gentoo auto-resync : 07:02:2023 - 15:25:18

4 files changed, 2 insertions, 102 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 6eef9cc97da1..0560a13dac53 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index a5f644979835..956a67cbce7a 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,5 +1,4 @@
 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
-EBUILD pymol-2.5.0-r1.ebuild 2601 BLAKE2B 83908a75d5952f4052aee7b1a6e356b6c7f35eabe0fce0d832c0d8458620bb16b06a4921fab8e9ceeda42a2becb71071bde9d515e2458900fdaf8f9977a38311 SHA512 45de3ba4a1af2797305cdf2aac0eb176b4cd09eccea3ecbae553164654102f9bde54ad213acfe150a0e97cb5419829c924f21d9cdc21ec7da2372c4c81bcea45
-EBUILD pymol-2.5.0.ebuild 2554 BLAKE2B ce41f9cb159999e7bd830108a2b529e12c0c1bb278bd68c13b969d3d387cdfac754c3affa5a2e991a2a03a967ca0b0540307ae549a9bbb8178177815d1f4ff01 SHA512 c7bb671b932b9d3a5994b2c201336fb6b1d5be5b6fc45dbab324c4bcaa671f1054b11d8ecb0d2a78d0d5c32d27b83ce61fa7ac8a4471378dcd7420fa5c0b76a9
+EBUILD pymol-2.5.0-r2.ebuild 2628 BLAKE2B d200613ec092f9ac5d2d4fb861157681cb5ee32ef4ed6b20f376ef28c6b7ca812a4410244f6f688981fd83c242c2b622b716e7a6ccd96d90d6af5695f9b4d270 SHA512 00afc275d1b5723b93fb93beb23cbe52fb5849dfbefc06ca0e00b197ce5f5ee3e81fb4b7443f41ef70b42983ae9ab4f4f58414737e81f1f28d29b3b164f89da0
 MISC metadata.xml 495 BLAKE2B 32d321e92c7e7c226747660c314f5cff9aabf9ee41c8a864064432ac9554879db7bf60640993dadae6e00a9b7d1367cb8ab228b63b8797ca84e5618eeeb192cc SHA512 36ef956d111c76182c70c81a830885f540fb2710f696b2711837d4bf1055a8792226f38b827f389a3a3861f259bae1394d6da50c2b33a0ddb4e6940262e1b25d
diff --git a/sci-chemistry/pymol/pymol-2.5.0-r1.ebuild b/sci-chemistry/pymol/pymol-2.5.0-r2.ebuild
index 287c6e3776bc..a4653ad70c83 100644
--- a/sci-chemistry/pymol/pymol-2.5.0-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-2.5.0-r2.ebuild
@@ -20,7 +20,7 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
 IUSE="+netcdf web"
 
 DEPEND="
-	dev-libs/msgpack[cxx(-)]
+	|| ( dev-cpp/msgpack-cxx dev-libs/msgpack[cxx(-)] )
 	dev-libs/mmtf-cpp
 	dev-python/pyopengl[${PYTHON_USEDEP}]
 	dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
diff --git a/sci-chemistry/pymol/pymol-2.5.0.ebuild b/sci-chemistry/pymol/pymol-2.5.0.ebuild
deleted file mode 100644
index febb99f21a88..000000000000
--- a/sci-chemistry/pymol/pymol-2.5.0.ebuild
+++ /dev/null
@@ -1,99 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{9..10} )
-DISTUTILS_USE_SETUPTOOLS=no
-
-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 -> ${P}.tar.gz
-	"
-RESTRICT="mirror"
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="+netcdf web"
-
-DEPEND="
-	dev-libs/msgpack[cxx(-)]
-	dev-libs/mmtf-cpp
-	dev-python/pyopengl[${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-${PV}
-
-python_prepare_all() {
-	sed \
-		-e "s:\"/usr:\"${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="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	sed \
-		-e '1i#!/usr/bin/env python' \
-		"${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
-}