From: Michał Górny Date: Sun, 18 Jan 2015 19:04:22 +0000 (+0000) Subject: Convert to python-single-r1. X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=0987237837248daa89016737fb5dbb7ef99b54fb;p=gentoo.git Convert to python-single-r1. Package-Manager: portage-2.2.15/cvs/Linux x86_64 Manifest-Sign-Key: 0xEFB4464E! --- diff --git a/sci-chemistry/ccp4-apps/ChangeLog b/sci-chemistry/ccp4-apps/ChangeLog index 272650b72d9a..6581570ca549 100644 --- a/sci-chemistry/ccp4-apps/ChangeLog +++ b/sci-chemistry/ccp4-apps/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-chemistry/ccp4-apps -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.42 2014/10/27 14:25:40 jlec Exp $ +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.43 2015/01/18 19:04:16 mgorny Exp $ + +*ccp4-apps-6.1.3-r13 (18 Jan 2015) + + 18 Jan 2015; Michał Górny +ccp4-apps-6.1.3-r13.ebuild: + Convert to python-single-r1. 27 Oct 2014; Justin Lecher ccp4-apps-6.1.3-r11.ebuild, ccp4-apps-6.1.3-r12.ebuild: @@ -206,4 +211,3 @@ +files/6.1.3-rename-rapper.patch, +files/6.1.3-rename-truncate.patch, +files/6.1.3-setup.patch, +ccp4-apps-6.1.3.ebuild, +metadata.xml: Splitted apps from ccp4 - diff --git a/sci-chemistry/ccp4-apps/Manifest b/sci-chemistry/ccp4-apps/Manifest index fb0232cc3b9f..06b142ce2bc2 100644 --- a/sci-chemistry/ccp4-apps/Manifest +++ b/sci-chemistry/ccp4-apps/Manifest @@ -1,5 +1,5 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA512 +Hash: SHA256 AUX 6.1.3-clipper-template.patch 2619 SHA256 a185a93f76c23ce06256866cfaf0e9854a5702b95a1e49e4d3a5f732e0d1e2a3 SHA512 27d2e1eeace0ba7e690ac218ba4272e668e693b20292d2824831c6472627fcbf7013409a9255bd514918921cdc9ac98d86709ecda73b255230ccadc8d66e45a9 WHIRLPOOL f1e0694ec4a582cf1b547d845e8c8a86791aa3f109429f6a4aadfb30142719a07fee92d01f3e3a8f0703cc55833aae8fb6c3c2e8503efe741ac94276feb1b3b4 AUX 6.1.3-dont-build-balbes.patch 489 SHA256 dfe1b810fb07bf536528b9c955e3162dc470a803513ae6fa69848ed6d64503c4 SHA512 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+SRC="ftp://ftp.ccp4.ac.uk/ccp4" +SRC_URI=" + ${SRC}/${PV}/${MY_P}-core-src.tar.gz + http://dev.gentooexperimental.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2" +# patch tarball from upstream + [[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" +# patches created by us + [[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" + +for i in $(seq $PATCH_TOT); do + NAME="PATCH${i}[1]" + SRC_URI="${SRC_URI} + ${SRC}/${PV}/patches/${!NAME}" +done + +LICENSE="ccp4" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="examples X" + +X11DEPS=" + x11-libs/libX11 + x11-libs/libXaw + x11-libs/libXt + x11-libs/libxdl_view" + +TKDEPS=" + >=dev-lang/tk-8.3 + >=dev-tcltk/blt-2.4 + dev-tcltk/iwidgets + dev-tcltk/itcl + dev-tcltk/itk + >=dev-tcltk/tdom-0.8 + dev-tcltk/tktreectrl" + +SCILIBS=" + ~sci-libs/ccp4-libs-${PV} + >=sci-libs/ccp4-libs-${PV}-r7 + sci-libs/clipper + sci-libs/fftw:2.1 + sci-libs/mmdb:0 + sci-libs/ssm + virtual/blas + virtual/lapack" + +SCIAPPS=" + sci-chemistry/pdb-extract + sci-chemistry/pymol + sci-chemistry/rasmol + >=sci-chemistry/oasis-4.0-r1" + +RDEPEND=" + ${TKDEPS} + ${SCILIBS} + app-shells/tcsh + dev-python/pyxml + dev-libs/libxml2:2 + dev-libs/libjwc_c + dev-libs/libjwc_f + dev-libs/boehm-gc + !app-office/sc + !