Version bump (see bug #124793).

(Portage version: 2.1_pre5-r4)

5 files changed, 140 insertions, 4 deletions

diff --git a/sci-chemistry/apbs/ChangeLog b/sci-chemistry/apbs/ChangeLog
index e5c1803efa75..feb6610b2353 100644
--- a/sci-chemistry/apbs/ChangeLog
+++ b/sci-chemistry/apbs/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/apbs
-# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.2 2005/12/13 00:51:08 markusle Exp $
+# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.3 2006/03/09 11:48:28 markusle Exp $
+
+*apbs-0.4.0 (08 Mar 2006)
+
+  08 Mar 2006; Markus Dittrich <markusle@gentoo.org> +apbs-0.4.0.ebuild, +apbs-examples-gentoo.patch:
+  Version bump. Thanks to je_fro <je_fro@yahoo.com> for the ebuild
+  (see bug #124793).
 
   13 Dec 2005; Markus Dittrich <markusle@gentoo.org> metadata.xml:
   marked apbs-0.3.2.ebuild as ~x86
diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest
index 1ccc4424d91a..bbd9fad7a541 100644
--- a/sci-chemistry/apbs/Manifest
+++ b/sci-chemistry/apbs/Manifest
@@ -1,4 +1,21 @@
-MD5 2cc3d0d1949d300f8b247f41fda43f49 ChangeLog 511
-MD5 df166a2ae1cb64196abc394d4fa522ed metadata.xml 272
+MD5 10f606fe70ac2376b31183119ba1f96f ChangeLog 729
+RMD160 17547f3f81ddd9bb4dc98e32c7b1a149c6732b3e ChangeLog 729
+SHA256 2d3d19c063c07e7235a9c2523c34e590fa1849c9d3f300f42a0c6d4e50c46408 ChangeLog 729
 MD5 401bb19a1a50e92cccd4580795528579 apbs-0.3.2.ebuild 1591
+RMD160 dcfc1d57d44ca4e83dec75311be034c5b49a96dc apbs-0.3.2.ebuild 1591
+SHA256 79d3bb1de04c812c238d74385633a22e9f15739584e87ff5bb5ba3302db1af6b apbs-0.3.2.ebuild 1591
+MD5 bbd3dbfc5068ef6402a5b75b4091b0f0 apbs-0.4.0.ebuild 2199
+RMD160 89a671b090e092fe27280fb1e2e706bd79c4cac9 apbs-0.4.0.ebuild 2199
+SHA256 ab2993653680f9dccf901855996adf9670285ab46d92770ffac35fdc9449d601 apbs-0.4.0.ebuild 2199
+MD5 43dd7c966e75cdbd40215b3616cfddf5 files/apbs-examples-gentoo.patch 1446
+RMD160 f0468219d3295cbaf90de7c0e3489d443f1ea144 files/apbs-examples-gentoo.patch 1446
+SHA256 1b12fdf855c4e80bb6e88d6b9c433a4c18eb406a5a6d1671146be897452863d4 files/apbs-examples-gentoo.patch 1446
 MD5 fe78d29b43ac5fd73de88376a5db2855 files/digest-apbs-0.3.2 63
+RMD160 c140373a787311656e2fb6bddfbb7bfcd1e74288 files/digest-apbs-0.3.2 63
+SHA256 91064ccf5f3996a97fbbbc9b108fa22ac94a95ca0428d13308653a733debc828 files/digest-apbs-0.3.2 63
+MD5 2ef0a41feb8be34beec568bf9fe062d6 files/digest-apbs-0.4.0 235
+RMD160 0606ae9bd4d8f291be73e669911da24e3cc0c457 files/digest-apbs-0.4.0 235
+SHA256 b0c6ba75ae65cac80987484dab6a0c0bb889d01b852c12dd7c4e59e6062f19f9 files/digest-apbs-0.4.0 235
+MD5 df166a2ae1cb64196abc394d4fa522ed metadata.xml 272
+RMD160 42331a21c1e7a31cfe105f705fe3073de14b6b14 metadata.xml 272
+SHA256 36ae23839abbf283daf51b7f9585af067c0504484f5ca61e2f08113912becb77 metadata.xml 272
diff --git a/sci-chemistry/apbs/apbs-0.4.0.ebuild b/sci-chemistry/apbs/apbs-0.4.0.ebuild
new file mode 100644
index 000000000000..e61251406059
--- /dev/null
+++ b/sci-chemistry/apbs/apbs-0.4.0.ebuild
@@ -0,0 +1,80 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/apbs-0.4.0.ebuild,v 1.1 2006/03/09 11:48:28 markusle Exp $
+
+inherit eutils fortran
+
+DESCRIPTION=" Software for evaluating the electrostatic properties of nanoscale biomolecular systems"
+LICENSE="GPL-2"
+HOMEPAGE="http://agave.wustl.edu/apbs/"
+SRC_URI="mirror:://sourceforge/${PN}/${P}.tar.gz"
+
+SLOT="0"
+IUSE="blas mpi"
+KEYWORDS="~x86"
+
+DEPEND="blas? ( virtual/blas )
+		sys-libs/readline
+		dev-libs/maloc
+		mpi? ( virtual/mpi )"
+
+pkg_setup() {
+	need_fortran g77
+
+	# the configure script has a weird MPI related behaviour:
+	# if maloc was compiled with mpi, apbs requires mpi as
+	# well and will bomb otherwise; if maloc was compiled
