[gentoo-commits] gentoo-x86 commit in sci-libs/cctbx: metadata.xml ChangeLog cctbx-2009.11.01.0123.ebuild

[Justin Lecher (jlec)]

jlec        10/02/04 22:56:27

  Added:                metadata.xml ChangeLog cctbx-2009.11.01.0123.ebuild
  Log:
  Computational Crystallography Toolbox
  Initially written by dberkholz
  (Portage version: 2.2_rc62/cvs/Linux x86_64)

Revision  Changes    Path
1.1                  sci-libs/cctbx/metadata.xml

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-libs/cctbx/metadata.xml?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-libs/cctbx/metadata.xml?rev=1.1&content-type=text/plain

Index: metadata.xml
===================================================================
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
	<herd>sci-chemistry</herd>
	<maintainer>
	  <email>jlec@g.o</email>
	  <name>Justin Lecher (jlec)</name>
	</maintainer>
	<longdescription>
	The Computational Crystallography Toolbox (cctbx) is being developed
	as the open source component of the PHENIX system. The goal of
	the PHENIX project is to advance automation of macromolecular structure
	determination. PHENIX depends on the cctbx, but not vice versa. This
	hierarchical approach enforces a clean design as a reusable library.
	The cctbx is therefore also useful for small-molecule crystallography
	and even general scientific applications.
	</longdescription>
</pkgmetadata>



1.1                  sci-libs/cctbx/ChangeLog

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-libs/cctbx/ChangeLog?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-libs/cctbx/ChangeLog?rev=1.1&content-type=text/plain

Index: ChangeLog
===================================================================
# ChangeLog for sci-libs/cctbx
# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/ChangeLog,v 1.1 2010/02/04 22:56:26 jlec Exp $

*cctbx-2009.11.01.0123 (04 Feb 2010)

  04 Feb 2010; Justin Lecher (jlec) <jlec@g.o>
  +cctbx-2009.11.01.0123.ebuild, +metadata.xml:
  New ebuild, initialy written by dberkholz




1.1                  sci-libs/cctbx/cctbx-2009.11.01.0123.ebuild

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-libs/cctbx/cctbx-2009.11.01.0123.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-libs/cctbx/cctbx-2009.11.01.0123.ebuild?rev=1.1&content-type=text/plain

Index: cctbx-2009.11.01.0123.ebuild
===================================================================
# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/cctbx-2009.11.01.0123.ebuild,v 1.1 2010/02/04 22:56:26 jlec Exp $

EAPI="3"
PYTHON_DEPEND="2"

inherit toolchain-funcs python eutils

MY_PV="${PV//./_}"

DESCRIPTION="Computational Crystallography Toolbox"
HOMEPAGE="http://cctbx.sourceforge.net/"
SRC_URI="http://cci.lbl.gov/cctbx_build/results/${MY_PV}/${PN}_bundle.tar.gz -> ${P}.tar.gz"

LICENSE="cctbx-2.0"
SLOT="0"
KEYWORDS="~x86 ~amd64"
IUSE="+minimal openmp threads"

RDEPEND="
	>dev-libs/boost-1.39
	sci-libs/fftw
	!minimal? (
		sci-chemistry/cns
		sci-chemistry/shelx )"
DEPEND="${RDEPEND}
	>=dev-util/scons-1.2"

S="${WORKDIR}"
MY_S="${WORKDIR}"/cctbx_sources
MY_B="${WORKDIR}"/cctbx_build

pkg_setup() {
	if use openmp &&
	[[ $(tc-getCC)$ == *gcc* ]] &&
		( [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]] ||
		! built_with_use sys-devel/gcc openmp )
	then
		ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 "
		ewarn "If you want to build ${PN} with OpenMP, abort now,"
		ewarn "and switch CC to an OpenMP capable compiler"
	fi
}

src_prepare() {
	local opts
	local optsld

	rm -rf "${MY_S}/scons"

	mkdir -p "${MY_S}"/scons/src/ "${MY_S}/boost"

	ln -sf "${EPREFIX}"/usr/$(get_libdir)/scons-* "${MY_S}"/scons/src/engine || die

	# Get CXXFLAGS in format suitable for substitition into SConscript
	for i in ${CXXFLAGS}; do
		opts="${opts} \"${i}\","
	done

	# Strip off the last comma
	opts=${opts%,}

	# Fix CXXFLAGS
	sed -i \
		-e "s:\"-O3\", \"-ffast-math\":${opts}:g" \
		${MY_S}/libtbx/SConscript

	# Get LDFLAGS in format suitable for substitition into SConscript
	for i in ${LDFLAGS}; do
		optsld="${optsld} \"${i}\","
	done

	optsld=${optsld%,}

	# Fix LDFLAGS which should be as-needed ready
	sed -i \
		-e "s:\"-shared\":\"-shared\", ${optsld}:g" \
		${MY_S}/libtbx/SConscript
}

src_configure() {
	local compiler
	local myconf

	myconf="${MY_S}/libtbx/configure.py"

