gentoo auto-resync : 24:11:2023 - 16:33:11

7 files changed, 343 insertions, 10 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index a08222bf93a5..05b003292226 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
index dae6544d80fa..acf0e93d7cce 100644
--- a/sci-chemistry/openbabel/Manifest
+++ b/sci-chemistry/openbabel/Manifest
@@ -3,6 +3,7 @@ AUX openbabel-python.cmake 4402 BLAKE2B 36c325a26f9b23c3957db22110628a0a922ad02b
 DIST openbabel-3.1.1_p20210225.tar.gz 36674527 BLAKE2B bb82fc96f704249d211bd86c73de0cf4e7cfe5e2ba5c745aa8b4f6f19583837e2181d85101377810095f6b71fc3b91bf2f6f5636726fc8271c6905f1f8c59e7b SHA512 9ff7cb4acbfad7a9c5c8d0dd8930ac0390d0d0f2758d1a6120009071f47ffe718f92ad620d37f26f196babb14649c52b5eb7bb161c342ef36aec655e0a172de4
 DIST openbabel.jpg 12159 BLAKE2B b701df2b8c29df607dc2bd3997a282aa9a726d56c789ff2db900d33234dc691f76b6af12a4c9ccda4f09984504b863c40c39e8bf91058939996714ede2dd37c7 SHA512 998ea526c8c92f87dd203527fdd9f4e001357e951409209f41ab68e0b730fe12d97f9079c12ca289be413854ea2abcf8bb691ae5af823a6f29d6a590e1a3e2b0
 DIST openbabel.png 29060 BLAKE2B 8d217d92125cc73462437411dd4e0cc05179cb0934f5ed15a307acc6b549b8ebab250a48a05ef7657f48c6df394f37da9b659de61efb1477b79b573a5b393ad3 SHA512 bbcaaa37663b526c9038ccb9edaf05ccc3ad1a861739a737f05f363098d8402a10b36e341fcc0aca636e809c6c32db99bf987b41719a0c756bf5e31444d3eb70
+EBUILD openbabel-3.1.1_p20210225-r1.ebuild 7464 BLAKE2B 6c5e196129c1d642ea25c2f6ae12079300c834daf4ffd00505a01713f22b0b069d35988db1ed8ce4e4b69666a8ed38ca965c69a83f569616c2c4ee320eef3606 SHA512 a1cd7f4be62712945005dd47fade839ff77215c22fabebb2928cf33fe29395fcae9072ddce2d0640c2d5564eec065de44589247f0a147e6c57882e9a0f2cf405
 EBUILD openbabel-3.1.1_p20210225.ebuild 7423 BLAKE2B 6a75f9e1ae79d6f393be360db155d6e84047ab3c3cd74f521c0b9fbd0af4046e3400ac05e110c4b4bcdade559e07a886af3abc48113f2559a8658d10fbaffddf SHA512 f2ca26f007b1ee9861c6666912579a8abead4d99c83c44e6eafcfc2f7fb184a5e88d281ef0237808b37f070c9b65dadf7fa4d2ba36a4337ec7e5b33af82bc2a7
-EBUILD openbabel-9999.ebuild 7313 BLAKE2B b60cd763b7909067365a5ee8d202d3d5642c7ee3ea0d460a6d5c60edced40ab531da09e585ad997487ffe907390d47be98f1eff6dbb244063fcb5880b6ed94be SHA512 971f59c9ba38f0b360bfa3cd2abb58a7bc86e5a97b41b1c57eb65274eb61728c8675b37eff181e36f250478bf2a1e7368838c25b68d18bb2917a9ea0b559c5ac
+EBUILD openbabel-9999.ebuild 7313 BLAKE2B 781d3eaf268a3a5608eb6f367ccfaf700b440f6ff14ab35da36ad23a88b89fc6acb0381388b4538d21dd78325eef635cb726d872fcc1940b2dc07caefd275289 SHA512 ada79b7c3cfa3f860b9838d3314cac533464c2aece7cbb21e09c992934d55593aca4aaf744a3aede7bc42b6d065454dcbca6087ba2978644662839a531ea391e
 MISC metadata.xml 921 BLAKE2B c0797440e50f813777c4858cc1ce893546d7785e57243318ec7d2c601c6ec2ecb7ec5ab3dbacce960c8b71196eef51ddce07802257fff0d4cba0293f940a773f SHA512 8ee8a50230f374904a9ddaaf7337caf018788ab25a1839dbf5a48b0e5c49ac4e285a1fa759900fa6d993bc220d3586a923ae21158687be971fc51a6c302f12ad
diff --git a/sci-chemistry/openbabel/openbabel-3.1.1_p20210225-r1.ebuild b/sci-chemistry/openbabel/openbabel-3.1.1_p20210225-r1.ebuild
new file mode 100644
index 000000000000..837978dbe580
--- /dev/null
