diff options
author | Justin Lecher <jlec@gentoo.org> | 2011-12-20 08:39:39 +0000 |
---|---|---|
committer | Justin Lecher <jlec@gentoo.org> | 2011-12-20 08:39:39 +0000 |
commit | 6b4ae6f9753bfe698b67cd262c7197e99436fcf0 (patch) | |
tree | b75a02a825e8ec0a683784473cfe3b283dae4b73 /sci-chemistry | |
parent | Version bump. Removed old (diff) | |
download | historical-6b4ae6f9753bfe698b67cd262c7197e99436fcf0.tar.gz historical-6b4ae6f9753bfe698b67cd262c7197e99436fcf0.tar.bz2 historical-6b4ae6f9753bfe698b67cd262c7197e99436fcf0.zip |
Todays Python Patches, cleaned old
Package-Manager: portage-2.2.0_alpha81/cvs/Linux x86_64
Diffstat (limited to 'sci-chemistry')
21 files changed, 27 insertions, 3687 deletions
diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog index b0b7f0fd0413..e1be611d98f2 100644 --- a/sci-chemistry/ccpn/ChangeLog +++ b/sci-chemistry/ccpn/ChangeLog @@ -1,6 +1,22 @@ # 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 1.76 2011/12/13 08:33:36 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.77 2011/12/20 08:39:39 jlec Exp $ + +*ccpn-2.2.1_p111220 (20 Dec 2011) +*ccpn-2.1.5_p111220 (20 Dec 2011) + + 20 Dec 2011; Justin Lecher <jlec@gentoo.org> -ccpn-2.1.5_p110602.ebuild, + -ccpn-2.1.5_p110629.ebuild, -ccpn-2.1.5_p110817.ebuild, + -ccpn-2.1.5_p110905.ebuild, -ccpn-2.1.5_p110926.ebuild, + -ccpn-2.1.5_p111011.ebuild, -ccpn-2.1.5_p111017.ebuild, + -ccpn-2.1.5_p111028.ebuild, -ccpn-2.1.5_p111124.ebuild, + +ccpn-2.1.5_p111220.ebuild, -ccpn-2.2.1_p110602.ebuild, + -ccpn-2.2.1_p110629.ebuild, -ccpn-2.2.1_p110817.ebuild, + -ccpn-2.2.1_p110905.ebuild, -ccpn-2.2.1_p110926.ebuild, + -ccpn-2.2.1_p111011.ebuild, -ccpn-2.2.1_p111017.ebuild, + -ccpn-2.2.1_p111019.ebuild, -ccpn-2.2.1_p111028.ebuild, + -ccpn-2.2.1_p111124.ebuild, +ccpn-2.2.1_p111220.ebuild: + Todays Python Patches, cleaned old *ccpn-2.2.1_p111213 (13 Dec 2011) *ccpn-2.1.5_p111213 (13 Dec 2011) diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest index 1489f0c83a2d..b3f9cff13393 100644 --- a/sci-chemistry/ccpn/Manifest +++ b/sci-chemistry/ccpn/Manifest @@ -19,55 +19,21 @@ DIST analysis2.1.3_1.tar.gz 18932918 RMD160 5f19ea6fe47c2910d16fcba8d1a78f0e1dea DIST analysis2.1.5.tar.gz 20338459 RMD160 b0706c859c1ee4da2ab80ee41534197268f73d44 SHA1 70dc5e6b2752d6b7d5c8673fc992ebd0a88e6ad0 SHA256 9f91f1bd56fb73fd24e71d396c96c0f0d31b92287664b6a2e756f6efc630b31b DIST analysis2.2.1.tar.gz 20974926 RMD160 5905f43fc1399a656f018808c4a2f8dd3d247ca9 SHA1 eed30da55a719ef6c29431e3b3c5a76f521010dc SHA256 d1252811b3db3a30d96a73368bae8abcb05de02fcd2f1f9c502d71dff5e00d13 DIST ccpn-update-100806.patch.bz2 187965 RMD160 3297162fe3314aa405ee58737ce45cda084834e5 SHA1 338423d9f36da3fb10dc9d9a3b8aeb932ae3bfd0 SHA256 5cea7899edb96237a6674f04a1beee6ad7b309e12964ea8b25d9ea6ff752d0d4 -DIST ccpn-update-2.1.5-110602.patch.bz2 81505 RMD160 2af0d5ca21828ccc3345ec763edfce81f2e12d11 SHA1 cf4a8613ecbb11421a4fb007500a6090b017fb2f SHA256 c8880d295914ac95c2ae2f0ffe3eb57e0e2b1b6c3c573eb31c8a40852c5cb886 -DIST ccpn-update-2.1.5-110629.patch.bz2 86224 RMD160 d4cb190ce84f62639d77f6592475746e8b9f6a0e SHA1 e20f3313853dff4a3de723a2efc70efe81c63861 SHA256 df847050c95ea925db16a5c6630861e308d39286cc7c207efc4360fce53e29b2 -DIST ccpn-update-2.1.5-110817.patch.bz2 88191 RMD160 9fe24e51a1416cdde25ac6d25c2764840c1a00ef SHA1 d16956e6ad7530d17c9e46b877eaf993959f49a2 SHA256 176fd4488c40d7eb426df353d85a05ddb8e4b4126f32264c9d536bf1799fe44c -DIST ccpn-update-2.1.5-110905.patch.bz2 99670 RMD160 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55038a1272f8e01ce54fefdba081ee51ec5d4f36 SHA1 0bbd8c029a98b282002d8b5385a85355722de323 SHA256 