sci-chemistry/pdb2pqr: Drop old

(Portage version: 2.2.15/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

5 files changed, 5 insertions, 548 deletions

diff --git a/sci-chemistry/pdb2pqr/ChangeLog b/sci-chemistry/pdb2pqr/ChangeLog
index 820a17b96385..e2208e020cac 100644
--- a/sci-chemistry/pdb2pqr/ChangeLog
+++ b/sci-chemistry/pdb2pqr/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-chemistry/pdb2pqr
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.46 2015/01/04 19:15:11 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.47 2015/01/04 19:17:35 jlec Exp $
+
+  04 Jan 2015; Justin Lecher <jlec@gentoo.org> -pdb2pqr-1.7.0.ebuild,
+  -pdb2pqr-1.7.0-r2.ebuild, -pdb2pqr-1.8.0-r1.ebuild, -pdb2pqr-1.9.0.ebuild:
+  Drop old
 
   04 Jan 2015; Justin Lecher <jlec@gentoo.org> pdb2pqr-1.9.0-r1.ebuild:
   Drop obsolete dep
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0-r2.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0-r2.ebuild
deleted file mode 100644
index ac9f5cf46b9c..000000000000
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0-r2.ebuild
+++ /dev/null
@@ -1,165 +0,0 @@
-# Copyright 1999-2012 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-r2.ebuild,v 1.2 2012/10/19 10:10:18 jlec Exp $
-
-EAPI=4
-
-PYTHON_DEPEND="2:2.5"
-SUPPORT_PYTHON_ABIS="1"
-PYTHON_EXPORT_PHASE_FUNCTIONS="1"
-RESTRICT_PYTHON_ABIS="2.4 3.* 2.7-pypy-*"
-
-inherit autotools eutils fortran-2 flag-o-matic python toolchain-funcs 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}/${MY_P}.tar.gz"
-
-SLOT="0"
-IUSE="doc examples opal +pdb2pka"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="
-	dev-python/numpy
-	sci-chemistry/openbabel
-	opal? ( dev-python/zsi )
-	pdb2pka? ( sci-chemistry/apbs[python,-mpi] )"
-DEPEND="${RDEPEND}"
-
-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 ${MAXATOMS} during calculations"
-	fi
-	python_pkg_setup
-	fortran-2_pkg_setup
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PN}-1.4.0-ldflags.patch \
-		"${FILESDIR}"/${PN}-1.4.0-automagic.patch \
-		"${FILESDIR}"/${PV}-install.patch
-	sed \
-		-e '50,200s:CWD:DESTDIR:g' \
-		-i Makefile.am || die
-
-	python_src_prepare
-
-	preparation() {
-		sed \
-			-e "s:python\$PY_VERSION:$(PYTHON):g" \
-			-i configure.ac || die
-
-		eautoreconf
-	}
-	python_execute_function -s preparation
-
-	tc-export CC
-}
-
-src_configure() {
-	# we need to compile the *.so as pic
-	append-flags -fPIC
-	FFLAGS="${FFLAGS} -fPIC"
-
-	configuration() {
-		# Avoid automagic to numeric
-		econf \
-			--enable-propka \
-			--with-max-atoms=${MAXATOMS:-10000} \
-			$(use_enable pdb2pka) \
-			$(use_with opal) \
-			NUMPY="${EPREFIX}/$(python_get_sitedir)" \
-			F77="$(tc-getFC)"
-	}
-	python_execute_function -s configuration
-}
-
-src_compile() {
-	python_execute_function -d -s
-}
-
-src_test() {
-	testing() {
-		emake -j1 test
-	}
-	python_execute_function -s testing
-}
-
-src_install() {
-	installation() {
-		dodir $(python_get_sitedir)/${PN}
-		emake -j1 DESTDIR="${ED}$(python_get_sitedir)/${PN}" \
-			PREFIX="" install
-
-		INPATH="$(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}-$(python_get_version)
-
-		insinto "${INPATH}" && doins __init__.py
-
-		exeinto "${INPATH}" && doexe ${PN}.py
-
-		insinto "${INPATH}"/dat && doins dat/*
-
-		exeinto "${INPATH}"/extensions && doexe extensions/*
-
-		insinto "${INPATH}"/src && doins src/*.py
-
-		exeinto "${INPATH}"/propka && doexe propka/_propkalib.so
-
-		insinto "${INPATH}"/propka && doins propka/propkalib.py propka/__init__.py
-
-		insinto "${INPATH}"/pdb2pka && doins pdb2pka/*.{py,so,DAT,h}
-
-		dosym ../../apbs/_apbs.so "${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
-		pushd doc > /dev/null
-		sh genpydoc.sh || die "genpydoc failed"
