Version Bump, tinker support removed

(Portage version: 2.2.0_alpha1/cvs/Linux x86_64)

7 files changed, 349 insertions, 13 deletions

diff --git a/sci-chemistry/apbs/ChangeLog b/sci-chemistry/apbs/ChangeLog
index 9cdb4283eaf1..e5ccc8e3b40e 100644
--- a/sci-chemistry/apbs/ChangeLog
+++ b/sci-chemistry/apbs/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/apbs
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.40 2010/07/09 16:09:03 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.41 2010/10/27 17:19:45 jlec Exp $
+
+*apbs-1.3 (27 Oct 2010)
+
+  27 Oct 2010; Justin Lecher <jlec@gentoo.org> apbs-1.2.1b-r4.ebuild,
+  +apbs-1.3.ebuild, +files/apbs-1.3-contrib.patch,
+  +files/apbs-1.3-link.patch, +files/apbs-1.3-openmp.patch,
+  +files/apbs-1.3-shared.patch:
+  Version Bump, tinker support removed
 
   09 Jul 2010; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Update metadata.xml
diff --git a/sci-chemistry/apbs/apbs-1.2.1b-r4.ebuild b/sci-chemistry/apbs/apbs-1.2.1b-r4.ebuild
index 34454d748029..151b2b833424 100644
--- a/sci-chemistry/apbs/apbs-1.2.1b-r4.ebuild
+++ b/sci-chemistry/apbs/apbs-1.2.1b-r4.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/apbs-1.2.1b-r4.ebuild,v 1.7 2010/07/09 13:36:47 fauli Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/apbs-1.2.1b-r4.ebuild,v 1.8 2010/10/27 17:19:45 jlec Exp $
 
 EAPI="3"
 
@@ -18,7 +18,7 @@ SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz"
 
 SLOT="0"
 LICENSE="BSD"
-IUSE="arpack doc mpi openmp python tinker tools"
+IUSE="arpack doc mpi openmp python tools"
 KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
 
 DEPEND="dev-libs/maloc[mpi=]
@@ -81,21 +81,15 @@ src_configure() {
 		--with-blas=-lblas \
 		$(use_enable openmp) \
 		$(use_enable python) \
-		$(use_enable tinker) \
 		$(use_enable tools) \
 		${myconf}
 }
 
 src_test() {
-	if use tinker; then
-		elog "tinker code make apbs to not reach the expected precission"
-		elog "https://sourceforge.net/tracker/?func=detail&aid=3019465&group_id=148472&atid=771704"
-	else
-		export LC_NUMERIC=C
-		cd examples && make test \
-			|| die "Tests failed"
-		grep -q 'FAILED' "${S}"/examples/TESTRESULTS.log && die "Tests failed"
-	fi
+	export LC_NUMERIC=C
+	cd examples && make test \
+		|| die "Tests failed"
+	grep -q 'FAILED' "${S}"/examples/TESTRESULTS.log && die "Tests failed"
 }
 