+++ b/sci-chemistry/openbabel/openbabel-3.1.1_p20210225-r1.ebuild
@@ -0,0 +1,280 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..11} )
+WX_GTK_VER=3.2-gtk3
+
+inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg-utils
+
+DESCRIPTION="Interconverts file formats used in molecular modeling"
+HOMEPAGE="https://openbabel.org/ https://github.com/openbabel/openbabel/"
+
+if [[ "${PV}" == *9999* ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/openbabel/${PN}.git"
+else
+	if [[ "${PV}" == *_p* ]]; then	# eg., openbabel-3.1.1_p20210325
+		# Set to commit hash
+		OPENBABEL_COMMIT=08e23f39b0cc39b4eebd937a5a2ffc1a7bac3e1b
+		SRC_URI="https://github.com/${PN}/${PN}/archive/${OPENBABEL_COMMIT}.tar.gz -> ${P}.tar.gz"
+		S="${WORKDIR}/${PN}-${OPENBABEL_COMMIT}"
+	else
+		MY_P="${PN}-$(ver_rs 1- -)"
+		SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz -> ${P}.tar.gz"
+		S="${WORKDIR}/${PN}-${MY_P}"
+	fi
+	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+fi
+
+SRC_URI="${SRC_URI}
+	https://openbabel.org/docs/dev/_static/babel130.png -> ${PN}.png
+	https://openbabel.org/OBTitle.jpg ->  ${PN}.jpg"
+
+# See src/CMakeLists.txt for LIBRARY_VERSION
+SLOT="0/7.0.0"
+LICENSE="GPL-2"
+IUSE="cpu_flags_arm_neon cpu_flags_x86_sse2 cpu_flags_x86_sse4_2 doc examples +inchi json minimal openmp perl png python test wxwidgets"
+
+RESTRICT="!test? ( test )"
+
+# Inaccurate dependency logic upstream
+REQUIRED_USE="
+	python? ( ${PYTHON_REQUIRED_USE} )
+	test? ( inchi json !minimal wxwidgets )
+"
+
+BDEPEND="
+	dev-lang/perl
+	doc? (
+		app-doc/doxygen
+		dev-texlive/texlive-latex
+	)
+	perl? ( >=dev-lang/swig-2 )
+	python? ( >=dev-lang/swig-2 )
+	test? ( dev-lang/python )
+"
+
+COMMON_DEPEND="
+	dev-cpp/eigen:3
+	dev-libs/libxml2:2
+	sys-libs/zlib:=
+	inchi? ( sci-libs/inchi )
+	json? ( >=dev-libs/rapidjson-1.1.0 )
+	png? ( x11-libs/cairo )
+	python? ( ${PYTHON_DEPS} )
+	wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] )
+"
+
+DEPEND="
+	${COMMON_DEPEND}
+	perl? ( dev-lang/perl )
+"
+
+RDEPEND="
+	${COMMON_DEPEND}
+	perl? (
+		dev-lang/perl:=
+		!sci-chemistry/openbabel-perl
+	)
+"
+
+PATCHES=(
+	"${FILESDIR}"/openbabel-3.1.1-fix-time-check-cmake.patch
+)
+
+pkg_pretend() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+prepare_python_bindings() {
+	mkdir -p scripts/${EPYTHON} || die
+	# Appends to scripts/CMakeLists.txt, substituting the correct tags, for
+	# each valid python implementation,
+	cat "${FILESDIR}"/${PN}-python.cmake | \
+		sed -e "s|@@EPYTHON@@|${EPYTHON}|" \
+			-e "s|@@PYTHON_INCUDE_DIR@@|$(python_get_includedir)|" \
+			-e "s|@@PYTHON_LIBS@@|$(python_get_LIBS)|" \
+			-e "s|@@PYTHON_SITEDIR@@|$(python_get_sitedir)|" >> \
+				scripts/CMakeLists.txt || die
+}
+
+src_prepare() {
+	cmake_src_prepare
+
+	if use perl; then
+		perl_set_version
+
+		sed -e "/\${LIB_INSTALL_DIR}\/auto/s|\${LIB_INSTALL_DIR}|${VENDOR_ARCH}|" \
+			-e "/\${LIB_INSTALL_DIR}\/Chemistry/s|\${LIB_INSTALL_DIR}|${VENDOR_ARCH}|" \
+			-i scripts/CMakeLists.txt || die
+	fi
+
+	if use python; then
+		# Skip the python bindings sections as we'll append our own
