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commit: 428de16e86460563d0e465331e301cc0dedf91ac |
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Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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AuthorDate: Sun May 16 20:41:00 2021 +0000 |
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Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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CommitDate: Sun May 16 20:41:15 2021 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=428de16e |
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|
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sci-chemistry/pymol: Version bump |
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|
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Package-Manager: Portage-3.0.18, Repoman-3.0.3 |
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Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org> |
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|
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sci-chemistry/pymol/Manifest | 1 + |
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sci-chemistry/pymol/pymol-2.5.0.ebuild | 111 +++++++++++++++++++++++++++++++++ |
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2 files changed, 112 insertions(+) |
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|
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diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest |
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index cfd2bae6b9a..dec8f0b1525 100644 |
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--- a/sci-chemistry/pymol/Manifest |
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+++ b/sci-chemistry/pymol/Manifest |
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@@ -1,2 +1,3 @@ |
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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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|
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diff --git a/sci-chemistry/pymol/pymol-2.5.0.ebuild b/sci-chemistry/pymol/pymol-2.5.0.ebuild |
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new file mode 100644 |
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index 00000000000..6d7ecd4e09c |
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--- /dev/null |
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+++ b/sci-chemistry/pymol/pymol-2.5.0.ebuild |
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@@ -0,0 +1,111 @@ |
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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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+ |
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+EAPI=7 |
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+ |
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+PYTHON_COMPAT=( python3_{7..9} ) |
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+DISTUTILS_USE_SETUPTOOLS=no |
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+ |
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+inherit desktop optfeature flag-o-matic xdg distutils-r1 |
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+ |
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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 -> ${P}.tar.gz |
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+ " |
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+RESTRICT="mirror" |
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+LICENSE="PSF-2.2" |
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+SLOT="0" |
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+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
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+IUSE="+netcdf web" |
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+ |
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+DEPEND=" |
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+ dev-libs/msgpack[cxx] |
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+ dev-libs/mmtf-cpp |
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+ dev-python/pyopengl[${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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+ |
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+S="${WORKDIR}"/${PN}-open-source-${PV} |
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+ |
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+python_prepare_all() { |
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+ sed \ |
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+ -e "s:\"/usr:\"${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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+ |
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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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+ |
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+ append-cxxflags -std=c++0x |
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+ |
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+ use !netcdf && mydistutilsargs=( --no-vmd-plugins ) |
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+ |
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+ distutils-r1_python_prepare_all |
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+} |
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+ |
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+python_install() { |
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+ distutils-r1_python_install \ |
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+ --pymol-path="${EPREFIX}/usr/share/pymol" |
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+ |
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+ sed \ |
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+ -e '1d' \ |
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+ -e "/APBS_BINARY_LOCATION/s:None:\"${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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+ |
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+python_install_all() { |
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+ distutils-r1_python_install_all |
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+ |
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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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+ |
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+ python_foreach_impl python_doscript "${T}"/${PN} |
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+ |
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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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+ |
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+ doenvd "${T}"/20pymol |
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+ |
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+ newicon "${WORKDIR}"/${PN}-1.8.4.0.png ${PN}.png |
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+ make_desktop_entry ${PN} PyMol ${PN} \ |
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+ "Graphics;Education;Science;Chemistry;" \ |
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+ "MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;" |
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+ |
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+ if ! use web; then |
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+ rm -rf "${D}/$(python_get_sitedir)/web" || die |
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+ fi |
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+ |
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+ rm -f "${ED}"/usr/share/${PN}/LICENSE || die |
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+} |
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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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+} |