[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/

["David Seifert" <soap@gentoo.org>]

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 <sebastian-keller@gmx.de>
-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
-}