+		sed -e '/^if (PYTHON_BINDINGS)$/s|PYTHON_BINDINGS|false|' \
+			-i {scripts,test}/CMakeLists.txt || die
+		if use test; then
+			# Problems with testbindings built with -O2
+			local test_skip="@unittest.skip('Similar to Issue #2138')"
+			sed -e "/def testTemplates/s|^|    ${test_skip}\\n|" \
+				-i test/testbindings.py || die
+			test_skip="@unittest.skip('Similar to Issue #2246')"
+			sed -e "/^def test_write_string/s|^|${test_skip}\\n|" \
+				-i test/testobconv_writers.py || die
+			fi
+		python_foreach_impl prepare_python_bindings
+	fi
+
+	# Remove dependency automagic
+	if ! use png; then
+		sed -e '/^find_package(Cairo/d' -i CMakeLists.txt || die
+	fi
+	if ! use wxwidgets; then
+		sed -e '/^find_package(wxWidgets/d' -i CMakeLists.txt || die
+	fi
+	if ! use inchi; then
+		sed -e '/^else()$/s|else\(\)|elseif\(false\)|' \
+			-i cmake/modules/FindInchi.cmake || die
+	fi
+
+	# Don't install example bins to /usr/bin
+	if use examples; then
+		sed -e "/RUNTIME DESTINATION/s|bin|share/doc/${PF}/examples|" \
+			-i doc/examples/CMakeLists.txt || die
+	fi
+
+	# boost is only used if building with gcc-3.x, which isn't supported in
+	# Gentoo. Still, it shouldn't look for, and include, its headers
+	sed -e '/find_package(Boost/d' -i {{tools,src}/,}CMakeLists.txt || die
+}
+
+src_configure() {
+	if use json; then
+		# -DOPTIMIZE_NATIVE=ON also forces -march=native so use
+		# cpu_flags to set defines instead
+		use cpu_flags_x86_sse2 && append-cppflags -DRAPIDJSON_SSE2
+		use cpu_flags_x86_sse4_2 && append-cppflags -DRAPIDJSON_SSE42
+		use cpu_flags_arm_neon && append-cppflags -DRAPIDJSON_NEON
+	fi
+
+	use wxwidgets && setup-wxwidgets
+
+	use_bindings() {
+		(use perl || use python) && (echo 'yes' || die) || (echo 'no' || die)
+	}
+
+	local mycmakeargs=(
+		-DBUILD_DOCS=$(usex doc)
+		-DBUILD_EXAMPLES=$(usex examples)
+		-DBUILD_GUI=$(usex wxwidgets)
+		-DENABLE_OPENMP=$(usex openmp)
+		-DENABLE_TESTS=$(usex test)
+		-DMINIMAL_BUILD=$(usex minimal)
+		# Set this, otherwise it defaults to true and forces WITH_INCHI=true
+		-DOPENBABEL_USE_SYSTEM_INCHI=$(usex inchi)
+		-DOPTIMIZE_NATIVE=OFF
+		-DPERL_BINDINGS=$(usex perl)
+		-DPYTHON_BINDINGS=$(usex python)
+		-DRUN_SWIG=$(use_bindings)
+		-DWITH_COORDGEN=false
+		-DWITH_INCHI=$(usex inchi)
+		-DWITH_JSON=$(usex json)
+		-DWITH_MAEPARSER=false
+	)
+
+	if use test; then
+		# Help cmake find the python interpreter when dev-lang/python-exec is built
+		# without native-symlinks support.
+		python_setup
+		mycmakeargs+=( -DPYTHON_EXECUTABLE="${PYTHON}" )
+	fi
+
+	cmake_src_configure
+}
+
+src_test() {
+	# Wierd deadlock causes system_load to keep rising
+	cmake_src_test -j1
+}
+
+openbabel-optimize() {
+	python_optimize "${D}/$(python_get_sitedir)"/openbabel || die
+}
+
+src_install() {
+	cmake_src_install
+
+	docinto html
+	for x in doc/*.html; do
+		[[ ${x} != doc/api*.html ]] && dodoc ${x}
+	done
+	# Rendered in some html pages
+	newdoc "${DISTDIR}"/${PN}.png babel130.png
+	newdoc "${DISTDIR}"/${PN}.jpg OBTitle.jpg
+
+	if use doc; then
+		cmake_src_install docs
+		docinto html/API
+		dodoc -r doc/API/html/.
