gentoo auto-resync : 24:11:2024 - 03:02:54

3 files changed, 3 insertions, 120 deletions

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 1352ddf62ff9..14721b14d7ae 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -5,8 +5,6 @@ AUX pymol-3.0.0-eof-maeffplugin.patch 1071 BLAKE2B b28941bd3fddb534fe150b3d98ef6
 AUX pymol-3.0.0-lto-molfile-plugin.patch 5585 BLAKE2B d9cedbb270184d562373fc9e8a2e1a75b08c5d1a956c28eac55662b424996a6770ea46d45b0645a7b96ab465af0f6aafac3120ed13a29f12daea5ab7c947da5d SHA512 babe47d4cbea390031d1880cf442c780f442d41bdeb181509df307550aa8d9c829af51a676665e8d55ed4cd6ab3f2cde363a087606cb064238bbc74be7e2fe51
 AUX pymol-3.0.0-numpy2.patch 1203 BLAKE2B bd06e70fea5a9a4940ecea226f2bd8d1f4753826ee246d6d418cd473c0ee738b9373c8f6e2f5e56e3708ab2934486286d43c33441e1e97f819c6ac0af731d060 SHA512 2c9445f013383fb534dca4306fa5f8ab8f55b33ed4bc53617e7765cb708a4ebc5380f8578ea1236f61e9e77a6d5a8e21588f7f081f6d6408195b9fa5b67c60b2
 AUX pymol-3.0.0-py3.12-progress.patch 985 BLAKE2B 77103dc94b2e9e304f65e429f5abb1cd2158d95a0b8b53e90d7e915b213a934ea8a598240355437b00cf95e0203c382d003034fa30a37dc00758351d13163e38 SHA512 ff7b75402a92d491145e1487fa018182a2a5a91f1736c63d07a194e6710d425f1bba59a7b4f0f49321e27db8c05e26feda7df12f42a66b1e1cdbf1e52f869a5b
-DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
 DIST pymol-3.0.0.tar.gz 29510174 BLAKE2B b67818e408045e386e44a203f29cd94a0ce34ec706776d29f78f1720bdc5c79d88f3b3e178882295b5a636d97fe70ff49eb1b021a9a6b96f0f4216bc392219d1 SHA512 eab05a46220339a05d8d4facdce6bfa08c6fc8a858a7b228236ef6c4054207059ef0f53a26bedebe4084a74b510015937fb4477f99612b21412cd75bf0c376a2
-EBUILD pymol-3.0.0-r1.ebuild 3372 BLAKE2B 378b1587c25a4592b6e2e503e7280f38d44696a899d5931c6f3e5a2ef11ed5f28d2bd9ba2e8024e6ed223d6bf504a2b76f7b730926eac7bbdbfbb29f986b3287 SHA512 597918ca799ceb6b2a29704ddc96e2b67464d66dd27ce6d32b00294854d34a4abbeb340848f2d3101464b6f263fb4dd07314c54d14fb87be57b07a27ae06522a
-EBUILD pymol-3.0.0.ebuild 2958 BLAKE2B 2eac68b0cf15c3369e243b7456e00b1c1119f0d8399bea7321794981f41911bd56bc10713c9102475a054e6a52353cef63c0f9416974bb1db5d91ddd9f6d2dfa SHA512 ca7a597cd909d5a04e77c0afb7e2c07413b13dd42d5788db97defabee23370695299e17193b431eb6190c87a0e06d8e741d2067de973652d1749b244cfeb0254
+EBUILD pymol-3.0.0-r1.ebuild 3373 BLAKE2B dcc30e9c9604b4572aaacbe3cab839874b6a76374b04cdad2131095dd3e5b4bf2a478e41c0357ecedec0427814002bae3b064b9591555a800aac175c4d615eb5 SHA512 7d9e6861bba0891e6f568ddc1a14f00f9a99725398e1b238a160ad6800e5d1d03eab72e583de285c17b110f686a532243060a7e3a31ec1c9ab29d06a9018bfd0
 MISC metadata.xml 495 BLAKE2B 32d321e92c7e7c226747660c314f5cff9aabf9ee41c8a864064432ac9554879db7bf60640993dadae6e00a9b7d1367cb8ab228b63b8797ca84e5618eeeb192cc SHA512 36ef956d111c76182c70c81a830885f540fb2710f696b2711837d4bf1055a8792226f38b827f389a3a3861f259bae1394d6da50c2b33a0ddb4e6940262e1b25d
diff --git a/sci-chemistry/pymol/pymol-3.0.0-r1.ebuild b/sci-chemistry/pymol/pymol-3.0.0-r1.ebuild
index aeb6bc85c7e1..ff2b8174eeb4 100644
--- a/sci-chemistry/pymol/pymol-3.0.0-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-3.0.0-r1.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..12} )
+PYTHON_COMPAT=( python3_{10..12} )
 DISTUTILS_USE_PEP517="setuptools"
 DISTUTILS_EXT=1
 
@@ -36,7 +36,7 @@ RDEPEND="
 	${DEPEND}
 	media-video/mpeg-tools
 	dev-python/pyopengl[${PYTHON_USEDEP}]
-	dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
+	dev-python/pyqt5[opengl,${PYTHON_USEDEP}]
 	dev-python/pmw[${PYTHON_USEDEP}]
 	sci-chemistry/chemical-mime-data
 "
diff --git a/sci-chemistry/pymol/pymol-3.0.0.ebuild b/sci-chemistry/pymol/pymol-3.0.0.ebuild
deleted file mode 100644
index b6ec9fbef1e3..000000000000
--- a/sci-chemistry/pymol/pymol-3.0.0.ebuild
+++ /dev/null
@@ -1,115 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{9..12} )
-DISTUTILS_USE_PEP517="setuptools"
-DISTUTILS_EXT=1
-
-inherit desktop flag-o-matic xdg distutils-r1
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="https://www.pymol.org/"
-SRC_URI="
-	https://dev.gentoo.org/~pacho/${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
-}