807cef8e8b2822e178d50695c7e234ea8c243264a4711610f6a95e30e1b40d12 +DIST ccpn-update-2.2.1-111220.patch.xz 82840 RMD160 c0fb328ad93d7f07e1f0d45215d7686204315f91 SHA1 7b2ef76c62e85fcb4c5c95be053a9e281bc3d59d SHA256 f8942568e4f859da71e5a38b279355222882de19328501a0297bcddefef75c9f EBUILD ccpn-2.1.3.1_p100806.ebuild 5188 RMD160 b66825e37b79a5f6ec6635b9f3236d1cda2da672 SHA1 458f516ffad25d9283b21c9dfb8e50c6323f4264 SHA256 ff57abefefd3bb128a3f96bf039cbaa5ed97350f6b41fdbdd4b4365ff9e68e51 -EBUILD ccpn-2.1.5_p110602.ebuild 5802 RMD160 b979b28541d4a52d52df45af0ac194c147e9e586 SHA1 bf731d3e076684670155ea7ed6f862785c961130 SHA256 a5b205266d47c77f3bcb2f4149a53e2866a665d28e49b5749dd0d3774d50cc38 -EBUILD ccpn-2.1.5_p110629.ebuild 5802 RMD160 99ce3cef5396276532ab3301e5442f72c379e39e SHA1 9efbd6e35633b15b92449228c17a82890d394c38 SHA256 f29088839b852119b20caa877a105aa4af4a447d60c429b8c7bd92e0918a9ea1 -EBUILD ccpn-2.1.5_p110817.ebuild 5802 RMD160 112485a848b98a5f8377b2d05c8555147de6dfd5 SHA1 1dfab5862dc3890a5d131f1f6e78c8f28f797ac1 SHA256 135ccefec5d55bedc301c2e9d1d61e31b09f17daec2d835f7f6e9f50272a42e9 -EBUILD ccpn-2.1.5_p110905.ebuild 5802 RMD160 4213a4957af30e78714604bed3cc565acc172a71 SHA1 579587f639367f3988f9f1925e78751bad08ad41 SHA256 dcf706cbadac4352090d7650838af11e0d5c03c6b42d71ba7d4906847b248f92 -EBUILD ccpn-2.1.5_p110926.ebuild 6010 RMD160 b1c16c451387a7f6aec29662843d79fa5ebbdd6e SHA1 e8c9aa2b897b7c0fff10cda35ce4cf6f561d2edf SHA256 0fd5352daa50a772138bff644cc3db9317cfbbb7dd4a2eea4bf02dd4487714a6 -EBUILD ccpn-2.1.5_p111011.ebuild 5766 RMD160 2de7124aa015e929939a35372841eca6b9c6b760 SHA1 d9d40612897662548f67fc05bf19a65ce893c8eb SHA256 1826ca6259f1f58f0b34d8e9baa785d4542e8cdd926370a9be4b36f9d0fc256b -EBUILD ccpn-2.1.5_p111017.ebuild 5773 RMD160 74770cdc30a513ca57b66667b9377883cc25ffd4 SHA1 1cc1c784d1921c3922a98548fc4f219327725248 SHA256 5da3935144bbb0b01bc826218c9b92de1148f799a0bd5965f83ca753cc7391e2 -EBUILD ccpn-2.1.5_p111028.ebuild 5773 RMD160 71c046eb48f2c1c88e619c4a7cb66ab08a792477 SHA1 9bd4d196cd738e823ef8e118e1620541f7a328fd SHA256 0285a567273fae510d241fc378be5822eef0f7b4319723d5df4e8803ea0f4a10 -EBUILD ccpn-2.1.5_p111124.ebuild 5773 RMD160 40602ef32b4690fc7cc940199f5a18f765d9ee79 SHA1 982e51c9cdcb02b292eebe546a9192f8adb81e01 SHA256 978cbd154039ca80c0b4fdcd11f93ba19f0b7edc7137147488b81177728220e6 EBUILD ccpn-2.1.5_p111213.ebuild 5773 RMD160 4fc120d9e6c5ecfd375a3df14a7b8b9afdebb3b5 SHA1 30bb2d2e22087ac6c93434863f1347db50f2514f SHA256 46de0ddcfd2fcb196dfb9ceb07c74c25ff3c8f4655b55f5e4b2f1d90a3787641 -EBUILD ccpn-2.2.1_p110602.ebuild 5817 RMD160 02a268d39e592e55955bd768c13d486fa37394df SHA1 4d419c6825b3eba1bbc9d1f21a441fee54633dcf SHA256 d01e038bb78efe67639c2fe0571f17ead32fb931cc14bf3f1a2d0140e322557c -EBUILD ccpn-2.2.1_p110629.ebuild 5817 RMD160 10a004a5f52097e30cceef012832dc31ac4a35ee SHA1 7d23a32e384549d53ab406c5e2ff96d6984e8b9c SHA256 99cb9b2c41b7c6cbb8405177b9d99b1c06ad140059bfa001ffbae68bc150b636 -EBUILD ccpn-2.2.1_p110817.ebuild 5817 RMD160 e9302ad7cb2e95a8c2e24359691a3c2371402a89 SHA1 923d0a52f358bf45de72d6b71fcb519f187f9298 SHA256 67c4e3e30cb978b5eb879ad532f3b30d3afcd14b3019bb5d27c779607914448c -EBUILD ccpn-2.2.1_p110905.ebuild 5817 RMD160 d3f9cc71971395a5e7b907c7081851d756f9ced8 SHA1 dd8c79e2b29af8f9de92edf4b0e9425f13fd6203 SHA256 4b8d550918003a3f3e25c043ed2625ea634c08ffc353a6354579a235c7a1e2a1 -EBUILD ccpn-2.2.1_p110926.ebuild 6025 RMD160 c8fbfe5b3e10a79447e86ff3fd49f1e7c5eb44d0 SHA1 dd9f901354a019ed1bb1731548264d3c8cfd833c SHA256 5b76872a98bb9e63db70bc96b22fd8acdf719c665e10a3e404af431f8693783d -EBUILD ccpn-2.2.1_p111011.ebuild 5781 RMD160 078beee165b07aa92753a05312179edc6ed82e2d SHA1 