diff options
author | Justin Lecher <jlec@gentoo.org> | 2010-09-21 13:11:31 +0000 |
---|---|---|
committer | Justin Lecher <jlec@gentoo.org> | 2010-09-21 13:11:31 +0000 |
commit | 352c061968e13b1d4aa32668d169c8ba3607a611 (patch) | |
tree | 495a912fd4e38651c66955c1c668b0bf505e0524 | |
parent | Split out from sci-chemistry/ccpn (diff) | |
download | historical-352c061968e13b1d4aa32668d169c8ba3607a611.tar.gz historical-352c061968e13b1d4aa32668d169c8ba3607a611.tar.bz2 historical-352c061968e13b1d4aa32668d169c8ba3607a611.zip |
Version Bump, splitted sci-libs/ccpn-data out, removed old
Package-Manager: portage-2.2_rc84/cvs/Linux x86_64
-rw-r--r-- | sci-chemistry/ccpn/ChangeLog | 13 | ||||
-rw-r--r-- | sci-chemistry/ccpn/Manifest | 31 | ||||
-rw-r--r-- | sci-chemistry/ccpn/ccpn-2.1.2.1_p100216.ebuild | 179 | ||||
-rw-r--r-- | sci-chemistry/ccpn/ccpn-2.1.3.1_p100607.ebuild | 186 | ||||
-rw-r--r-- | sci-chemistry/ccpn/ccpn-2.1.3.1_p100628.ebuild | 186 | ||||
-rw-r--r-- | sci-chemistry/ccpn/ccpn-2.1.3.1_p100806.ebuild (renamed from sci-chemistry/ccpn/ccpn-2.1.3.1_p100713.ebuild) | 2 | ||||
-rw-r--r-- | sci-chemistry/ccpn/ccpn-2.1.5_p100921.ebuild (renamed from sci-chemistry/ccpn/ccpn-2.1.3.1_p100519.ebuild) | 74 | ||||
-rw-r--r-- | sci-chemistry/ccpn/files/2.1.5-parallel.patch | 38 | ||||
-rw-r--r-- | sci-chemistry/ccpn/files/depositionFileImporter | 8 | ||||
-rw-r--r-- | sci-chemistry/ccpn/files/extendNmr | 8 |
10 files changed, 131 insertions, 594 deletions
diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog index 1bd7ec1c0d97..5dcfb210f15a 100644 --- a/sci-chemistry/ccpn/ChangeLog +++ b/sci-chemistry/ccpn/ChangeLog @@ -1,6 +1,17 @@ # 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 1.32 2010/09/16 17:23:05 scarabeus Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.33 2010/09/21 13:11:31 jlec Exp $ + +*ccpn-2.1.5_p100921 (21 Sep 2010) +*ccpn-2.1.3.1_p100806 (21 Sep 2010) + + 21 Sep 2010; Justin Lecher <jlec@gentoo.org> +files/2.1.5-parallel.patch, + -ccpn-2.1.2.1_p100216.ebuild, -ccpn-2.1.3.1_p100519.ebuild, + -ccpn-2.1.3.1_p100607.ebuild, -ccpn-2.1.3.1_p100628.ebuild, + -ccpn-2.1.3.1_p100713.ebuild, +ccpn-2.1.3.1_p100806.ebuild, + +ccpn-2.1.5_p100921.ebuild, +files/depositionFileImporter, + +files/extendNmr: + Version Bump, splitted sci-libs/ccpn-data out, removed old 16 Sep 2010; Tomáš Chvátal <scarabeus@gentoo.org> ccpn-2.1.2.1_p100216.ebuild, ccpn-2.1.3.1_p100519.ebuild, diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest index c2ce5f2a3d5a..7272dd07b663 100644 --- a/sci-chemistry/ccpn/Manifest +++ b/sci-chemistry/ccpn/Manifest @@ -1,23 +1,30 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX 2.1.3_1-dynamics.patch 825 RMD160 1941257b998a1063c4a7cce796bdf67415a0380f SHA1 d76089c3280906507c29af9307d35aabce1cd01b SHA256 53577b6f9621a707b1b5d676d57ed16f3963f3172598d944b823133908226edb AUX 2.1.3_1-impl-dec.patch 2818 RMD160 182cb26478750711916c73b7f9ba5e0caeb30bde SHA1 078fee172d7b9cf9f6bd653b53c87351b4625aba SHA256 f175a1b4a9cc4f1636bf36928883d37a266af830234aa3d7676f4fe4f7f1ddd8 AUX 2.1.3_1-parallel.patch 577 RMD160 8bafa14bec766aaca0e55f33f9b51f10f5f29c43 SHA1 e95891313f669e0908374aa98a725596140150cf SHA256 7e650ef2fa1ff0626349affdf1bc9578fe1da3b8cee7dd9125d33a2164978b69 +AUX 2.1.5-parallel.patch 850 RMD160 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683bdfb17d14979eb6477aaa99e4c4af5003beb2 SHA256 bbc1ba5434f896d38b6745c1dc9adc470a78d3be7b879160edcd635a19228b74 -DIST ccpn-update-100216.patch.bz2 37914 RMD160 92d2845f9a21a5ddc9fd71cf56928b61f497530c SHA1 de61701435675d10165826cf4cd590dca336cbb2 SHA256 13e062188e953ea62e779b7d89004ce103db61daf228cf6b9f7d3c77f39947fc -DIST ccpn-update-100519.patch.bz2 136871 RMD160 34e91278eaa0f29eaca569033a3960440060b729 SHA1 32a6647b8e166748c539e990c0b2d1b21b995a23 SHA256 69f8d647ab0bb7d6d7fbc6f8a23b8164d97916dcef3b0b50137902084ad2b99e -DIST ccpn-update-100607.patch.bz2 148229 RMD160 5154191926916e592ae3f3bede35937b93ec33be SHA1 0035824a5901276ba9b0d2efeee5e30d88264d32 SHA256 d9ed5dc5c56ea1f65a6e8d567d177a6ed5733d1281cb798e8e4c00f066f86821 -DIST ccpn-update-100628.patch.bz2 171691 RMD160 a7cd100c5fa5a3d5d3bda8eb7c5ef813e5a4c476 SHA1 c975d3f1125eca2983e558780e63d400f17fb341 SHA256 aec560829b43d1f4d9facc8a13f54c0e47799f21d67aceb05be30aeb647d9c15 -DIST ccpn-update-100713.patch.bz2 187527 RMD160 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548eebcdcadd930b5f206fb56c75d5d32d11b7ef8aa2b696c60d9f35cd45b8f4 +EBUILD ccpn-2.1.3.1_p100806.ebuild 5190 RMD160 b9572b61f8c53505b63b1c99ce9ea73cf38472fc SHA1 9d8df54514655824e09e3e65fdaf51ad32f97d91 SHA256 ca80063e4810c499416ffc8ade6b187a3df9bfb470d03f9aa26105c379476b68 +EBUILD ccpn-2.1.5_p100921.ebuild 5596 RMD160 44595e67dc3d5586a91071758c3b0abae7e4cdbb SHA1 b839a43dc31fd6fa25f47d97298820534f8e9a53 SHA256 07eeb612f65160513d436c1b3c4767896bfa70ef2eac7ed125ae023fa0d3eb50 +MISC ChangeLog 6238 RMD160 997f6a3b8c72aa155c8d11ee74d9f7831e3a8f79 SHA1 727899d2a3046ba08158d3dcff04858f53df86e9 SHA256 29ab17f86a0aed5c9b7059d0c082bc4ff7cfb0c93b3bf1e78a1d8aacc06867b3 MISC metadata.xml 226 RMD160 0355d90bd8d1c106a19b136045ebdf970a0a2485 SHA1 1db0b2a470657641079d6613829df49a5c043ed6 SHA256 094a3ac740c81b9afbff3c855ba93cc20a593cad2392f6f4404715608a836fa1 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.16 (GNU/Linux) + +iEYEARECAAYFAkyYrwgACgkQgAnW8HDreRaoUACghjBc2DToo+27PYmtspSBJa8P +VSkAoKGxWV1q6+IHDU87XFOwdeKWMMHF +=q2BS +-----END PGP SIGNATURE----- diff --git a/sci-chemistry/ccpn/ccpn-2.1.2.1_p100216.ebuild b/sci-chemistry/ccpn/ccpn-2.1.2.1_p100216.ebuild deleted file mode 100644 index 0ba27172cbfe..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.1.2.1_p100216.ebuild +++ /dev/null @@ -1,179 +0,0 @@ -# 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-2.1.2.1_p100216.ebuild,v 1.3 2010/09/16 17:23:05 scarabeus Exp $ - -EAPI="3" -PYTHON_DEPEND="2:2.5" -SUPPORT_PYTHON_ABIS="1" -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 _ ${PV%%_p*})" - -DESCRIPTION="The Collaborative Computing Project for NMR" -SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz" - [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/distfiles/ccpn-update-${PATCHSET}.patch.bz2" -HOMEPAGE="http://www.ccpn.ac.uk/ccpn" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86" -IUSE="+opengl" - -RDEPEND=" - dev-lang/tk - dev-python/numpy - dev-tcltk/tix - opengl? ( media-libs/freeglut )" -DEPEND="${RDEPEND}" -RESTRICT_PYTHON_ABIS="2.4 3.