Version bump and removed old ebuilds.

(Portage version: 2.1.7.3/cvs/Linux x86_64)

8 files changed, 133 insertions, 208 deletions

diff --git a/sci-chemistry/pdb2pqr/ChangeLog b/sci-chemistry/pdb2pqr/ChangeLog
index fb5b45682d24..ea14f1c4dcc6 100644
--- a/sci-chemistry/pdb2pqr/ChangeLog
+++ b/sci-chemistry/pdb2pqr/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/pdb2pqr
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.18 2009/09/24 23:43:11 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.19 2009/11/03 05:40:25 markusle Exp $
+
+*pdb2pqr-1.5.0 (03 Nov 2009)
+
+  03 Nov 2009; Markus Dittrich <markusle@gentoo.org> -pdb2pqr-1.1.2.ebuild,
+  -files/pdb2pqr-1.1.2-fpic-gentoo.patch, -files/pdb2pqr-gcc4-gentoo.patch,
+  -files/pdb2pqr-1.1.2-gcc4-gentoo.patch, -pdb2pqr-1.2.1.ebuild,
+  -files/pdb2pqr-propka-gentoo.patch, +pdb2pqr-1.5.0.ebuild:
+  Version bump and removed old ebuilds.
 
   24 Sep 2009; Markus Dittrich <markusle@gentoo.org>
   pdb2pqr-1.4.0-r1.ebuild, files/pdb2pqr-1.4.0-automagic.patch:
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.1.2-fpic-gentoo.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.1.2-fpic-gentoo.patch
deleted file mode 100644
index 254041a7b586..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.1.2-fpic-gentoo.patch
+++ /dev/null
@@ -1,18 +0,0 @@
---- pdb2pqr-1.1.2/propka/Makefile.in	2006-06-23 10:16:25.000000000 -0400
-+++ pdb2pqr-1.1.2-new/propka/Makefile.in	2006-07-01 14:15:29.000000000 -0400
-@@ -210,13 +210,13 @@
- 	-rm -f *.tab.c
- 
- .c.o:
--	$(COMPILE) -c `test -f '$<' || echo '$(srcdir)/'`$<
-+	$(COMPILE) -fPIC -c `test -f '$<' || echo '$(srcdir)/'`$<
- 
- .c.obj:
- 	$(COMPILE) -c `if test -f '$<'; then $(CYGPATH_W) '$<'; else $(CYGPATH_W) '$(srcdir)/$<'`
- 
- .f.o:
--	$(F77COMPILE) -c -o $@ `test -f '$<' || echo '$(srcdir)/'`$<
-+	$(F77COMPILE) -fPIC -c -o $@ `test -f '$<' || echo '$(srcdir)/'`$<
- 
- .f.obj:
- 	$(F77COMPILE) -c -o $@ `if test -f '$<'; then $(CYGPATH_W) '$<'; else $(CYGPATH_W) '$(srcdir)/$<'`
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.1.2-gcc4-gentoo.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.1.2-gcc4-gentoo.patch
deleted file mode 100644
index 6c59bf8b4d71..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.1.2-gcc4-gentoo.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- pdb2pqr-1.1.2/propka/configure	2006-06-23 09:16:25.000000000 -0500
-+++ pdb2pqr-1.1.2-patched/propka/configure	2006-06-28 05:40:50.000000000 -0500
-@@ -2819,7 +2819,7 @@
- ac_link='$F77 -o conftest$ac_exeext $FFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
- ac_compiler_gnu=$ac_cv_f77_compiler_gnu
- if test -n "$ac_tool_prefix"; then
--  for ac_prog in g77 f77 xlf frt pgf77 fl32 af77 fort77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 lf95 g95
-+  for ac_prog in g77 f77 gfortran xlf frt pgf77 fl32 af77 fort77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 lf95 g95
-   do
-     # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
- set dummy $ac_tool_prefix$ac_prog; ac_word=$2
-@@ -2861,7 +2861,7 @@
- fi
- if test -z "$F77"; then
-   ac_ct_F77=$F77
--  for ac_prog in g77 f77 xlf frt pgf77 fl32 af77 fort77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 lf95 g95
-+  for ac_prog in g77 f77 gfortran xlf frt pgf77 fl32 af77 fort77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 lf95 g95
- do
-   # Extract the first word of "$ac_prog", so it can be a program name with args.
- set dummy $ac_prog; ac_word=$2
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-gcc4-gentoo.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-gcc4-gentoo.patch
deleted file mode 100644
index a909cf6d70b1..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-gcc4-gentoo.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naur pdb2pqr-1.0.2/propka/configure pdb2pqr-1.0.2-new/propka/configure
---- pdb2pqr-1.0.2/propka/configure	2005-12-16 09:50:58.000000000 -0600
-+++ pdb2pqr-1.0.2-new/propka/configure	2006-03-21 09:18:26.000000000 -0600
-@@ -2861,7 +2861,7 @@
- fi
- if test -z "$F77"; then
-   ac_ct_F77=$F77
--  for ac_prog in g77 f77 xlf frt pgf77 fl32 af77 fort77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 lf95 g95
-+  for ac_prog in g77 f77 gfortran xlf frt pgf77 fl32 af77 fort77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 lf95 g95
- do
-   # Extract the first word of "$ac_prog", so it can be a program name with args.