+	fi
+
+	if use examples; then
+		# no compression since we want ready-to-run scripts
+		docompress -x /usr/share/doc/${PF}/examples
+
+		# ${PV} doesn't correspond to the internal BABEL_VERSION for
+		# live or patch release builds so we grep it
+		local babel_ver=$(
+			grep '^#define BABEL_VERSION' < \
+				"${BUILD_DIR}"/include/openbabel/babelconfig.h | \
+				cut -d \" -f 2 || die
+		)
+		docinto examples/povray
+		dodoc doc/dioxin.* doc/README*.pov*
+		# Needed by the povray example
+		dosym ../../../../${PN}/${babel_ver}/babel_povray3.inc \
+			/usr/share/doc/${PF}/examples/povray/babel31.inc
+
+	fi
+
+	if use perl; then
+		docinto /
+		newdoc scripts/perl/Changes Changes.perl
+		newdoc scripts/perl/README README.perl
+		if use examples; then
+			docinto examples/perl
+			dodoc -r scripts/perl/examples/.
+		fi
+	fi
+
+	if use python; then
+		python_foreach_impl openbabel-optimize
+		docinto /
+		newdoc scripts/python/README.rst README.python.rst
+		docinto html
+		dodoc scripts/python/*.html
+		if use examples; then
+			docinto examples/python
+			dodoc -r scripts/python/examples/.
+		fi
+	fi
+
+	if use wxwidgets; then
+		make_desktop_entry obgui "Open Babel" ${PN}
+		doicon "${DISTDIR}"/${PN}.png
+	fi
+}
+
+pkg_postinst() {
+	use wxwidgets && xdg_desktop_database_update
+}
+
+pkg_postrm() {
+	use wxwidgets && xdg_desktop_database_update
+}
diff --git a/sci-chemistry/openbabel/openbabel-9999.ebuild b/sci-chemistry/openbabel/openbabel-9999.ebuild
index 735a5e868ea5..b4641769ecfa 100644
--- a/sci-chemistry/openbabel/openbabel-9999.ebuild
+++ b/sci-chemistry/openbabel/openbabel-9999.ebuild
@@ -4,7 +4,7 @@
 EAPI=8
 
 PYTHON_COMPAT=( python3_{9..11} )
-WX_GTK_VER=3.0-gtk3
+WX_GTK_VER=3.2-gtk3
 
 inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg-utils
 
diff --git a/sci-chemistry/wxmacmolplt/Manifest b/sci-chemistry/wxmacmolplt/Manifest
index 50709d193a75..15e8ec679986 100644
--- a/sci-chemistry/wxmacmolplt/Manifest
+++ b/sci-chemistry/wxmacmolplt/Manifest
@@ -1,4 +1,6 @@
 AUX wxmacmolplt-7.5-glew.patch 232 BLAKE2B 9e0bd2849cc20664ca4a6b6678d2d78a723ae3e730225355dd70db0cac56d501c14aaa34d86d2ff87932feb950178a7245a943b763bde728f64a07a49ed4ba29 SHA512 cf1f77f9a86224b866f55154316a044314fda47a82de9b5be4ee58ed4ea8f4a07f9540e7060f477249b773e147739f15f43df293110045bdbca9567c60fbd5dc
 DIST wxmacmolplt-7.5.tar.gz 1965376 BLAKE2B 01033266ae66a215582a62690e792ca4ae82c8a8885fe277e2e77ee67ff70f02f6a9c10467ea6f3cee15933c6c89ba3c6137c9d29e47322ac4f395a3efd41383 SHA512 a1064d5068136b2a91328c7f912ff57d4741081d6d61437e7b4567fbf732917485b391493d637b8892bdad50b539363cfa9c778bb35407a9c0a2bfed20e42bc0
+DIST wxmacmolplt-7.7.2.tar.gz 2012054 BLAKE2B 0e419d9700dd6461a4520722f43cc36cdaa2f51920868a868bdd58db169ed92f88c71d4ce0d79446c4c564eb794f7327b0eef5f87d9ab5a639829287b29482d6 SHA512 bf4b3126bbc8657a604f8dee8b022a17dbf4633a877318ceb45d803456acb0da007c2edae23f581fb6eeafd6ea411d147fbc076acb07aba3dcb8ee55b9c486fa
 EBUILD wxmacmolplt-7.5-r1.ebuild 986 BLAKE2B 67cccea1d2e7886ee67f78ac54548047c2fe889dedfef45956a4614149d5597fd0376f0f01fd59085c9f925faa2284c2c22d4bae2d8ee98f2eca3be6b06e96ed SHA512 6e1d9051621a36deb7aeb997aa93a0b5becea1b3f7512fc56d2ee97788b5a9bedace25fb40a7a7b4e77a76830e7f8aa61ad0c32ea3e1afdb66b744197d50daf0
