gentoo auto-resync : 20:07:2023 - 13:07:51

3 files changed, 125 insertions, 0 deletions

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 496faac919ff..27ab37bd4be7 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,4 +1,6 @@
+AUX pymol-2.5.0-format-security.patch 562 BLAKE2B 566f653ca3abd4498f9ee5d7255e1b06d8df320bd25a569620b1ee33da0cfb6a969fd3e0a65fbce7116cd6567d9a544c57f4d6d399bec00b9effa8273a52153c SHA512 4e93a0449470abdbd2d943ef0a5fac7f302485ca42c6d9ccdf1ab9a879029d5185c3f1a3a2e237fd8b3b3bf0a306bce07db3226257360127c97546480c233c4f
 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-r3.ebuild 2617 BLAKE2B d79d2bcdbb284b0eb6bb3eb4863288aaaebfa94c65b3d9205e60caf607195fd7631b7b29cc7a27ff25b25f4236ea211b99b96dbafe084042b4a0d20c613edb05 SHA512 4ec711441b124b5abc0a062dac1293385dfecf83db6c1c7380907d2ae680f4a064cbb08260bd2b058741764dd25be1570e8fbb402c3204da58f08bf7efd48678
+EBUILD pymol-2.5.0-r4.ebuild 2826 BLAKE2B 3a5a557058ff0f552e3160c8a127bdbfd257d1fc47530b4cc79b0ac5751b3a2959822c8562aca0d66aafa4c3e48a287784e0b968c3c9cbdc6fa980db49768735 SHA512 1f219a9ea5ee7946626c15bfb3e0e01501bf16dd08c1763bd986a6766e0cce92846c3ac9ed9e1e88fa19467b35a0d21b67ef0c58dbd81bd002968f609f802e78
 MISC metadata.xml 495 BLAKE2B 32d321e92c7e7c226747660c314f5cff9aabf9ee41c8a864064432ac9554879db7bf60640993dadae6e00a9b7d1367cb8ab228b63b8797ca84e5618eeeb192cc SHA512 36ef956d111c76182c70c81a830885f540fb2710f696b2711837d4bf1055a8792226f38b827f389a3a3861f259bae1394d6da50c2b33a0ddb4e6940262e1b25d
diff --git a/sci-chemistry/pymol/files/pymol-2.5.0-format-security.patch b/sci-chemistry/pymol/files/pymol-2.5.0-format-security.patch
new file mode 100644
index 000000000000..080e5e8960e4
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-2.5.0-format-security.patch
@@ -0,0 +1,15 @@
+Author: Michael Banck <mbanck@debian.org>
+Description: Fix "error: format not a string literal and no format arguments [-Werror=format-security]" (#759860)
+Forwarded: yes
+
+--- a/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp
++++ b/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp
+@@ -2004,7 +2004,7 @@ namespace {
+       }
+     }
+     catch (std::exception &e) {
+-      fprintf(stderr, "%s", e.what());
++      fprintf(stderr, "Cannot write timestamp to mae file: %s\n", e.what());
+       return MOLFILE_ERROR;
+     }
+     return MOLFILE_SUCCESS;
diff --git a/sci-chemistry/pymol/pymol-2.5.0-r4.ebuild b/sci-chemistry/pymol/pymol-2.5.0-r4.ebuild
new file mode 100644
index 000000000000..e4b4d3e2eadb
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-2.5.0-r4.ebuild
@@ -0,0 +1,108 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..11} )
+DISTUTILS_USE_PEP517="setuptools"
+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 -> ${P}.tar.gz
+	"
+LICENSE="BitstreamVera BSD freedist HPND OFL public-domain UoI-NCSA" #844991
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="+netcdf web"
+
+DEPEND="
+	dev-cpp/msgpack-cxx
+	dev-libs/mmtf-cpp
+	dev-python/pyopengl[${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-${PV}
+
+PATCHES=(
+	"${FILESDIR}/${PN}-2.5.0-format-security.patch"
+)
+
+python_prepare_all() {
+	sed \
+		-e "s:\"/usr:\"${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}"/${PN}
+}
+
+python_install_all() {
+	distutils-r1_python_install_all
+
+	# Move data to correct location
+	dodir /usr/share/pymol
+	mv "${D}/$(python_get_sitedir)"/pymol/pymol_path/* "${ED}/usr/share/pymol" || die
+
+	# 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
+}