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

6 files changed, 136 insertions, 3 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 49923e459714..34c9f044e402 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest
index 4443a56326f2..0a4268c4203e 100644
--- a/sci-chemistry/dssp/Manifest
+++ b/sci-chemistry/dssp/Manifest
@@ -3,10 +3,10 @@ AUX dssp-2.1.0-gentoo.patch 1513 BLAKE2B aabdcfff1083d7552392c35897eb8a84b07323c
 AUX dssp-2.2.1-boost-1.65-tr1-removal.patch 2126 BLAKE2B dc59d21a6be26ee96b636c13645163478999d5122f09d3a72963843be773210ea225e374941bd057ef6f083a13fb77980bd4390174df2a0c715f0386da7232e0 SHA512 8f84c6e163888d6a8192683a6555f7d6003634854f5cde0f6f962744e531165c7e0b2b08c55cbfb9c396d167c44317dd2e7a8290e4defd2c8def0a6511fbbd6c
 DIST dssp-2.2.1.tgz 47141 BLAKE2B 34d8b2db8797a8c23763766c0214337f03584c4be52c1bc820a0df0db6a5f78ac0229aafdd47a60b8fd6f4832abf0399663c53f9e898c75f08ecbe22b141c8da SHA512 4a273714d6b3230daea166caa7f4117d5ccb225bea0cf1bc2eb61539b6cc8e227d0ba19047d61f0ad0d1d6bc2efdec9c193bd44341e15ef0950acb4a22498811
 DIST dssp-3.0.11.tar.gz 168085 BLAKE2B e1c42fd22cfb2287f10b5deae48b56a4583d4a67737a3485dcbd160d1597a15c2d5105c3794c875d8001abede1c014efb4f7f5b7c250f867bdf9ed95a0860217 SHA512 a0cfe44e517ff1f909ef2928b62ae2c639c6bddfd8a0fb538883f647fd2771e00da68e0fd2521aa02ba3c6d1b0c9b784b7fe142392af3a3abf6ea89f1546bd9d
-DIST dssp-4.2.2.1.tar.gz 144413 BLAKE2B 97c587bc0b4ef3d212ae81d568f817aab54f1dd2a77d170746e9b0d3f1bd63873d21fb0a7fc38c0300fc091f21241820d5d009d42a9e3e33dcc608c046185d9f SHA512 6daa41aea766940bf40afaee068daef341a7f79cae79d967b8da00e7002bdb602deaed40e452a5f0cea9aa2041a5c8678dfcae2e0f595cc5a0856392162dcdff
 DIST dssp-4.3.1.tar.gz 226842 BLAKE2B 86318f05b8381d94fa9c65a956f5fb607ef8072b0395d912e20697ba36836c449ddff31a4a64d0005bbfe34899f71853c0f15a911042389fc894934c08fc34c8 SHA512 4dc1a3f5c7ba258ebf548674c7b33c36b0e3a7d14911394eb8d2955c235f3cb1d6c50cb03f411db55a8a9d7aa93e4d03354c47f9f0126b0bdcbf40dc9391d403
+DIST dssp-4.4.0.tar.gz 161773 BLAKE2B 87673be73f3163ba6fa090cc7acd4f864d41922033da9d126535b84e2da4defaaa8781a8cda6e80103dc75359718cd867b9baf90c74ae3ff923e212b520998a2 SHA512 1b09306c05587c278fcd881e0d3c169d44d960d8578f310adbd79b054683c257d0ee00d6bdfb5b0d7cd81c224f3572c2c7538a42d964817d587632128b96daa9
