sci-chemistry/cns: Stabilize; drop pre EAPI=5 ebuilds, #478584; add longdescription, #511734

(Portage version: 2.2.10/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

4 files changed, 16 insertions, 467 deletions

diff --git a/sci-chemistry/cns/ChangeLog b/sci-chemistry/cns/ChangeLog
index 8709f966b04f..d900e61ea061 100644
--- a/sci-chemistry/cns/ChangeLog
+++ b/sci-chemistry/cns/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-chemistry/cns
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.54 2013/10/09 14:33:46 jlec Exp $
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.55 2014/06/08 08:27:31 jlec Exp $
+
+  08 Jun 2014; Justin Lecher <jlec@gentoo.org> -cns-1.2.1-r7.ebuild,
+  -cns-1.3_p7.ebuild, metadata.xml:
+  Stabilize; drop pre EAPI=5 ebuilds, #478584; add longdescription, #511734
 
 *cns-1.3_p7-r1 (09 Oct 2013)
 *cns-1.2.1-r8 (09 Oct 2013)
diff --git a/sci-chemistry/cns/cns-1.2.1-r7.ebuild b/sci-chemistry/cns/cns-1.2.1-r7.ebuild
deleted file mode 100644
index b01e7cccc969..000000000000
--- a/sci-chemistry/cns/cns-1.2.1-r7.ebuild
+++ /dev/null
@@ -1,241 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.2.1-r7.ebuild,v 1.7 2012/11/27 13:17:37 jlec Exp $
-
-EAPI=3
-
-inherit eutils fortran-2 toolchain-funcs versionator flag-o-matic
-
-MY_PN="${PN}_solve"
-MY_PV="$(delete_version_separator 2)"
-MY_P="${MY_PN}_${MY_PV}"
-
-DESCRIPTION="Crystallography and NMR System"
-HOMEPAGE="http://cns.csb.yale.edu/"
-SRC_URI="
-	${MY_P}_all-mp.tar.gz
-	aria? ( aria2.3.2.tar.gz )"
-
-SLOT="0"
-LICENSE="cns"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE="aria openmp"
-
-RDEPEND="app-shells/tcsh"
-DEPEND="${RDEPEND}"
-
-FORTRAN_NEED_OPENMP=1
-
-S="${WORKDIR}/${MY_P}"
-
-RESTRICT="fetch test"
-
-pkg_nofetch() {
-	elog "Fill out the form at http://cns.csb.yale.edu/cns_request/"
-	use aria && elog "and http://aria.pasteur.fr/"
-	elog "and place these files:"
-	elog ${A}
-	elog "in ${DISTDIR}."
-}
-
-get_fcomp() {
-	case $(tc-getFC) in
-		*gfortran* )
-			FCOMP="gfortran" ;;
-		ifort )
-			FCOMP="ifc" ;;
-		* )
-			FCOMP=$(tc-getFC) ;;
-	esac
-}
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	get_fcomp
-}
-
-get_bitness() {
-	echo > "${T}"/test.c
-	$(tc-getCC) ${CFLAGS} -c "${T}"/test.c -o "${T}"/test.o
-	case $(file "${T}"/test.o) in
-		*64-bit*|*ppc64*|*x86_64*) export _bitness="64";;
-		*32-bit*|*ppc*|*i386*) export _bitness="32";;
-		*) die "Failed to detect whether your arch is 64bits or 32bits, disable distcc if you're using it, please";;
-	esac
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PV}-gentoo.patch \
-		"${FILESDIR}"/${PV}-parallel.patch
-
-	get_bitness
-
-	if use aria; then
-	pushd "${WORKDIR}"/aria* >& /dev/null
-		# Update the cns sources in aria for version 1.2.1
-		epatch "${FILESDIR}"/1.2.1-aria2.3.patch
-
-		# Update the code with aria specific things
-		cp -rf cns/src/* "${S}"/source/
-	popd >& /dev/null
-	fi
-
-	# the code uses Intel-compiler-specific directives
-	if [[ $(tc-getFC) =~ gfortran ]]; then
-		epatch "${FILESDIR}"/${PV}-allow-gcc-openmp.patch
-		use openmp && \
-			append-flags -fopenmp && append-ldflags -fopenmp
-		COMP="gfortran"
-		[[ ${_bitness} == 64 ]] && \
-			append-fflags -fdefault-integer-8
-	elif [[ $(tc-getFC) == if* ]]; then
-		epatch "${FILESDIR}"/${PV}-ifort.patch
-		use openmp && \
-			append-flags -openmp && append-ldflags -openmp
-		COMP="ifort"
-		[[ ${_bitness} == 64 ]] && append-fflags -i8
-	fi
-
-	[[ ${_bitness} == 64 ]] && \
-		append-cflags "-DINTEGER='long long int'"
-
-	# Set up location for the build directory
-	# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
-	cp "${FILESDIR}"/cns_solve_env_sh "${T}"/
-	sed -i \
-		-e "s:_CNSsolve_location_:${S}:g" \
-		-e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \
-		"${S}"/cns_solve_env
-	sed -i \
-		-e "s:_CNSsolve_location_:${S}:g" \
-		-e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \
-		"${T}"/cns_solve_env_sh
-
-	einfo "Fixing shebangs..."