 src_install() {
diff --git a/sci-chemistry/apbs/apbs-1.3.ebuild b/sci-chemistry/apbs/apbs-1.3.ebuild
new file mode 100644
index 000000000000..20063b3c0a8e
--- /dev/null
+++ b/sci-chemistry/apbs/apbs-1.3.ebuild
@@ -0,0 +1,140 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/apbs-1.3.ebuild,v 1.1 2010/10/27 17:19:45 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="python? 2"
+FORTRAN="g77 gfortran ifc"
+
+inherit autotools eutils flag-o-matic fortran python versionator
+
+MY_PV=$(get_version_component_range 1-3)
+MY_P="${PN}-${MY_PV}"
+
+DESCRIPTION="Software for evaluating the electrostatic properties of nanoscale biomolecular systems"
+HOMEPAGE="http://apbs.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+IUSE="arpack doc mpi openmp python tools"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+
+DEPEND="dev-libs/maloc[mpi=]
+	virtual/blas
+	sys-libs/readline
+	arpack? ( sci-libs/arpack )
+	mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/"${MY_P}-source"
+
+pkg_setup() {
+	use python && python_set_active_version 2
+	fortran_pkg_setup
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-openmp.patch \
+		"${FILESDIR}"/${PN}-1.2.1b-install-fix.patch \
+		"${FILESDIR}"/${P}-contrib.patch \
+		"${FILESDIR}"/${P}-link.patch \
+		"${FILESDIR}"/${PN}-1.2.1b-autoconf-2.64.patch \
+		"${FILESDIR}"/${P}-shared.patch \
+		"${FILESDIR}"/${PN}-1.2.1b-multilib.patch \
+		"${FILESDIR}"/${PN}-1.2.1b-parallelbuild.patch
+	sed "s:GENTOO_PKG_NAME:${PN}:g" \
+		-i Makefile.am || die "Cannot correct package name"
+	# this test is broken
+	sed '/ion-pmf/d' -i examples/Makefile.am || die
+	eautoreconf
+	find . -name "._*" -exec rm -f '{}' \;
+}
+
+src_configure() {
+	local myconf="--docdir=${EPREFIX}/usr/share/doc/${PF}"
+	use arpack && myconf="${myconf} --with-arpack=${EPREFIX}/usr/$(get_libdir)"
+
+	# check which mpi version is installed and tell configure
+	if use mpi; then
+		export CC="${EPREFIX}/usr/bin/mpicc"
+		export F77="${EPREFIX}/usr/bin/mpif77"
+
+		if has_version sys-cluster/mpich; then
+	 		myconf="${myconf} --with-mpich=${EPREFIX}/usr"
+		elif has_version sys-cluster/mpich2; then
+			myconf="${myconf} --with-mpich2=${EPREFIX}/usr"
+		elif has_version sys-cluster/openmpi; then
+			myconf="${myconf} --with-openmpi=${EPREFIX}/usr"
+		fi
+	fi || die "Failed to select proper mpi implementation"
+
+	# we need the tools target for python
+	if use python && ! use tools; then
+		myconf="${myconf} --enable-tools"
+	fi
+
+	econf \
+		--disable-maloc-rebuild \
+		--enable-shared \
+		--with-blas=-lblas \
+		$(use_enable openmp) \
+		$(use_enable python) \
+		$(use_enable tools) \
+		${myconf}
+}
+
+src_test() {
+	export LC_NUMERIC=C
+	cd examples && make test \
+		|| die "Tests failed"
+	grep -q 'FAILED' "${S}"/examples/TESTRESULTS.log && die "Tests failed"
+}
+
+src_install() {
+	emake -j1 DESTDIR="${D}" install \
+		|| die "make install failed"
+
+	if use tools; then
+		mv tools/mesh/{,mesh-}analysis || die
+		dobin tools/mesh/* || die
+
+		if use arpack; then
+			dobin tools/arpack/* || die
+		fi
+
+		insinto /usr/share/${PN}
+		doins -r tools/conversion || die
+		doins -r tools/visualization/opendx || die
+
+		dobin tools/manip/{born,coulomb} || die
+
+		doins -r tools/matlab || die
+	fi
+
+	insinto $(python_get_sitedir)/${PN}
+	doins tools/manip/*.py || die
+
+	if use python && ! use mpi; then
+		insinto $(python_get_sitedir)/${PN}
+		doins tools/python/{*.py,*.pqr,*.so} || die
+		doins tools/python/*/{*.py,*.so} || die
+	fi
+
+	dodoc AUTHORS INSTALL README NEWS ChangeLog \
+		|| die "Failed to install docs"
+
+	if use doc; then
+		dohtml -r doc/* || die "Failed to install html docs"
+	fi
+}
+
+pkg_postinst() {
+	python_mod_optimize ${PN}
+}
+
+pkg_postrm() {
+	python_mod_cleanup ${PN}
+}