379e2840780bb9b5f86e8ddf134eec03174a93e3 SHA256 eb6ad46393d8e0efd724dd5d966363c2aa17c4ccef30b4c3a6de62f35970fb2c -EBUILD ccpn-2.2.1_p111017.ebuild 5788 RMD160 f83ad913229aeb54667bf55ec2d5b1563b511492 SHA1 9dbce4e6f7c1e90e84fc389873261410e882fc1d SHA256 6a85c4e9c4ca84325bd2cb6627b7f82d0d245a893ab43bd8fdb39fed74f2876a -EBUILD ccpn-2.2.1_p111019.ebuild 5788 RMD160 1199938733ab49962a7cda42f86cb9d1d4d99840 SHA1 ebed2c4883b8c8c4f3788ba4b160df136b1c5d35 SHA256 08dc643197243a4836c440c37258be1651fe1d8b96d46ef4da668ae03d65cdd3 -EBUILD ccpn-2.2.1_p111028.ebuild 5788 RMD160 c9d9075636aa52e8e92d3fb1ab7f0800bcfdc3ef SHA1 bb2a99f8bef3327ed15bc118304aec4210a52024 SHA256 bf0fbf5f6558d780925e95b722575f1c3d32607244af1f744c85f58f452fa4ed -EBUILD ccpn-2.2.1_p111124.ebuild 5788 RMD160 67c30d743b838b890dd3499e36f28b0380e9e644 SHA1 37ea9409000485c057cbbd7d160e02f783b1b3fd SHA256 23aa3778bf05b3bc9a21bcbc79f2bd17516c0b1a82ecd078a8ca6988a846201d +EBUILD ccpn-2.1.5_p111220.ebuild 5773 RMD160 726f13ab2aa4532df15cbdc5a96b15293e53791e SHA1 5038f1c70ee0979181278ad3bbc9cdafff54d81c SHA256 7c21ffd5368b3a1c46ee838be8b970c6f7af371ea1048a253eca9c4c73af40c8 EBUILD ccpn-2.2.1_p111213.ebuild 5788 RMD160 49f50c489d3eee93f80e1548c66fe2acf1131e20 SHA1 fe36614826a38746d32f32071f8583744fa263fd SHA256 2f25c2e6e348f37d95bc89dc36137303def1c66a02ff1603eedb8c32f61867e4 -MISC ChangeLog 15010 RMD160 69c0a89d67873d1ed305f172bdeeda14de6671e4 SHA1 08af23375e54832c13b03edecd575aed79a5ca62 SHA256 c717826240b6edf5f6a573e219eda7db43c0c7fef4595d72e635d53d1c2746f2 +EBUILD ccpn-2.2.1_p111220.ebuild 5788 RMD160 abb85d91207669ef94be18d38b4e9efc5dca135b SHA1 e07108a62c4867be2d4538a0ecf09bf5ac4dd968 SHA256 37885cacf0a4e97d05201b18949b87889c5e5965f04434399a2e52b24d30cf98 +MISC ChangeLog 15772 RMD160 c68edc0742245f733471de2f8a86ece12bf87eaa SHA1 d89dbad83be0b61e2d45f28aa8880ac6cd3b2e41 SHA256 cc398ca99864b9d79c0e4d305c0e73b535b35ed265b79859e6d148e9ca936667 MISC metadata.xml 322 RMD160 9fd5fba7405b689fc39a089d81ffdaa9f961b514 SHA1 0c31132b25fca04cff97ef11fdc11940f90c77d0 SHA256 7468ba4c27b879e7ed5f82274f5837e51f1f389673a33b9e26e1756a6b0783df -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.18 (GNU/Linux) -iEYEAREKAAYFAk7nDeYACgkQgAnW8HDreRbNcwCgnuaNufAbEgOugaw76YudZySC -ynUAnRENqyT5onSNL3SABwabzd8L6Umn -=CDS1 +iEYEAREKAAYFAk7wSdEACgkQgAnW8HDreRZj1QCfXIwKGWDwVPFSOBFie1P44pQN +HMIAoKmvPclmOC7NgfuAyVdqJKgk/QXz +=iA0C -----END PGP SIGNATURE----- diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p110602.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p110602.ebuild deleted file mode 100644 index faf270c21216..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.1.5_p110602.ebuild +++ /dev/null @@ -1,213 +0,0 @@ -# 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_p110602.ebuild,v 1.3 2011/10/07 19:29:31 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" -HOMEPAGE="http://www.ccpn.ac.uk/ccpn" -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" - -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-2.3.2 - 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-2.1.5_p110629.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p110629.ebuild deleted file mode 100644 index cc3b7fd65f68..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.1.5_p110629.ebuild +++ /dev/null @@ -1,213 +0,0 @@ -# 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_p110629.ebuild,v 1.2 2011/10/07 19:29:31 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" -HOMEPAGE="http://www.ccpn.ac.uk/ccpn" -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" - -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-2.3.2 - 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-2.1.5_p110817.