sci-chemistry/ccpn: Todays python patches

Package-Manager: portage-2.2.15/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 1e90314da9c5c58af5db736da5bda42225234a3d..abd63f597c3ea350dbf0e2413f586836035c2280 100644 (file)
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/ccpn
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.153 2014/11/17 08:01:09 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.154 2014/12/04 08:20:03 jlec Exp $
+
+*ccpn-2.4.1_p141204 (04 Dec 2014)
+
+  04 Dec 2014; Justin Lecher <jlec@gentoo.org> +ccpn-2.4.1_p141204.ebuild:
+  Todays python patches
 
 *ccpn-2.4.1_p141117 (17 Nov 2014)
 

diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 5d757fd44875ae101238052206cabaa858d12b15..ce7785355710e0268a971587a5a2fd3d98ba9b86 100644 (file)
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -29,6 +29,7 @@ DIST ccpn-update-2.4.1-141008.patch.xz 960 SHA256 e838cfe46b4897939fbcb631225adc
 DIST ccpn-update-2.4.1-141020.patch.xz 1900 SHA256 e01a911ba78d972b471a146dae2c35e0ddb756b0f46959dc8f28733caa4ece2d SHA512 6ab67ed68377f17d11c02cbb635e60814e9bd1e9fe0fdb87b1ad96309e18eb6dceb89dfe734aeb81ec0d6cdc7ae735965aef7d9da67be35ffe85db4d43bddd63 WHIRLPOOL 95edc9f6f5a192a58929fb2d52636e774818f8e10583ab3fa19648b7f97ec9ff72c8ab6a761552efd6c17bd448ab93d6ffde14122d643f11a2e49f37a2d60f59
 DIST ccpn-update-2.4.1-141022.patch.xz 2552 SHA256 6ec6ab3246b42ebe385056b8d25559ae42ae70481052a28d9afaa1bdd9af9b6b SHA512 926b7953aa8464ba9e1d08cbe88fbecf4b90d54991c87da6cbc052fc5b5eb8db3da553c8890c8540f0a80dc467e8d66f96b0f474c8251cea8b8deeb43eca91ef WHIRLPOOL a08980934a8fc3c2f57d30a9ae1184e14bda691f27820f67d3bb8e5981f2b59d3fd2c86e0abe8089a32d9f62ab39cc7d5f0a25d82361c31e11a7b894eca6b294
 DIST ccpn-update-2.4.1-141117.patch.xz 5120 SHA256 ce02985d32f1764ee7e05b8aa0628ac263fbe56da10411217cadeabccf0de17f SHA512 7762c479e23f9f54760d003099bfa3449b3f32a2c0ac464ec3d26bff54a1cc86f0b0b34d909b48726e849f45b4bcc54ad897380d1d9f895ff05f4c1eba75f579 WHIRLPOOL 7acb7233abcf48ce6eed6985ebad1f5ebeab255f45100803f2ea89c05d53e6c97dd62f56747d96aadf450509f97eac9e060e4b66a329ae8f5cb2eb833a7b20bb
+DIST ccpn-update-2.4.1-141204.patch.xz 6460 SHA256 502cba7654e415d8d1e08ca48ca966b2b5a25eb4238c03c0457a9633044d5aa0 SHA512 a5af54cc8b9056546c65463e335f28f9d0fe63db2edbab95b9b0a673f602970be635b8f571bd0522ddbe1fac24cdbc1553a596a49a17b0b3c2b569d06802c29c WHIRLPOOL 0e85f6f80b304ef578e319b0e6d08901860671ca707fa4149c3f05aab91c4d941aa2c8cb736a4b5d902f604eb8fad22476fbb0e0bdab6d19cbb7d27d06090477
 EBUILD ccpn-2.3.1_p140425.ebuild 4703 SHA256 8bdc74da4c23ab1c25147abd87ef87a8567bdf21a15a511d1ee966f09ef2c6c3 SHA512 a22af894d808cb5ca19190fb9dfdfe21e47b3626e2b18eebc1946fca28bbd463fb1bd4fca0a2b2ff57558ec2f004798c58253ccc7740f18174df258d07499ef8 WHIRLPOOL abc9ac85b431e2acc5ec8bf760ff52ae77c60df8e72dab823cb83c0040f895b6234b28b7e63ca854422bd311cf17079cacf03e702d3cc6e5907bcd13080b2208
 EBUILD ccpn-2.4.0_p140915.ebuild 4692 SHA256 32847b9452cab2d8579eb372548812497425f25715f4597a9c967abdf8ccf687 SHA512 67b2c0c969cf83194435667dfb92719d8b75be049cafa708c124e91a60519ae8b43843278004ecac92dc1035cd8391cd8531f58b82cf1fffe5151d0a4595b340 WHIRLPOOL e5de10a8838cfee05a23e81f1f3f032e23263633b67504afe71ae5a7d06a4097eba4ec32714907380ce17d82619fb8db9e0217b16952e19f0babe19dd3e30c79
 EBUILD ccpn-2.4.0_p140917.ebuild 4692 SHA256 9f4acfd7e56f6f0ccd12037b91bbd7e739e932e4543b8f34214273c0d2954012 SHA512 a7abfe87f100596d9f1c1bb22c43f35833a7f256c153fe2e52d2be4570eecb82b641081b35fd62478800a579ce4a5eb84f917095cd6172665b1d3e6c6db117ec WHIRLPOOL f0bc39c7ffd2b4b74919eec8d4b5bb619c3b45d1fc19f6cc5de6ca762b13189e5067e0e397f0ffe2e13e46ddfa6d18df78e8ef2def28426bdeab479bd9aee075
