From 783262a5da5c41f73420607786a7ddb811c38aa0 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Thu, 4 Dec 2014 08:20:04 +0000 Subject: [PATCH] sci-chemistry/ccpn: Todays python patches Package-Manager: portage-2.2.15/cvs/Linux x86_64 Manifest-Sign-Key: 0xB9D4F231BD1558AB! --- sci-chemistry/ccpn/ChangeLog | 7 +- sci-chemistry/ccpn/Manifest | 32 ++-- sci-chemistry/ccpn/ccpn-2.4.1_p141204.ebuild | 166 +++++++++++++++++++ 3 files changed, 189 insertions(+), 16 deletions(-) create mode 100644 sci-chemistry/ccpn/ccpn-2.4.1_p141204.ebuild diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog index 1e90314da9c5..abd63f597c3e 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 1.153 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 +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 5d757fd44875..ce7785355710 100644 --- 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 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+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 +} -- 2.26.2