From 1b1f83a0313f4fe8f2d36ba6e18bb5a491d4d31d Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Mon, 13 Apr 2015 08:01:39 +0000 Subject: [PATCH] Today's python patches Package-Manager: portage-2.2.18/cvs/Linux x86_64 Manifest-Sign-Key: 0xB9D4F231BD1558AB! --- sci-chemistry/ccpn/ChangeLog | 7 +- sci-chemistry/ccpn/Manifest | 32 ++-- sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild | 166 +++++++++++++++++++ 3 files changed, 189 insertions(+), 16 deletions(-) create mode 100644 sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog index 63b90667bbb6..38c9de4d2379 100644 --- a/sci-chemistry/ccpn/ChangeLog +++ b/sci-chemistry/ccpn/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-chemistry/ccpn # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.166 2015/04/07 14:36:39 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.167 2015/04/13 08:01:37 jlec Exp $ + +*ccpn-2.4.2_p150413 (13 Apr 2015) + + 13 Apr 2015; Justin Lecher +ccpn-2.4.2_p150413.ebuild: + Today's python patches *ccpn-2.4.2_p150325 (25 Mar 2015) diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest index 843d8168b08f..12478e132d2b 100644 --- a/sci-chemistry/ccpn/Manifest +++ b/sci-chemistry/ccpn/Manifest @@ -16,27 +16,29 @@ DIST analysis2.4.1.tar.gz 36088236 SHA256 1cb089dcc739e8536d938a68536f556094f5d7 DIST analysis2.4.2.tar.gz 36390919 SHA256 14941131033cbd4b0b13d6d4fe3f9253360a7c2ace8ece9194be00c1fe4b2903 SHA512 694faefd3c085b559b6bb4729141a9ab885334f578bfbb0ebf260366dbca38c31738d5f5af50b5c7ea16b304b27adf80411082859796a5afeec630c36d56bd8b WHIRLPOOL 4499dcb074d445bfc972f9dea43e6f3e3c28722d513dce0fec4e1b2b5dab8be098f53f82565d86a4e7935f0595ef303465668230aa61021cf88e13cce8606214 DIST ccpn-update-2.4.1-150226.patch.xz 10732 SHA256 74e8723d310d336cd4215ed4e9a1a1c0b2c0efdb4c03aaacba7ecd0575b38287 SHA512 60eb4acf6179f80207a72076ff5d5d733d3c3e804c1ce0a48701dd6e923146af49cd6759a529c8125f4b26eb3f8f83b35acc0c48b88a3e3034b25b5438a04feb WHIRLPOOL 3a2357d4fcb086206d45edd5b9cc807313b5f62be2f2a70e8f011f5521cf8729371b8c7149837c4ea1f6f059e26a49c1d20492f338a844e15f38ccf543faf6e1 DIST ccpn-update-2.4.2-150325.patch.xz 2096 SHA256 d33676fd93aaa5814aa43179f221df69f4bae9b8ec98ce5b6cc57ce6aacab732 SHA512 c544e0a4a93d0e3275a22d07d21bf3bb5ed90cf041f40bf08fbc687b431640ad5c56180eadd4b43e4023b08ef42afe5a874423becc6f9313a0b1f642a4b97873 WHIRLPOOL f2e9780eb3216185cc6b89ca490e14c2de1130393eda4308fc71e6a2eb0460fc97f83ab3c92fb6a488a1926ba2f3099c7ae5f0a4bd216f8ffa24bfd87e360838 +DIST ccpn-update-2.4.2-150413.patch.xz 3132 SHA256 c0796e1f739f799003304c8b8d23ea0ee42b2e0a6dd59b292cb2a1167b5725f5 SHA512 99893ca009ff76b015017b29cfd97e0ae935ed2d62aa5a99d52dd9a5f22cf0d369e5019273fe3c3811c28b32568721fb64f71c5927eb57d0cc91dcea44b0288d WHIRLPOOL 48a355ef4824d41517d618178be4cd4efc42a6f5e190bac88348041504da0807aa1b34bafbc3937d7f6fc3b5b52fe469431fb6ce9df40bb1c56d7faad88cfe51 EBUILD ccpn-2.4.1_p150226.ebuild 4668 SHA256 5b0cda2b0270173831f07760c9c3d39f46e8e84a5ef3a4ada3ff5b3435375147 SHA512 59e43c3c2f9c6dce01633f4c3a6bbd51e14ec98b962777e027e634f70405013737cd2741b7e0cc78d407ab954fa9869a45a0daa2583d3306b030433896132dba WHIRLPOOL 64febf20e9b842370f16d848ce7087d3e663f87e2836e2eea4d10940919bd34638497b731cbd8c121237781e90ddc272b45cd39ea999f94b18420bba4713cce9 EBUILD ccpn-2.4.2.ebuild 4661 SHA256 2d389f8474981d4f9b5888a2c1a54ef7615d7ef98db4ab919bafe5c694d925d2 SHA512 baecfdc6617a5c3e353fe9b459ed3fdec5bfc84ebc62418dbcc2ffb6e245e1c2c229721e305a54de9a02b1610d7e7dcd69aef953f4f5840ce58eb8d58bd60a2a WHIRLPOOL 334210c94184145054f84a2b0863d4a4cafbddce30ee862c257fc2eec50794eef2e297d7f6250d7fb54a01d75704b00fa1cc4ccf7248376cdb683672af7ac436 EBUILD