+	# without mpi, apbs will silently disable mpi even if
+	# USE="mpi" is forced
+	if use mpi; then
+		if ! built_with_use dev-libs/maloc mpi; then
+			die 'USE="mpi" requires dev-libs/maloc built with mpi'
+		fi
+	else
+		if built_with_use dev-libs/maloc mpi; then
+			die 'USE="-mpi" requires dev-libs/maloc built without mpi'
+		fi
+	fi
+}
+
+src_unpack() {
+	unpack ${A}
+	epatch "${FILESDIR}"/apbs-examples-gentoo.patch
+}
+
+src_compile() {
+	# use blas
+	use blas && local myconf="--with-blas=-lblas"
+
+	use mpi && myconf="${myconf} --with-mpiinc=/usr/include"
+
+	# configure 
+	econf ${myconf} || die "configure failed"
+
+	# build
+	make || die "make failed"
+}
+
+src_install() {
+
+	# install apbs binary
+	dobin bin/apbs || die "failed to install apbs binary"
+
+	# fix up and install examples
+	find ./examples -name 'test.sh' -exec rm -f {} \; || \
+		die "Failed to remove test.sh files"
+	find ./examples -name 'Makefile*' -exec rm -f {} \; || \
+		die "Failed to remove Makefiles"
+	insinto /usr/share/doc/${PF}/examples
+	doins -r examples/* || die "failed to install examples"
+
+	# install docs
+	insinto /usr/share/doc/${PF}/html/programmer
+	doins doc/html/programmer/* || die "failed to install html docs"
+
+	insinto /usr/share/doc/${PF}/html/tutorial
+	doins doc/html/tutorial/* || die "failed to install html docs"
+
+	insinto /usr/share/doc/${PF}/html/user-guide
+	doins doc/html/user-guide/* || die "failed to install html docs"
+}
diff --git a/sci-chemistry/apbs/files/apbs-examples-gentoo.patch b/sci-chemistry/apbs/files/apbs-examples-gentoo.patch
new file mode 100644
index 000000000000..5c82bc2882ab
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-examples-gentoo.patch
@@ -0,0 +1,30 @@
+diff -Naur apbs-0.4.0/examples/born/runme apbs-0.4.0-new/examples/born/runme
+--- apbs-0.4.0/examples/born/runme	2002-08-13 14:35:41.000000000 +0000
++++ apbs-0.4.0-new/examples/born/runme	2006-03-09 03:15:09.000000000 +0000
+@@ -8,5 +8,5 @@
+   echo "Generating ion with $i radius..."
+   echo "ATOM      1  I   ION     1       0.000   0.000  0.000  1.00  $i" \
+     > ion.pqr
+-  ${bindir}/apbs apbs.in > OUTPUT-${i} 2>&1 
++  /usr/bin/apbs apbs.in > OUTPUT-${i} 2>&1 
+ done
+diff -Naur apbs-0.4.0/examples/ion-pmf/runme apbs-0.4.0-new/examples/ion-pmf/runme
+--- apbs-0.4.0/examples/ion-pmf/runme	2002-08-13 14:35:41.000000000 +0000
++++ apbs-0.4.0-new/examples/ion-pmf/runme	2006-03-09 03:16:11.000000000 +0000
+@@ -14,5 +14,5 @@
+   echo "ATOM      1  I   ION     1      $i    0.000   0.000  1.00 2.00"\
+      > mol2.pqr
+   cat mol1.pqr mol2.pqr > complex.pqr
+-  ${bindir}/apbs apbs.in > OUTPUT_${i} 2>&1
++  /usr/bin/apbs apbs.in > OUTPUT_${i} 2>&1
+ done
+diff -Naur apbs-0.4.0/examples/point-pmf/runme.sh apbs-0.4.0-new/examples/point-pmf/runme.sh
+--- apbs-0.4.0/examples/point-pmf/runme.sh	2004-02-12 17:14:02.000000000 +0000
++++ apbs-0.4.0-new/examples/point-pmf/runme.sh	2006-03-09 03:17:11.000000000 +0000
+@@ -20,5 +20,5 @@
+   echo "ATOM      1  I   ION     1      $i    0.000   0.000  1.00 0.00"\
+      > mol2.pqr
+   cat mol1.pqr mol2.pqr > complex.pqr
+-  ${bindir}/apbs apbs.in > OUTPUT_${i} 2>&1
++  /usr/bin/apbs apbs.in > OUTPUT_${i} 2>&1
+ done
diff --git a/sci-chemistry/apbs/files/digest-apbs-0.4.0 b/sci-chemistry/apbs/files/digest-apbs-0.4.0
new file mode 100644
index 000000000000..26b788e6d2cc
--- /dev/null
+++ b/sci-chemistry/apbs/files/digest-apbs-0.4.0
@@ -0,0 +1,3 @@
+MD5 a9d5f8b24a40087998267c9df3eecceb apbs-0.4.0.tar.gz 6490858
+RMD160 259c89efed2296eb20af1f8076adc767ef35228c apbs-0.4.0.tar.gz 6490858
+SHA256 d1f6637e10b3051e6f618abaa14063f8f9bafbbbad75058645866b606d708acc apbs-0.4.0.tar.gz 6490858