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p110817.ebuild deleted file mode 100644 index 59cf2d672f31..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.1.5_p110817.ebuild +++ /dev/null @@ -1,213 +0,0 @@ -# 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_p110817.ebuild,v 1.2 2011/10/07 19:29:31 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" -HOMEPAGE="http://www.ccpn.ac.uk/ccpn" -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" - -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-2.3.2 - 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-2.1.5_p110905.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p110905.ebuild deleted file mode 100644 index 312267b7a9d2..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.1.5_p110905.ebuild +++ /dev/null @@ -1,213 +0,0 @@ -# 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_p110905.ebuild,v 1.2 2011/10/07 19:29:31 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" -HOMEPAGE="http://www.ccpn.ac.uk/ccpn" -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" - -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-2.3.2 - 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-2.1.5_p110926.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p110926.ebuild deleted file mode 100644 index 6a05a896dcbe..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.1.5_p110926.ebuild +++ /dev/null @@ -1,220 +0,0 @@ -# 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 1.3 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" -HOMEPAGE="http://www.ccpn.ac.uk/ccpn" -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" - -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-"${MY_MAJOR}"* - sci-biology/psipred - x11-libs/libXext - x11-libs/libX11 - opengl? ( - media-libs/freeglut - dev-python/pyglet )" -# We need to fix this -# sci-chemistry/mdd -DEPEND="${RDEPEND}" -PDEPEND=" - extendnmr? ( - <=sci-chemistry/aria-2.3.2 - 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=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara" - use extendnmr && _wrapper="${_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 ${in_path}/c - - ebegin "Installing main files" - doins -r python || die "main files installation failed" - eend - dosym ../../../..//share/doc/ccpn-data-${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-2.1.5_p111011.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p111011.ebuild deleted file mode 100644 index bdb3bf68f7b6..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.1.5_p111011.ebuild +++ /dev/null @@ -1,214 +0,0 @@ -# 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 1.2 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" -HOMEPAGE="http://www.ccpn.ac.uk/ccpn" -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" - -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-"${MY_MAJOR}"* - >=sci-libs/ccpn-data-${PVR} - 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="${RDEPEND}" -PDEPEND=" - extendnmr? ( - <=sci-chemistry/aria-2.3.2 - sci-chemistry/prodecomp )" - -RESTRICT="mirror" - -S="${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=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara" - use extendnmr && _wrapper="${_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} -} diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p111017.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p111017.ebuild deleted file mode 100644 index 6d841300e841..