diff options
| -rw-r--r-- | sci-chemistry/ccpn/ChangeLog | 9 | ||||
| -rw-r--r-- | sci-chemistry/ccpn/ccpn-2.1.5_p110222.ebuild | 213 | ||||
| -rw-r--r-- | sci-chemistry/ccpn/ccpn-2.2.1_p110222.ebuild | 213 | ||||
| -rw-r--r-- | sci-chemistry/ccpn/files/2.2.1-parallel.patch | 38 | ||||
| -rw-r--r-- | sci-chemistry/ccpn/files/xeasy2azara | 8 |
5 files changed, 480 insertions, 1 deletions
diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog index 9381500a9aa3..752dcf0b75d0 100644 --- a/sci-chemistry/ccpn/ChangeLog +++ b/sci-chemistry/ccpn/ChangeLog @@ -1,6 +1,13 @@ # 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 1.56 2011/02/17 11:39:12 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.57 2011/02/22 10:35:38 jlec Exp $ + +*ccpn-2.2.1_p110222 (22 Feb 2011) +*ccpn-2.1.5_p110222 (22 Feb 2011) + + 22 Feb 2011; Justin Lecher <jlec@gentoo.org> +files/2.2.1-parallel.patch, + +files/xeasy2azara, +ccpn-2.1.5_p110222.ebuild, +ccpn-2.2.1_p110222.ebuild: + Version Bump and python patches *ccpn-2.1.5_p110217 (17 Feb 2011) diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p110222.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p110222.ebuild new file mode 100644 index 000000000000..80608cf7391d --- /dev/null +++ b/sci-chemistry/ccpn/ccpn-2.1.5_p110222.ebuild @@ -0,0 +1,213 @@ +# 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_p110222.ebuild,v 1.1 2011/02/22 10:35:38 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.bz2" +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-"${MY_MAJOR}"* + x11-libs/libXext + x11-libs/libX11 + opengl? ( + media-libs/freeglut + dev-python/pyglet )" +# We need to fix this +# sci-chemistry/mdd +DEPEND="${RDEPEND}" +PDEPEND=" + extendnmr? ( + sci-chemistry/aria + 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 + + 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://:/: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 ${in_path}/c + + ebegin "Installing main files" + doins -r python || die "main files installation failed" + eend + dosym ../../../..//share/doc/ccpn-data-${MY_MAJOR}/html ${in_path}/doc || die + for i in ${pydocs}; do + dosym /usr/share/doc/ccpn-data-${MY_MAJOR}/html/${i} ${in_path}/${i} + done + + dosym /usr/share/ccpn/data ${in_path}/data + dosym /usr/share/ccpn/model ${in_path}/model + + 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_p110222.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p110222.ebuild new file mode 100644 index 000000000000..5c6451c73318 --- /dev/null +++ b/sci-chemistry/ccpn/ccpn-2.2.1_p110222.ebuild @@ -0,0 +1,213 @@ +# 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_p110222.ebuild,v 1.1 2011/02/22 10:35:38 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.bz2" +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-"${MY_MAJOR}"* + x11-libs/libXext + x11-libs/libX11 + opengl? ( + media-libs/freeglut + dev-python/pyglet )" +# We need to fix this +# sci-chemistry/mdd +DEPEND="${RDEPEND}" +PDEPEND=" + extendnmr? ( + sci-chemistry/aria + 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 + + 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://:/: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 ${in_path}/c + + ebegin "Installing main files" + doins -r python || die "main files installation failed" + eend + dosym ../../../..//share/doc/ccpn-data-${MY_MAJOR}/html ${in_path}/doc || die + for i in ${pydocs}; do + dosym /usr/share/doc/ccpn-data-${MY_MAJOR}/html/${i} ${in_path}/${i} + done + + dosym /usr/share/ccpn/data ${in_path}/data + dosym /usr/share/ccpn/model ${in_path}/model + + 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/files/2.2.1-parallel.patch b/sci-chemistry/ccpn/files/2.2.1-parallel.patch new file mode 100644 index 000000000000..9223ea8828c2 --- /dev/null +++ b/sci-chemistry/ccpn/files/2.2.1-parallel.patch @@ -0,0 +1,38 @@ +diff --git a/ccpnmr2.2/c/Makefile b/ccpnmr2.2/c/Makefile +index 01fb25a..8e8e1fe 100644 +--- a/ccpnmr2.2/c/Makefile ++++ b/ccpnmr2.2/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 ++ $(MAKE) -C other/cambridge/bayes + + clean: global_clean structure_clean analysis_clean clouds_clean dynamics_clean bayes_clean + diff --git a/sci-chemistry/ccpn/files/xeasy2azara b/sci-chemistry/ccpn/files/xeasy2azara new file mode 100644 index 000000000000..68db2bf57695 --- /dev/null +++ b/sci-chemistry/ccpn/files/xeasy2azara @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export LD_LIBRARY_PATH=gentoolibdir +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccp/format/spectra/params/XeasyData.py $1 $2 $3 $4 $5 $6 |