sci-chemistry/pymol: Fix netcdf handling

Also fix upstream bug and use xdg.eclass to not need to redefine every pkg_
phase

Closes: https://bugs.gentoo.org/757798
Thanks-to: Soren Harward
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Pacho Ramos <pacho@gentoo.org>

2 files changed, 151 insertions, 0 deletions

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
new file mode 100644
index 000000000000..62512053fd71
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-2.4.0-fix_bug119.patch
@@ -0,0 +1,34 @@
+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
new file mode 100644
index 000000000000..540097824ec7
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild
@@ -0,0 +1,117 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{6..9} )
+DISTUTILS_USE_SETUPTOOLS=no
+
+inherit distutils-r1 desktop optfeature flag-o-matic xdg
+
+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 -> ${P}.tar.gz
+	"
+RESTRICT="mirror"
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="+netcdf web"
+
+DEPEND="
+	dev-libs/msgpack[cxx]
+	dev-libs/mmtf-cpp
+	dev-python/pyopengl[${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" \
+		-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
+
+	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
+}