Configure fixes, removed unnecessary installed files. Make tools optional

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

6 files changed, 246 insertions, 6 deletions

diff --git a/sci-chemistry/apbs/ChangeLog b/sci-chemistry/apbs/ChangeLog
index 832f53684647..3e07b3b682d2 100644
--- a/sci-chemistry/apbs/ChangeLog
+++ b/sci-chemistry/apbs/ChangeLog
@@ -1,6 +1,13 @@
 # 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 1.25 2010/02/20 09:33:57 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.26 2010/03/29 19:00:29 jlec Exp $
+
+*apbs-1.2.1b-r2 (28 Mar 2010)
+
+  28 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  +apbs-1.2.1b-r2.ebuild, +files/apbs-1.2.1b-install-fix.patch,
+  +files/apbs-1.2.1b-openmp.patch:
+  Configure fixes, removed unnecessary installed files. Make tools optional
 
 *apbs-1.2.1b-r1 (20 Feb 2010)
 
diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest
index 831c773a7c0d..058e763b8569 100644
--- a/sci-chemistry/apbs/Manifest
+++ b/sci-chemistry/apbs/Manifest
@@ -9,19 +9,22 @@ AUX apbs-1.2.0-contrib.patch 382 RMD160 4c0c75e57fb6a0c298606d87785a5b9daa8db457
 AUX apbs-1.2.0-install-fix.patch 1417 RMD160 4dbf96c23c2c2b150d48dc2983c293aac8be5492 SHA1 591339b9f994ee3853f6f6c38ab2cb4a280d3216 SHA256 cb805d3b12b7457c9c9a28277159516b5ea3724b6c5647b567c9683865a160b8
 AUX apbs-1.2.0-link.patch 1716 RMD160 904e7123d32f628171aa728a761c9d7fd95e967d SHA1 63265d0c7c636749292d90efe6a989e7e48251b6 SHA256 37faa758d6439f22853aa9d4524e3e8770437d3986e00649a193b0a97f369bba
 AUX apbs-1.2.1b-autoconf-2.64.patch 952 RMD160 80ed2f351c52764b1c3221b4f5f0e152652c8637 SHA1 dbe725035299182efe82d6ab4a8dcb721601592c SHA256 d9855b84b5b3ca404c463ad9ada7d75d7076d11a929b53bd61f42ed427be9984
+AUX apbs-1.2.1b-install-fix.patch 1467 RMD160 0ed57415822554b888f642b4e3afb296418ead1e SHA1 b7de15116e16c440c7b689182fa465c55fb4a628 SHA256 f67dfdbdff6f89c616c01890efcb059e104be94a33bc8a538275fa4360831d9f
+AUX apbs-1.2.1b-openmp.patch 1431 RMD160 d72a7dad56c1d2ce4e13c4eb03b2cb5e58ebcdf0 SHA1 94ca5f758749c3d71ab783041624256b8d4e8092 SHA256 ae6ba8acc1de36372e3e2af00bac23beca6354cbfbcf2140d9c65bf8e2c3bff6
 DIST apbs-1.0.0-source.tar.gz 11541303 RMD160 1eeb79f93a591835281bf8395308cddc065dac93 SHA1 fbcfe664defb09165e0eae3ff913a9d5a17cb27e SHA256 bd3803183ffb2bede9fca242d5432acb60b3cb8668eeccdbbced69aaf7a57604
 DIST apbs-1.2-source.tar.gz 10593537 RMD160 62cb82da9ca5276c3d7127a4d1f9737747dac315 SHA1 43e766a8c6166288c25229e0615a72dca5e8a3b5 SHA256 b8b74d80f8b4e553cd2e51727efc79436152cd4f5e02be076e7cdf994aa5424e
 DIST apbs-1.2.1b-source.tar.gz 40647966 RMD160 4ba1f72a7f9adcf7b283dc18743488143025b398 SHA1 dc3e6933a987ff9fdf88db510db79b3dacb100d6 SHA256 7d088def1ed7689127eb64014ea44069b9d7bfc995941fe5800ff753d48c87be
 EBUILD apbs-1.0.0-r1.ebuild 1995 RMD160 0efbe531fe27749a65a23d17958c411bcd15ad74 SHA1 9ff5761e0d8d01cdb49518cdf5d3372977c0f9ad SHA256 34b2bd026da29cec1224c91d9b4c86bdac3bec95747e167b2127aa329de2f4b2
 EBUILD apbs-1.2.0.ebuild 2514 RMD160 860994d50bc8a5d1657a5f3f6fa0dfef3c1e76e4 SHA1 d917e489ecc0e245e02796097a6aef07617e73ff SHA256 4f4229963c163b60012c091e84cf456a1215680358e3852174f2a972554546bf
 EBUILD apbs-1.2.1b-r1.ebuild 2666 RMD160 147ace2cedc979ae431e0e2e83ace236c320c7a0 SHA1 7889ebff83224c531315123dae972d3e503270bf SHA256 c9b404e8870a7461b38139785f62a05db8227464fc6b6bd918467655ed959b8e
+EBUILD apbs-1.2.1b-r2.ebuild 3333 RMD160 7f429bc43e097adac47c8991d9baa7939f8b18b6 SHA1 0440981bb40ab26db895348f74a9534318480fea SHA256 ce9ad9d236ac80b44f6895e1fb2bc54e3bf86479f620f0a0128d7160e79cf360
