From 0c2a5cb0f6a062b7da6f9a90cbb06e3784df29a6 Mon Sep 17 00:00:00 2001 From: Michał Górny Date: Sat, 8 Feb 2020 13:36:34 +0100 Subject: sci-chemistry/pdb2pqr: Switch to python-single-r1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Use python-single-r1 as requiered for the dep on sci-chemistry/apbs. Signed-off-by: Michał Górny --- sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r2.ebuild | 132 -------------------------- sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild | 114 ++++++++++++++++++++++ 2 files changed, 114 insertions(+), 132 deletions(-) delete mode 100644 sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r2.ebuild create mode 100644 sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild (limited to 'sci-chemistry/pdb2pqr') diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r2.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r2.ebuild deleted file mode 100644 index ad95f8f410fa..000000000000 --- a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r2.ebuild +++ /dev/null @@ -1,132 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit scons-utils fortran-2 flag-o-matic python-r1 toolchain-funcs - -DESCRIPTION="Automated pipeline for performing Poisson-Boltzmann electrostatics calculations" -HOMEPAGE="https://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 x86 ~amd64-linux ~x86-linux" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - || ( - dev-python/numpy-python2[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - ) - 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" - -PATCHES=( - "${FILESDIR}"/${P}-flags.patch - "${FILESDIR}"/${P}-install-py.patch -) - -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 -} - -src_prepare() { - find -type f \( -name "*\.pyc" -o -name "*\.pyo" \) -delete || die - - export CXXFLAGS="${CXXFLAGS}" - export LDFLAGS="${LDFLAGS}" - - epatch "${PATCHES[@]}" - tc-export CXX - rm -rf scons || die - - python_copy_sources -} - -src_configure() { - python_configure() { - cd "${BUILD_DIR}" || die - - cat > build_config.py <<- EOF - PREFIX="${D}/$(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 - } - - python_foreach_impl python_configure -} - -src_compile() { - python_compile() { - cd "${BUILD_DIR}" || die - escons - } - python_foreach_impl python_compile -} - -src_test() { - python_test() { - local myesconsargs=( -j1 ) - cd "${BUILD_DIR}" || die - escons test - escons advtest - escons complete-test - } - python_foreach_impl python_test -} - -src_install() { - dodir /usr/share/doc/${PF}/html - python_install() { - local lib - - cd "${BUILD_DIR}" || die - - escons install - - find "${D}$(python_get_sitedir)"/${PN}/{jmol,examples,doc,contrib} -delete || die - - python_doscript "${FILESDIR}"/{${PN},pdb2pka} - - for lib in apbslib.py{,c,o}; do - dosym ../../apbs/${lib} $(python_get_sitedir)/${PN}/pdb2pka/${lib} - done - dosym ../../_apbslib.so $(python_get_sitedir)/${PN}/pdb2pka/_apbslib.so - python_optimize - } - python_foreach_impl python_install - - if use doc; then - pushd doc > /dev/null - docinto html - dodoc -r *.html images pydoc - popd > /dev/null - fi - - use examples && \ - insinto /usr/share/${PN}/ && \ - doins -r examples - - dodoc *md NEWS -} diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild new file mode 100644 index 000000000000..179e6448d605 --- /dev/null +++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild @@ -0,0 +1,114 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit scons-utils fortran-2 flag-o-matic python-single-r1 toolchain-funcs + +DESCRIPTION="Automated pipeline for performing Poisson-Boltzmann electrostatics calculations" +HOMEPAGE="https://www.poissonboltzmann.org/" +SRC_URI="https://github.com/Electrostatics/apbs-${PN}/releases/download/${P}/${PN}-src-${PV}.tar.gz" + +SLOT="0" +LICENSE="BSD" +IUSE="doc examples opal +pdb2pka" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + $(python_gen_cond_dep ' + || ( + dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}] + dev-python/numpy[${PYTHON_MULTI_USEDEP}] + ) + sci-chemistry/openbabel-python[${PYTHON_MULTI_USEDEP}] + opal? ( dev-python/zsi[${PYTHON_MULTI_USEDEP}] ) + ') + pdb2pka? ( sci-chemistry/apbs[${PYTHON_SINGLE_USEDEP},-mpi] )" +DEPEND="${RDEPEND} + dev-lang/swig:0" + +PATCHES=( + "${FILESDIR}"/${P}-flags.patch + "${FILESDIR}"/${P}-install-py.patch +) + +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 + + export CXXFLAGS="${CXXFLAGS}" + export LDFLAGS="${LDFLAGS}" + + epatch "${PATCHES[@]}" + tc-export CXX + rm -rf scons || die +} + +src_configure() { + cat > build_config.py <<- EOF + PREFIX="${D}/$(python_get_sitedir)/${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=$(usex pdb2pka True False) + REBUILD_SWIG=True + EOF +} + +src_compile() { + escons +} + +src_test() { + local myesconsargs=( -j1 ) + escons test + escons advtest + escons complete-test +} + +src_install() { + dodir /usr/share/doc/${PF}/html + local lib + + escons install + + find "${D}$(python_get_sitedir)"/${PN}/{jmol,examples,doc,contrib} -delete || die + + python_doscript "${FILESDIR}"/{${PN},pdb2pka} + + for lib in apbslib.py{,c,o}; do + dosym ../../apbs/${lib} $(python_get_sitedir)/${PN}/pdb2pka/${lib} + done + dosym ../../_apbslib.so $(python_get_sitedir)/${PN}/pdb2pka/_apbslib.so + python_optimize + + if use doc; then + pushd doc > /dev/null + docinto html + dodoc -r *.html images pydoc + popd > /dev/null + fi + + use examples && \ + insinto /usr/share/${PN}/ && \ + doins -r examples + + dodoc *md NEWS +} -- cgit v1.2.3-65-gdbad