sci-chemistry/pymol: add 3.1.0

Closes: https://bugs.gentoo.org/950338
Signed-off-by: Pacho Ramos <pacho@gentoo.org>

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

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
+}