*" - -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)" - - python_copy_sources - - preparation() { - sed \ - -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:^\(GLUT_NEED_INIT =\).*:\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" \ - -e "s:^\(GL_LIB_FLAGS =\).*:\1 -L${EPREFIX}/usr/$(get_libdir):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 - - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - for wrapper in analysis dangle dataShifter 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:${EPREFIX}/usr/bin/python:g" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}" - done - - installation() { - local in_path - local files - - in_path=$(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} - done - - insinto ${in_path} - - dodir ${in_path}/c - - ebegin "Installing main files" - doins -r data model python || die "main files installation failed" - eend - - dohtml -r doc/* || die - dosym ../../../../share/doc/${PF}/html ${in_path}/doc || die - - einfo "Adjusting permissions" - - files="ccpnmr/c/ContourFile.so - ccpnmr/c/ContourLevels.so - ccpnmr/c/ContourStyle.so - ccpnmr/c/PeakList.so - ccpnmr/c/SliceFile.so - ccpnmr/c/WinPeakList.so - ccpnmr/c/AtomCoordList.so - ccpnmr/c/AtomCoord.so - ccpnmr/c/Bacus.so - ccpnmr/c/CloudUtil.so - ccpnmr/c/DistConstraintList.so - ccpnmr/c/DistConstraint.so - ccpnmr/c/DistForce.so - ccpnmr/c/Dynamics.so - ccpnmr/c/Midge.so - ccp/c/StructAtom.so - ccp/c/StructBond.so - ccp/c/StructStructure.so - ccp/c/StructUtil.so - memops/c/BlockFile.so - memops/c/FitMethod.so - memops/c/GlHandler.so - memops/c/MemCache.so - memops/c/PdfHandler.so - memops/c/PsHandler.so - memops/c/ShapeFile.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} -} diff --git a/sci-chemistry/ccpn/ccpn-2.1.3.1_p100607.ebuild b/sci-chemistry/ccpn/ccpn-2.1.3.1_p100607.ebuild deleted file mode 100644 index 26ed180bef61..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.1.3.1_p100607.ebuild +++ /dev/null @@ -1,186 +0,0 @@ -# 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-2.1.3.1_p100607.ebuild,v 1.2 2010/09/16 17:23:05 scarabeus Exp $ - -EAPI="3" -PYTHON_DEPEND="2:2.5" -SUPPORT_PYTHON_ABIS="1" -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 _ ${PV%%_p*})" - -DESCRIPTION="The Collaborative Computing Project for NMR" -SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz" - [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${PATCHSET}.patch.bz2" -HOMEPAGE="http://www.ccpn.ac.uk/ccpn" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="+opengl" - -RDEPEND=" - dev-lang/tk - dev-python/numpy - dev-tcltk/tix - x11-libs/libXext - x11-libs/libX11 - opengl? ( media-libs/freeglut )" -DEPEND="${RDEPEND}" -RESTRICT_PYTHON_ABIS="2.4 3.*" - -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}"/${MY_PV}-parallel.patch - epatch "${FILESDIR}"/${MY_PV}-dynamics.patch - - local tk_ver - local myconf - - tk_ver="$(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)" - - 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$(python_get_version):g" \ - c/environment_default.txt > c/environment.txt - } - python_execute_function -s preparation -} - -src_compile() { - building() { - emake -C c all links - } - python_execute_function -s building -} - -src_install() { - local libdir - local tkver - - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - for wrapper in analysis dangle dataShifter eci formatConverter pipe2azara; do - sed -e "s:gentoo_sitedir:${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" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}" - done - - installation() { - local in_path - local files - - in_path=$(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} - done - - insinto ${in_path} - - dodir ${in_path}/c - - ebegin "Installing main files" - doins -r data model python || die "main files installation failed" - eend - - dohtml -r doc/* || die - dosym ../../../../share/doc/${PF}/html ${in_path}/doc || die - - einfo "Adjusting permissions" - - files="ccpnmr/c/ContourFile.so - ccpnmr/c/ContourLevels.so - ccpnmr/c/ContourStyle.so - ccpnmr/c/PeakList.so - ccpnmr/c/SliceFile.so - ccpnmr/c/WinPeakList.so - ccpnmr/c/AtomCoordList.so - ccpnmr/c/AtomCoord.so - ccpnmr/c/Bacus.so - ccpnmr/c/CloudUtil.so - ccpnmr/c/DistConstraintList.so - ccpnmr/c/DistConstraint.so - ccpnmr/c/DistForce.so - ccpnmr/c/Dynamics.so - ccpnmr/c/Midge.so - ccp/c/StructAtom.so - ccp/c/StructBond.so - ccp/c/StructStructure.so - ccp/c/StructUtil.so - memops/c/BlockFile.so - memops/c/FitMethod.so - memops/c/GlHandler.so - memops/c/MemCache.so - memops/c/PdfHandler.so - memops/c/PsHandler.so - memops/c/ShapeFile.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} -} diff --git a/sci-chemistry/ccpn/ccpn-2.1.3.1_p100628.ebuild b/sci-chemistry/ccpn/ccpn-2.1.3.1_p100628.ebuild deleted file mode 100644 index be8759aaf139..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.1.3.1_p100628.ebuild +++ /dev/null @@ -1,186 +0,0 @@ -# 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-2.1.3.1_p100628.ebuild,v 1.2 2010/09/16 17:23:05 scarabeus Exp $ - -EAPI="3" -PYTHON_DEPEND="2:2.5" -SUPPORT_PYTHON_ABIS="1" -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 _ ${PV%%_p*})" - -DESCRIPTION="The Collaborative Computing Project for NMR" -SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz" - [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${PATCHSET}.patch.bz2" -HOMEPAGE="http://www.ccpn.ac.uk/ccpn" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="+opengl" - -RDEPEND=" - dev-lang/tk - dev-python/numpy - dev-tcltk/tix - x11-libs/libXext - x11-libs/libX11 - opengl? ( media-libs/freeglut )" -DEPEND="${RDEPEND}" -RESTRICT_PYTHON_ABIS="2.4 3.*" - -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}"/${MY_PV}-parallel.patch - epatch "${FILESDIR}"/${MY_PV}-dynamics.patch - - local tk_ver - local myconf - - tk_ver="$(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)" - - 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$(python_get_version):g" \ - c/environment_default.txt > c/environment.txt - } - python_execute_function -s preparation -} - -src_compile() { - building() { - emake -C c all links - } - python_execute_function -s building -} - -src_install() { - local libdir - local tkver - - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - for wrapper in analysis dangle dataShifter eci formatConverter pipe2azara; do - sed -e "s:gentoo_sitedir:${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" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}" - done - - installation() { - local in_path - local files - - in_path=$(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} - done - - insinto ${in_path} - - dodir ${in_path}/c - - ebegin "Installing main files" - doins -r data model python || die "main files installation failed" - eend - - dohtml -r doc/* || die - dosym ../../../../share/doc/${PF}/html ${in_path}/doc || die - - einfo "Adjusting permissions" - - files="ccpnmr/c/ContourFile.so - ccpnmr/c/ContourLevels.so - ccpnmr/c/ContourStyle.so - ccpnmr/c/PeakList.so - ccpnmr/c/SliceFile.so - ccpnmr/c/WinPeakList.so - ccpnmr/c/AtomCoordList.so - ccpnmr/c/AtomCoord.so - ccpnmr/c/Bacus.so - ccpnmr/c/CloudUtil.so - ccpnmr/c/DistConstraintList.so - ccpnmr/c/DistConstraint.so - ccpnmr/c/DistForce.so - ccpnmr/c/Dynamics.so - ccpnmr/c/Midge.so - ccp/c/StructAtom.so - ccp/c/StructBond.so - ccp/c/StructStructure.so - ccp/c/StructUtil.so - memops/c/BlockFile.so - memops/c/FitMethod.so - memops/c/GlHandler.so - memops/c/MemCache.so - memops/c/PdfHandler.so - memops/c/PsHandler.so - memops/c/ShapeFile.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} -} diff --git a/sci-chemistry/ccpn/ccpn-2.1.3.1_p100713.ebuild b/sci-chemistry/ccpn/ccpn-2.1.3.1_p100806.ebuild index 0756ff8b760c..5ba343da7182 100644 --- a/sci-chemistry/ccpn/ccpn-2.1.3.1_p100713.ebuild +++ b/sci-chemistry/ccpn/ccpn-2.1.3.1_p100806.ebuild @@ -1,6 +1,6 @@ # 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-2.1.3.1_p100713.ebuild,v 1.2 2010/09/16 17:23:05 scarabeus Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.3.1_p100806.ebuild,v 1.1 2010/09/21 13:11:31 jlec Exp $ EAPI="3" PYTHON_DEPEND="2:2.5" diff --git a/sci-chemistry/ccpn/ccpn-2.1.3.1_p100519.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p100921.ebuild index 63f2e47d11ae..4da316a88732 100644 --- a/sci-chemistry/ccpn/ccpn-2.1.3.1_p100519.ebuild +++ b/sci-chemistry/ccpn/ccpn-2.1.5_p100921.ebuild @@ -1,11 +1,13 @@ # 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-2.1.3.1_p100519.ebuild,v 1.2 2010/09/16 17:23:05 scarabeus Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p100921.ebuild,v 1.1 2010/09/21 13:11:31 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 @@ -24,14 +26,14 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="+opengl" RDEPEND=" - dev-lang/tk - dev-python/numpy - dev-tcltk/tix + dev-lang/tk[threads] + >=dev-python/numpy-1.4 + >=dev-tcltk/tix-8.4.3 + =sci-libs/ccpn-data-2.1.5* x11-libs/libXext x11-libs/libX11 opengl? ( media-libs/freeglut )" DEPEND="${RDEPEND}" -RESTRICT_PYTHON_ABIS="2.4 3.*" RESTRICT="mirror" S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV}) @@ -41,7 +43,6 @@ src_prepare() { epatch "${WORKDIR}"/ccpn-update-${PATCHSET}.patch epatch "${FILESDIR}"/${MY_PV}-parallel.patch - epatch "${FILESDIR}"/${MY_PV}-dynamics.patch local tk_ver local myconf @@ -65,6 +66,7 @@ src_prepare() { GLUT_NOT_IN_GL="" GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" + rm -rf data model doc license || die python_copy_sources preparation() { @@ -105,7 +107,7 @@ src_install() { libdir=$(get_libdir) tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - for wrapper in analysis dangle dataShifter eci