commit: 95a31681e14af07ba21add4cdb655fe3211eedeb Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Oct 24 11:20:28 2021 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Oct 24 11:20:28 2021 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=95a31681
sci-chemistry/pymol: drop 2.4.0-r1 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-chemistry/pymol/Manifest | 1 - .../pymol/files/pymol-2.4.0-fix_bug119.patch | 34 ------ sci-chemistry/pymol/pymol-2.4.0-r1.ebuild | 116 --------------------- 3 files changed, 151 deletions(-) diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest index dec8f0b1525..2c6723b71c2 100644 --- a/sci-chemistry/pymol/Manifest +++ b/sci-chemistry/pymol/Manifest @@ -1,3 +1,2 @@ DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c -DIST pymol-2.4.0.tar.gz 10552539 BLAKE2B 34e31dce99c1e838b00389c3d7c29657534dd037349769bd6c8cb17028cfaaa856d5729760d3768fd43f61086cac30749a864fb4156c14eda07f9027430f0523 SHA512 2b19294197d58a808bf7bb7fa9f829c2ec582ba47a4380783a2b1eedda2ce4118cd398e01885db8c449e7fd5e4c08a1c40508e679ef42d8e183a6a52b031c02a DIST pymol-2.5.0.tar.gz 10470268 BLAKE2B ad3721432001053be93afe755f531ae47348213b042e84dae33cd79580428c9ac3d00629afa0222e4081807dc80e2dd69c3963a457666b5975b6263b988d02d9 SHA512 19f21b8f735fda5314abf202d56f3c81c7251bf6ef0df73ccee534d9c08035f4ef6155ffb68e09d7717a0fb5ba7289bbfa440691bea4cec0de7199c9e858ea91 diff --git a/sci-chemistry/pymol/files/pymol-2.4.0-fix_bug119.patch b/sci-chemistry/pymol/files/pymol-2.4.0-fix_bug119.patch deleted file mode 100644 index 62512053fd7..00000000000 --- a/sci-chemistry/pymol/files/pymol-2.4.0-fix_bug119.patch +++ /dev/null @@ -1,34 +0,0 @@ -From 885891cf60371674406cdff16b395e25cc13d8ae Mon Sep 17 00:00:00 2001 -From: Sebastian Keller <[email protected]> -Date: Tue, 28 Jul 2020 22:50:53 +0200 -Subject: [PATCH] Don't drop the last model when updating the selector table - -The last assigned model in the Obj vector was at position modelCnt. -Resizing the vector to modelCnt removes the last model, which later -results in a crash when trying to access it. - -See https://github.com/schrodinger/pymol-open-source/issues/119 ---- - layer3/Selector.cpp | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/layer3/Selector.cpp b/layer3/Selector.cpp -index 546725b..637cd60 100644 ---- a/layer3/Selector.cpp -+++ b/layer3/Selector.cpp -@@ -7284,11 +7284,11 @@ static sele_array_t SelectorUpdateTableSingleObject(PyMOLGlobals * G, ObjectMole - result[obj->SeleBase + at] = tag; - } - } - } - } -- I->Obj.resize(modelCnt); -+ I->Obj.resize(modelCnt + 1); - I->Table.resize(c); - - PRINTFD(G, FB_Selector) - "SelectorUpdateTableSingleObject-Debug: leaving...\n" ENDFD; - --- -libgit2 1.0.1 - diff --git a/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild b/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild deleted file mode 100644 index c710896747d..00000000000 --- a/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild +++ /dev/null @@ -1,116 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) -DISTUTILS_USE_SETUPTOOLS=no - -inherit desktop optfeature 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 -> ${P}.tar.gz - " -RESTRICT="mirror" -LICENSE="PSF-2.2" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" -IUSE="+netcdf web" - -DEPEND=" - dev-libs/msgpack[cxx] - dev-libs/mmtf-cpp - dev-python/pyopengl[${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-${PV} - -PATCHES=( - # https://github.com/schrodinger/pymol-open-source/issues/119 - "${FILESDIR}/${P}-fix_bug119.patch" -) - -python_prepare_all() { - sed \ - -e "s:\"/usr:\"${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++0x - - use !netcdf && mydistutilsargs=( --no-vmd-plugins ) - - distutils-r1_python_prepare_all -} - -python_install() { - distutils-r1_python_install \ - --pymol-path="${EPREFIX}/usr/share/pymol" - - sed \ - -e '1d' \ - -e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \ - -e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \ - -e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \ - -i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die -} - -python_install_all() { - distutils-r1_python_install_all - - sed \ - -e '1i#!/usr/bin/env python' \ - "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die - - python_foreach_impl python_doscript "${T}"/${PN} - - # 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} 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 -} - -pkg_postinst() { - xdg_pkg_postinst - optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr -}
