diff options
Diffstat (limited to 'sci-chemistry')
-rw-r--r-- | sci-chemistry/ccpn/ChangeLog | 7 | ||||
-rw-r--r-- | sci-chemistry/ccpn/Manifest | 10 | ||||
-rw-r--r-- | sci-chemistry/ccpn/ccpn-2.1.5_p101013.ebuild | 212 |
3 files changed, 224 insertions, 5 deletions
diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog index bfba83c51e8b..96cd6f2119eb 100644 --- a/sci-chemistry/ccpn/ChangeLog +++ b/sci-chemistry/ccpn/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-chemistry/ccpn # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.40 2010/09/30 20:04:11 maekke Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.41 2010/10/13 07:40:31 jlec Exp $ + +*ccpn-2.1.5_p101013 (13 Oct 2010) + + 13 Oct 2010; Justin Lecher <jlec@gentoo.org> +ccpn-2.1.5_p101013.ebuild: + Todays Python Patches 30 Sep 2010; Markus Meier <maekke@gentoo.org> ccpn-2.1.3.1_p100806.ebuild: x86 stable, bug #338528 diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest index f5fa9a860b1d..6febc730e7cd 100644 --- a/sci-chemistry/ccpn/Manifest +++ b/sci-chemistry/ccpn/Manifest @@ -19,16 +19,18 @@ DIST ccpn-update-100806.patch.bz2 187965 RMD160 3297162fe3314aa405ee58737ce45cda DIST ccpn-update-100921.patch.bz2 17693 RMD160 a1c2de812ce524969b9148d5e0f6e0c5c24fce91 SHA1 b04c9a1af7a7de9139ef74914deab80b44f24f7f SHA256 548eebcdcadd930b5f206fb56c75d5d32d11b7ef8aa2b696c60d9f35cd45b8f4 DIST ccpn-update-100924.patch.bz2 20846 RMD160 e914a04322bad3d1eaefd5250ff70c10e7d50dbb SHA1 765e4e8590b471152f6acdbe0f088df5e2bbd541 SHA256 762a95cdb410c8b08dd4d4d17f76595549e890031c7f8bf379ab78d5850228f8 DIST ccpn-update-100927.patch.bz2 20853 RMD160 e6b8c606504a7607c01487ba992353951d94681d SHA1 5dd5648286575abf39e34d054d54f552615b88bb SHA256 831295d28f827636b2ad9620556190f58ffcb607b373147c3715c80a9a292cce +DIST ccpn-update-101013.patch.bz2 36926 RMD160 d1cd280599cd66ee0729f1bcb47b3a4647c0d83c SHA1 9a63a95c2b2281084ac9e98edba28c1e9ff1bdf1 SHA256 288ec2995ea7d49c3a477be57f509f9cd32719b2a10ab50745069a321f8f5c88 EBUILD ccpn-2.1.3.1_p100806.ebuild 5190 RMD160 c1dd4e2443ab5cf8386627a9feba25be6e61b715 SHA1 0d9700191a04c6ed5f106e2712b010d499315827 SHA256 ed26ef362193f91d4726fd49a1c4b19c1f975c3847b0616ada2e64ce7a90ffa5 EBUILD ccpn-2.1.5_p100921-r2.ebuild 5815 RMD160 83a020277c866ae39a093a1745cf5b7f4cb38b44 SHA1 10d4161af742915be2715c23d3be4756a5ec4152 SHA256 c1b15892c449205a8bf94a544481d86059ecd9352db2e454790abd90214b2df1 EBUILD ccpn-2.1.5_p100924.ebuild 5812 RMD160 19790f131cc251e4fc637ca3cb78ab8797488625 SHA1 b7f322f97dfdea15b553a00e6fb1db13a120d553 SHA256 89c2201e7fa61902d7db063ce499a85e1aab1b6f87451e0568eb6024401561c0 EBUILD ccpn-2.1.5_p100927.ebuild 5871 RMD160 3b636e724225f9749b3469dddf2259bea5299566 SHA1 0d378b29421a4668fa430cacc16285ae63e2762d SHA256 d4df7a1404a685d59339db2d0a300994664e204a309ca1002351d019c8101d9f -MISC ChangeLog 6842 RMD160 44a12fe0ca85a5b9d8e3f888678a5a948c1f33e9 SHA1 fb3a79ad06e8db51a0b327c9251732cc2ad6e9a6 SHA256 316e9714a9e93dba496aa07c5b6b26a320887cc06183a688b2df4f7867deeb34 +EBUILD ccpn-2.1.5_p101013.ebuild 5871 RMD160 4b09dca2f1831086d1c244a2ed7e0e3408b75218 SHA1 24a5408a535bd09af7681bf19ef748ddf6eb5d3d SHA256 