[gentoo-commits] gentoo-x86 commit in sci-chemistry/pdb2pqr: metadata.xml ChangeLog pdb2pqr-1.7.0-r1.ebuild

[Justin Lecher (jlec)]

jlec        10/11/04 09:35:20

  Modified:             metadata.xml ChangeLog
  Added:                pdb2pqr-1.7.0-r1.ebuild
  Log:
  Added support for psb2pka
  
  (Portage version: 2.2.0_alpha3/cvs/Linux x86_64)

Revision  Changes    Path
1.5                  sci-chemistry/pdb2pqr/metadata.xml

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/metadata.xml?rev=1.5&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/metadata.xml?rev=1.5&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/metadata.xml?r1=1.4&r2=1.5

Index: metadata.xml
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/metadata.xml,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- metadata.xml	11 Mar 2010 22:47:07 -0000	1.4
+++ metadata.xml	4 Nov 2010 09:35:19 -0000	1.5
@@ -3,6 +3,7 @@
 <pkgmetadata>
 <herd>sci-chemistry</herd>
 <use>
-        <flag name='opal'>Add web interface via opal</flag>
+	<flag name='opal'>Add web interface via opal</flag>
+	<flag name='pdb2pka'>Install experimental pdb2pka interface</flag>
 </use>
 </pkgmetadata>



1.29                 sci-chemistry/pdb2pqr/ChangeLog

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog?rev=1.29&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog?rev=1.29&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog?r1=1.28&r2=1.29

Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v
retrieving revision 1.28
retrieving revision 1.29
diff -u -r1.28 -r1.29
--- ChangeLog	15 Oct 2010 18:56:50 -0000	1.28
+++ ChangeLog	4 Nov 2010 09:35:19 -0000	1.29
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/pdb2pqr
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.28 2010/10/15 18:56:50 ranger Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.29 2010/11/04 09:35:19 jlec Exp $
+
+*pdb2pqr-1.7.0-r1 (04 Nov 2010)
+
+  04 Nov 2010; Justin Lecher <jlec@g.o> +pdb2pqr-1.7.0-r1.ebuild,
+  metadata.xml:
+  Added support for psb2pka
 
   15 Oct 2010; Brent Baude <ranger@g.o> pdb2pqr-1.5.0-r2.ebuild:
   stable ppc, bug 321897



1.1                  sci-chemistry/pdb2pqr/pdb2pqr-1.7.0-r1.ebuild

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0-r1.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0-r1.ebuild?rev=1.1&content-type=text/plain

Index: pdb2pqr-1.7.0-r1.ebuild
===================================================================
# 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-1.7.0-r1.ebuild,v 1.1 2010/11/04 09:35:20 jlec Exp $

EAPI="3"

SUPPORT_PYTHON_ABIS="1"
PYTHON_EXPORT_PHASE_FUNCTIONS="1"
RESTRICT_PYTHON_ABIS="2.4 3.*"

inherit eutils fortran multilib flag-o-matic distutils python versionator toolchain-funcs

FORTRAN="g77 gfortran"

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 +pdb2pka"
KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"

RDEPEND="
	dev-python/numpy
	sci-chemistry/openbabel
	opal? ( dev-python/zsi )
	pdb2pka? ( sci-chemistry/apbs[python,-mpi] )"
DEPEND="${DEPEND}"

S="${WORKDIR}/${MY_P}"

pkg_setup() {
	if [[ -z ${MAXATOMS} ]]; then
		einfo "If you like to have support for more then 10000 atoms,"
		einfo "export MAXATOMS=\"your value\""
	else
		einfo "Allow usage of ${MAXATOMS} during calculations"
	fi
	python_pkg_setup
}

src_prepare() {
	epatch "${FILESDIR}"/${PN}-1.4.0-ldflags.patch
	epatch "${FILESDIR}"/${PN}-1.4.0-automagic.patch
	epatch "${FILESDIR}"/${PV}-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
	tc-export CC
}

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="${FORTRANC}" \
			econf \
			--enable-propka \
			--with-max-atoms=${MAXATOMS:-10000} \
			$(use_enable pdb2pka) \
			$(use_with opal) || \
			die "econf failed"
	}
	python_execute_function -s configuration
}

src_test() {
	testing() {
		emake -j1 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

		cat >> "${T}"/pdb2pka-$(python_get_version) <<-EOF
			#!/bin/sh
			$(PYTHON) ${EPREFIX}${INPATH}/pdb2pka/pka.py \$*
		EOF

		dobin "${T}"/{${PN},pdb2pka}-$(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."

		dosym ../../apbs/_apbslib.so "${INPATH}"/pdb2pka/_apbslib.so
		dosym ../../apbs/apbslib.py "${INPATH}"/pdb2pka/apbslib.py
		dosym ../../apbs/apbslib.pyc "${INPATH}"/pdb2pka/apbslib.pyc
		dosym ../../apbs/apbslib.pyo "${INPATH}"/pdb2pka/apbslib.pyo
	}
	python_execute_function -s installation

	dosym ${PN}-$(python_get_version -f) /usr/bin/${PN}
	dosym pdb2pka-$(python_get_version -f) /usr/bin/pdb2pka

	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"
}