ccpn-2.4.2_p150325.ebuild 4668 SHA256 e5db889d53056bb80310bdbeacfa0dd942785eff48fbb5057aa5afd8b74c0316 SHA512 d297d0508eb624102f74a062cac56cac2193b2102ed1036669f9d0cabfa74717f0de312455f8bd7ed8392313c7afac2d4d670b5696f38555f18c075724737ce7 WHIRLPOOL 0da3cabff804429a020401b88d12240b8ad7eb973005a92bc3b2a51b71ce8f4889bced5f81962c11391a180e7d051ae8b428756cb060ed9387d5c3583c8d5af6 -MISC ChangeLog 31285 SHA256 9d71031fdec750bf101dee74a2e5922c3c7d1ad6e33f1fd350a62f72d3c0dc0f SHA512 d644b8653fc3e99e0f1e8cf59e9b4646e41d911722b0900ee828fbdfc241139de15a63507c63d1c459cabc6a6b0d38f76a773259e3a5dab62b43670682b4654d WHIRLPOOL 467ddc41bb70bc3dd3baa89fb50c9e47a9ad48d045ee5297274e8c0f71d2c92385899b6ef2436bc8ebc6eb5ef520e3dcfdb26a2265f2575088fa6ffb43430ec0 +EBUILD ccpn-2.4.2_p150413.ebuild 4668 SHA256 378d49c75aa0b89d9c615125c36c479f3584b70913d50ecb3ddfcfa8b59a3df6 SHA512 f9ee3e61a27bf424e64dfd36e70834ec8e82aa99cbf160a8c49e0de37372ad7bed5d9a837b1892e1925fa9a68c937fc101078afd3931853955c68bf1c01474bc WHIRLPOOL 73c94ed2eeb89ce2f8a96e6a440dfcb19793402ff772c3a757dff0aa9236fe5743029c9a64092fe5e68788911657514e4f70aebfd89b088d90054fadffbb3641 +MISC ChangeLog 31421 SHA256 770b12176f120a35eba8cc5ee481407b7c1679422d8369a49ce7469cae205dcf SHA512 5966f3136c575a5a0d057518c8ee09cc4d520216ff8453672cb8a7b41fd508fd649a39131b053197ea785b59f1726e2c3c5b1130b017be486b500a8ae09baa49 WHIRLPOOL f65579fb6c34b2a1f028eab3a006d4a7e3d586d0f29294f0a275751b1137ebe07997ed2ebc2c9d32bf5a875517934884713e5791824732964593e3f39d27af18 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0 -iQJ8BAEBCgBmBQJVI+t4XxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w +iQJ8BAEBCgBmBQJVK3fgXxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w ZW5wZ3AuZmlmdGhob3JzZW1hbi5uZXQyQ0JDQjFGMzBDQ0UxMjFGNENDNDgxMDdC -OUQ0RjIzMUJEMTU1OEFCAAoJELnU8jG9FVirXRIQAKBB/MOjWRLzfnmXyeYhdJgH -+1fETmCZY+dHEbw7Ad46UPVLrPgkOOxwIUzdovL5QtPNMvovM5O9DeNiSzfWXZpi -39rTflBow5gcpD9Pf3Dwnc90nQryA8QgI/Z/h4tRDQdC07iwTGhNt3rxfOsqTL84 -yyj4MqdhEolCo0UBd9MTMHKMF4WX5lUNBtu4FZYie417tq+awUPqqjVeE97jMwps -0iFH94pxQggifO9o1rS1WoKMA/Jhw72Odm7Lw9oWD212osmFgQCLl1B3h9zFDSHT -PgOqZO4oGOZVQ3jqxgA8Ax+MluIz+Klnaqs8HnoJxEsi21VCGvde+JyUy+M7kSr5 -sqcNsK5CyLHDWhhsCnG/stFMgyeakD3EHgmre25+kX1mdcmCqr+lLtdsu3okYErY -VMOATTa6bnyd7VQF2sbJSP9EH5C0G6g5n8Nx/V90oimvNmQsyccZmtKjTHIdBS25 -glwj/D2fzFTgGOdSlwToAVg3ffu57VYSltmeAHeALp0PmaeD2Y4wO42dt7tpVNXM -ma1Z7Cqxp1ChpKbFACtLY7QWfgIoZeeQ2r4d25QnzNtUNekLSuvpSSB991mzUuhh -dDTXcuwaOCgHCyIEWU7Pj9AbHsi3Cu/PGsTNvwVK3178bED95xU5bM9HiphyDsva -vpeHyeeqUJ3ZafdXI6v1 -=681d +OUQ0RjIzMUJEMTU1OEFCAAoJELnU8jG9FVirxzIP/3upsNeJ6Q4dRSOOM9ZkEULd +R+KrTimT8wCsOwn11JUP7CLc845mlA4jxcVkuvZAplR3E5jdK3nI/UHeWfKo8CkB +DJGIPiA/smLT/LUN26SgOSzAGBDW5B0QMJTTWrL/qTuIjTPjt7HLtp1uY64FWtkk +Jc1wxY3G/qRZyUcou+mqujGROnrsmYLF5jubSPBn7+xdGldZVgY0KXwsRkP/6ym/ +h8g/oSOKtrPkjueCEm+fSm+mQwdjllrJnQOwT6aE6ZYB6ahXwPk54bgJVo/AMCxb +cLMQNy2dXiuF4ScqFiPvrYFY8gPaUtqhoJv6diKtAUphBWJ/A5DC3rDQU8vl5djJ +ZIt1NJ+jJRkQYcnfBzacg4Xw0+tVIcHDp+RMAsm521YP5nXVMLGzrdlqu0HKZBiS +hMecW9qbdOSt5MkATjyMA/gWRU9WgsuG5gv3bi5F2Ao68d1OSQha4QrfMEjnNYOD +a2598OZ9jS+RNcFZRMRgNq78CoFElTmQUMQW7azG8VFO8B7/qCaGU7soXtC8A6nL +/QsHafuFJb1XDBt6jNumyu7P2HIeSRbtKUiIKChJSbc27dqvKoG5RfXIAUyDL591 +MS+DMnRHK4D4/jE749BIiBQu6tCb3nGT6uNVRkyMxPJRBuc3qQYgHAsOgLYhDct+ +IFEhCWV9aWLjHVpsM6ax +=dTwb -----END PGP SIGNATURE----- diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild new file mode 100644 index 000000000000..85c7de5946d7 --- /dev/null +++ b/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild @@ -0,0 +1,166 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild,v 1.1 2015/04/13 08:01:37 jlec Exp $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="ssl,tk" + +inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator + +PATCHSET="${PV##*_p}" +MY_PN="${PN}mr" +MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" +MY_MAJOR="$(get_version_component_range 1-3)" + +DESCRIPTION="The Collaborative Computing Project for NMR" +HOMEPAGE="http://www.ccpn.ac.uk/ccpn" +SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" +[[ -n ${PATCHSET} ]] \ + && SRC_URI+=" http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+opengl" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-lang/tk:0=[threads] + dev-python/numpy[${PYTHON_USEDEP}] + dev-tcltk/tix + =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] + sci-biology/psipred + x11-libs/libXext + x11-libs/libX11 + opengl? ( + media-libs/freeglut + dev-python/pyglet[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch + + epatch "${FILESDIR}"/2.3.1-parallel.patch + + append-lfs-flags + + sed \ + -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ + -e "s:weights_s:weights:g" \ + -i python/ccpnmr/analysis/wrappers/Psipred.py || die + + local tk_ver + local myconf + + tk_ver="$(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="${EPREFIX}/usr" + GL_LIB="-lglut -lGLU -lGL" + GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" + GL_LIB_FLAGS="" + else + IGNORE_GL_FLAG="-DIGNORE_GL" + GL_FLAG="-DUSE_GL_FALSE" + fi + + GLUT_NOT_IN_GL="" + GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" + + rm -rf data model doc license || die + + sed \ + -e "s|/usr|${EPREFIX}/usr|g" \ + -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ + -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ + -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ + -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ + -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ + -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ + -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ + -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ + -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ + -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ + -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ + -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ + -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ + -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ + c/environment_default.txt > c/environment.txt || die + + sed \ + -e 's:ln -s:cp -f:g' \ + -i $(find python -name linkSharedObjs) || die +} + +src_compile() { + emake -C c all + emake -C c links +} + +src_install() { + local libdir + local tkver + local _wrapper + + find . -name "*.pyc" -type f -delete || die + + libdir=$(get_libdir) + tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) + + _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" + for wrapper in ${_wrapper}; do + sed \ + -e "s|gentoo_sitedir|$(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|${EPYTHON}|g" \ + -e "s|gentoousr|${EPREFIX}/usr|g" \ + -e "s|//|/|g" \ + "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" + dobin "${T}"/${wrapper} + done + + local in_path=$(python_get_sitedir)/${PN} + local files + local pydocs + + pydocs="$(find python -name doc -type d)" + rm -rf ${pydocs} || die + + for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do + sed \ + -e 's|#from __future__|from __future__|g' \ + -i ${i} || die + done + + dodir ${in_path#${EPREFIX}}/c + + ebegin "Installing main files" + python_moduleinto ${PN} + python_domodule python + eend + + ebegin "Adjusting permissions" + for _file in $(find "${ED}" -type f -name "*so"); do + chmod 755 ${_file} + done + eend + python_optimize +} -- 2.26.2