adea7d4adefea50c2b4d1024eb7b289942afd2574eb506ea3fb32c6107f977e2 +MISC ChangeLog 6975 RMD160 4fa62c222f2ba5aef518b41b6bdb2cdb95a4403f SHA1 7208f44652f8ce50bbf7bf94c3ad9972bd3c3c6f SHA256 830e9b6629e0f2fa2b214fa1505721d47889ae24823c59ba86a328bf275f90f5 MISC metadata.xml 226 RMD160 0355d90bd8d1c106a19b136045ebdf970a0a2485 SHA1 1db0b2a470657641079d6613829df49a5c043ed6 SHA256 094a3ac740c81b9afbff3c855ba93cc20a593cad2392f6f4404715608a836fa1 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.16 (GNU/Linux) -iEYEARECAAYFAkyk7PEACgkQkKaRLQcq0GII0QCgroUokc5mFclOH1n7wUTuxrB3 -pygAni2YX2qFVroH/wSby+cVNYWWuUuX -=j9+0 +iEYEARECAAYFAky1YnQACgkQgAnW8HDreRaMMgCgngA5KVO/W1V1iEQ07Lg0sd7p +2XsAnjBQ0RiK29rZ/QreIN0gmaaKT31C +=yyFp -----END PGP SIGNATURE----- diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p101013.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p101013.ebuild new file mode 100644 index 000000000000..c9e6b8a02b74 --- /dev/null +++ b/sci-chemistry/ccpn/ccpn-2.1.5_p101013.ebuild @@ -0,0 +1,212 @@ +# Copyright 1999-2010 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_p101013.ebuild,v 1.1 2010/10/13 07:40:31 jlec Exp $ + +EAPI="3" + +PYTHON_DEPEND="2:2.5" +SUPPORT_PYTHON_ABIS="1" +PYTHON_USE_WITH="ssl tk" +RESTRICT_PYTHON_ABIS="2.4 3.*" + +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-${PATCHSET}.patch.bz2" +HOMEPAGE="http://www.ccpn.ac.uk/ccpn" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+opengl" + +RDEPEND=" + dev-lang/tk[threads] + >=dev-python/numpy-1.4 + >=dev-tcltk/tix-8.4.3 + =sci-libs/ccpn-data-"${MY_MAJOR}"* + x11-libs/libXext + x11-libs/libX11 + opengl? ( + media-libs/freeglut + dev-python/pyglet )" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" +S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV}) + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + epatch "${WORKDIR}"/ccpn-update-${PATCHSET}.patch + + epatch "${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_FALSE" + 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 + python_copy_sources + + preparation() { + 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\$(PYTHON_DIR)/include/python$(python_get_version):g" \ + -e "s:^\(PYTHON_LIB =\).*:\1 -lpython$(python_get_version):g" \ + c/environment_default.txt > c/environment.txt + } + python_execute_function -s preparation +} + +src_compile() { + building() { + emake -C c all links + } + python_execute_function -s building +} + +src_install() { + local libdir + local tkver + + find . -name "*.pyc" -type d -delete + + libdir=$(get_libdir) + tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) + + for wrapper in analysis dangle dataShifter depositionFileImporter extendNmr eci formatConverter pipe2azara; do + sed -e "s:gentoo_sitedir:${EPREFIX}$(python_get_sitedir -f):g" \ + -e "s:gentoolibdir:${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 ${wrapper}" + done + + installation() { + local in_path + local files + local pydocs + + pydocs="$(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 + } + python_execute_function -s installation +} + +pkg_postinst() { + python_mod_optimize ${PN} +} + +pkg_postrm() { + python_mod_cleanup ${PN} +} |