[gentoo-commits] proj/sci:ccp4 commit in: sci-chemistry/phaser/

[gentoo-commits] proj/sci:ccp4 commit in: sci-chemistry/phaser/

[Justin Lecher]

commit:     f7a40496bd93e6d5d52fd0acf4cf764f40eb9e32
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 16 14:52:31 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 16 14:52:31 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f7a40496

BUmp but evuild is still broken
Build system changed
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 sci-chemistry/phaser/phaser-2.1.4.ebuild           | 114 ---------------------
 ...{phaser-2.1.4-r1.ebuild => phaser-2.5.0.ebuild} |  31 +++---
 2 files changed, 17 insertions(+), 128 deletions(-)

diff --git a/sci-chemistry/phaser/phaser-2.1.4.ebuild b/sci-chemistry/phaser/phaser-2.1.4.ebuild
deleted file mode 100644
index 73f18f4..0000000
--- a/sci-chemistry/phaser/phaser-2.1.4.ebuild
+++ /dev/null
@@ -1,114 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit eutils python toolchain-funcs
-
-DESCRIPTION="Phasing macromolecular crystal structures with maximum likelihood methods"
-SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/6.1.1/${P}-cctbx-src.tar.gz"
-HOMEPAGE="http://www-structmed.cimr.cam.ac.uk/phaser/"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="~x86 ~amd64"
-IUSE="openmp"
-
-DEPEND="dev-util/scons"
-RDEPEND="sci-libs/cctbx"
-
-S="${WORKDIR}"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	rm -rf lib/*
-	cp -rf $CCP4/lib/cctbx/cctbx_sources/libtbx "${WORKDIR}"
-
-	mkdir -p "${WORKDIR}"/scons/src/
-	ln -sf /usr/$(get_libdir)/scons-1.2.0 "${WORKDIR}"/scons/src/engine || die
-
-	epatch "${FILESDIR}"/${PV}-sadf.patch
-}
-
-src_compile(){
-	python_version
-
-	local MYCONF
-	local MAKEOPTS_EXP
-	local OPTS
-	local OPTSLD
-
-	MYCONF="${S}/libtbx/configure.py"
-
-	MYCONF="${MYCONF} --repository ${S}/ccp4-6.1.1/src/${PN}/source --repository /usr/$(get_libdir)/cctbx/cctbx_sources/ \
-	--build=release ccp4io=${CCP4}/$(get_libdir)/cctbx/cctbx_sources/ccp4io/"
-
-	MAKEOPTS_EXP=${MAKEOPTS/j/j }
-	MAKEOPTS_EXP=${MAKEOPTS_EXP%-l[0-9]*}
-
-	# 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:opts = \[.*\]$:opts = \[${OPTS}\]:g" \
-	"${S}"/libtbx/SConscript
-
-	# Get LDFLAGS in format suitable for substitition into SConscript
-	for i in ${LDFLAGS}; do
-	OPTSLD="${OPTSLD} \"${i}\","
-	done
-
-	# Fix LDFLAGS which should be as-needed ready
-	sed -i \
-	-e "s:env_etc.shlinkflags .* \"-shared\":env_etc.shlinkflags = \[ ${OPTSLD} \"-shared\":g" \
-	"${S}"/libtbx/SConscript
-
-	# Get compiler in the right way
-	COMPILER=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
-	MYCONF="${MYCONF} --compiler=${COMPILER}"
-
-	# 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} ${USE_threads} --scan-boost"
-
-	MYCONF="${MYCONF} phaser"
-	einfo "configuring with ${python} ${MYCONF}"
-
-	${python} ${MYCONF} \
-	|| die "configure failed"
-
-	source setpaths_all.sh
-
-	einfo "compiling with libtbx.scons ${MAKEOPTS_EXP}"
-	libtbx.scons ${MAKEOPTS_EXP} .|| die "make failed"
-}
-
-src_install() {
-	rm lib/libboost*
-	dolib.so lib/*.so || die
-	dolib.a lib/*.a || die
-	dobin exe/phaser || die
-}
-
-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-chemistry/phaser/phaser-2.1.4-r1.ebuild b/sci-chemistry/phaser/phaser-2.5.0.ebuild
similarity index 86%
rename from sci-chemistry/phaser/phaser-2.1.4-r1.ebuild
rename to sci-chemistry/phaser/phaser-2.5.0.ebuild
index 2f8cafa..d277cf9 100644
--- a/sci-chemistry/phaser/phaser-2.1.4-r1.ebuild
+++ b/sci-chemistry/phaser/phaser-2.5.0.ebuild
@@ -2,27 +2,31 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI="2"
+EAPI=5
 
-inherit base flag-o-matic python
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit base flag-o-matic python-any-r1
+
+CCP4_VERSION="6.3.0"
+CCP4_TAG="ccp4-${CCP4_VERSION}"
 
 DESCRIPTION="A program for phasing macromolecular crystal structures"
 HOMEPAGE="http://www-structmed.cimr.cam.ac.uk/phaser"
-SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/6.1.1/${PN}-${PV}-cctbx-src.tar.gz"
+SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/${CCP4_VERSION}/${CCP4_TAG}-${PN}-cctbx-src.tar.gz -> ${P}-${CCP4_TAG}.tar.gz"
 
 LICENSE="|| ( phaser phaser-com ccp4 )"
-
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-
 IUSE="openmp"
-RDEPEND=""
+
+RDEPEND="${PYTHON_DEPS}"
 DEPEND="${RDEPEND}
-		  app-shells/tcsh"
+	app-shells/tcsh"
 
-S="${WORKDIR}"/ccp4-6.1.1
+S="${WORKDIR}"/${CCP4_TAG}
 
-PATCHES=(
+_PATCHES=(
 	"${FILESDIR}"/phaser-2.1.4-chmod.patch
 	)
 
@@ -80,8 +84,7 @@ src_compile() {
 	# frequently.  Perhaps better to link statically to the bundled
 	# cctbx.
 	einfo "Configuring phaser components"
-	python_version
-	${python} "libtbx/configure.py" \
+	${PYTHON} "libtbx/configure.py" \
 		--build=release \
 		--compiler=${compiler} \
 		--repository="${S}"/src/${PN}/source \
@@ -113,7 +116,7 @@ src_compile() {
 #	einfo "Creating env.sh"
 	cat >> "${T}"/53${PN} <<- EOF
 
-	PHASER="/usr/bin"
+	PHASER="${EPREFIX}/usr/bin"
 	PHASER_ENVIRONMENT="1"
 	PHASER_MTYPE="${mtype}"
 	PHASER_MVERSION="${mversion}"
@@ -127,8 +130,8 @@ src_compile() {
 # cctbx ebuild tests.
 src_test() {
 	cd "${S}//build" && \
-	source setpaths.sh && \
-	csh ./run_tests.csh || die "run_test.csh failed"
+		source setpaths.sh && \
+		csh ./run_tests.csh || die "run_test.csh failed"
 }
 
 # This is a bit thin.  Maybe install other files from the distribution