 EBUILD apbs-1.2.1b.ebuild 2583 RMD160 03d49d8d7d7a5a7ab71164e40bdde4a0c3e8632e SHA1 7712bc2d3faed84eb914d7466769be38076d11ed SHA256 9fa004e87205630e756762a82e6f6ffa969d77970aab2210b9688a8a295ef2a7
-MISC ChangeLog 4405 RMD160 1c4c2df9e925161088e226e613bcebcc51cca777 SHA1 1005881f7c02a5367af3ded357379332819a6cb2 SHA256 87545af36d57b0575b88867a4c16483474e9980edf56229d5e3d6a8d9a06a41e
-MISC metadata.xml 358 RMD160 b98e2ce84589bbc6b62f9fb91007bae907f019bc SHA1 c15f33b50d731bda2c2f58a1fe601e0b23f7288c SHA256 9f33e69a8a217ad31fcad567e0d0889693c680631d9245c7bd9774caac95a74e
+MISC ChangeLog 4666 RMD160 c83ce4d1179de50d1b22555ce798e781760ff661 SHA1 842a19cc34a81f56a4b93b665e45b18f12781e9c SHA256 b6caf32916d704bce84da20143903dfabc492cd5a11508a81069a57d0d15f4c1
+MISC metadata.xml 409 RMD160 61627921d41b6b81c937da90c975be2f5ec76aee SHA1 d76210f2bb303a7f277cb8c75697cf1f242af3ff SHA256 cd86d7db6f944fe5339d452a49ef9f707c163b323a844c21ab4d2d8fbeceb9f4
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diff --git a/sci-chemistry/apbs/apbs-1.2.1b-r2.ebuild b/sci-chemistry/apbs/apbs-1.2.1b-r2.ebuild
new file mode 100644
index 000000000000..c9727e661f38
--- /dev/null
+++ b/sci-chemistry/apbs/apbs-1.2.1b-r2.ebuild
@@ -0,0 +1,128 @@
+# 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-r2.ebuild,v 1.1 2010/03/29 19:00:29 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="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}/${P}-source.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+IUSE="arpack blas doc mpi openmp python tools"
+KEYWORDS="~x86 ~amd64 ~ppc ~amd64-linux ~x86-linux"
+
+DEPEND="
+	dev-libs/maloc[mpi=]
+	blas? ( virtual/blas )
+	python? ( dev-lang/python )
+	sys-libs/readline
+	arpack? ( sci-libs/arpack )
+	mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/"${MY_P}-source"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-openmp.patch
+	epatch "${FILESDIR}"/${P}-install-fix.patch
+	epatch "${FILESDIR}"/${PN}-1.2.0-contrib.patch
+	epatch "${FILESDIR}"/${PN}-1.2.0-link.patch
+	epatch "${FILESDIR}"/${P}-autoconf-2.64.patch
+	sed "s:GENTOO_PKG_NAME:${PN}:g" \
+		-i Makefile.am || die "Cannot correct package name"
+	eautoreconf
+	find . -name "._*" -exec rm -f '{}' \;
+}
+
+src_configure() {
+	local myconf="--docdir=${EPREFIX}/usr/share/doc/${PF}"
+	use blas && myconf="${myconf} --with-blas=-lblas"
+	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=${EPREFIX}/usr"
+		elif has_version sys-cluster/lam-mpi; then
+			myconf="${myconf} --with-lam=${EPREFIX}/usr"
+		elif has_version sys-cluster/openmpi; then
+			myconf="${myconf} --with-openmpi=${EPREFIX}/usr"
+		fi
+	fi || die "Failed to select proper mpi implementation"
+
+	econf $(use_enable python) \
+		--disable-maloc-rebuild \
+		$(use_enable openmp) \
+		$(use_enable tools) \
+		${myconf}
+}
+
+src_compile() {
+	emake -j1 || die "make failed"
+}
+
+src_test() {
+	cd examples && make test \
+		|| die "Tests failed"
+}
+
+src_install() {
+	emake -j1 DESTDIR="${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/${PN}
+		doins -r tools/conversion || die
+		doins -r tools/visualization/opendx || die
+
+		dobin tools/manip/{born,coulomb} || die
+
+		doins -r tools/matlab || die
+	fi
+
+	insinto /usr/$(python_get_sitedir)/${PN}
+	doins tools/manip/*.py || die
+
+	if use python && ! use mpi; then
+		insinto /usr/$(python_get_sitedir)/${PN}
+		doins tools/python/{*.py,*.pqr,*.so} || die
+		doins tools/python/*/{*.py,*.so} || die
+	fi
+
+	dodoc AUTHORS INSTALL README NEWS ChangeLog \
+		|| die "Failed to install docs"
+
+	if use doc; then
+		dohtml -r doc/* || die "Failed to install html docs"