	# Get compiler in the right way
	compiler=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
	myconf="${myconf} --compiler=${compiler}"

	# Precompiling python scripts. It is done in upstreams install script.
	# Perhaps use python_mod_compile, but as this script works we should stick to it.
	${EPREFIX}/usr/bin/python "${MY_S}/libtbx/command_line/py_compile_all.py"

	# Additional USE flag usage
	check_use openmp
	myconf="${myconf} --enable-openmp-if-possible=${USE_openmp}"

	use threads && USEthreads="--enable-boost-threads" && \
		ewarn "If using boost threads openmp support is disabled"

	myconf="${myconf} ${USE_threads} --scan-boost"

	mkdir "${MY_B}" && myconf="${myconf} --current_working_directory=${MY_B}"
	cd "${MY_B}"

	myconf="${myconf} --build=release fftw3tbx rstbx smtbx mmtbx clipper"
	einfo "configuring with ${python} ${myconf}"

	${EPREFIX}/usr/bin/python ${myconf} \
		|| die "configure failed"
}

src_compile() {
	local makeopts_exp

	cd "${MY_B}"

	makeopts_exp=${MAKEOPTS/j/j }
	makeopts_exp=${makeopts_exp%-l[0-9]*}

	source setpaths_all.sh

	einfo "compiling with libtbx.scons ${makeopts_exp}"
	libtbx.scons ${makeopts_exp} .|| die "make failed"
}

src_test(){
	source "${MY_B}"/setpaths_all.sh
	libtbx.python $(libtbx.show_dist_paths boost_adaptbx)/tests/tst_rational.py && \
	libtbx.python ${SCITBX_DIST}/run_tests.py ${MAKEOPTS_EXP} && \
	libtbx.python ${CCTBX_DIST}/run_tests.py  ${MAKEOPTS_EXP} \
	|| die "test failed"
}

src_install(){
	# This is what Bill Scott does in the fink package. Do we need this as well?
#	-e "s:prepend:append:g" \

	find cctbx_build/ -type f \( -name "*.py" -o -name "*sh" \) -exec \
	sed -e "s:${MY_S}:${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_sources:g" \
	    -e "s:${MY_B}:${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build:g"  \
	    -i '{}' \; || die "Fail to correct path"

	ebegin "removing unnessary files"
		rm -r "${S}"/cctbx_sources/scons || die "failed to remove uneeded scons"
		find "${S}" -type f -name "*conftest*" -exec rm -f '{}' \; || die "failed to remove uneeded *.o"
		find "${S}" -type f -name "*.o" -exec rm -f '{}' \; || die "failed to remove uneeded *.o"
		find "${S}" -type f -name "*.c" -exec rm -f '{}' \; || die "failed to remove uneeded *.c"
		find "${S}" -type f -name "*.cpp" -exec rm -f '{}' \; || die "failed to remove uneeded *.cpp"
		find "${S}" -type f -name "*.pyc" -exec rm -f '{}' \; || die "failed to remove uneeded *.pyc"
	eend

	insinto /usr/$(get_libdir)/${PN}
	doins -r cctbx_sources cctbx_build || die

# fperms cannot handle wildcards
	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/*sh && \
	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/lib/* && \
	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/scitbx/array_family/* && \
	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/scitbx/serialization/* && \
	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/scitbx/error/* && \
	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/scitbx/fftpack/timing/* && \
	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/scitbx/lbfgs/* && \
	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/chiltbx/handle_test && \
	chmod 775 "${D}"/usr/$(get_libdir)/${PN}/cctbx_build/bin/* || \
	die

	insinto /etc/profile.d/
	newins "${MY_B}"/setpaths.sh 30cctbx.sh || die
	newins "${MY_B}"/setpaths.csh 30cctbx.csh || die

	cat >> "${T}"/30cctbx <<- EOF
	LDPATH="${EPREFIX}/usr/$(get_libdir)/${PN}/cctbx_build/lib"
	EOF

	doenvd "${T}"/30cctbx || die
}

pkg_postinst () {
	python_need_rebuild
	python_mod_optimize /usr/$(get_libdir)/${PN}/cctbx_sources
}

pkg_postrm () {
	python_mod_cleanup /usr/$(get_libdir)/${PN}/cctbx_sources
}

check_use() {
	for var in $@; do
		if use ${var}; then
			printf -v "USE_$var" True
		else
			printf -v "USE_$var" False
		fi
	shift
	done
}