sci-chemistry/pymol: pymol works with py3

Package-Manager: Portage-2.3.88, Repoman-2.3.20
Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>

diff --git a/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild b/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
index 36cc913f7b0962a0c45c7b0fd7be1b7ada07a4fd..5eadc9a8512d4e43221fe6093fab854b2cef09d2 100644 (file)
--- a/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
+++ b/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
@@ -29,7 +29,6 @@ DEPEND="
        dev-python/pmw:py2[${PYTHON_USEDEP}]
        dev-python/pyopengl[${PYTHON_USEDEP}]
        dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
-       dev-python/numpy[${PYTHON_USEDEP}]
        media-libs/freetype:2
        media-libs/glew:0=
        media-libs/glm

diff --git a/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild b/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
new file mode 100644 (file)
index 0000000..675c8b3
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
@@ -0,0 +1,113 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{6,7} )
+
+inherit distutils-r1 desktop eutils flag-o-matic xdg-utils
+
+DESCRIPTION="A Python-extensible molecular graphics system"
+HOMEPAGE="https://www.pymol.org/"
+SRC_URI="
+       https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz
+       https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz
+       "
+RESTRICT="mirror"
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="web"
+
+DEPEND="
+       dev-libs/msgpack[cxx]
+       dev-libs/mmtf-cpp
+       dev-python/pyopengl[${PYTHON_USEDEP}]
+       dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
+       dev-python/numpy[${PYTHON_USEDEP}]
+       media-libs/freetype:2
+       media-libs/glew:0=
+       media-libs/glm
+       media-libs/libpng:0=
+       media-video/mpeg-tools
+       sys-libs/zlib
+"
+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" \
+               -e "/import/s:argparse:argparseX: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_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 >> "${T}"/20pymol <<- EOF
+               PYMOL_PATH="${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_desktop_database_update
+       xdg_mimeinfo_database_update
+       optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
+}
+
+pkg_postrm() {
+       xdg_desktop_database_update
+       xdg_mimeinfo_database_update
+}