& /dev/null + ccp_patch "${DISTDIR}/${p}" + popd >& /dev/null + done + einfo "Done." + echo + + [[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch + + einfo "Applying Gentoo patches ..." + + # it tries to create libdir, bindir etc on live system in configure + ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch + + # We already have sci-chemistry/rasmol + # Also remember to create the bindir. + ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch + + # libraries come from sci-libs/ccp4-libs + ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch + + # We have seperate ebuilds for those + for bin in molref xia scala imosflm balbes; do + ccp_patch "${FILESDIR}"/${PV}-dont-build-${bin}.patch + done + + # don't configure what is not build + ccp_patch "${FILESDIR}"/${PV}-dont-configure.patch + + # Set python paths correctly + ccp_patch "${FILESDIR}"/${PV}-pythonpath.patch + + # Set python paths correctly + ccp_patch "${FILESDIR}"/${PV}-pisa.patch + + # Set python paths correctly + ccp_patch "${FILESDIR}"/${PV}-clipper-template.patch + + # Fix upstreams code + ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch + + # Not renaming, but unbundling libs + ccp_patch "${FILESDIR}"/${PV}-rename-rapper-ng.patch + + # Use pkg-config to detect BLAS/LAPCK + ccp_patch "${FILESDIR}"/${PV}-lapack.patch + + # unbundle libs + ccp_patch "${FILESDIR}"/${PV}-unbundle.patch + + # tcl-8.6 + ccp_patch "${FILESDIR}"/${P}-tcl8.6.patch + + # Update things for oasis 4 usage + epatch "${WORKDIR}"/${PV}-oasis4.0.patch + sed 's: oasis : :g' -i src/Makefile.in || die + + einfo "Done." # done applying Gentoo patches + echo + + find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete + + sed \ + -e "s:/usr:${EPREFIX}/usr:g" \ + -e 's:-Wl,-rpath,$CLIB::g' \ + -e 's: -rpath $CLIB::g' \ + -e 's: -I${srcdir}/include/cpp_c_headers::g' \ + -e 's:sleep 1:sleep .2:g' \ + -e 's:\\$(XCIF_LIB):-L$srcdir/lib/ccif -lccif:g' \ + -e 's:\\$(XLAPACK_LIB):${XLAPACK_LIB}:g' \ + -e 's:\\$(CXX_LIBS):\${CXX_LIBS}:g' \ + -e 's:\\$(XLDFLAGS):\${XLDFLAGS}:g' \ + -i configure || die + + sed \ + -e '/o crunch2/s:$: ${XLAPACK_LIB}:g' \ + -i src/Makefile* || die + + find "${S}" -name "Makefile.*" \ + -exec sed -e 's|_FLAGS-|_FLAGS:-|g' -e "s:\(eval \$([[:alnum:]]*)\):\1 \$(GENTOOLDFLAGS):g" -i '{}' \; + + # Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version + sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure || die + + # Rapper bundles libxml2 and boehm-gc. Don't build, use or install those. + pushd src/rapper 2>/dev/null + eautoreconf + popd 2>/dev/null + + gnuconfig_update + + python_fix_shebang -f . +} + +src_configure() { + # Build system is broken if we set LDFLAGS + export GENTOOLDFLAGS="${LDFLAGS}" + unset LDFLAGS + + # These are broken with ./src/procheck/ps.f + filter-flags "-floop-*" + + # GENTOO_OSNAME can be one of: + # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd + # linux_compaq_compilers linux_intel_compilers generic Darwin + # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers + if [[ "$(tc-getFC)" = "ifort" ]]; then + if use ia64; then + GENTOO_OSNAME="ia64_linux_intel" + else + # Should be valid for x86, maybe amd64 + GENTOO_OSNAME="linux_intel_compilers" + fi + else + # Should be valid for x86 and amd64, at least + GENTOO_OSNAME="linux" + fi + + # Sets up env + ln -s \ + ccp4.setup-bash \ + "${S}"/include/ccp4.setup + + # We agree to the license by emerging this, set in LICENSE + sed -i \ + -e "s~^\(^agreed=\).*~\1yes~g" \ + "${S}"/configure || die + + # Fix up variables -- need to reset CCP4_MASTER at install-time + sed -i \ + -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ + -e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ + -e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ + -e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ + -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \ + "${S}"/include/ccp4.setup* || die + + # Set up variables for build + source "${S}"/include/ccp4.setup-sh + + export CC=$(tc-getCC) + export CXX=$(tc-getCXX) + export COPTIM=${CFLAGS} + export