sci-chemistry/pymol: Update to 3.0.0 and drop old

Closes: https://bugs.gentoo.org/862441
Closes: https://bugs.gentoo.org/910511
Closes: https://bugs.gentoo.org/929762
Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>

3 files changed, 6 insertions, 105 deletions

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 2c6723b71c25..2ef25b2b27fa 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,2 +1,2 @@
 DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
-DIST pymol-2.5.0.tar.gz 10470268 BLAKE2B ad3721432001053be93afe755f531ae47348213b042e84dae33cd79580428c9ac3d00629afa0222e4081807dc80e2dd69c3963a457666b5975b6263b988d02d9 SHA512 19f21b8f735fda5314abf202d56f3c81c7251bf6ef0df73ccee534d9c08035f4ef6155ffb68e09d7717a0fb5ba7289bbfa440691bea4cec0de7199c9e858ea91
+DIST pymol-3.0.0.tar.gz 29510174 BLAKE2B b67818e408045e386e44a203f29cd94a0ce34ec706776d29f78f1720bdc5c79d88f3b3e178882295b5a636d97fe70ff49eb1b021a9a6b96f0f4216bc392219d1 SHA512 eab05a46220339a05d8d4facdce6bfa08c6fc8a858a7b228236ef6c4054207059ef0f53a26bedebe4084a74b510015937fb4477f99612b21412cd75bf0c376a2
diff --git a/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild b/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild
deleted file mode 100644
index 317350640580..000000000000
--- a/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild
+++ /dev/null
@@ -1,100 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{9..11} )
-DISTUTILS_USE_SETUPTOOLS=no
-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 -> ${P}.tar.gz
-	"
-LICENSE="BitstreamVera BSD freedist HPND OFL-1.0 public-domain UoI-NCSA" #844991
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="+netcdf web"
-
-DEPEND="
-	dev-cpp/msgpack-cxx
-	dev-libs/mmtf-cpp
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pmw[${PYTHON_USEDEP}]
-	media-libs/freetype:2
-	media-libs/glew:0=
-	media-libs/glm
-	media-libs/libpng:0=
-	media-video/mpeg-tools
-	sys-libs/zlib
-	netcdf? ( sci-libs/netcdf:0= )
-"
-RDEPEND="${DEPEND}
-	sci-chemistry/chemical-mime-data
-"
-
-S="${WORKDIR}"/${PN}-open-source-${PV}
-
-python_prepare_all() {
-	sed \
-		-e "s:\"/usr:\"${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++0x
-
-	distutils-r1_python_prepare_all
-}
-
-python_configure_all() {
-	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}"/${PN}
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${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
-}
diff --git a/sci-chemistry/pymol/pymol-2.5.0-r5.ebuild b/sci-chemistry/pymol/pymol-3.0.0.ebuild
index 3e0e1d344ac6..150f7732d930 100644
--- a/sci-chemistry/pymol/pymol-2.5.0-r5.ebuild
+++ b/sci-chemistry/pymol/pymol-3.0.0.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{9..12} )
 DISTUTILS_USE_PEP517="setuptools"
 DISTUTILS_EXT=1
 
@@ -15,6 +15,9 @@ 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"
@@ -39,8 +42,6 @@ RDEPEND="${DEPEND}
 	sci-chemistry/chemical-mime-data
 "
 
-S="${WORKDIR}"/${PN}-open-source-${PV}
-
 PATCHES=(
 	"${FILESDIR}/${PN}-2.5.0-format-security.patch"
 )
@@ -59,7 +60,7 @@ python_prepare_all() {
 		-e "s:\['msgpackc'\]:\['msgpack'\]:g" \
 		-i setup.py || die
 
-	append-cxxflags -std=c++0x
+	append-cxxflags -std=c++17
 
 	distutils-r1_python_prepare_all
 }