formatConverter pipe2azara; do + for wrapper in analysis dangle dataShifter depositionFileImporter extendNmr eci formatConverter pipe2azara; do sed -e "s:gentoo_sitedir:${EPREFIX}/$(python_get_sitedir -f):g" \ -e "s:gentoolibdir:${EPREFIX}/usr/${libdir}:g" \ -e "s:gentootk:${EPREFIX}/usr/${libdir}/tk${tkver}:g" \ @@ -118,13 +120,17 @@ src_install() { 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} + -i ${i} || die done insinto ${in_path} @@ -132,40 +138,50 @@ src_install() { dodir ${in_path}/c ebegin "Installing main files" - doins -r data model python || die "main files installation failed" + doins -r python || die "main files installation failed" eend - dohtml -r doc/* || die - dosym ../../../../share/doc/${PF}/html ${in_path}/doc || die + dosym ../../../..//share/doc/ccpn-data-${PV}/html ${in_path}/doc || die + for i in ${pydocs}; do + dosym /usr/share/doc/ccpn-data-${PV}/html/${i} ${in_path}/${i} + done einfo "Adjusting permissions" - files="ccpnmr/c/ContourFile.so - ccpnmr/c/ContourLevels.so + files=" + 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/PeakList.so + ccpnmr/c/ContourLevels.so ccpnmr/c/SliceFile.so - ccpnmr/c/WinPeakList.so - ccpnmr/c/AtomCoordList.so - ccpnmr/c/AtomCoord.so + ccpnmr/c/PeakCluster.so + ccpnmr/c/Dynamics.so ccpnmr/c/Bacus.so - ccpnmr/c/CloudUtil.so - ccpnmr/c/DistConstraintList.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/Dynamics.so - ccpnmr/c/Midge.so - ccp/c/StructAtom.so - ccp/c/StructBond.so - ccp/c/StructStructure.so - ccp/c/StructUtil.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/FitMethod.so - memops/c/GlHandler.so - memops/c/MemCache.so memops/c/PdfHandler.so + memops/c/MemCache.so + memops/c/FitMethod.so memops/c/PsHandler.so - memops/c/ShapeFile.so + memops/c/GlHandler.so memops/c/StoreFile.so memops/c/StoreHandler.so memops/c/TkHandler.so" diff --git a/sci-chemistry/ccpn/files/2.1.5-parallel.patch b/sci-chemistry/ccpn/files/2.1.5-parallel.patch new file mode 100644 index 000000000000..2bffed78b11d --- /dev/null +++ b/sci-chemistry/ccpn/files/2.1.5-parallel.patch @@ -0,0 +1,38 @@ +diff --git a/ccpnmr2.1/c/Makefile b/ccpnmr2.1/c/Makefile +index 01fb25a..8e8e1fe 100644 +--- a/ccpnmr2.1/c/Makefile ++++ b/ccpnmr2.1/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 ++ $(MAKE) -C other/cambridge/bayes + + clean: global_clean structure_clean analysis_clean clouds_clean dynamics_clean bayes_clean + diff --git a/sci-chemistry/ccpn/files/depositionFileImporter b/sci-chemistry/ccpn/files/depositionFileImporter new file mode 100644 index 000000000000..86ceb9dd8571 --- /dev/null +++ b/sci-chemistry/ccpn/files/depositionFileImporter @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${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/pdbe/deposition/dataFileImport/dataFileImportGui.py $@ diff --git a/sci-chemistry/ccpn/files/extendNmr b/sci-chemistry/ccpn/files/extendNmr new file mode 100644 index 000000000000..1c3edb64d243 --- /dev/null +++ b/sci-chemistry/ccpn/files/extendNmr @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export LD_LIBRARY_PATH=gentoolibdir +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +gentoopython -O -i -O ${CCPNMR_TOP_DIR}/ccpn/python/extendNmr/ExtendNmrGui.py $@ |