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.1.5_p111017.ebuild +++ /dev/null @@ -1,214 +0,0 @@ -# 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 1.2 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" -HOMEPAGE="http://www.ccpn.ac.uk/ccpn" -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" - -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-"${MY_MAJOR}"* - >=sci-libs/ccpn-data-2.1.5_p111011 - sci-biology/psipred - x11-libs/libXext - x11-libs/libX11 - opengl? ( - media-libs/freeglut - dev-python/pyglet )" -# We need to fix this -# sci-chemistry/mdd -DEPEND="${RDEPEND}" -PDEPEND=" - extendnmr? ( - <=sci-chemistry/aria-2.3.2 - 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=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara" - use extendnmr && _wrapper="${_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} -} diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p111028.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p111028.ebuild deleted file mode 100644 index 8d2ee4842c7c..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.1.5_p111028.ebuild +++ /dev/null @@ -1,214 +0,0 @@ -# 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_p111028.ebuild,v 1.1 2011/10/28 08:50:29 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" -HOMEPAGE="http://www.ccpn.ac.uk/ccpn" -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" - -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-"${MY_MAJOR}"* - >=sci-libs/ccpn-data-2.1.5_p111011 - sci-biology/psipred - x11-libs/libXext - x11-libs/libX11 - opengl? ( - media-libs/freeglut - dev-python/pyglet )" -# We need to fix this -# sci-chemistry/mdd -DEPEND="${RDEPEND}" -PDEPEND=" - extendnmr? ( - <=sci-chemistry/aria-2.3.2 - 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=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara" - use extendnmr && _wrapper="${_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} -} diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p111124.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p111220.ebuild index c1ecb9ceaede..1ae1679ac13f 100644 --- a/sci-chemistry/ccpn/ccpn-2.1.5_p111124.ebuild +++ b/sci-chemistry/ccpn/ccpn-2.1.5_p111220.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_p111124.ebuild,v 1.1 2011/11/24 08:36:43 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p111220.ebuild,v 1.1 2011/12/20 08:39:39 jlec Exp $ EAPI="3" diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p110602.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p110602.ebuild deleted file mode 100644 index ed92da57f330..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.2.1_p110602.ebuild +++ /dev/null @@ -1,213 +0,0 @@ -# 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_p110602.ebuild,v 1.3 2011/10/07 19:29:31 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-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 - - 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/ccpn-2.2.1_p110629.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p110629.ebuild deleted file mode 100644 index 06b9f66d1ba4..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.2.1_p110629.ebuild +++ /dev/null @@ -1,213 +0,0 @@ -# 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_p110629.ebuild,v 1.2 2011/10/07 19:29:31 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-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 - - 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/ccpn-2.2.1_p110817.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p110817.ebuild deleted file mode 100644 index bb0a5d8b74e3..