+	fi
+}
+
+pkg_postinst() {
+	python_mod_optimize /usr/$(python_get_sitedir)/${PN}
+}
+
+pkg_postrm() {
+	python_mod_cleanup /usr/$(python_get_sitedir)/${PN}
+}
diff --git a/sci-chemistry/apbs/files/apbs-1.2.1b-install-fix.patch b/sci-chemistry/apbs/files/apbs-1.2.1b-install-fix.patch
new file mode 100644
index 000000000000..636c685f1b9a
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.2.1b-install-fix.patch
@@ -0,0 +1,53 @@
+diff --git a/Makefile.am b/Makefile.am
+index 437402d..b400095 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -27,11 +27,30 @@ clean-ac:
+ install-exec-local:
+ 	-rm -f ./bin/apbs
+ 
+-install-data-local:
+-	mkdir -p ${prefix}/share
+-	-cp -rf examples ${prefix}/share 
+-	-cp -rf doc ${prefix}/share 
+-	-cp -rf tools ${prefix}/share
++install-data-local: install-cleanup
++	-rm -f doc/LICENSE.txt
++
++install-cleanup:
++	-rm -f tools/manip/*.pyc
++	-rm -f tools/**/*.o
++	-rm -f tools/**/*.c
++	-rm -f tools/**/*.f
++	-rm -f tools/**/*Makefile*
++	-rm -f tools/**/**/*.o
++	-rm -f tools/**/**/*.c
++	-rm -f tools/**/**/*.f
++	-rm -f tools/**/**/*Makefile*
++	-rm -f tools/*Makefile*
++	-rm -f examples/*Makefile*
++	-rm -f examples/**/*Makefile*
++
++install-tools:
++	mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/tools
++	-cp -rf tools $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/
++
++install-examples:
++	mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/examples 
++	-cp -rf examples $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/
+ 
+ test:
+ 	cd examples; make test
+diff --git a/bin/Makefile.am b/bin/Makefile.am
+index 7b2f3ee..0470525 100644
+--- a/bin/Makefile.am
++++ b/bin/Makefile.am
+@@ -40,6 +40,4 @@ includedir = ${prefix}/include/apbs
+ include_HEADERS = routines.h
+ 	
+ install-data-local:
+-	-cp -p ${top_apbsdir}/bin/ApbsClient.py ${prefix}/bin
+-	-chmod 755 ${prefix}/bin/ApbsClient.py
+-	-rm -f ${prefix}/bin/wsdl2py 
+\ No newline at end of file
++	-rm -f $(DESTDIR)${prefix}/bin/wsdl2py 
diff --git a/sci-chemistry/apbs/files/apbs-1.2.1b-openmp.patch b/sci-chemistry/apbs/files/apbs-1.2.1b-openmp.patch
new file mode 100644
index 000000000000..e202725b6056
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.2.1b-openmp.patch
@@ -0,0 +1,48 @@
+diff --git a/configure.ac b/configure.ac
+index 24748bd..bd1b608 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -976,7 +976,6 @@ 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"$enable_tools" != "xno"; then
+@@ -1134,22 +1133,17 @@ AC_MSG_CHECKING([for --disable-openmp])
+ AC_ARG_ENABLE(
+ 	[openmp],
+ 	AS_HELP_STRING([--disable-openmp],[disables OpenMP compiler support]),,
+-	[disable_openmp=yes]
+ )
+-if test x"$disable_openmp" != "xyes"; then
+-    AC_MSG_RESULT([yes])
+-else
++if test x"$enable_openmp" != "xno"; then
+     AC_MSG_RESULT([no])
+ 	if [[ "${CC}" = "icc" ] && [ "${F77}" = "ifort" ]]; then
+ 		CFLAGS="${CFLAGS} -openmp"
+ 		FFLAGS="${FFLAGS} -openmp -assume cc_omp"
+ 		LDFLAGS="${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"
+@@ -1159,6 +1153,9 @@ else
+ 			AC_MSG_RESULT([WARNING])
+ 		fi
+ 	fi
++else
++    AC_MSG_RESULT([yes])
++    disable_openmp=yes
+ fi
+ 
+ dnl # -----------------------
diff --git a/sci-chemistry/apbs/metadata.xml b/sci-chemistry/apbs/metadata.xml
index cc7f93f699b0..c6c79fd71ace 100644
--- a/sci-chemistry/apbs/metadata.xml
+++ b/sci-chemistry/apbs/metadata.xml
@@ -8,5 +8,6 @@
 	<herd>sci-chemistry</herd>
 	<use>
 		<flag name='arpack'>Include support for arpack libs</flag>
+		<flag name='tools'>Install optional tools</flag>
 	</use>
 </pkgmetadata>