commit: c97fc2c54ef33dc846378ef57fff770947317fc2 Author: Pacho Ramos <pacho <AT> gentoo <DOT> org> AuthorDate: Sat Jun 28 11:27:03 2025 +0000 Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org> CommitDate: Sat Jun 28 11:27:03 2025 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c97fc2c5
sci-chemistry/pymol: add 3.1.0 Closes: https://bugs.gentoo.org/950338 Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org> sci-chemistry/pymol/Manifest | 1 + sci-chemistry/pymol/pymol-3.1.0.ebuild | 121 +++++++++++++++++++++++++++++++++ 2 files changed, 122 insertions(+) diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest index 7b6fd1d91c5d..9cb6b70b1b94 100644 --- a/sci-chemistry/pymol/Manifest +++ b/sci-chemistry/pymol/Manifest @@ -1 +1,2 @@ DIST pymol-3.0.0.tar.gz 29510174 BLAKE2B b67818e408045e386e44a203f29cd94a0ce34ec706776d29f78f1720bdc5c79d88f3b3e178882295b5a636d97fe70ff49eb1b021a9a6b96f0f4216bc392219d1 SHA512 eab05a46220339a05d8d4facdce6bfa08c6fc8a858a7b228236ef6c4054207059ef0f53a26bedebe4084a74b510015937fb4477f99612b21412cd75bf0c376a2 +DIST pymol-3.1.0.tar.gz 29550866 BLAKE2B 0ad054407ac74bf2d088b1d4f7857bfd021ac283b05b95189aae7e9db2d6af8bf34d8b1ceb944af74d66a2d7b4481fa0b7dc42021d653d27d8661e00b1a44fbf SHA512 2eab9f12b0d716ae807659ebf4475f5a4748d4aa9db8266cea25059679898ce6f4c566d304ddaacf069b56baebc0f7c029c4bd1b2e983b8f7226c0d5cea5d097 diff --git a/sci-chemistry/pymol/pymol-3.1.0.ebuild b/sci-chemistry/pymol/pymol-3.1.0.ebuild new file mode 100644 index 000000000000..92bf696f3d13 --- /dev/null +++ b/sci-chemistry/pymol/pymol-3.1.0.ebuild @@ -0,0 +1,121 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{11..13} ) +DISTUTILS_USE_PEP517="standalone" +DISTUTILS_EXT=1 + +inherit desktop xdg distutils-r1 + +DESCRIPTION="A Python-extensible molecular graphics system" +HOMEPAGE="https://www.pymol.org/"; +SRC_URI="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 MIT-0 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[${PYTHON_USEDEP}] + >=dev-python/pillow-10.3.0[${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= ) +" +BDEPEND="test? ( >=dev-cpp/catch-2:0 ) + dev-python/setuptools[${PYTHON_USEDEP}] + dev-python/wheel[${PYTHON_USEDEP}] +" +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 +" + +distutils_enable_tests pytest + +# FIXME: We need to still figure out about how to make all the tests pass +# https://bugs.gentoo.org/932127 +RESTRICT="test" + +python_prepare_all() { + sed \ + -e 's/no_launcher = False/no_launcher = True/' \ + -i setup.py || die + + if use !netcdf; then + sed -e 's/vmd_plugins = True/vmd_plugins = False/' \ + -i setup.py || die + fi + + 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 + + distutils-r1_python_prepare_all +} + +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}"/${PN} +} + +python_test() { + "${EPYTHON}" -m pymol -ckqy testing/testing.py --offline --no-mmlibs --no-undo --run all || die +} + +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 "${S}"/data/pymol/icons/icon2.svg ${PN}.svg + make_desktop_entry "${PN} %u" PyMol ${PN} \ + "Graphics;Education;Science;Chemistry;" \ + "MimeType=chemical/x-pdb;chemical/pdby;chemical/x-mdl-sdfile;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;chemical/x-macromodel-input;chemical/x-vmd;" + + if ! use web; then + rm -rf "${D}/$(python_get_sitedir)/web" || die + fi + + rm -f "${ED}"/usr/share/${PN}/LICENSE || die +}
