From: Justin Lecher Date: Sun, 4 Jan 2015 19:17:40 +0000 (+0000) Subject: sci-chemistry/pdb2pqr: Drop old X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=90bc9c07c4657fd07b7da035f311ebc82635fe8f;p=gentoo.git sci-chemistry/pdb2pqr: Drop old Package-Manager: portage-2.2.15/cvs/Linux x86_64 Manifest-Sign-Key: 0xB9D4F231BD1558AB! --- 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 -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 pdb2pqr-1.9.0-r1.ebuild: Drop obsolete dep diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest index 7e28efb2a0b5..ad9f02c1401f 100644 --- a/sci-chemistry/pdb2pqr/Manifest +++ b/sci-chemistry/pdb2pqr/Manifest @@ -12,33 +12,27 @@ AUX pdb2pqr-1.8.0-ldflags.patch 1098 SHA256 b9ab2740e062b130c4b61d385b762d4ce54e AUX pdb2pqr-1.9.0-flags.patch 1392 SHA256 478b86cf3871e39b9d231a10474abbcade07eceb32db2a83c0e68bbd2c1f5f32 SHA512 deed0aef88dc43515745204f2b4209bd6b42702d9004d48797d642b8f497229424bd0bb92017982cec54c448ea35de563bd42017cd5dc042840acae8495d135b WHIRLPOOL 7280c677dbfeb309c6c66d495c857a581fbac80801f9241c20ff17a2c6f4e051929f675807ec30f8dce1fd5337937c76e857b955570f2c1f134855a2b7c0ec2c AUX pdb2pqr-1.9.0-install-py.patch 578 SHA256 c82c11eb421a839710d40bfb3de4d99852ef69dc9b35b1ac31f7b51b36ff512d SHA512 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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)/${PN}" - #URL="http:///pdb2pqr/" - APBS="${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 -}