Moved to EAPI=3 for PREFIX support, keyworded for *-linux, tested by me

Package-Manager: portage-2.2_rc65/cvs/Linux x86_64

3 files changed, 160 insertions, 3 deletions

diff --git a/sci-chemistry/pdb2pqr/ChangeLog b/sci-chemistry/pdb2pqr/ChangeLog
index ea14f1c4dcc6..01d9f24ee831 100644
--- a/sci-chemistry/pdb2pqr/ChangeLog
+++ b/sci-chemistry/pdb2pqr/ChangeLog
@@ -1,6 +1,11 @@
 # 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 1.19 2009/11/03 05:40:25 markusle Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.20 2010/03/07 12:26:12 jlec Exp $
+
+*pdb2pqr-1.5.0-r1 (07 Mar 2010)
+
+  07 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org> +pdb2pqr-1.5.0-r1.ebuild:
+  Moved to EAPI=3 for prefix support, keyworded for *-linux, adopted to new python.eclass style
 
 *pdb2pqr-1.5.0 (03 Nov 2009)
 
diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest
index 0adde96b8588..ad32eb49bcac 100644
--- a/sci-chemistry/pdb2pqr/Manifest
+++ b/sci-chemistry/pdb2pqr/Manifest
@@ -1,3 +1,6 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX pdb2pqr-1.3.0-gcc4.3.patch 349 RMD160 a7e241b288738faaee678609c61968dba990b9a3 SHA1 95e0dcb30e926f0bab2068bff550427a1a3a623e SHA256 4e65916b3370bc3c4690ca9424629a928f9753879939f0ebb881304331fab946
 AUX pdb2pqr-1.3.0-ldflags.patch 803 RMD160 ecc52d97bae89e1a961531eb5e4c87d456e87919 SHA1 ba777c53835045fd4538f3e1104a18d12df8d935 SHA256 8d2cf1f0d206e4162193877dd577ff0835f8e390d779ddfa4b73d30734dede77
 AUX pdb2pqr-1.4.0-automagic.patch 3526 RMD160 c4d662e68352d93f913fdc83b5c733a555a9bc17 SHA1 64598bff69e627a27ffa550ad5f3b38898a3a9cf SHA256 f145bc6222d56410035240e2d8be9fbbb0d70dabccad5c5efc5d4dacd602670a
@@ -9,6 +12,14 @@ DIST pdb2pqr-1.4.0.tar.gz 5471743 RMD160 4d5596da5f9bdb2c657e7d0d88d91d20d00569e
 DIST pdb2pqr-1.5.tar.gz 5747178 RMD160 543545513811bae058e23cfe1f24e02eaa094b87 SHA1 5249064cf4ebfb2291a382121ecea4d457e65e6a SHA256 2a83433b50a57aa0a05102c425cd7b4bb6750487327195ab719992f4186281c5
 EBUILD pdb2pqr-1.3.0.ebuild 1981 RMD160 d9e8eb2f45aa12cd478e4e27e99ddf66aa202c5a SHA1 39de5c8e05de1827ab618959f73b256fd915fe8d SHA256 831d3e176306826bd44146f489030186beba521d00d7a87864ebb13272edfd17
 EBUILD pdb2pqr-1.4.0-r1.ebuild 2771 RMD160 95b243244ebf8167bb3d1d3a233f52985046345a SHA1 5ee56fc36c834c8a11d5b06d5d57404c9c844435 SHA256 3dc0ffb3b9e414f15b6aaee11e03309ec40558ad001a0bd2225465a5da028a26
+EBUILD pdb2pqr-1.5.0-r1.ebuild 3463 RMD160 d0a7d9fa2de0adef7bb80e601918299ed39bb5fe SHA1 542d1799bf9197d5699e6eb65eb2368dfd093c5c SHA256 f6ab7d172760337d62c9efb021a02e7a6d9df07b3f2c5de892d24eea9dc62cc6
 EBUILD pdb2pqr-1.5.0.ebuild 3000 RMD160 689ae4c01f4c258899a1fdf3fe87d515513957ea SHA1 8fef56d1a8f1a6c6b1dd0c10b0a0f4c085f7b76d SHA256 6d2743f05a5370be804df774e315eb5d89fcce4016f10453ad89bc75c4270874
-MISC ChangeLog 3194 RMD160 a0f98e51028a5f56e2bb315594e0d32dc4c58bdf SHA1 d13a3bc79fb94e7717e2ed7bbc2983cde81c03fa SHA256 f0b6b3e272274f708daff7ff28130c16f9b3419d4d09d6552b4d79528f21a565
