4 files changed, 262 insertions, 1 deletions
diff --git a/sci-chemistry/cns/ChangeLog b/sci-chemistry/cns/ChangeLog
index 4f872ee93f4a..88656a204e5f 100644
--- a/sci-chemistry/cns/ChangeLog
+++ b/sci-chemistry/cns/ChangeLog
@@ -1,6 +1,17 @@
 # ChangeLog for sci-chemistry/cns
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.20 2010/03/07 09:54:15 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.21 2010/03/20 13:33:12 jlec Exp $
+
+  20 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  +files/1.2.1-aria2.3.patch, +cns-1.2.1-r3.ebuild,
+  +files/1.2.1-parallel.patch:
+  Included new version of aria
+
+*cns-1.2.1-r3 (20 Mar 2010)
+
+  20 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  +files/1.2.1-aria2.3.patch, +cns-1.2.1-r3.ebuild:
+  Bump to new aria-2.3
 
   07 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org> cns-1.2.1-r2.ebuild:
   Moved to EAPI=3 for PREFIX support, keyworded for *-linux, tested by me
diff --git a/sci-chemistry/cns/cns-1.2.1-r3.ebuild b/sci-chemistry/cns/cns-1.2.1-r3.ebuild
new file mode 100644
index 000000000000..e6cbce88bf7a
--- /dev/null
+++ b/sci-chemistry/cns/cns-1.2.1-r3.ebuild
@@ -0,0 +1,211 @@
+# Copyright 1999-2010 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-r3.ebuild,v 1.1 2010/03/20 13:33:12 jlec Exp $
+
+EAPI="3"
+
+inherit eutils fortran 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="${MY_P}_all-mp.tar.gz
+	aria? ( aria2.3.1.tar.gz )"
+
+SLOT="0"
+LICENSE="cns"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="aria openmp"
+
+RDEPEND="app-shells/tcsh
+	!app-text/dos2unix"
+DEPEND="${RDEPEND}"
+PDEPEND="aria? ( ~sci-chemistry/aria-2.3.1 )"
+
+RESTRICT="fetch"
+S="${WORKDIR}/${MY_P}"
+
+FORTRAN="g77 gfortran"
+
+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}."
+}
+
+pkg_setup() {
+	fortran_pkg_setup
+
+	if [[ $(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 "Switch CC to an OpenMP capable compiler"
+	fi
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-gentoo.patch
+	epatch "${FILESDIR}"/${PV}-parallel.patch
+
+	pushd "${WORKDIR}"/aria* >& /dev/null
+	if use aria; then
+		# Update the cns sources in aria for version 1.2.1
+		epatch "${FILESDIR}"/1.2.1-aria2.3.patch
+
+		# Update the code with aria specific things
+		cp -rf cns/src/* "${S}"/source/
+	fi
+	popd >& /dev/null
+
+	use openmp && append-fflags -fopenmp
+
+	# the code uses Intel-compiler-specific directives
+	epatch "${FILESDIR}"/${PV}-allow-gcc-openmp.patch
+
+	use openmp && OMPLIB="-lgomp"
+
+	use amd64 && \
+		append-cflags "-DINTEGER='long long int'" && \
+		append-fflags -fdefault-integer-8
+
+	# Set up location for the build directory
+	# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
+	cp "${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 [[ ${FORTRANC} = g77 ]]; then
+		GLOBALS="-fno-globals"
+		MALIGN='\$(CNS_MALIGN_I86)'
+	fi
+
+	# Set up the compiler to use
+	pushd instlib/machine/unsupported/g77-unix 2>/dev/null
+	ln -s Makefile.header Makefile.header.${FORTRANC} || 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="$(tc-getCC)" \
+		F77="${FORTRANC}" \
+		LD="${FORTRANC}" \
+		CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
+		LDFLAGS="${LDFLAGS}" \
+		F77OPT="${FFLAGS:- -O2} ${MALIGN}" \
+		F77STD="${GLOBALS}" \
+		OMPLIB="${OMPLIB}" \
+		g77install \
+		|| 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() {
+	# 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/${PF}:g" \
+		-e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \
+		-e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \
+		-e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \
+		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
+		"${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/${PF}:g" \
+		-e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \
+		-e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \
+		-e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \
+		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
+		"${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}"/*_g77/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 "${S}"/*_g77/utils/Makefile
+
+	dobin "${S}"/*_g77/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 "${T}"/cns_solve_env_sh cns_solve_env.sh || die
+
+	dohtml \
+		-A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \
+		-f all_cns_info_template,omac,def \
+		-r doc/html/* || die
+}
+
+pkg_info() {
+	if use openmp; then
+		elog "Set OMP_NUM_THREADS to the number of threads you want."
+		elog "If you get segfaults on large structures, set the GOMP_STACKSIZE"
+		elog "variable if using gcc (16384 should be good)."
+	fi
+}
+
+pkg_postinst() {
+	pkg_info
+}
diff --git a/sci-chemistry/cns/files/1.2.1-aria2.3.patch b/sci-chemistry/cns/files/1.2.1-aria2.3.patch
new file mode 100644
index 000000000000..8c6939d8eb92
--- /dev/null
+++ b/sci-chemistry/cns/files/1.2.1-aria2.3.patch
@@ -0,0 +1,22 @@
+diff --git a/cns/src/cns.f b/cns/src/cns.f
+index a3c2cbe..51a34f8 100644
+--- a/cns/src/cns.f
++++ b/cns/src/cns.f
+@@ -470,6 +470,7 @@ C local
+       INTEGER      HNLEN, TMP, PTRSZ, STLEN
+       CHARACTER*(1) CNSPTMP
+       CHARACTER*(4) ST
++!$    integer omp_get_max_threads
+ C
+ C write header
+       WRITE(6,'(10X,A)')
+@@ -526,6 +527,9 @@ C
+       WRITE(6,'(10X,7A)')
+      & ' Running on machine: ',HOSTNM(1:HNLEN),
+      & ' (',SYSNM(1:TMP),',',ST(1:STLEN),'-bit)'
++!$    write(6,'(31x,a,i3,a)') 'with',omp_get_max_threads(),
++!$   &  ' threads'
++!$C (to change use setenv OMP_NUM_THREADS x)
+ C
+       CALL GETNAM(USERNM,12,TMP)
+       WRITE(6,'(10X,2A)')
diff --git a/sci-chemistry/cns/files/1.2.1-parallel.patch b/sci-chemistry/cns/files/1.2.1-parallel.patch
new file mode 100644
index 000000000000..dfaa40021d66
--- /dev/null
+++ b/sci-chemistry/cns/files/1.2.1-parallel.patch
@@ -0,0 +1,17 @@
+diff --git a/instlib/source/Makefile.proto b/instlib/source/Makefile.proto
+index 0d0dd3e..ae9e422 100644
+--- a/instlib/source/Makefile.proto
++++ b/instlib/source/Makefile.proto
+@@ -19,9 +19,9 @@ DEPENDS = $(OBJS) dmemory.o machine_c.o
+ 
+ # the default is to make the cns executable
+ cns_solve:
+-	@ make -k printflags       F77BUG="$(debug)" DEBUG="$(debug)"
+-	@ make -k ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)"
+-	@ make -k exepurge
++	@ make printflags       F77BUG="$(debug)" DEBUG="$(debug)"
++	@ make ${MAKEOPTS} ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)"
++	@ make exepurge
+ 
+ # rule for the fortran routines
+ $(OBJS):