- set dummy $ac_prog; ac_word=$2
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-propka-gentoo.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-propka-gentoo.patch
deleted file mode 100644
index c57b8e210d6e..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-propka-gentoo.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naur pdb2pqr-1.0.2/pdb2pqr.py pdb2pqr-1.0.2-new/pdb2pqr.py
---- pdb2pqr-1.0.2/pdb2pqr.py	2005-12-16 09:50:57.000000000 -0600
-+++ pdb2pqr-1.0.2-new/pdb2pqr.py	2006-03-21 10:09:52.000000000 -0600
-@@ -37,6 +37,8 @@
- from src.protein import *
- from src.server import *
- from StringIO import *
-+from propka import propkalib
-+from propka.propkalib import *
- 
- def usage(rc):
-     """
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.1.2.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.1.2.ebuild
deleted file mode 100644
index 24ef55bdcf14..000000000000
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.1.2.ebuild
+++ /dev/null
@@ -1,77 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.1.2.ebuild,v 1.10 2009/05/24 07:50:41 je_fro Exp $
-
-inherit eutils fortran multilib flag-o-matic distutils
-
-DESCRIPTION="pdb2pqr is an automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
-LICENSE="GPL-2"
-HOMEPAGE="http://pdb2pqr.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86"
-
-DEPEND="dev-lang/python
-		dev-python/numpy"
-
-RDEPEND="${DEPEND}"
-
-FORTRAN="g77 gfortran"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	epatch "${FILESDIR}"/${P}-gcc4-gentoo.patch
-	epatch "${FILESDIR}"/${P}-fpic-gentoo.patch
-}
-
-src_compile() {
-	econf || die "econf failed"
-	emake || die "emake failed"
-}
-
-src_install() {
-	python_version
-	INPATH="/usr/$(get_libdir)/python${PYVER}/site-packages/${PN}"
-
-	insinto "${INPATH}"
-	doins __init__.py || \
-		die "Setting up the pdb2pqr site-package failed."
-
-	exeinto "${INPATH}"
-	doexe ${PN}.py || die "Installing pdb2pqr failed."
-
-	exeinto "${INPATH}"/propka
-	doexe propka/_propkalib.so || \
-		die "Failed to install propka."
-
-	exeinto "${INPATH}"/extensions
-	doexe extensions/* || \
-		die "Failed to install extensions."
-
-	insinto "${INPATH}"/propka
-	doins propka/propkalib.py propka/__init__.py || \
-		die "Failed to install propka."
-
-	insinto "${INPATH}"/src
-	doins src/* || die "Installing of python scripts failed."
-
-	insinto "${INPATH}"/dat
-	doins dat/* || die "Installing data failed."
-
-	# generate pdb2pqr wrapper
-	cat >> "${T}"/${PN} << EOF
-#!/bin/sh
-${python} ${INPATH}/${PN}.py \$*
-EOF
-
-	exeinto /usr/bin
-	doexe "${T}"/${PN} || die "Failed to install pdb2pqr wrapper."
-
-	dodoc ChangeLog NEWS README AUTHORS || \
-		die "Failed to install docs"
-	dohtml -r doc/* || die "Failed to install html docs."
-}
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.2.1.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.2.1.ebuild
deleted file mode 100644
index a0e7ef896c5a..000000000000
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.2.1.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.2.1.ebuild,v 1.5 2009/05/24 07:50:41 je_fro Exp $
-
-inherit eutils fortran multilib flag-o-matic distutils
-
-DESCRIPTION="pdb2pqr is an automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
-LICENSE="GPL-2"
-HOMEPAGE="http://pdb2pqr.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="dev-lang/python"
-
-RDEPEND="${DEPEND}"
-
-FORTRAN="g77 gfortran"
-
-src_compile() {
-	econf || die "econf failed"
-	emake || die "emake failed"
-}
-
-src_install() {
-	python_version
-	INPATH="/usr/$(get_libdir)/python${PYVER}/site-packages/${PN}"
-
-	insinto "${INPATH}"
-	doins __init__.py || \
-		die "Setting up the pdb2pqr site-package failed."
-
-	exeinto "${INPATH}"
-	doexe ${PN}.py || die "Installing pdb2pqr failed."
-
-	exeinto "${INPATH}"/propka
-	doexe propka/_propkalib.so || \
-		die "Failed to install propka."
-
-	exeinto "${INPATH}"/extensions
-	doexe extensions/* || \
-		die "Failed to install extensions."
