From d42200bec37eef2a7478d88988ff00addd0a9202 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sat, 25 Jan 2020 11:50:47 +0000 Subject: gentoo resync : 25.01.2020 --- sci-chemistry/pdb2pqr/Manifest | 2 +- sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild | 132 -------------------------- sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r2.ebuild | 132 ++++++++++++++++++++++++++ 3 files changed, 133 insertions(+), 133 deletions(-) delete mode 100644 sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild create mode 100644 sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r2.ebuild (limited to 'sci-chemistry/pdb2pqr') diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest index 87ce3397495f..911dbff7ccca 100644 --- a/sci-chemistry/pdb2pqr/Manifest +++ b/sci-chemistry/pdb2pqr/Manifest @@ -3,5 +3,5 @@ AUX pdb2pqr 263 BLAKE2B 3cbd33cf9fb9fd6469c71d8d167ed0fb85ad7b87b6caf27dabb2490b AUX pdb2pqr-1.9.0-flags.patch 1392 BLAKE2B b6b6ac64f98944d85fc93c076d7258c8f980a0391d2cf086edc46bca3f4ef15a5cb720ef8ae2dc38007962a462fb88e92eb4f439c4f3267a5d1d83de5a848dd6 SHA512 deed0aef88dc43515745204f2b4209bd6b42702d9004d48797d642b8f497229424bd0bb92017982cec54c448ea35de563bd42017cd5dc042840acae8495d135b AUX pdb2pqr-1.9.0-install-py.patch 578 BLAKE2B 91ad4b40ce3d13b574ad6d9ea84e55b08803fa018490a7327dae5621a371adfeda509188c049144301cbc023f4407f6c0daf7b57e7d3c10d95d78ab570a6f540 SHA512 902ad717e32790e9c691851dc4b92412f07ac79caf74b2b5794a10fa75cca7fa19e8814df4d8ba71bd2ecc98a3d777d0b79e6e43009171a32e8c99756d81d4d2 DIST pdb2pqr-src-1.9.0.tar.gz 9051969 BLAKE2B bacb2c65d319fb918a7a15b772c250398ffa991a93ee731ec15c8ae907304daf57282bf83c24f84d11945349a7f93f6f934575c117d4ce24d6530f14e60f3730 SHA512 7f3f191cca9879a0e166e82700c706f8c99bb66558a218e54845f10c3324b6c45d413da80b0782d96a8d56df1463262609db075aba3768db3942cb928ee7b98f -EBUILD pdb2pqr-1.9.0-r1.ebuild 2961 BLAKE2B b8aa0bba7cb9d94f8a8fcc3246ae63d6c8a92f8148fbf28b73b683425b00bedb58069250b06e6e08e21ca483343723738c70c8c7e19309559d05c032c5bb4d62 SHA512 5e613fe7a2e927634fde7f685a8ab9429f171d469280a21c8004dd718a22e4ed5bcfb30e0d5ea6426744e0a75f4ffd366ae93d7c458d6bd72e0269e7dcb006a4 +EBUILD pdb2pqr-1.9.0-r2.ebuild 2961 BLAKE2B b8aa0bba7cb9d94f8a8fcc3246ae63d6c8a92f8148fbf28b73b683425b00bedb58069250b06e6e08e21ca483343723738c70c8c7e19309559d05c032c5bb4d62 SHA512 5e613fe7a2e927634fde7f685a8ab9429f171d469280a21c8004dd718a22e4ed5bcfb30e0d5ea6426744e0a75f4ffd366ae93d7c458d6bd72e0269e7dcb006a4 MISC metadata.xml 511 BLAKE2B 70a1bf9ff6db44bdbae39b1f58ac5b80769738b2ce8fbb19b3bcb9fbf7cec2a9eab215a7a922025b9110673cb834255240adf10613fd78a8fea47fa7be4fbba9 SHA512 11a010eea3bbbaaf4150a23dadcd10c45737745d51a3341cd7e69cc8537215f313d1ab57059eff265e73e34aeaef435585bb652f5497508dd12b99f67b8580c0 diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild deleted file mode 100644 index ad95f8f410fa..000000000000 --- a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.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/${PN}/ && \ - doins -r examples - - dodoc *md NEWS -} diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r2.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r2.ebuild new file mode 100644 index 000000000000..ad95f8f410fa --- /dev/null +++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r2.ebuild @@ -0,0 +1,132 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit scons-utils fortran-2 flag-o-matic python-r1 toolchain-funcs + +DESCRIPTION="Automated pipeline for performing Poisson-Boltzmann electrostatics calculations" +HOMEPAGE="https://www.poissonboltzmann.org/" +SRC_URI="https://github.com/Electrostatics/apbs-${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 +} -- cgit v1.2.3