Today's python patches

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 63b90667bbb69e53ed0d96439b692be02b46091a..38c9de4d2379019d4048b07e373de687d5379fc7 100644 (file)
--- 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 <jlec@gentoo.org> +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 843d8168b08fcc5546fec67fdeb3869daaf0f375..12478e132d2b5ba929a4e640a73f2f34acea9fa9 100644 (file)
--- 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
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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 (file)
index 0000000..85c7de5
--- /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
+}