-		dohtml -r *.html images pydoc
-		popd > /dev/null
-	fi
-
-	use examples && \
-		insinto /usr/share/${PN}/ && \
-		doins -r examples
-
-	dodoc ChangeLog NEWS README AUTHORS
-}
-
-pkg_postinst() {
-	python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
-	python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0.ebuild
deleted file mode 100644
index 180ca27d19d3..000000000000
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0.ebuild
+++ /dev/null
@@ -1,159 +0,0 @@
-# Copyright 1999-2012 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.ebuild,v 1.9 2012/10/19 10:10:18 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-SUPPORT_PYTHON_ABIS="1"
-PYTHON_EXPORT_PHASE_FUNCTIONS="1"
-RESTRICT_PYTHON_ABIS="2.4 3.*"
-
-inherit autotools eutils fortran-2 flag-o-matic python toolchain-funcs 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}/${MY_P}.tar.gz"
-
-SLOT="0"
-IUSE="doc examples opal"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="
-	dev-python/numpy
-	sci-chemistry/openbabel
-	opal? ( dev-python/zsi )"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	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
-}
-
-src_configure() {
-	# we need to compile the *.so as pic
-	append-flags -fPIC
-	FFLAGS="${FFLAGS} -fPIC"
-
-	configuration() {
-		# Avoid automagic to numeric
-		NUMPY="${EPREFIX}/$(python_get_sitedir)" \
-			F77="$(tc-getFC)" \
-			econf \
-			$(use_with opal)
-	}
-	python_execute_function -s configuration
-}
-
-src_compile() {
-	compilation() {
-		emake || die
-	}
-	python_execute_function -s compilation
-}
-
-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}/${PN}.py \$*
-		EOF
-
-		dobin "${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"
-}
-
-pkg_postinst() {
-	python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
-	python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.8.0-r1.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.8.0-r1.ebuild
deleted file mode 100644
index 4a3004f21dd7..000000000000
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.8.0-r1.ebuild
+++ /dev/null
@@ -1,114 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.8.0-r1.ebuild,v 1.1 2014/10/24 12:06:42 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools eutils fortran-2 flag-o-matic python-single-r1 toolchain-funcs versionator
-
-MY_PV=$(get_version_component_range 1-2)
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
-LICENSE="BSD"
-HOMEPAGE="http://www.poissonboltzmann.org/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-SLOT="0"
-IUSE="doc examples opal +pdb2pka"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-chemistry/openbabel[python]
-	opal? ( dev-python/zsi[${PYTHON_USEDEP}] )
-	pdb2pka? ( sci-chemistry/apbs[${PYTHON_USEDEP},-mpi] )"
-DEPEND="${RDEPEND}"
-
-S="${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 ${MAXATOMS} during calculations"
-	fi
-	fortran-2_pkg_setup
-	python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	rm -rf contrib/* || die
-	epatch \
-		"${FILESDIR}"/${P}-ldflags.patch \
-		"${FILESDIR}"/${PN}-1.4.0-automagic.patch \
-		"${FILESDIR}"/1.7.0-install.patch
-	sed \
-		-e '50,200s:CWD:DESTDIR:g' \
-		-i Makefile.am || die
-
-	eautoreconf
-
-	tc-export CC
-}
-
-src_configure() {
-	# we need to compile the *.so as pic
-	append-flags -fPIC
-	FFLAGS="${FFLAGS} -fPIC"
-	econf \
-		--with-max-atoms=${MAXATOMS:-10000} \
-		--with-python="${PYTHON}" \
-		$(usex pdb2pka "" --disable-pdb2pka) \
-		$(use_with opal) \
-		NUMPY="${EPREFIX}/$(python_get_sitedir)" \
-		F77="$(tc-getFC)"
-}
-
-src_compile() {
-	default
-	if use doc; then
-		pushd doc > /dev/null
-		sh genpydoc.sh || die "genpydoc failed"
-		popd > /dev/null
-	fi
-}
-
-src_test() {