-	find "${S}" -type f \
-		-exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' \; || die
-}
-
-src_compile() {
-	local GLOBALS
-	local MALIGN
-	if [[ $(tc-getFC) =~ g77 ]]; then
-		GLOBALS="-fno-globals"
-		MALIGN='\$(CNS_MALIGN_I86)'
-	fi
-
-	# Set up the compiler to use
-	pushd instlib/machine/unsupported/g77-unix 2>/dev/null
-	ln -s Makefile.header Makefile.header.${FCOMP} || die
-	popd 2>/dev/null
-
-	# make install really means build, since it's expected to be used in-place
-	# -j1 doesn't mean we do no respect MAKEOPTS!
-	emake -j1 \
-		CC="$(tc-getCC)" \
-		F77=$(tc-getFC) \
-		LD=$(tc-getFC) \
-		CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
-		LDFLAGS="${LDFLAGS}" \
-		F77OPT="${FCFLAGS} ${MALIGN}" \
-		F77STD="${GLOBALS}" \
-		OMPLIB="${OMPLIB}" \
-		compiler="${COMP}" \
-		install \
-		|| die "emake failed"
-}
-
-src_test() {
-	# We need to force on g77 manually, because we can't get aliases working
-	# when we source in a -c
-	einfo "Running tests ..."
-	csh -c \
-		"export CNS_G77=ON; source ${S}/cns_solve_env; make run_tests" \
-		|| die "tests failed"
-	einfo "Displaying test results ..."
-	cat "${S}"/*_g77/test/*.diff-test
-}
-
-src_install() {
-	# Install to locations resembling FHS
-	sed -i \
-		-e "s:${S}:usr:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_ROOT ${EPREFIX}/usr:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DATA \$CNS_ROOT/share/cns:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DOC \$CNS_ROOT/share/doc/${PF}:g" \
-		-e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \
-		-e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \
-		-e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \
-		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
-		-e "/^g77on/d" \
-		"${S}"/cns_solve_env
-	# I don't entirely understand why the sh version requires a leading /
-	# for CNS_SOLVE and CNS_ROOT, but it does
-	sed -i \
-		-e "s:${S}:/usr:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_ROOT=${EPREFIX}/usr:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DATA=\$CNS_ROOT/share/cns:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DOC=\$CNS_ROOT/share/doc/${PF}:g" \
-		-e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \
-		-e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \
-		-e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \
-		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
-		-e "/^g77on/d" \
-		-e "/^g77off/d" \
-		"${T}"/cns_solve_env_sh
-
-	# Get rid of setup stuff we don't need in the installed script
-	sed -i \
-		-e "83,$ d" \
-		-e "37,46 d" \
-		"${S}"/cns_solve_env
-	sed -i \
-		-e "84,$ d" \
-		-e "39,50 d" \
-		"${T}"/cns_solve_env_sh
-
-	newbin "${S}"/*linux*/bin/cns_solve* cns_solve \
-		|| die "install cns_solve failed"
-
-	# Can be run by either cns_solve or cns
-	dosym cns_solve /usr/bin/cns
-
-	# Don't want to install this
-	rm -f "${S}"/*linux*/utils/Makefile
-
-	dobin "${S}"/*linux*/utils/* || die "install utils failed"
-
-	sed -i \
-		-e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \
-		"${S}"/bin/cns_web || die
-
-	dobin "${S}"/bin/cns_{edit,header,transfer,web} || die "install bin failed"
-
-	insinto /usr/share/cns
-	doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib || die
-	doins "${S}"/bin/cns_info || die
-
-	insinto /etc/profile.d
-	newins "${S}"/cns_solve_env cns_solve_env.csh || die
-	newins "${T}"/cns_solve_env_sh cns_solve_env.sh || die
-
-	dohtml \
-		-A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \
-		-f all_cns_info_template,omac,def \
-		-r doc/html/* || die
-	# Conflits with app-text/dos2unix
-	rm -f "${D}"/usr/bin/dos2unix
-}
-
-pkg_info() {
-	if use openmp; then
-		elog "Set OMP_NUM_THREADS to the number of threads you want."
-		elog "If you get segfaults on large structures, set the GOMP_STACKSIZE"
-		elog "variable if using gcc (16384 should be good)."
