# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 PYTHON_COMPAT=( python3_{9..12} ) DISTUTILS_USE_PEP517="setuptools" DISTUTILS_EXT=1 inherit desktop 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 -> ${P}.tar.gz " S="${WORKDIR}"/${PN}-open-source-${PV} LICENSE="BitstreamVera BSD freedist HPND OFL-1.0 public-domain UoI-NCSA" #844991 SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" IUSE="+netcdf web" DEPEND=" dev-cpp/msgpack-cxx dev-libs/mmtf-cpp dev-python/numpy[${PYTHON_USEDEP}] sys-libs/zlib media-libs/freetype:2 media-libs/glew:0= media-libs/glm media-libs/libpng:0= netcdf? ( sci-libs/netcdf:0= ) " RDEPEND=" ${DEPEND} media-video/mpeg-tools dev-python/pyopengl[${PYTHON_USEDEP}] dev-python/PyQt5[opengl,${PYTHON_USEDEP}] dev-python/pmw[${PYTHON_USEDEP}] sci-chemistry/chemical-mime-data " PATCHES=( "${FILESDIR}/${PN}-2.5.0-format-security.patch" ) 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++17 distutils-r1_python_prepare_all } python_configure_all() { # -Werror=odr # https://bugs.gentoo.org/933235 # https://github.com/schrodinger/pymol-open-source/issues/395 filter-lto use !netcdf && DISTUTILS_ARGS=( --no-vmd-plugins ) } python_install() { distutils-r1_python_install \ --pymol-path="${EPREFIX}/usr/share/pymol" sed \ -e '1i#!/usr/bin/env python' \ "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die python_doscript "${T}"/${PN} } python_install_all() { distutils-r1_python_install_all # Move data to correct location dodir /usr/share/pymol mv "${D}/$(python_get_sitedir)"/pymol/pymol_path/* "${ED}/usr/share/pymol" || die # 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} %u" 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 }