-	emake -j1 test
-}
-
-src_install() {
-	local lib
-	dodir $(python_get_sitedir)/${PN}
-	emake -j1 \
-		DESTDIR="${ED}$(python_get_sitedir)/${PN}" \
-		PREFIX="" install
-		INPATH="$(python_get_sitedir)/${PN}"
-
-	make_wrapper ${PN} "${PYTHON} /$(python_get_sitedir)/${PN}/${PN}.py"
-	make_wrapper pdb2pka "${PYTHON} /$(python_get_sitedir)/${PN}/pdb2pka/pka.py"
-
-	for lib in _apbs.so apbslib.py{,c,o}; do
-		dosym /usr/share/apbs/tools/python/${lib} $(python_get_sitedir)/${PN}/pdb2pka/${lib}
-	done
-
-	if use doc; then
-		pushd doc > /dev/null
-		dohtml -r *.html images pydoc
-		popd > /dev/null
-	fi
-
-	use examples && \
-		insinto /usr/share/${PN}/ && \
-		doins -r examples
-
-	dodoc ChangeLog NEWS README AUTHORS
-
-	python_optimize
-}
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0.ebuild
deleted file mode 100644
index bce2a68f8450..000000000000
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0.ebuild
+++ /dev/null
@@ -1,109 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0.ebuild,v 1.3 2014/10/29 02:42:21 patrick Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit scons-utils fortran-2 flag-o-matic python-single-r1 toolchain-funcs
-
-DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
-HOMEPAGE="http://www.poissonboltzmann.org/"
-SRC_URI="https://github.com/Electrostatics/apbs-${PN}/releases/download/${P}/${PN}-src-${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-IUSE="doc examples opal +pdb2pka"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-chemistry/openbabel[python]
-	sci-chemistry/openbabel-python[${PYTHON_USEDEP}]
-	opal? ( dev-python/zsi[${PYTHON_USEDEP}] )
-	pdb2pka? ( sci-chemistry/apbs[${PYTHON_USEDEP},-mpi] )"
-DEPEND="${RDEPEND}
-	dev-lang/swig:0"
-
-pkg_setup() {
-	if [[ -z ${MAXATOMS} ]]; then
-		einfo "If you like to have support for more then 10000 atoms,"
-		einfo "export MAXATOMS=\"your value\""
-		export MAXATOMS=10000
-	else
-		einfo "Allow usage of ${MAXATOMS} during calculations"
-	fi
-	fortran-2_pkg_setup
-	python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	find -type f \( -name "*\.pyc" -o -name "*\.pyo" \) -delete || die
-
-	cat > build_config.py <<- EOF
-	PREFIX="${ED}/$(python_get_sitedir)/${PN}"
-	#URL="http://<COMPUTER NAME>/pdb2pqr/"
-	APBS="${EPREFIX}/usr/bin/apbs"
-	#OPAL="http://nbcr-222.ucsd.edu/opal2/services/pdb2pqr_1.8"
-	#APBS_OPAL="http://nbcr-222.ucsd.edu/opal2/services/apbs_1.3"
-	MAX_ATOMS=${MAXATOMS}
-	BUILD_PDB2PKA=$(usex pdb2pka True False)
-	REBUILD_SWIG=True
-	EOF
-
-	export CXXFLAGS="${CXXFLAGS}"
-	export LDFLAGS="${LDFLAGS}"
-
-	epatch "${FILESDIR}"/${P}-flags.patch
-	tc-export CXX
-	rm -rf scons || die
-}
-
-src_compile() {
-	escons
-}
-
-src_test() {
-	local myesconsargs=( -j1 )
-	escons test
-	escons advtest
-	escons complete-test
-}
-
-src_install() {
-	escons install
-
-	local lib
-
-	make_wrapper ${PN} "${PYTHON} /$(python_get_sitedir)/${PN}/${PN}.py"
-	make_wrapper pdb2pka "${PYTHON} /$(python_get_sitedir)/${PN}/pdb2pka/pka.py"
-
-	for lib in apbslib.py{,c,o}; do
-		dosym ../../apbs/${lib} $(python_get_sitedir)/${PN}/pdb2pka/${lib}
-	done
-	dosym ../../_apbslib.so $(python_get_sitedir)/${PN}/pdb2pka/_apbslib.so
-
-	if use doc; then
-		pushd doc > /dev/null
-		dohtml -r *.html images pydoc
-		popd > /dev/null
-	fi
-
-	use examples && \
-		insinto /usr/share/${PN}/ && \
-		doins -r examples
-
-	dodir /usr/share/doc/${PF}/html
-	mv "${ED}"$(python_get_sitedir)/${PN}/doc/pydoc/* "${ED}"/usr/share/doc/${PF}/html || die
-	rmdir "${ED}"$(python_get_sitedir)/${PN}/doc/pydoc || die
-	mv "${ED}"$(python_get_sitedir)/${PN}/doc/* "${ED}"/usr/share/doc/${PF}/ || die
-
-	dodoc *md NEWS
-
-	find "${ED}"$(python_get_sitedir)/${PN}/contrib -delete || die
-
-	python_optimize
-}