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authorJustin Lecher <jlec@gentoo.org>2014-01-31 09:07:59 +0000
committerJustin Lecher <jlec@gentoo.org>2014-01-31 09:07:59 +0000
commit0fd3d5cd04abb66c3dd9614158b52bf42380a2ff (patch)
treec623335b0ab3ec688b8f7dfd5fef59b5c630c4a4 /sci-chemistry
parentDeclare mod_proxy_balancer dep on mod_proxy_balancer #460434 by Jaco Kroon. (diff)
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Add todays Python patches
(Portage version: 2.2.8-r1/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)
Diffstat (limited to 'sci-chemistry')
-rw-r--r--sci-chemistry/ccpn/ChangeLog7
-rw-r--r--sci-chemistry/ccpn/ccpn-2.3.1_p140131.ebuild166
2 files changed, 172 insertions, 1 deletions
diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 202d300e33a3..9136a07a8452 100644
--- 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 1.130 2014/01/20 10:38:50 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.131 2014/01/31 09:07:59 jlec Exp $
+
+*ccpn-2.3.1_p140131 (31 Jan 2014)
+
+ 31 Jan 2014; Justin Lecher <jlec@gentoo.org> +ccpn-2.3.1_p140131.ebuild:
+ Add todays Python patches
*ccpn-2.3.1_p140120 (20 Jan 2014)
diff --git a/sci-chemistry/ccpn/ccpn-2.3.1_p140131.ebuild b/sci-chemistry/ccpn/ccpn-2.3.1_p140131.ebuild
new file mode 100644
index 000000000000..c57dcbcb0602
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.3.1_p140131.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-2.3.1_p140131.ebuild,v 1.1 2014/01/31 09:07:59 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_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}r2.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 ${PATCHSET} ]] && \
+ epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
+
+ epatch "${FILESDIR}"/${MY_PV}-parallel.patch "${FILESDIR}"/talosn.patch
+
+ append-lfs-flags
+
+ sed \
+ -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
+ -e "s:weights_s:weights:g" \
+ -i python/ccpnmr/analysis/wrappers/Psipred.py || die
+
+ local tk_ver
+ local myconf
+
+ tk_ver="$(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
+}