 EBUILD dssp-2.2.1-r3.ebuild 870 BLAKE2B 9b7542d9ec45b60f5671830e5068e1d1cbcca4b82cf22cc0e2d9804c221f9977cfade439cc6e41a67375b438faca3ffa64fdec23db2b417b58615513fd60ad44 SHA512 964bfd70d98a80e6afd7f28fc6bf7359bbde105e77903211cec04c5adcdce273f1d7142a6d206d644300a1185cba1352bf584499d864809dadad69b2023e50d0
 EBUILD dssp-3.0.11.ebuild 875 BLAKE2B 6344416239b93804755b1829dcfcb9e8e461606c217938945bb2fc75e9680f2849b39bdbf0ed361592e703fea493a2dacabca498b26e696c969735a585e5d183 SHA512 353f4f5d7b1b195753c738ecc9fb17b429cdeada757806f5cf9a3da65c6318e3885d2c92fa904d5b3a546756eb87ec90787d158e8a9450b4730dd97b45af970d
-EBUILD dssp-4.2.2.1.ebuild 788 BLAKE2B a5db07b22d8d27e6c3ada69a8cb7764a9ff0d9acbbb0bb308d6bc4713e08ea427b10179ec24ed8b02c5766ede5c9061b9620e3f2d6e6fe7ff491780c66eee3c9 SHA512 829f9775b9a11d09305a28c4ce8bc1cb050b2155a5ca10c5abb24e0831cd62d3005623eac95f8018dac8e3e182f21716ac5e89cc0b797a0e574e6d5721fcd0ef
 EBUILD dssp-4.3.1.ebuild 900 BLAKE2B d99a9024e58e5b2c53cbbfebb662a3fc546dd2a7b16a31394b312a2320bde8df9b62ecdef82295d924141e8427aee56a1e7277132e7767f481041dde6fd7c292 SHA512 1ac6d76fc9c37d5af8eecede2225d86517d27cd96a65ea4a6c9f1ce45eaf2e48fe0772838154639eebdbbccde3dd92bc6f5c9f8b2c37e3c9ca158534e5f8b8fc
+EBUILD dssp-4.4.0.ebuild 900 BLAKE2B d99a9024e58e5b2c53cbbfebb662a3fc546dd2a7b16a31394b312a2320bde8df9b62ecdef82295d924141e8427aee56a1e7277132e7767f481041dde6fd7c292 SHA512 1ac6d76fc9c37d5af8eecede2225d86517d27cd96a65ea4a6c9f1ce45eaf2e48fe0772838154639eebdbbccde3dd92bc6f5c9f8b2c37e3c9ca158534e5f8b8fc
 MISC metadata.xml 295 BLAKE2B 4355bbe00822cc702acdf70031ab9cd1f2a8f6e076d71016c1783f2a6c052c2da0a1a4a1860062562bb837161787f2481fa6f49c4319c546482a263ebe149bb0 SHA512 ace35ca21c614a7c0cbdea2496be3190a907295053566707c1875836a306cc9e9c96816cca6ce2b514935f6fcd494d2e813f4d94ba88552cd7b86831f30501f4
diff --git a/sci-chemistry/dssp/dssp-4.2.2.1.ebuild b/sci-chemistry/dssp/dssp-4.4.0.ebuild
index 32167a786c22..daf7c4f9314d 100644
--- a/sci-chemistry/dssp/dssp-4.2.2.1.ebuild
+++ b/sci-chemistry/dssp/dssp-4.4.0.ebuild
@@ -16,11 +16,19 @@ IUSE=""
 BDEPEND="
 	dev-libs/boost:=[zlib]
 	>=dev-libs/libmcfp-1.2.2
-	>=sci-libs/libcifpp-5.0.8
+	>=sci-libs/libcifpp-5.1.0
 "
 DEPEND=""
 RDEPEND="${BDEPEND}"
 
+src_configure() {
+	# gxrio not packaged
+	local mycmakeargs=(
+		-DBUILD_WEBSERVER=OFF
+	)
+	cmake_src_configure
+}
+
 pkg_postinst() {
 	if has_version "<=sci-chemistry/gromacs-2022"; then
 		ewarn "DSSP > 3.0.x is not compatible with gmx do_dssp:"
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
+}