccpn-2.2.1_p111017 (17 Oct 2011)
 *ccpn-2.1.5_p111017 (17 Oct 2011)
diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p110926.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p110926.ebuild
index 3e99c2a9f6ae..6a05a896dcbe 100644
--- a/sci-chemistry/ccpn/ccpn-2.1.5_p110926.ebuild
+++ b/sci-chemistry/ccpn/ccpn-2.1.5_p110926.ebuild
@@ -1,6 +1,6 @@
 # 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_p110926.ebuild,v 1.2 2011/10/07 19:29:31 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p110926.ebuild,v 1.3 2011/10/19 07:25:58 jlec Exp $
 
 EAPI="3"
 
@@ -59,6 +59,7 @@ src_prepare() {
 
 	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
diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p111011.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p111011.ebuild
index afcbfe58f1ff..bdb3bf68f7b6 100644
--- a/sci-chemistry/ccpn/ccpn-2.1.5_p111011.ebuild
+++ b/sci-chemistry/ccpn/ccpn-2.1.5_p111011.ebuild
@@ -1,6 +1,6 @@
 # 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_p111011.ebuild,v 1.1 2011/10/11 19:28:28 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p111011.ebuild,v 1.2 2011/10/19 07:25:58 jlec Exp $
 
 EAPI="3"
 
@@ -60,6 +60,7 @@ src_prepare() {
 
 	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
diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p111017.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p111017.ebuild
index 29908be3c9f1..6d841300e841 100644
--- a/sci-chemistry/ccpn/ccpn-2.1.5_p111017.ebuild
+++ b/sci-chemistry/ccpn/ccpn-2.1.5_p111017.ebuild
@@ -1,6 +1,6 @@
 # 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_p111017.ebuild,v 1.1 2011/10/17 15:38:40 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p111017.ebuild,v 1.2 2011/10/19 07:25:58 jlec Exp $
 
 EAPI="3"
 
@@ -60,6 +60,7 @@ src_prepare() {
 
 	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
diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p110926.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p110926.ebuild
index 530b99d9a109..81bba68c28b7 100644
--- a/sci-chemistry/ccpn/ccpn-2.2.1_p110926.ebuild
+++ b/sci-chemistry/ccpn/ccpn-2.2.1_p110926.ebuild
@@ -1,6 +1,6 @@
 # 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_p110926.ebuild,v 1.2 2011/10/07 19:29:31 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p110926.ebuild,v 1.3 2011/10/19 07:25:58 jlec Exp $
 
 EAPI="3"
 
@@ -59,6 +59,7 @@ src_prepare() {
 
 	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
diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p111011.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p111011.ebuild
index 23c0825dce7f..d0ae0c549ab9 100644
--- a/sci-chemistry/ccpn/ccpn-2.2.1_p111011.ebuild
+++ b/sci-chemistry/ccpn/ccpn-2.2.1_p111011.ebuild
@@ -1,6 +1,6 @@
 # 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_p111011.ebuild,v 1.1 2011/10/11 19:28:28 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p111011.ebuild,v 1.2 2011/10/19 07:25:58 jlec Exp $
 
 EAPI="3"
 
@@ -60,6 +60,7 @@ src_prepare() {
 
 	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
diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p111017.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p111017.ebuild
index 28849630e1fe..e4f4f13a7c63 100644
--- a/sci-chemistry/ccpn/ccpn-2.2.1_p111017.ebuild
+++ b/sci-chemistry/ccpn/ccpn-2.2.1_p111017.ebuild
@@ -1,6 +1,6 @@
 # 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_p111017.ebuild,v 1.1 2011/10/17 15:38:40 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p111017.ebuild,v 1.2 2011/10/19 07:25:58 jlec Exp $
 
 EAPI="3"
 
@@ -60,6 +60,7 @@ src_prepare() {
 
 	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
diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p111019.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p111019.ebuild
new file mode 100644
index 000000000000..51c99204e671
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.2.1_p111019.ebuild
@@ -0,0 +1,214 @@
+# 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_p111019.ebuild,v 1.1 2011/10/19 07:25:58 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}
+}