diff --git a/sci-chemistry/apbs/files/apbs-1.3-contrib.patch b/sci-chemistry/apbs/files/apbs-1.3-contrib.patch
new file mode 100644
index 000000000000..9971f032dcbc
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.3-contrib.patch
@@ -0,0 +1,12 @@
+diff --git a/contrib/Makefile.am b/contrib/Makefile.am
+index bddb563..6a882ca 100644
+--- a/contrib/Makefile.am
++++ b/contrib/Makefile.am
+@@ -9,6 +9,6 @@
+ AUTOMAKE_OPTIONS = no-dependencies
+ SUFFIXES = .H .h .C .c .f .o
+ 
+-always_built_SUBDIRS = @apbs_do_blas@ @apbs_do_maloc@ pmgZ aqua opal @zlib@
++always_built_SUBDIRS = @apbs_do_blas@ @apbs_do_maloc@ pmgZ aqua
+ 
+ SUBDIRS = $(always_built_SUBDIRS) .
diff --git a/sci-chemistry/apbs/files/apbs-1.3-link.patch b/sci-chemistry/apbs/files/apbs-1.3-link.patch
new file mode 100644
index 000000000000..54b66235a2d0
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.3-link.patch
@@ -0,0 +1,25 @@
+diff --git a/tools/python/Makefile.am b/tools/python/Makefile.am
+index 73d25f7..431640c 100644
+--- a/tools/python/Makefile.am
++++ b/tools/python/Makefile.am
+@@ -15,5 +15,5 @@ SUBDIRS          = vgrid
+ 
+ noinst_PROGRAMS       = _apbslib.so
+ _apbslib_so_SOURCES   = apbslib.c
+-_apbslib_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
+-_apbslib_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a ${top_builddir}/contrib/lib/libmaloc.a ${top_builddir}/contrib/blas/.libs/libapbsblas.a $(PY_LDFLAGS) ${z_lib} 
++_apbslib_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
++_apbslib_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS) ${z_lib} 
+diff --git a/tools/python/vgrid/Makefile.am b/tools/python/vgrid/Makefile.am
+index b573268..b31c9b6 100644
+--- a/tools/python/vgrid/Makefile.am
++++ b/tools/python/vgrid/Makefile.am
+@@ -15,6 +15,6 @@ CLEANFILES       = _vgrid.so
+ if PY_PRESENT
+    noinst_PROGRAMS     = _vgrid.so
+    _vgrid_so_SOURCES   = vgridlib.c
+-   _vgrid_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
+-   _vgrid_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS) ${top_builddir}/contrib/lib/libmaloc.a @lib_list@
++   _vgrid_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
++   _vgrid_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a @lib_list@
+ endif
diff --git a/sci-chemistry/apbs/files/apbs-1.3-openmp.patch b/sci-chemistry/apbs/files/apbs-1.3-openmp.patch
new file mode 100644
index 000000000000..d5aefd893325
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.3-openmp.patch
@@ -0,0 +1,61 @@
+diff --git a/configure.ac b/configure.ac
+index 6020fbf..73fbe21 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -982,7 +982,6 @@ AC_MSG_CHECKING([for --disable-tools])
+ AC_ARG_ENABLE(
+ 	[tools],
+ 	AS_HELP_STRING([--disable-tools],[disable tool compilation]),,
+-	[enable_tools=yes]
+ )
+ apbs_do_tools=""
+ if test x"$enable_tools" != "xno"; then
+@@ -1048,7 +1047,6 @@ AC_MSG_CHECKING([--disable-zlib])
+ AC_ARG_ENABLE(
+ 	[zlib],
+ 	AS_HELP_STRING([--disable-zlib], [disable zlib compilation]),,
+-	[disable_zlib=no]
+ )
+ if test x"$disable_zlib" == "xno"; then
+ 	AC_MSG_RESULT([yes])
+@@ -1160,11 +1158,8 @@ AC_MSG_CHECKING([for --disable-openmp])
+ AC_ARG_ENABLE(
+ 	[openmp],
+ 	AS_HELP_STRING([--disable-openmp],[disables OpenMP compiler support]),,
+-	[disable_openmp=yes]
+ )
+-if test x"$disable_openmp" != "xyes"; then
+-    AC_MSG_RESULT([yes])
+-else
++if test x"$disable_openmp" != "xno"; then
+     AC_MSG_RESULT([no])
+ 	if [[ "${CC}" = "icc" ] && [ "${F77}" = "ifort" ]]; then
+ 		CFLAGS="${CFLAGS} -openmp"
+@@ -1172,20 +1167,25 @@ else
+ 		LDFLAGS="${LDFLAGS} -static-intel"
+ 	fi
+ 	
+-	if [[ "${CC}" = "gcc" ] && [ "${F77}" = "gfortran" ]]; then
+-		gcc_version=`gcc --version`
++	if [[[ "${CC}" = *gcc* ]]] && [[[ "${F77}" = *gfortran* ]]]; then
++		gcc_version=`${CC} --version`