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.2.1_p110817.ebuild +++ /dev/null @@ -1,213 +0,0 @@ -# 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_p110817.ebuild,v 1.2 2011/10/07 19:29:31 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-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 - - 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/ccpn-2.2.1_p110905.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p110905.ebuild deleted file mode 100644 index aa65d086692d..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.2.1_p110905.ebuild +++ /dev/null @@ -1,213 +0,0 @@ -# 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_p110905.ebuild,v 1.2 2011/10/07 19:29:31 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-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 - - 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/ccpn-2.2.1_p110926.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p110926.ebuild deleted file mode 100644 index 81bba68c28b7..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.2.1_p110926.ebuild +++ /dev/null @@ -1,220 +0,0 @@ -# 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 1.3 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.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-"${MY_MAJOR}"* - sci-biology/psipred - x11-libs/libXext - x11-libs/libX11 - opengl? ( - media-libs/freeglut - dev-python/pyglet )" -# We need to fix this -# sci-chemistry/mdd -DEPEND="${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 ${in_path}/c - - ebegin "Installing main files" - doins -r python || die "main files installation failed" - eend - dosym ../../../..//share/doc/ccpn-data-${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_p111011.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p111011.ebuild deleted file mode 100644 index d0ae0c549ab9..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.2.1_p111011.ebuild +++ /dev/null @@ -1,214 +0,0 @@ -# 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 1.2 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-"${MY_MAJOR}"* - >=sci-libs/ccpn-data-${PVR} - 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} -} diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p111017.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p111017.ebuild deleted file mode 100644 index e4f4f13a7c63..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.2.1_p111017.ebuild +++ /dev/null @@ -1,214 +0,0 @@ -# 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 1.2 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} -} diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p111019.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p111019.ebuild deleted file mode 100644 index 51c99204e671..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.2.1_p111019.ebuild +++ /dev/null @@ -1,214 +0,0 @@ -# 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} -} diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p111028.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p111028.ebuild deleted file mode 100644 index 479a8991247c..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.2.1_p111028.ebuild +++ /dev/null @@ -1,214 +0,0 @@ -# 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_p111028.ebuild,v 1.1 2011/10/28 08:50:29 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} -} diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p111124.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p111220.ebuild index 14650a1952d9..e1600d68538f 100644 --- a/sci-chemistry/ccpn/ccpn-2.2.1_p111124.ebuild +++ b/sci-chemistry/ccpn/ccpn-2.2.1_p111220.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_p111124.ebuild,v 1.1 2011/11/24 08:36:43 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p111220.ebuild,v 1.1 2011/12/20 08:39:39 jlec Exp $ EAPI="3" |