Computational Crystallography Toolbox

Initially written by dberkholz
Package-Manager: portage-2.2_rc62/cvs/Linux x86_64

4 files changed, 241 insertions, 0 deletions

diff --git a/sci-libs/cctbx/ChangeLog b/sci-libs/cctbx/ChangeLog
new file mode 100644
index 000000000000..29e98d81c5a8
--- /dev/null
+++ b/sci-libs/cctbx/ChangeLog
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+# 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@gentoo.org>
+  +cctbx-2009.11.01.0123.ebuild, +metadata.xml:
+  New ebuild, initialy written by dberkholz
+
diff --git a/sci-libs/cctbx/Manifest b/sci-libs/cctbx/Manifest
new file mode 100644
index 000000000000..fffa4885a3ef
--- /dev/null
+++ b/sci-libs/cctbx/Manifest
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+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+DIST cctbx-2009.11.01.0123.tar.gz 14604079 RMD160 77cc84d4b9e35e7a87f807d8669efb939b2e82ce SHA1 7db71a62786b82f47999919a9411938b123d5b4d SHA256 31e7f79424360f963c6eae528a9d289db4b53c1f7fe4aa9de71201e9d14bc5af
+EBUILD cctbx-2009.11.01.0123.ebuild 5809 RMD160 dce578bd21bd49bcc205df65457d97066ac44955 SHA1 83245e05e828c408ef15172827d364a647569541 SHA256 96c81826c7aa8bf7f487d913d1c8414be1cfe7451f40e6ab60df72cb7764a980
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+MISC metadata.xml 767 RMD160 c2fc3bcc534e407e6066ee98beb6878d78a0f6e9 SHA1 a653677e160cf0726e1747b06b5d0cd95e51ac5f SHA256 ef36fc1a1d5d657ba67f88b303f08eef5a1a814d22a2091c07616dc16928e3fa
+-----BEGIN PGP SIGNATURE-----
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+-----END PGP SIGNATURE-----
diff --git a/sci-libs/cctbx/cctbx-2009.11.01.0123.ebuild b/sci-libs/cctbx/cctbx-2009.11.01.0123.ebuild
new file mode 100644
index 000000000000..096c0892f755
--- /dev/null
+++ b/sci-libs/cctbx/cctbx-2009.11.01.0123.ebuild
@@ -0,0 +1,199 @@
+# 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
+}
diff --git a/sci-libs/cctbx/metadata.xml b/sci-libs/cctbx/metadata.xml
new file mode 100644
index 000000000000..4f0ff73f95b4
--- /dev/null
+++ b/sci-libs/cctbx/metadata.xml
@@ -0,0 +1,18 @@
+<?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@gentoo.org</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>