-	fi
-}
-
-pkg_postinst() {
-	pkg_info
-}
diff --git a/sci-chemistry/cns/cns-1.3_p7.ebuild b/sci-chemistry/cns/cns-1.3_p7.ebuild
deleted file mode 100644
index 0caa1251ad4c..000000000000
--- a/sci-chemistry/cns/cns-1.3_p7.ebuild
+++ /dev/null
@@ -1,224 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.3_p7.ebuild,v 1.3 2012/11/27 13:17:37 jlec Exp $
-
-EAPI=3
-
-inherit eutils fortran-2 toolchain-funcs versionator flag-o-matic
-
-MY_PN="${PN}_solve"
-MY_PV="$(delete_version_separator 2)"
-MY_P="${MY_PN}_${MY_PV}"
-
-DESCRIPTION="Crystallography and NMR System"
-HOMEPAGE="http://cns.csb.yale.edu/"
-SRC_URI="
-	${MY_P/p7}_all.tar.gz
-	aria? ( aria2.3.1.tar.gz )"
-
-SLOT="0"
-LICENSE="cns"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="aria openmp"
-
-RDEPEND="app-shells/tcsh"
-DEPEND="${RDEPEND}"
-
-FORTRAN_NEED_OPENMP=1
-
-S="${WORKDIR}/${MY_P/p7}"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	elog "Fill out the form at http://cns.csb.yale.edu/cns_request/"
-	use aria && elog "and http://aria.pasteur.fr/"
-	elog "and place these files:"
-	elog ${A}
-	elog "in ${DISTDIR}."
-}
-
-get_fcomp() {
-	case $(tc-getFC) in
-		*gfortran* )
-			FCOMP="gfortran" ;;
-		ifort )
-			FCOMP="ifc" ;;
-		* )
-			FCOMP=$(tc-getFC) ;;
-	esac
-}
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	get_fcomp
-}
-
-get_bitness() {
-	echo > "${T}"/test.c
-	$(tc-getCC) ${CFLAGS} -c "${T}"/test.c -o "${T}"/test.o
-	case $(file "${T}"/test.o) in
-		*64-bit*|*ppc64*|*x86_64*) export _bitness="64";;
-		*32-bit*|*ppc*|*i386*) export _bitness="32";;
-		*) die "Failed to detect whether your arch is 64bits or 32bits, disable distcc if you're using it, please";;
-	esac
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PV}-gentoo.patch \
-		"${FILESDIR}"/${PV}-delete.patch
-
-	get_bitness
-
-	if use aria; then
-		pushd "${WORKDIR}"/aria* >& /dev/null
-			# Update the cns sources in aria for version 1.2.1
-			epatch "${FILESDIR}"/1.2.1-aria2.3.patch
-
-			# Update the code with aria specific things
-			cp -rf cns/src/* "${S}"/source/
-		popd >& /dev/null
-	fi
-
-	# the code uses Intel-compiler-specific directives
-	if [[ $(tc-getFC) =~ gfortran ]]; then
-		use openmp && \
-			append-flags -fopenmp && append-ldflags -fopenmp
-		COMP="gfortran"
-		[[ ${_bitness} == 64 ]] && \
-			append-fflags -fdefault-integer-8
-	elif [[ $(tc-getFC) == if* ]]; then
-		use openmp && \
-			append-flags -openmp && append-ldflags -openmp
-		COMP="ifort"
-		[[ ${_bitness} == 64 ]] && append-fflags -i8
-	fi
-
-	[[ ${_bitness} == 64 ]] && \
-		append-cflags "-DINTEGER='long long int'"
-
-	# Set up location for the build directory
-	# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
-	cp "${FILESDIR}"/cns_solve_env_sh-${PV} "${T}"/cns_solve_env_sh || die
-	sed -i \
-		-e "s:_CNSsolve_location_:${S}:g" \
-		-e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \
-		"${S}"/cns_solve_env || die
-	sed -i \
-		-e "s:_CNSsolve_location_:${S}:g" \
-		-e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \
-		-e "s:setenv OMP_STACKSIZE 256m:export OMP_STACKSIZE= 256m:g" \
-		-e "s:limit:ulimit:g" \
-		"${T}"/cns_solve_env_sh || die
-
-	ebegin "Fixing shebangs..."
-		find "${S}" -type f \
-			-exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' \; || die
-		find . -name "Makefile*" \
-			-exec \
-				sed \
-					-e "s:^SHELL=/bin/sh:SHELL=${EPREFIX}/bin/sh:g" \
-					-e "s:/bin/ls:ls:g" \
-					-e "s:/bin/rm:rm:g" \
-					-i '{}' \; || die
-	eend
-}
-
-src_compile() {
-	local GLOBALS
-	local MALIGN
-
-	# Set up the compiler to use
-	pushd instlib/machine/unsupported/g77-unix 2>/dev/null
-	ln -s Makefile.header Makefile.header.${FCOMP} || die
-	popd 2>/dev/null
-
-	# make install really means build, since it's expected to be used in-place
-	# -j1 doesn't mean we do no respect MAKEOPTS!