CXXOPTIM=${CXXFLAGS} + # Default to -O2 if FFLAGS is unset + export FC=$(tc-getFC) + export FOPTIM=${FFLAGS:- -O2} + export BINSORT_SCR="${T}" + export CCP4_MASTER="${WORKDIR}" + export CCP4I_TCLTK="${EPREFIX}/usr/bin" + export MAKE="make ${MAKEOPTS} ${EXTRA_EMAKE}" + + # Can't use econf, configure rejects unknown options like --prefix + ./configure \ + $(use_enable X x) \ + --with-shared-libs \ + --with-fftw="${EPREFIX}/usr" \ + --with-warnings \ + --disable-pdb_extract \ + --disable-cctbx \ + --disable-phaser \ + --disable-diffractionImg \ + --disable-clipper \ + --disable-ssm \ + --disable-mosflm \ + --disable-mrbump \ + --tmpdir="${TMPDIR}" \ + ${GENTOO_OSNAME} || die "configure failed" + + # We do this manually, since disabling the clipper libraries also + # disables the clipper programs + pushd src/clipper_progs 2>/dev/null + econf \ + --prefix="${S}" \ + --bindir="${ED}"/usr/libexec/ccp4/bin \ + --with-ccp4="${S}" \ + --with-clipper="${EPREFIX}/usr" \ + --with-fftw="${EPREFIX}/usr" \ + --with-mmdb="${EPREFIX}/usr" \ + CXX=$(tc-getCXX) + popd 2>/dev/null +} + +src_compile() { + # fsplit is required for the programs + pushd lib/src 2>/dev/null + emake fsplit -j1 || die + popd 2>/dev/null + + # We do this manually, since disabling the clipper libraries also + # disables the clipper programs + pushd src/clipper_progs 2>/dev/null + emake || die + popd 2>/dev/null + + emake -j1 || die "emake failed" +} + +src_install() { + # Set up variables for build + source "${S}"/include/ccp4.setup-sh + + # if we don't make this, a ton of programs fail to install + mkdir "${S}"/bin || die + + # We do this manually, since disabling the clipper libraries also + # disables the clipper programs + pushd "${S}"/src/clipper_progs 2>/dev/null + emake install || die + popd 2>/dev/null + + einstall || die "install failed" + + # Collision with sci-chemistry/mrbump + rm -f "${S}"/bin/{mrbump,pydbviewer} || die + + # Bins + exeinto /usr/libexec/ccp4/bin/ + doexe "${S}"/bin/* || die + + # Libs + for file in "${S}"/lib/*; do + if [[ -d ${file} ]]; then + continue + elif [[ -x ${file} ]]; then + dolib.so ${file} || die + else + insinto /usr/$(get_libdir) + doins ${file} || die + fi + done + + rm -f "${S}"/include/ccp4.setup* + + # smartie -- log parsing + insinto /usr/share/ccp4 + doins -r "${S}"/share/smartie || die + + # Install docs and examples + local _man + pushd "${S}"/man/cat1 > /dev/null + for _man in *; do + newman ${_man} ${_man%??}-ccp4${_man:${#_man}-2:2} + done + popd > /dev/null + + mv "${S}"/manual/README "${S}"/manual/README-manual + dodoc manual/* README CHANGES doc/* examples/README || die + + rm "${ED}"/usr/share/doc/${PF}/GNUmakefile.* + rm "${ED}"/usr/share/doc/${PF}/COPYING.* + + dohtml -r "${S}"/html/* + + if use examples; then + for i in data rnase toxd; do + docinto examples/${i} + dodoc "${S}"/examples/${i}/* + done + + docinto examples/tutorial + dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css + for i in data results; do + docinto examples/tutorial/${i} + dodoc "${S}"/examples/tutorial/${i}/* + done + + for i in non-runnable runnable; do + docinto examples/unix/${i} + dodoc "${S}"/examples/unix/${i}/* + done + fi + # Needed for ccp4i docs to work + dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples || die + dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html || die + + cat >> "${T}"/baubles <<- EOF + #!${EPREFIX}/bin/bash + exec "${EPYTHON}" "\${CCP4}/share/ccp4/smartie/baubles.py" + EOF + + exeinto /usr/libexec/ccp4/bin/ + doexe "${T}"/baubles || die +} + +# Epatch wrapper for bulk patching +ccp_patch() { + EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} +}