gentoo resync : 25.10.2021

6 files changed, 11 insertions, 163 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 9179b0b9fb77..249ae0cf5547 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/cluster/Manifest b/sci-chemistry/cluster/Manifest
index d640d1a734fd..c89146efc997 100644
--- a/sci-chemistry/cluster/Manifest
+++ b/sci-chemistry/cluster/Manifest
@@ -1,5 +1,5 @@
 AUX 1.3.081231-includes.patch 245 BLAKE2B 6bbe0621d49bc7af8091a5594ebcd52d29d99cc00567eab523186b24c387f5c9af241c7ee53d235c1b56b6a6ea6759d3aeea814e87dd591d585413243be735e2 SHA512 a1261ed2b3f867fe464e1501fa9bc0b1f2909eaf736475e717da95ddbc34ae2938346c0044f7b6d84264a0d85ea5f7b1214caf1c2b12c544876912ff10e2302a
 AUX 1.3.081231-ldflags.patch 842 BLAKE2B 67085c3dd9ca5e97b28481fbf06a0f9b6294bd519eb3639c54b10cd9b11a4c44a48dbfa907cdf9ff8ec68761164e82d415c44ad0c3a551842416759c76d4b7a9 SHA512 9937f88e65ae94595ba2889e7f57d3b295e025d2ebd83817300a7f74a674fab84358e3b7fc9619ba473c586c51bd106e303b096cdb267d8fda05670f7815e9e4
 DIST cluster.1.3.081231.src.tgz 8860 BLAKE2B 4bfc6fe9efa3dbde106ad12df7b23990a748fee5446f16fe4e3cf9232697313bd513366a2283ac732cf0c7306ac65af578155328d0b04e4b5b99536553c9b903 SHA512 af5851ef467458d45ee5f2309c6344ae16145ac371a1b9d0a3d8b5769a18b98877cf7cb65b85f71108d927b0e6c363e06b85a67e7cb2e5e0b41af375cb2db7ac
-EBUILD cluster-1.3.081231-r1.ebuild 661 BLAKE2B 2c4054b677172ab3d6dd2e6decae4841e20ac1596d2a92b2bbd5ee633b4934db454fd8e21bd5dc71269224037eee673327b0a95433c19c7e3a0d699e38b15e92 SHA512 81883b09e3159cc2ee01756e4809265723ce9176c78de7fa0dc3c56477c25dcc45b73161268bd9972d881bfb008d9c9df406abe12fe347415a8ec5ecc60edc20
+EBUILD cluster-1.3.081231-r1.ebuild 655 BLAKE2B a97073c0f49b08a1183f1459c439194773c6deff4e40c86bbd84cf5445a17157aa6cc771926d4b39d8519f086df4b2e6fc8673f5c1581dbe5805fd210c1f2270 SHA512 240111447ab33153123bd4c2ba17be974e495fb37fa6af000b3439adcae24624f9f030442d15c5fd2b40930b0f5befb7dc51b68d4952740a2cf0897a35259774
 MISC metadata.xml 662 BLAKE2B 66db8e72eb84b709acc99788eaa9be84f4427db7cafb71acafae25f7bfe4dc42e54a9249d2adb58c35c2a0a815012e6fcb131de953791a9b8465b038da1e3836 SHA512 139bb6061d66da9e10c479d02c0df1df6f296d423dfc0db33c8eb76706888a8eccab587fe81269a3d90020425953c5cbe32bf94ef0b3ad157dabe25446fd5df2
diff --git a/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild b/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild
index d274ed0d3787..b5f0395734e0 100644
--- a/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild
+++ b/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild
@@ -1,26 +1,27 @@
 # Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=8
 
-inherit epatch toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="Build lists of collections of interacting items"
 HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php"
 SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${PN}.${PV}.src.tgz"
+S="${WORKDIR}"/${PN}1.3src
 
-SLOT="0"
 LICENSE="richardson"
+SLOT="0"
 KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE=""
 
-S="${WORKDIR}"/${PN}1.3src
+PATCHES=(
+	"${FILESDIR}"/${PV}-ldflags.patch
+	"${FILESDIR}"/${PV}-includes.patch
+)
 
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PV}-ldflags.patch \
-		"${FILESDIR}"/${PV}-includes.patch
+src_configure() {
 	tc-export CXX
+	default
 }
 
 src_install() {
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 89ea6a33ac66..7fa22a257f67 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,7 +1,4 @@
-AUX pymol-2.4.0-fix_bug119.patch 1078 BLAKE2B 78ed2953dcb20197de0a06c2c9c4c9f59be79cecbedfc910e7e530e5ad58452aab0da8540f4a4737023a3d56eba51530dfb1f2dfd59cdaf91192b6cd90383610 SHA512 ff4adb6de9c03f165e062698fe6359ab187ccf7cccba05c2e90363b44a53e5d4371e4942f21f26dd89ca8d1b7f9865f48e18f7d9a0214a5c6f453bee0ab49bb7
 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
-EBUILD pymol-2.4.0-r1.ebuild 3106 BLAKE2B ca3e75218437da7eecb7f6cd4feb737386cfed4a002121659cf4147f141fc380dac3d3c18b9a0ea1dd3d614dd05df391545b3cad65905d1d7a52beace3c54b97 SHA512 cd03c112d9210fa24206de44e55dc8ed1bfde7a51c4278902355f01fd5d5846fb12afb3318796c9e4f57b1e5e7cae58812cf81267d9c7f776c5a35f6a0eb3082
 EBUILD pymol-2.5.0.ebuild 3092 BLAKE2B 911add60f71e41659a1bf0754fa1e263ed3b8bb1222b83401ed192db2c4679629b41ec4476e552e23d0c7f85063adcc4380be16cd920a50ce1ba5ef7ee4da1c1 SHA512 2326993a095b2dda7de7b0049d192a57c5a4e28cd323629344e8723090c621fe10b1e767c50c50a3941d2241bb06a7c393210c0093bf0d5810e20419737ca30e
 MISC metadata.xml 440 BLAKE2B ee3a427d21cd25ce455b61c40767eec9ded9718fa835f545b0849e24451d2004a149bd25df36e59c94d53f3fc27b3d747ac051f82db6aec593645e54a335d884 SHA512 848b215441a66d3ebcda4c06733dc6ce879b738e5210f9e20d309d2aed11f1dd6f2d267e0a4ecb702b43dc5cc9925cb026aff2a16ded4b35dce7c38607438417
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 62512053fd71..000000000000
--- 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 c710896747d8..000000000000
--- 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
-}