-	emake -j1 \
-		CC="$(tc-getCC)" \
-		CXX="$(tc-getCXX)" \
-		F77=$(tc-getFC) \
-		LD=$(tc-getFC) \
-		CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
-		CXXFLAGS="${CXXFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
-		LDFLAGS="${LDFLAGS}" \
-		F77OPT="${FCFLAGS} ${MALIGN}" \
-		F77STD="${GLOBALS}" \
-		OMPLIB="${OMPLIB}" \
-		compiler="${COMP}" \
-		install \
-		|| die "emake failed"
-}
-
-src_test() {
-	# We need to force on g77 manually, because we can't get aliases working
-	# when we source in a -c
-	einfo "Running tests ..."
-	sh -c \
-		"export CNS_G77=ON; source ${T}/cns_solve_env_sh; make run_tests" \
-		|| die "tests failed"
-	einfo "Displaying test results ..."
-	cat "${S}"/*_g77/test/*.diff-test
-}
-
-src_install() {
-	cat >> "${T}"/66cns <<- EOF
-	CNS_SOLVE="${EPREFIX}/usr"
-	CNS_ROOT="${EPREFIX}/usr"
-	CNS_DATA="${EPREFIX}/usr/share/cns"
-	CNS_DOC="${EPREFIX}/usr/share/doc/cns-1.3"
-	CNS_LIB="${EPREFIX}/usr/share/cns/libraries"
-	CNS_MODULE="${EPREFIX}/usr/share/cns/modules"
-	CNS_TOPPAR="${EPREFIX}/usr/share/cns/libraries/toppar"
-	CNS_CONFDB="${EPREFIX}/usr/share/cns/libraries/confdb"
-	CNS_XTALLIB="${EPREFIX}/usr/share/cns/libraries/xtal"
-	CNS_NMRLIB="${EPREFIX}/usr/share/cns/libraries/nmr"
-	CNS_XRAYLIB="${EPREFIX}/usr/share/cns/libraries/xray"
-	CNS_XTALMODULE="${EPREFIX}/usr/share/cns/modules/xtal"
-	CNS_NMRMODULE="${EPREFIX}/usr/share/cns/modules/nmr"
-	CNS_HELPLIB="${EPREFIX}/usr/share/cns/helplib"
-	EOF
-
-	doenvd "${T}"/66cns || die
-
-	# Don't want to install this
-	rm -f "${S}"/*linux*/utils/Makefile
-
-	sed -i \
-		-e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \
-		"${S}"/bin/cns_web || die
-
-	newbin "${S}"/*linux*/bin/cns_solve* cns_solve \
-		|| die "install cns_solve failed"
-
-	# Can be run by either cns_solve or cns
-	dosym cns_solve /usr/bin/cns
-
-	dobin \
-		"${S}"/*linux*/utils/* \
-		"${S}"/bin/cns_{edit,header,import_cif,transfer,web} || die "install bin failed"
-
-	insinto /usr/share/cns
-	doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib "${S}"/bin/cns_info || die
-
-	dohtml \
-		-A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \
-		-f all_cns_info_template,omac,def \
-		-r doc/html/* || die
-	# Conflits with app-text/dos2unix
-	rm -f "${D}"/usr/bin/dos2unix || die
-}
-
-pkg_info() {
-	if use openmp; then
-		elog "Set OMP_NUM_THREADS to the number of threads you want."
-		elog "If you get segfaults on large structures, set the GOMP_STACKSIZE"
-		elog "variable if using gcc (16384 should be good)."
-	fi
-}
-
-pkg_postinst() {
-	pkg_info
-}
diff --git a/sci-chemistry/cns/metadata.xml b/sci-chemistry/cns/metadata.xml
index 3102a32e4dd1..a9cb92ec3f79 100644
--- a/sci-chemistry/cns/metadata.xml
+++ b/sci-chemistry/cns/metadata.xml
@@ -8,4 +8,14 @@
   <use>
     <flag name="aria"> Support patch for sci-chemistry/aria</flag>
   </use>
+  <longdescription>
+Crystallography and NMR System (CNS) is the result of an international
+collaborative effort among several research groups. The program has 
+been designed to provide a flexible multi-level hierachical approach for the
+most commonly used algorithms in macromolecular structure determination. 
+Highlights include heavy atom searching, experimental phasing (including 
+MAD and MIR), density modification, crystallographic refinement with maximum
+likelihood targets, and NMR structure calculation using NOEs, J-coupling, 
+chemical shift, and dipolar coupling data.
+</longdescription>
 </pkgmetadata>