sci-chemistry/pymol: drop 2.4.0-r1
Signed-off-by: David Seifert <soap@gentoo.org>
This commit is contained in:
David Seifert
parent
400f153a09
commit
95a31681e1
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DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
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DIST pymol-2.4.0.tar.gz 10552539 BLAKE2B 34e31dce99c1e838b00389c3d7c29657534dd037349769bd6c8cb17028cfaaa856d5729760d3768fd43f61086cac30749a864fb4156c14eda07f9027430f0523 SHA512 2b19294197d58a808bf7bb7fa9f829c2ec582ba47a4380783a2b1eedda2ce4118cd398e01885db8c449e7fd5e4c08a1c40508e679ef42d8e183a6a52b031c02a
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DIST pymol-2.5.0.tar.gz 10470268 BLAKE2B ad3721432001053be93afe755f531ae47348213b042e84dae33cd79580428c9ac3d00629afa0222e4081807dc80e2dd69c3963a457666b5975b6263b988d02d9 SHA512 19f21b8f735fda5314abf202d56f3c81c7251bf6ef0df73ccee534d9c08035f4ef6155ffb68e09d7717a0fb5ba7289bbfa440691bea4cec0de7199c9e858ea91
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@ -1,34 +0,0 @@
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From 885891cf60371674406cdff16b395e25cc13d8ae Mon Sep 17 00:00:00 2001
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From: Sebastian Keller <sebastian-keller@gmx.de>
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Date: Tue, 28 Jul 2020 22:50:53 +0200
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Subject: [PATCH] Don't drop the last model when updating the selector table
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The last assigned model in the Obj vector was at position modelCnt.
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Resizing the vector to modelCnt removes the last model, which later
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results in a crash when trying to access it.
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See https://github.com/schrodinger/pymol-open-source/issues/119
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---
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layer3/Selector.cpp | 2 +-
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1 file changed, 1 insertion(+), 1 deletion(-)
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diff --git a/layer3/Selector.cpp b/layer3/Selector.cpp
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index 546725b..637cd60 100644
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--- a/layer3/Selector.cpp
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+++ b/layer3/Selector.cpp
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@@ -7284,11 +7284,11 @@ static sele_array_t SelectorUpdateTableSingleObject(PyMOLGlobals * G, ObjectMole
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result[obj->SeleBase + at] = tag;
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}
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}
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}
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}
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- I->Obj.resize(modelCnt);
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+ I->Obj.resize(modelCnt + 1);
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I->Table.resize(c);
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PRINTFD(G, FB_Selector)
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"SelectorUpdateTableSingleObject-Debug: leaving...\n" ENDFD;
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--
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libgit2 1.0.1
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@ -1,116 +0,0 @@
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# Copyright 1999-2021 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=7
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PYTHON_COMPAT=( python3_{7..9} )
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DISTUTILS_USE_SETUPTOOLS=no
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inherit desktop optfeature flag-o-matic xdg distutils-r1
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DESCRIPTION="A Python-extensible molecular graphics system"
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HOMEPAGE="https://www.pymol.org/"
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SRC_URI="
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https://dev.gentoo.org/~pacho/${PN}/${PN}-1.8.4.0.png.xz
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https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz
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"
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RESTRICT="mirror"
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LICENSE="PSF-2.2"
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SLOT="0"
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KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
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IUSE="+netcdf web"
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DEPEND="
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dev-libs/msgpack[cxx]
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dev-libs/mmtf-cpp
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dev-python/pyopengl[${PYTHON_USEDEP}]
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dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
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dev-python/numpy[${PYTHON_USEDEP}]
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dev-python/pmw[${PYTHON_USEDEP}]
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media-libs/freetype:2
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media-libs/glew:0=
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media-libs/glm
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media-libs/libpng:0=
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media-video/mpeg-tools
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sys-libs/zlib
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netcdf? ( sci-libs/netcdf:0= )
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"
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RDEPEND="${DEPEND}
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sci-chemistry/chemical-mime-data
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"
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S="${WORKDIR}"/${PN}-open-source-${PV}
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PATCHES=(
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# https://github.com/schrodinger/pymol-open-source/issues/119
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"${FILESDIR}/${P}-fix_bug119.patch"
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)
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python_prepare_all() {
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sed \
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-e "s:\"/usr:\"${EPREFIX}/usr:g" \
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-e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
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-i setup.py || die
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sed \
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-e "s:/opt/local:${EPREFIX}/usr:g" \
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-e '/ext_comp_args/s:\[.*\]:[]:g' \
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-i setup.py || die
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sed \
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-e "s:\['msgpackc'\]:\['msgpack'\]:g" \
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-i setup.py || die
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append-cxxflags -std=c++0x
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use !netcdf && mydistutilsargs=( --no-vmd-plugins )
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distutils-r1_python_prepare_all
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}
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python_install() {
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distutils-r1_python_install \
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--pymol-path="${EPREFIX}/usr/share/pymol"
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sed \
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-e '1d' \
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-e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \
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-e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \
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-e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \
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-i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die
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}
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python_install_all() {
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distutils-r1_python_install_all
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sed \
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-e '1i#!/usr/bin/env python' \
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"${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die
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python_foreach_impl python_doscript "${T}"/${PN}
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# These environment variables should not go in the wrapper script, or else
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# it will be impossible to use the PyMOL libraries from Python.
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cat >> "${T}"/20pymol <<- EOF || die
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PYMOL_PATH="${EPREFIX}/usr/share/pymol"
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PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
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PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
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EOF
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doenvd "${T}"/20pymol
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newicon "${WORKDIR}"/${PN}-1.8.4.0.png ${PN}.png
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make_desktop_entry ${PN} PyMol ${PN} \
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"Graphics;Education;Science;Chemistry;" \
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"MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;"
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if ! use web; then
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rm -rf "${D}/$(python_get_sitedir)/web" || die
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fi
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rm -f "${ED}"/usr/share/${PN}/LICENSE || die
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}
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pkg_postinst() {
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xdg_pkg_postinst
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optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
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}
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