commit: dfe0f62750dadf6273bd4146db194c7165181781 Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> AuthorDate: Fri May 17 19:20:35 2024 +0000 Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> CommitDate: Fri May 17 19:20:35 2024 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=dfe0f627
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 <AT> gentoo.org> sci-chemistry/pymol/Manifest | 2 +- sci-chemistry/pymol/pymol-2.5.0-r3.ebuild | 100 --------------------- .../{pymol-2.5.0-r5.ebuild => pymol-3.0.0.ebuild} | 9 +- 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/${PN}/LICENSE || die -} diff --git a/sci-chemistry/pymol/pymol-2.5.0-r5.ebuild b/sci-chemistry/pymol/pymol-3.0.0.ebuild similarity index 97% rename from sci-chemistry/pymol/pymol-2.5.0-r5.ebuild rename to sci-chemistry/pymol/pymol-3.0.0.ebuild index 3e0e1d344ac6..150f7732d930 100644 --- a/sci-chemistry/pymol/pymol-2.5.0-r5.ebuild +++ b/sci-chemistry/pymol/pymol-3.0.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{9..11} ) +PYTHON_COMPAT=( python3_{9..12} ) DISTUTILS_USE_PEP517="setuptools" DISTUTILS_EXT=1 @@ -15,6 +15,9 @@ SRC_URI=" https://dev.gentoo.org/~pacho/${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 }
