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authorAlexey Shvetsov <alexxy@gentoo.org>2024-05-17 22:20:35 +0300
committerAlexey Shvetsov <alexxy@gentoo.org>2024-05-17 22:20:35 +0300
commitdfe0f62750dadf6273bd4146db194c7165181781 (patch)
tree8e87924adde251ccc9810678da132de6fb792d03 /sci-chemistry
parentmedia-libs/libpano13: remove old (diff)
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sci-chemistry/pymol: Update to 3.0.0 and drop old
Closes: https://bugs.gentoo.org/862441 Closes: https://bugs.gentoo.org/910511 Closes: https://bugs.gentoo.org/929762 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
Diffstat (limited to 'sci-chemistry')
-rw-r--r--sci-chemistry/pymol/Manifest2
-rw-r--r--sci-chemistry/pymol/pymol-2.5.0-r3.ebuild100
-rw-r--r--sci-chemistry/pymol/pymol-3.0.0.ebuild (renamed from sci-chemistry/pymol/pymol-2.5.0-r5.ebuild)9
3 files changed, 6 insertions, 105 deletions
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 2c6723b71c25..2ef25b2b27fa 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,2 +1,2 @@
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
+DIST pymol-3.0.0.tar.gz 29510174 BLAKE2B b67818e408045e386e44a203f29cd94a0ce34ec706776d29f78f1720bdc5c79d88f3b3e178882295b5a636d97fe70ff49eb1b021a9a6b96f0f4216bc392219d1 SHA512 eab05a46220339a05d8d4facdce6bfa08c6fc8a858a7b228236ef6c4054207059ef0f53a26bedebe4084a74b510015937fb4477f99612b21412cd75bf0c376a2
diff --git a/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild b/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild
deleted file mode 100644
index 317350640580..000000000000
--- a/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild
+++ /dev/null
@@ -1,100 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{9..11} )
-DISTUTILS_USE_SETUPTOOLS=no
-DISTUTILS_EXT=1
-
-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 -> ${P}.tar.gz
- "
-LICENSE="BitstreamVera BSD freedist HPND OFL-1.0 public-domain UoI-NCSA" #844991
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="+netcdf web"
-
-DEPEND="
- dev-cpp/msgpack-cxx
- dev-libs/mmtf-cpp
- dev-python/pyopengl[${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
-
- distutils-r1_python_prepare_all
-}
-
-python_configure_all() {
- use !netcdf && DISTUTILS_ARGS=( --no-vmd-plugins )
-}
-
-python_install() {
- distutils-r1_python_install \
- --pymol-path="${EPREFIX}/usr/share/pymol"
-
- sed \
- -e '1i#!/usr/bin/env python' \
- "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die
- python_doscript "${T}"/${PN}
-}
-
-python_install_all() {
- distutils-r1_python_install_all
-
- # These environment variables should not go in the wrapper script, or else
- # it will be impossible to use the PyMOL libraries from Python.
- cat >> "${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} %u" 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/${PN}/LICENSE || die
-}
diff --git a/sci-chemistry/pymol/pymol-2.5.0-r5.ebuild b/sci-chemistry/pymol/pymol-3.0.0.ebuild
index 3e0e1d344ac6..150f7732d930 100644
--- a/sci-chemistry/pymol/pymol-2.5.0-r5.ebuild
+++ b/sci-chemistry/pymol/pymol-3.0.0.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{9..12} )
DISTUTILS_USE_PEP517="setuptools"
DISTUTILS_EXT=1
@@ -15,6 +15,9 @@ SRC_URI="
https://dev.gentoo.org/~pacho/${PN}/${PN}-1.8.4.0.png.xz
https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz
"
+
+S="${WORKDIR}"/${PN}-open-source-${PV}
+
LICENSE="BitstreamVera BSD freedist HPND OFL-1.0 public-domain UoI-NCSA" #844991
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
@@ -39,8 +42,6 @@ RDEPEND="${DEPEND}
sci-chemistry/chemical-mime-data
"
-S="${WORKDIR}"/${PN}-open-source-${PV}
-
PATCHES=(
"${FILESDIR}/${PN}-2.5.0-format-security.patch"
)
@@ -59,7 +60,7 @@ python_prepare_all() {
-e "s:\['msgpackc'\]:\['msgpack'\]:g" \
-i setup.py || die
- append-cxxflags -std=c++0x
+ append-cxxflags -std=c++17
distutils-r1_python_prepare_all
}