@@ -38,24 +39,25 @@ EBUILD ccpn-2.4.1_p141008.ebuild 4692 SHA256 2d54fa5ca4f5edbe071d0576e923152806c
 EBUILD ccpn-2.4.1_p141020.ebuild 4692 SHA256 e5c79ece1d0c4fca0fc3cd1d0ddc0b28c7b37ba8d30deaa415b706ac61841f3a SHA512 1cf610b842a1ca89e16954bbc542679bb815db95c4fb9aed3c3c71b09cd2543508944a74c849d87e9753343516b0b933366c4c6584fc916b7ed0482327a12b22 WHIRLPOOL e32844cef4a2c5587da0c469b5da7ef93bd71190827a98a4589109f14e286695b6f7738ffeaf7df03cfe8a756d60e080dc0c2293a457d987467b553cf324e231
 EBUILD ccpn-2.4.1_p141022.ebuild 4692 SHA256 bc559064a91bf4d92d17714c6d67f1dd7b480de7296193d0cdcc797460463baf SHA512 1a42358e098a73eb7937edf2cbd3f73b8a165f2cce550779d7219f2676188200460e25706b728c6b2d429a58447e5d3c9796e5d9bf876352c2a2f4ef9cd8b9ad WHIRLPOOL 31c669333d7a633babc226aceff380686ff72bc5977a5754ab5b857267874a5cc672c11ce035dc3fce34b2b8f47cb7bf8c5626fc790a89017e8eb0dbb8334c02
 EBUILD ccpn-2.4.1_p141117.ebuild 4692 SHA256 9ddc2b8b9fef6302f5adaea918a05b6c5307663f4c41e099a68c1a113f4cd440 SHA512 cfb181c616ff4d80a6a22b0f5d0e2321ff4fd61e50bd1cfce3502db45056f55c50d57c57079a51d559d0660bd93496e308f66eefcf22220d9a0376f9aa3e57ae WHIRLPOOL 42b842692007dfe752b37301acba95455febf8da2ddac27ed163c099a9b9be8db1cd0cfee196ab668df25830a4826362c4328c5e624c40f2a1325ef38d597e85
-MISC ChangeLog 28883 SHA256 320377ab098af4e1c49b59bddac669770f26f8d0f171b3c23a85b263b1fe875d SHA512 243bc3ef0507965d67df56394134643bad6eb0ec5adffc67c5d2c0f498bfa306e8362ef63dcc68f4594a5283e005df3600d8944af818e5ee6088daca2bc7acb6 WHIRLPOOL d580fc1cc36afd11ad21fdd3e22560b5cf2bc3537c8bc14a48a0acece663cae9a1ba9b9c59ab931cd18acd3c6f9645141620a1839e25324a6dd22524fee1c883
+EBUILD ccpn-2.4.1_p141204.ebuild 4692 SHA256 dce86e7384ab436c6da05d38d2668eb71607d58ad0edb89e5970f0399cc17012 SHA512 0f4052811f3aa6c033984263b81e37e962539f68403ffe7e98ca79cea9fd309044d0d0ffbd8005092a70a9cefdd8debfe260da78a0db2a85b4632c17dac3c25e WHIRLPOOL 6f1f347073a25b622ed7d966a9e7b252cb6d674d8e8c11ff4ce5675c3ebc1b6476ddbabcb3067de257260109a29ee59fccc9cff9ae354fb40b27b8f046df72c7
+MISC ChangeLog 29018 SHA256 87e5fc3bfa652212f3540119c34093085c0165b12a54b2e9f2b3f75ca02ea9c8 SHA512 00c21b2824896107ae3583a938f1857ddfe6fd120d608e9b4e153d80df45a16310ac4f474cb0d3fe69c8cbb9949634c361e719979bfd8687df912dafb84ec239 WHIRLPOOL 0198dac4fd5598f49d2b05ff13215891d2dfbf004210c2e74c3f4d9f19a29fb331eb0b63c4a4eb60bc51403d61c0e38ee8dff052a1f6a89d100e4ab8768fd10a
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
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diff --git a/sci-chemistry/ccpn/ccpn-2.4.1_p141204.ebuild b/sci-chemistry/ccpn/ccpn-2.4.1_p141204.ebuild
new file mode 100644 (file)
index 0000000..a6def8a
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.4.1_p141204.ebuild
@@ -0,0 +1,166 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.4.1_p141204.ebuild,v 1.1 2014/12/04 08:20:03 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="
+       ${PYTHON_DEPS}
+       dev-lang/tk[threads]
+       dev-python/numpy[${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="${EPREFIX}/usr"
+               GL_LIB="-lglut -lGLU -lGL"
+               GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
+               GL_LIB_FLAGS="-L\$(GL_DIR)/$(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 ${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
+}