+MISC ChangeLog 3400 RMD160 ddb35ab0d573432a36f50adcc6a72c49b21a828b SHA1 d897ac5436358df6d07acf75a1e77ffd6cc5516c SHA256 fd01b9015fc9f7d976ef6a642aadf37dfb66a2f9baa6032bab7c737ad0c977f4
 MISC metadata.xml 239 RMD160 c9646b9b2171a8eeac8517b70efe2d2f8b6aa0f0 SHA1 48e78f37fbb221dc94978bf1ea4a9ba874a52464 SHA256 5dd1bfe10b60a7f631b103e6755e771471fea0334312522ef256db4ddb6923c2
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.14 (GNU/Linux)
+
+iEYEARECAAYFAkuTm2oACgkQgAnW8HDreRYw7QCeMFcXrpopsbNVfizkuJXCldTB
+cOwAoKmDDsmbN2EALQQ7f4uf9fHF/6cD
+=w7dB
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0-r1.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0-r1.ebuild
new file mode 100644
index 000000000000..c8caf3e0a63b
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0-r1.ebuild
@@ -0,0 +1,141 @@
+# Copyright 1999-2010 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-r1.ebuild,v 1.1 2010/03/07 12:26:12 jlec Exp $
+
+EAPI="3"
+
+SUPPORT_PYTHON_ABIS="1"
+PYTHON_EXPORT_PHASE_FUNCTIONS="1"
+
+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}/${MY_P}.tar.gz"
+
+SLOT="0"
+IUSE="doc examples opal"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+DEPEND="
+	dev-python/numpy
+	opal? ( dev-python/zsi )"
+RDEPEND="${DEPEND}"
+RESTRICT_PYTHON_ABIS="2.4 3.*"
+
+FORTRAN="g77 gfortran"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	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"
+	python_src_prepare
+	preparation() {
+		eautoreconf
+	}
+	python_execute_function -s preparation
+}
+
+src_configure() {
+	# we need to compile the *.so as pic
+	append-flags -fPIC
+	FFLAGS="${FFLAGS} -fPIC"
+
+	configuration() {
+		# Avoid automagic to numeric
+		NUMPY="${EPREFIX}/$(python_get_sitedir)" \
+			F77="${FORTRANC}" \
+			econf \
+			$(use_with opal) || \
+			die "econf failed"
+	}
+	python_execute_function -s configuration
+}
+
+src_test() {
+	testing() {
+		emake -j1 test && \
+			F77="${FORTRANC}" emake -j1 adv-test \
+			|| die "tests failed"
+	}
+	python_execute_function -s testing
+}
+
+src_install() {
+	installation() {
+		dodir $(python_get_sitedir)/${PN}
+		emake -j1 DESTDIR="${ED}$(python_get_sitedir)/${PN}" \
+			PREFIX=""  install || die "install failed"
+
+		INPATH="$(python_get_sitedir)/${PN}"
+
+		# generate pdb2pqr wrapper
+		cat >> "${T}"/${PN}-$(python_get_version) <<-EOF
+			#!/bin/sh
+			${PYTHON} ${EPREFIX}/${INPATH}/${PN}.py \$*
+		EOF
+
+		dobin "${T}"/${PN}-$(python_get_version) || die "Failed to install pdb2pqr wrapper."
+
+		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."
+	}
+	python_execute_function -s installation
+
+	dosym ${PN}-$(python_get_version -f) /usr/bin/${PN}
+
+	if use doc; then
+		cd doc
+		sh genpydoc.sh \
+			|| die "genpydoc failed"
+		dohtml -r *.html images pydoc \
+			|| die "failed to install html docs"
+		cd -
+	fi
+
+	if use examples; then
+		insinto /usr/share/${PN}/
+		doins -r examples || die "Failed to install examples."
+	fi
+
+	dodoc ChangeLog NEWS README AUTHORS || \
+		die "Failed to install docs"
+}