diff options
Diffstat (limited to 'sci-chemistry')
| -rw-r--r-- | sci-chemistry/ccpn/ChangeLog | 11 | ||||
| -rw-r--r-- | sci-chemistry/ccpn/Manifest | 14 | ||||
| -rw-r--r-- | sci-chemistry/ccpn/ccpn-2.2.2_p130110.ebuild | 4 | ||||
| -rw-r--r-- | sci-chemistry/ccpn/ccpn-2.2.2_p130116.ebuild | 174 | ||||
| -rw-r--r-- | sci-chemistry/ccpn/metadata.xml | 3 |
5 files changed, 193 insertions, 13 deletions
diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog index c0dc7ce3b597..def0157fb74a 100644 --- a/sci-chemistry/ccpn/ChangeLog +++ b/sci-chemistry/ccpn/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-chemistry/ccpn # 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 $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.101 2013/01/16 11:43:05 jlec Exp $ + +*ccpn-2.2.2_p130116 (16 Jan 2013) + + 16 Jan 2013; Justin Lecher <jlec@gentoo.org> ccpn-2.2.2_p130110.ebuild, + +ccpn-2.2.2_p130116.ebuild, metadata.xml: + Todays python patches; fix for generic tcl/tk; drop unused local use + description *ccpn-2.2.2_p130110 (10 Jan 2013) @@ -8,7 +15,7 @@ -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 + Todays python patches, Drop old *ccpn-2.2.2_p121125 (25 Nov 2012) diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest index 4a1fcacf8953..39437e80fa9e 100644 --- a/sci-chemistry/ccpn/Manifest +++ b/sci-chemistry/ccpn/Manifest @@ -20,15 +20,17 @@ DIST analysis2.2.2.tar.gz 21044504 SHA256 8e46d12b8fb7763d282933e14ddfa9ce197954 DIST ccpn-update-100806.patch.bz2 187965 SHA256 5cea7899edb96237a6674f04a1beee6ad7b309e12964ea8b25d9ea6ff752d0d4 SHA512 ab145f14137955bcb4dcc4d242eb718a806152bf3376e4cc9ff5e8186ed54812051ad07de1c9d2316ce3379c8c74db4af36f714aa3291ea7a1d11d4f432df06f WHIRLPOOL 2a0cbf62aca74e22fc0e00a0a91c3c185c10fb07277ba30791511565a2fa645b123a8c5164389eb9fb5a2d1f591e26c6416c46038acceefa2f1ecf347b631a66 DIST ccpn-update-2.2.2-121125.patch.xz 223556 SHA256 996f453d7d6a143715a94b1201bd7b8b9c037f6d0baa342f5c0645d500aa5c79 SHA512 d213e072a63110ec478c3ee64792b01c818d3c9052ae6d7dac903508536f78c432c72d5a4756665045579d72f4f54ef5ac9db1fb02eb5ea3111eaa47e72866b0 WHIRLPOOL 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8406a93562897aadfefd03e098b393af5fb29f9bfde8e5727b73ceb6cbe004b73cfd97b61e942189d9fba717761b20cc4914e5c9d858f36bbdbdeea1369490e7 WHIRLPOOL 112e9cab77898ef9246b127d5ef8529948cfaf91157a25bbe39899560af8340f8e5cbd1e2a3935dae083a9291f0d569d3cc5b7588dc2029f3342ecbe5590cb0f +EBUILD ccpn-2.2.2_p130116.ebuild 4649 SHA256 b1832e30ba4cf40a79a8781f0e84c49f35245ea36a42e7ca5adf2019bcacfdca SHA512 52fe7e59bb3a801ac30f0fb1d503622a0d6e18357fec14a73c9b83d05fdbac33d594e636ab5e72df6eea15dc796ab90c113d0715f1dc06d3ecebfcfcf9fc186e WHIRLPOOL 617306f09808d9bdad288990ffc3da5cacfcae8bfa8c07dbde20c879d9e5308a4d7d9d64afb217be0ef46801d22230a2b8a6152b461332b94448a01f813e4ffd +MISC ChangeLog 20064 SHA256 097eda07f9ccd3723001d60016ddfc5ca57fec3d54dafedc4e3e16f6bb962a48 SHA512 f72b72f595897f10e799817e48ba9ec06eb18168453a586f7e3c52fef4a838e3785aafedcecafddf7f0f3dd581b0a9da0a4ee0c57abeff94bddb9da95892b59a WHIRLPOOL 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a/sci-chemistry/ccpn/ccpn-2.2.2_p130110.ebuild +++ b/sci-chemistry/ccpn/ccpn-2.2.2_p130110.ebuild @@ -1,6 +1,6 @@ # 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_p130110.ebuild,v 1.1 2013/01/10 17:41:33 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.2_p130110.ebuild,v 1.2 2013/01/16 11:43:05 jlec Exp $ EAPI=4 @@ -97,7 +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|^\(TK_LIB =\).*|\1 -ltk|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" \ diff --git a/sci-chemistry/ccpn/ccpn-2.2.2_p130116.ebuild b/sci-chemistry/ccpn/ccpn-2.2.2_p130116.ebuild new file mode 100644 index 000000000000..9e83f3d33e37 --- /dev/null +++ b/sci-chemistry/ccpn/ccpn-2.2.2_p130116.ebuild @@ -0,0 +1,174 @@ +# 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_p130116.ebuild,v 1.1 2013/01/16 11:43:05 jlec Exp $ + +EAPI=5 + +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 ${PATCHSET} ]] \ + && SRC_URI+=" http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+opengl" + +RDEPEND=" + dev-lang/tk[threads] + dev-python/numpy + dev-tcltk/tix + =sci-libs/ccpn-data-"${MY_MAJOR}"* + sci-biology/psipred + x11-libs/libXext + x11-libs/libX11 + opengl? ( + media-libs/freeglut + dev-python/pyglet )" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${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|^\(TK_LIB =\).*|\1 -ltk|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 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/metadata.xml b/sci-chemistry/ccpn/metadata.xml index 8a82c7657734..ae9ec7c5f6a4 100644 --- a/sci-chemistry/ccpn/metadata.xml +++ b/sci-chemistry/ccpn/metadata.xml @@ -5,7 +5,4 @@ <maintainer> <email>jlec@gentoo.org</email> </maintainer> - <use> - <flag name="extendnmr">Install needed packages for extendNMR support</flag> - </use> </pkgmetadata> |