[gentoo-commits] gentoo-x86 commit in sci-chemistry/pdb2pqr: ChangeLog pdb2pqr-1.5.0.ebuild pdb2pqr-1.1.2.ebuild pdb2pqr-1.2.1.ebuild

[gentoo-commits] gentoo-x86 commit in sci-chemistry/pdb2pqr: ChangeLog pdb2pqr-1.5.0.ebuild pdb2pqr-1.1.2.ebuild pdb2pqr-1.2.1.ebuild

[Markus Dittrich (markusle)]

markusle    09/11/03 05:40:26

  Modified:             ChangeLog
  Added:                pdb2pqr-1.5.0.ebuild
  Removed:              pdb2pqr-1.1.2.ebuild pdb2pqr-1.2.1.ebuild
  Log:
  Version bump and removed old ebuilds.
  (Portage version: 2.1.7.3/cvs/Linux x86_64)

Revision  Changes    Path
1.19                 sci-chemistry/pdb2pqr/ChangeLog

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog?rev=1.19&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog?rev=1.19&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog?r1=1.18&r2=1.19

Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v
retrieving revision 1.18
retrieving revision 1.19
diff -u -r1.18 -r1.19
--- ChangeLog	24 Sep 2009 23:43:11 -0000	1.18
+++ ChangeLog	3 Nov 2009 05:40:25 -0000	1.19
@@ -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:



1.1                  sci-chemistry/pdb2pqr/pdb2pqr-1.5.0.ebuild

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0.ebuild?rev=1.1&content-type=text/plain

Index: pdb2pqr-1.5.0.ebuild
===================================================================
# 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."
}