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author | Alexey Shvetsov <alexxy@gentoo.org> | 2021-05-16 23:41:00 +0300 |
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committer | Alexey Shvetsov <alexxy@gentoo.org> | 2021-05-16 23:41:15 +0300 |
commit | 428de16e86460563d0e465331e301cc0dedf91ac (patch) | |
tree | ddc9c08640b86b71dc0813d7fa39b04d3714c8f7 /sci-chemistry/pymol/pymol-2.5.0.ebuild | |
parent | x11-apps/igt-gpu-tools: use ${EPYTHON}, not python3 (diff) | |
download | gentoo-428de16e86460563d0e465331e301cc0dedf91ac.tar.gz gentoo-428de16e86460563d0e465331e301cc0dedf91ac.tar.bz2 gentoo-428de16e86460563d0e465331e301cc0dedf91ac.zip |
sci-chemistry/pymol: Version bump
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
Diffstat (limited to 'sci-chemistry/pymol/pymol-2.5.0.ebuild')
-rw-r--r-- | sci-chemistry/pymol/pymol-2.5.0.ebuild | 111 |
1 files changed, 111 insertions, 0 deletions
diff --git a/sci-chemistry/pymol/pymol-2.5.0.ebuild b/sci-chemistry/pymol/pymol-2.5.0.ebuild new file mode 100644 index 000000000000..6d7ecd4e09c5 --- /dev/null +++ b/sci-chemistry/pymol/pymol-2.5.0.ebuild @@ -0,0 +1,111 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_{7..9} ) +DISTUTILS_USE_SETUPTOOLS=no + +inherit desktop optfeature flag-o-matic xdg distutils-r1 + +DESCRIPTION="A Python-extensible molecular graphics system" +HOMEPAGE="https://www.pymol.org/" +SRC_URI=" + https://dev.gentoo.org/~pacho/${PN}/${PN}-1.8.4.0.png.xz + https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz + " +RESTRICT="mirror" +LICENSE="PSF-2.2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="+netcdf web" + +DEPEND=" + dev-libs/msgpack[cxx] + dev-libs/mmtf-cpp + dev-python/pyopengl[${PYTHON_USEDEP}] + dev-python/PyQt5[opengl,${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pmw[${PYTHON_USEDEP}] + media-libs/freetype:2 + media-libs/glew:0= + media-libs/glm + media-libs/libpng:0= + media-video/mpeg-tools + sys-libs/zlib + netcdf? ( sci-libs/netcdf:0= ) +" +RDEPEND="${DEPEND} + sci-chemistry/chemical-mime-data +" + +S="${WORKDIR}"/${PN}-open-source-${PV} + +python_prepare_all() { + sed \ + -e "s:\"/usr:\"${EPREFIX}/usr:g" \ + -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \ + -i setup.py || die + + sed \ + -e "s:/opt/local:${EPREFIX}/usr:g" \ + -e '/ext_comp_args/s:\[.*\]:[]:g' \ + -i setup.py || die + sed \ + -e "s:\['msgpackc'\]:\['msgpack'\]:g" \ + -i setup.py || die + + append-cxxflags -std=c++0x + + use !netcdf && mydistutilsargs=( --no-vmd-plugins ) + + distutils-r1_python_prepare_all +} + +python_install() { + distutils-r1_python_install \ + --pymol-path="${EPREFIX}/usr/share/pymol" + + sed \ + -e '1d' \ + -e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \ + -e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \ + -e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \ + -i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die +} + +python_install_all() { + distutils-r1_python_install_all + + sed \ + -e '1i#!/usr/bin/env python' \ + "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die + + python_foreach_impl python_doscript "${T}"/${PN} + + # These environment variables should not go in the wrapper script, or else + # it will be impossible to use the PyMOL libraries from Python. + cat >> "${T}"/20pymol <<- EOF || die + PYMOL_PATH="${EPREFIX}/usr/share/pymol" + PYMOL_DATA="${EPREFIX}/usr/share/pymol/data" + PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts" + EOF + + doenvd "${T}"/20pymol + + newicon "${WORKDIR}"/${PN}-1.8.4.0.png ${PN}.png + make_desktop_entry ${PN} PyMol ${PN} \ + "Graphics;Education;Science;Chemistry;" \ + "MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;" + + if ! use web; then + rm -rf "${D}/$(python_get_sitedir)/web" || die + fi + + rm -f "${ED}"/usr/share/${PN}/LICENSE || die +} + +pkg_postinst() { + xdg_pkg_postinst + optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr +} |