-
-	insinto "${INPATH}"/propka
-	doins propka/propkalib.py propka/__init__.py || \
-		die "Failed to install propka."
-
-	insinto "${INPATH}"/src
-	doins src/* || die "Installing of python scripts failed."
-
-	insinto "${INPATH}"/dat
-	doins dat/* || die "Installing data failed."
-
-	# generate pdb2pqr wrapper
-	cat >> "${T}"/${PN} << EOF
-#!/bin/sh
-${python} ${INPATH}/${PN}.py \$*
-EOF
-
-	exeinto /usr/bin
-	doexe "${T}"/${PN} || die "Failed to install pdb2pqr wrapper."
-
-	dodoc ChangeLog NEWS README AUTHORS || \
-		die "Failed to install docs"
-	dohtml -r doc/* || die "Failed to install html docs."
-}
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0.ebuild
new file mode 100644
index 000000000000..898517a899cd
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0.ebuild
@@ -0,0 +1,124 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0.ebuild,v 1.1 2009/11/03 05:40:25 markusle Exp $
+
+inherit eutils fortran multilib flag-o-matic distutils python versionator
+
+MY_PV=$(get_version_component_range 1-2)
+MY_P="${PN}-${MY_PV}"
+
+DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
+LICENSE="BSD"
+HOMEPAGE="http://pdb2pqr.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
+
+SLOT="0"
+IUSE="doc examples opal"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="dev-lang/python
+	dev-python/numpy
+	opal? ( dev-python/zsi )"
+RDEPEND="${DEPEND}"
+
+FORTRAN="g77 gfortran"
+
+S="${WORKDIR}/${MY_P}"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}"/${PN}-1.4.0-ldflags.patch
+	epatch "${FILESDIR}"/${PN}-1.4.0-automagic.patch
+	epatch "${FILESDIR}"/${PN}-1.4.0-install.patch
+	sed '50,200s:CWD:DESTDIR:g' -i Makefile.am \
+		|| die "Failed to fix Makefile.am"
+	eautoreconf
+}
+
+src_compile() {
+	# we need to compile the *.so as pic
+	append-flags -fPIC
+	FFLAGS="${FFLAGS} -fPIC"
+
+	# Avoid automagic to numeric
+	NUMPY="$(python_get_sitedir)" \
+		F77="${FORTRANC}" \
+		econf \
+		$(use_with opal) || \
+		die "econf failed"
+	emake || die "emake failed"
+}
+
+src_test() {
+	emake -j1 test && \
+		F77="${FORTRANC}" emake -j1 adv-test \
+		|| die "tests failed"
+}
+
+src_install() {
+	dodir $(python_get_sitedir)/${PN}
+	emake -j1 DESTDIR="${D}$(python_get_sitedir)/${PN}" \
+		PREFIX=""  install || die "install failed"
+
+	if use doc; then
+		cd doc
+		sh genpydoc.sh \
+			|| die "genpydoc failed"
+		dohtml -r *.html images pydoc \
+			|| die "failed to install html docs"
+		cd -
+	fi
+
+	if use examples; then
+		insinto /usr/share/${PN}/
+		doins -r examples || die "Failed to install examples."
+	fi
+
+	INPATH="$(python_get_sitedir)/${PN}"
+
+	# generate pdb2pqr wrapper
+	cat >> "${T}"/${PN} <<-EOF
+		#!/bin/sh
+		${python} ${INPATH}/${PN}.py \$*
+	EOF
+
+	exeinto /usr/bin
+	doexe "${T}"/${PN} || die "Failed to install pdb2pqr wrapper."
+
+	dodoc ChangeLog NEWS README AUTHORS || \
+		die "Failed to install docs"
+
+	insinto "${INPATH}"
+	doins __init__.py || \
+		die "Setting up the pdb2pqr site-package failed."
+
+	exeinto "${INPATH}"
+	doexe ${PN}.py || die "Installing pdb2pqr failed."
+
+	insinto "${INPATH}"/dat
+	doins dat/* || die "Installing data failed."
+
+	exeinto "${INPATH}"/extensions
+	doexe extensions/* || \
+		die "Failed to install extensions."
+
+	insinto "${INPATH}"/src
+	doins src/*.py || die "Installing of python scripts failed."
+
+	exeinto "${INPATH}"/propka
+	doexe propka/_propkalib.so || \
+		die "Failed to install propka."
+
+	insinto "${INPATH}"/propka
+	doins propka/propkalib.py propka/__init__.py || \
+		die "Failed to install propka."
+
+	insinto "${INPATH}"/pdb2pka
+	doins pdb2pka/*.{py,so,DAT,h} || \
+		die "Failed to install pdb2pka."
+
+	insinto "${INPATH}"/pdb2pka/
+	doins pdb2pka/*.{py,so,DAT,h} || \
+		die "Failed to install pdb2pka."
+}