* [gentoo-commits] gentoo-x86 commit in sci-chemistry/pdb2pqr: metadata.xml ChangeLog pdb2pqr-1.7.0-r1.ebuild
@ 2010-11-04 9:35 Justin Lecher (jlec)
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From: Justin Lecher (jlec) @ 2010-11-04 9:35 UTC (permalink / raw
To: gentoo-commits
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@gentoo.org> +pdb2pqr-1.7.0-r1.ebuild,
+ metadata.xml:
+ Added support for psb2pka
15 Oct 2010; Brent Baude <ranger@gentoo.org> 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"
}
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2010-11-04 9:35 [gentoo-commits] gentoo-x86 commit in sci-chemistry/pdb2pqr: metadata.xml ChangeLog pdb2pqr-1.7.0-r1.ebuild Justin Lecher (jlec)
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