+ 		gcc_complete_version=`echo ${gcc_version} | awk '{printf("%s",$3)}' | awk -F'.' '{print $1$2}'`
+ 		
+ 		if test ["${gcc_complete_version}" -ge 42]; then
+ 			CFLAGS="${CFLAGS} -fopenmp"
+ 			FFLAGS="${FFLAGS} -fopenmp"
++			OPENMP_LIBS="-lgomp"
+ 		else
+ 		    AC_MSG_RESULT([WARNING])
+ 			AC_MSG_RESULT([WARNING Version of gcc/gfortran does not support OpenMP. Disabling.])
+ 			AC_MSG_RESULT([WARNING])
+ 		fi
+ 	fi
++else
++    AC_MSG_RESULT([yes])
++    disable_openmp=yes
+ fi
++AC_SUBST(OPENMP_LIBS)
+ 
+ dnl # -----------------------
+ dnl # CHECK FOR WINDOWS SPECIFIC LIBRARIES
diff --git a/sci-chemistry/apbs/files/apbs-1.3-shared.patch b/sci-chemistry/apbs/files/apbs-1.3-shared.patch
new file mode 100644
index 000000000000..1a237b066345
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.3-shared.patch
@@ -0,0 +1,96 @@
+diff --git a/Makefile.am b/Makefile.am
+index b400095..9e6d698 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -16,6 +16,9 @@ SUFFIXES = .H .h .C .cc .c .f .o
+ 
+ SUBDIRS = contrib src bin @apbs_do_tools@ 
+ 
++pkgconfigdir = @pkgconfigdir@
++pkgconfig_DATA = apbs.pc
++
+ distclean-local: clean-local
+ 
+ clean-local: clean-ac
+diff --git a/apbs.pc.in b/apbs.pc.in
+new file mode 100644
+index 0000000..c177512
+--- /dev/null
++++ b/apbs.pc.in
+@@ -0,0 +1,11 @@
++prefix=@prefix@
++exec_prefix=@exec_prefix@
++libdir=@libdir@
++includedir=@includedir@/apbs
++
++Name: apbs
++Description: apbs
++Version: @PACKAGE_VERSION@
++Libs: -L${libdir} -lapbsmainroutines -lapbs
++Libs.private: @LIBS@
++Cflags: -I${includedir}
+diff --git a/configure.ac b/configure.ac
+index 73fbe21..31a0053 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -71,7 +71,10 @@ AM_CONFIG_HEADER(src/aaa_inc/apbscfg.h)
+ AC_CONFIG_AUX_DIR(config)
+ AC_PREFIX_DEFAULT(${HOME})
+ AC_CANONICAL_SYSTEM
+-
++LT_INIT
++LT_LANG([Fortran 77])
++AC_F77_DUMMY_MAIN
++AC_F77_LIBRARY_LDFLAGS
+ dnl ##########################################################################
+ dnl 1. automake initialization (uncomment only if rebuilding Makefile.in's)
+ dnl ##########################################################################
+@@ -1037,6 +1040,7 @@ else
+ 	blas_lib=${contrib_path}/blas/.libs/libapbsblas.a
+ fi
+ AC_SUBST(apbs_do_blas)
++AC_SUBST(blas_lib)
+ 
+ dnl # --------------------------------
+ dnl # HANDLE ZLIB COMPILATION
+@@ -1284,6 +1288,17 @@ else
+ fi
+ AC_SUBST(apbs_build_libraries)
+ 
++# Additional arguments (and substitutions)
++# Allow the pkg-config directory to be set
++AC_ARG_WITH(pkgconfigdir,
++        AC_HELP_STRING([--with-pkgconfigdir],
++        [Use the specified pkgconfig dir (default is libdir/pkgconfig)]),
++        [pkgconfigdir=${withval}],
++        [pkgconfigdir='${libdir}/pkgconfig'])
++
++AC_SUBST([pkgconfigdir])
++AC_MSG_NOTICE([pkgconfig directory is ${pkgconfigdir}])
++
+ dnl ##########################################################################
+ dnl 11. generate the makefiles
+ dnl ##########################################################################
+@@ -1332,6 +1347,8 @@ AC_CONFIG_FILES([
+     
+     bin/Makefile
+ 
++    apbs.pc:apbs.pc.in
++
+ ])
+ AC_OUTPUT
+ 
+diff --git a/src/aaa_lib/Makefile.am b/src/aaa_lib/Makefile.am
+index 2c5026b..d8d0650 100644
+--- a/src/aaa_lib/Makefile.am
++++ b/src/aaa_lib/Makefile.am
+@@ -22,7 +22,8 @@ libdir = ${prefix}/lib
+ lib_LTLIBRARIES = libapbs.la
+ 
+ libapbs_la_SOURCES = apbs_link.c
+-libapbs_la_LIBADD  = ${GEN_LIBS} ${FEM_LIBS} ${MG_LIBS} ${PMGZ_LIBS} ${AQUA_LIBS} ${BLAS_LIBS}
++libapbs_la_LIBADD  = ${GEN_LIBS} ${FEM_LIBS} ${MG_LIBS} ${PMGZ_LIBS} ${AQUA_LIBS} ${BLAS_LIBS} \
++		     @OPENMP_LIBS@ @maloc_lib@
+ libapbs_la_LDFLAGS = -version-info ${APBS_VERSION}
+ 
+ INCLUDES         = -I${top_srcdir}/src/generic -I${top_srcdir}/src/mg -I${top_srcdir}/src/fem @inc_list@