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121 lines
3.2 KiB
Bash
121 lines
3.2 KiB
Bash
# Copyright 1999-2025 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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PYTHON_COMPAT=( python3_{11..13} )
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DISTUTILS_USE_PEP517="standalone"
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DISTUTILS_EXT=1
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inherit desktop xdg distutils-r1
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DESCRIPTION="A Python-extensible molecular graphics system"
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HOMEPAGE="https://www.pymol.org/"
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SRC_URI="https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz"
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S="${WORKDIR}"/${PN}-open-source-${PV}
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LICENSE="BitstreamVera BSD freedist HPND MIT-0 OFL-1.0 public-domain UoI-NCSA" #844991
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SLOT="0"
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KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
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IUSE="+netcdf web"
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DEPEND="
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dev-cpp/msgpack-cxx
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dev-libs/mmtf-cpp
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dev-python/numpy[${PYTHON_USEDEP}]
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>=dev-python/pillow-10.3.0[${PYTHON_USEDEP}]
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sys-libs/zlib
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media-libs/freetype:2
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media-libs/glew:0=
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media-libs/glm
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media-libs/libpng:0=
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netcdf? ( sci-libs/netcdf:0= )
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"
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BDEPEND="test? ( >=dev-cpp/catch-2:0 )
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dev-python/setuptools[${PYTHON_USEDEP}]
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dev-python/wheel[${PYTHON_USEDEP}]
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"
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RDEPEND="
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${DEPEND}
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media-video/mpeg-tools
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dev-python/pyopengl[${PYTHON_USEDEP}]
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dev-python/pyqt5[opengl,${PYTHON_USEDEP}]
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dev-python/pmw[${PYTHON_USEDEP}]
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sci-chemistry/chemical-mime-data
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"
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distutils_enable_tests pytest
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# FIXME: We need to still figure out about how to make all the tests pass
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# https://bugs.gentoo.org/932127
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RESTRICT="test"
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python_prepare_all() {
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sed \
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-e 's/no_launcher = False/no_launcher = True/' \
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-i setup.py || die
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if use !netcdf; then
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sed -e 's/vmd_plugins = True/vmd_plugins = False/' \
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-i setup.py || die
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fi
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sed \
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-e "s:\"/usr:\"${EPREFIX}/usr:g" \
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-e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
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-i setup.py || die
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sed \
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-e "s:/opt/local:${EPREFIX}/usr:g" \
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-e '/ext_comp_args/s:\[.*\]:[]:g' \
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-i setup.py || die
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sed \
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-e "s:\['msgpackc'\]:\['msgpack'\]:g" \
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-i setup.py || die
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distutils-r1_python_prepare_all
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}
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python_install() {
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distutils-r1_python_install \
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--pymol-path="${EPREFIX}/usr/share/pymol"
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sed \
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-e '1i#!/usr/bin/env python' \
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"${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die
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python_doscript "${T}"/${PN}
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}
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python_test() {
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"${EPYTHON}" -m pymol -ckqy testing/testing.py --offline --no-mmlibs --no-undo --run all || die
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}
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python_install_all() {
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distutils-r1_python_install_all
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# Move data to correct location
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dodir /usr/share/pymol
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mv "${D}/$(python_get_sitedir)"/pymol/pymol_path/* "${ED}/usr/share/pymol" || die
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# These environment variables should not go in the wrapper script, or else
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# it will be impossible to use the PyMOL libraries from Python.
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cat >> "${T}"/20pymol <<- EOF || die
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PYMOL_PATH="${EPREFIX}/usr/share/pymol"
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PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
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PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
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EOF
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doenvd "${T}"/20pymol
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newicon "${S}"/data/pymol/icons/icon2.svg ${PN}.svg
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make_desktop_entry "${PN} %u" PyMol ${PN} \
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"Graphics;Education;Science;Chemistry;" \
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"MimeType=chemical/x-pdb;chemical/pdby;chemical/x-mdl-sdfile;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;chemical/x-macromodel-input;chemical/x-vmd;"
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if ! use web; then
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rm -rf "${D}/$(python_get_sitedir)/web" || die
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fi
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rm -f "${ED}"/usr/share/${PN}/LICENSE || die
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}
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