-MISC metadata.xml 640 BLAKE2B 36baa8ff8acb725922fb1b813cb795478ebf394c55d7b4fad21ad38e8f74e48411ec23a478ac7eb3a7a1ac7deb4fdb6ae9335782731bf6004ce42819e037d6b0 SHA512 4111c51ac4c0dbf3e819bf9fb4d14a9fe26464d15014ab5d8053836070d4b280c6cec75afe573aa1f03ea4b031ec5accaf187c8fab8b1ff9297b373f316f8136
+EBUILD wxmacmolplt-7.7.2.ebuild 982 BLAKE2B edc3b4383a20ec6039472319273947988aa77de31622a40bd604857560684612d79dd6743c2048fc423e928c5a9c8b45e38899568a68de32069591b7593ef2b7 SHA512 99e5cf215f4ef74d6c7480b9aa1732cc1eda079634e2e09e61b83f080b9093febea8d48c77d4e5dbf20bc32c3eecfef9e26b233ec7e549818b3714b13e8ac82f
+MISC metadata.xml 717 BLAKE2B e2344ebd6332d01a309edb0951483adff1342584fd1a9a6b6890c4cae7bba86f8e9f874b4200726845c1aed7712a4459fddda27ae544ee98da63098e897b499e SHA512 169c1aa0ff6cdfe7ed5e155bd1bdb2ea817c59501dde6c7caa1d25bc4826341516731e3082bf7960cc6f87fdf2a26983c04e26baea21b7bdff815eef45e4521b
diff --git a/sci-chemistry/wxmacmolplt/metadata.xml b/sci-chemistry/wxmacmolplt/metadata.xml
index 289dce2bea98..209998764618 100644
--- a/sci-chemistry/wxmacmolplt/metadata.xml
+++ b/sci-chemistry/wxmacmolplt/metadata.xml
@@ -1,11 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <longdescription>
-  wxMacMolPlt is a program for plotting 3D molecular structures and normal modes (vibrations), various orbitals and electron density maps. It reads a variety of file formats including any GAMESS input, log or IRC file directly to create animations. It has a simple GAMESS input (.inp) builder and a primitive molecule builder.
-  </longdescription>
+	<maintainer type="project">
+		<email>sci-chemistry@gentoo.org</email>
+		<name>Gentoo Chemistry Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">brettbode/wxmacmolplt</remote-id>
+	</upstream>
+	<longdescription>
+	wxMacMolPlt is a program for plotting 3D molecular structures and normal modes (vibrations), various orbitals and electron density maps. It reads a variety of file formats including any GAMESS input, log or IRC file directly to create animations. It has a simple GAMESS input (.inp) builder and a primitive molecule builder.
+	</longdescription>
 </pkgmetadata>
diff --git a/sci-chemistry/wxmacmolplt/wxmacmolplt-7.7.2.ebuild b/sci-chemistry/wxmacmolplt/wxmacmolplt-7.7.2.ebuild
new file mode 100644
index 000000000000..d233a257b76e
--- /dev/null
+++ b/sci-chemistry/wxmacmolplt/wxmacmolplt-7.7.2.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+WX_GTK_VER="3.2-gtk3"
+inherit autotools desktop toolchain-funcs wxwidgets
+
+DESCRIPTION="Chemical 3D graphics program with GAMESS input builder"
+HOMEPAGE="http://brettbode.github.io/wxmacmolplt/"
+SRC_URI="https://github.com/brettbode/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	media-libs/glew:0=
+	media-libs/mesa[X(+)]
+	x11-libs/wxGTK:${WX_GTK_VER}[X,opengl]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+	default
+	sed \
+		-e "/^dist_doc_DATA/d" \
+		-i Makefile.am || die "Failed to disable installation of LICENSE file"
+	eautoreconf
+}
+
+src_configure() {
+	tc-export PKG_CONFIG
+
+	setup-wxwidgets unicode
+	econf \
+		--with-glew \
+		--without-ming
+}
+
+src_install() {
+	default
+
+	doicon resources/${PN}.png
+	make_desktop_entry ${PN} wxMacMolPlt ${PN} "Science;DataVisualization;"
+}