Adding metadata

9 files changed, 0 insertions, 972 deletions

diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
deleted file mode 100644
index 336f074b2917..000000000000
--- a/sci-chemistry/openbabel/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST openbabel-3.1.1_p20241221.tar.gz 36864825 BLAKE2B 55e6fbdd5c50a557c40fd5ffaca41753f73175b2b4eea22abe5c2b0031363e3c133acf9a8daf5b1cb362a3adb6398204497af036b9a7ba3630c1d8ccbce0f9d3 SHA512 44340c3d08b22783cf6a702c192480869b73fef21104641feaf5cbcd51f693fd17bb05ad31a3520f330aa57733d6f4be707b3c1243b3010d6ceccca8974e732f
diff --git a/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-cmake4.patch b/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-cmake4.patch
deleted file mode 100644
index 822213a7bddb..000000000000
--- a/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-cmake4.patch
+++ /dev/null
@@ -1,78 +0,0 @@
-https://github.com/openbabel/openbabel/pull/2784.patch
-From fda825d390af8b5eaf79d7b7c39c19ab5ce317ac Mon Sep 17 00:00:00 2001
-From: Nicolas PARLANT <nicolas.parlant@parhuet.fr>
-Date: Wed, 26 Mar 2025 10:24:42 +0000
-Subject: [PATCH] cmake4 compat :
-
-* up cmake_minimum_required to 3.10
-* delete CMP0042 because OLD behavior is removed in cmake-4 and
-is no longer used.
-* set ENABLE_EXPORTS for test_runner (OLD behavior for CMP0065 is removed
-in cmake4)
-
-Signed-off-by: Nicolas PARLANT <nicolas.parlant@parhuet.fr>
----
- CMakeLists.txt                                | 7 ++-----
- doc/examples/static_executable/CMakeLists.txt | 2 +-
- scripts/CMakeLists.txt                        | 2 +-
- test/CMakeLists.txt                           | 1 +
- 4 files changed, 5 insertions(+), 7 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 9d2a9f143e..f8440e412e 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -1,6 +1,6 @@
--# Please ensure that any changes remain compliant with 3.1.
-+# Please ensure that any changes remain compliant with 3.10.
- if(NOT EMBED_OPENBABEL)
--  cmake_minimum_required(VERSION 3.1)
-+  cmake_minimum_required(VERSION 3.10)
- endif()
- 
- project(openbabel)
-@@ -10,9 +10,6 @@ set (CMAKE_CXX_STANDARD 11)
- 
- if(COMMAND cmake_policy)
-   cmake_policy(SET CMP0003 NEW)
--  if(POLICY CMP0042)
--    cmake_policy(SET CMP0042 OLD)
--  endif()
- endif()
- 
- include (CheckCXXCompilerFlag)
-diff --git a/doc/examples/static_executable/CMakeLists.txt b/doc/examples/static_executable/CMakeLists.txt
-index 0ed21beaaf..63dae2a468 100644
---- a/doc/examples/static_executable/CMakeLists.txt
-+++ b/doc/examples/static_executable/CMakeLists.txt
-@@ -25,7 +25,7 @@
- #
- 
- # This line is required for cmake backwards compatibility.
--cmake_minimum_required(VERSION 2.6)
-+cmake_minimum_required(VERSION 3.10)
- 
- # Name of your project
- project(myproject)
-diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
-index 792e4592d0..eafda66c5a 100644
---- a/scripts/CMakeLists.txt
-+++ b/scripts/CMakeLists.txt
-@@ -1,4 +1,4 @@
--cmake_minimum_required(VERSION 2.6.0)
-+cmake_minimum_required(VERSION 3.10.0)
- # Library versioning (used in Mac Python bindings)x
- set(SOVERSION 4)
- 
-diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
-index 2ecf0dbe22..280eac471f 100644
---- a/test/CMakeLists.txt
-+++ b/test/CMakeLists.txt
-@@ -152,6 +152,7 @@ endif()
- 
- add_executable(test_runner ${srclist} obtest.cpp)
- target_link_libraries(test_runner ${libs})
-+set_target_properties(test_runner PROPERTIES ENABLE_EXPORTS TRUE)
- 
- if(NOT BUILD_SHARED AND NOT BUILD_MIXED)
-   set_target_properties(test_runner PROPERTIES LINK_SEARCH_END_STATIC TRUE)
diff --git a/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_examples.patch b/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_examples.patch
deleted file mode 100644
index b61d3bc29b98..000000000000
--- a/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_examples.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-prevent installation of examples in /usr/bin
-all files from examples are 'RUNTIME', no lib
---- a/doc/examples/CMakeLists.txt
-+++ b/doc/examples/CMakeLists.txt
-@@ -7,7 +7,7 @@
-   add_executable(${example} ${example}.cpp)
-   target_link_libraries(${example} ${BABEL_LIBRARY})
-   install(TARGETS ${example}
--    RUNTIME DESTINATION bin
-+    RUNTIME DESTINATION ${CMAKE_INSTALL_DOCDIR}/examples
-     LIBRARY DESTINATION lib
-     ARCHIVE DESTINATION lib
-   )
diff --git a/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_pybind.patch b/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_pybind.patch
deleted file mode 100644
index ab1a24499306..000000000000
--- a/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_pybind.patch
+++ /dev/null
@@ -1,25 +0,0 @@
---- a/scripts/CMakeLists.txt
-+++ b/scripts/CMakeLists.txt
-@@ -69,13 +69,9 @@
- 
- if (DO_PYTHON_BINDINGS)
- 
--    include_directories(
--        ${PYTHON_INCLUDE_PATH}
--    )
--
-     if(RUN_SWIG)
-       add_custom_command(OUTPUT ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel.py
--      COMMAND ${SWIG_EXECUTABLE} -python -c++ ${doxygen_switch} -small -O -templatereduce -naturalvar -I${openbabel_SOURCE_DIR}/include -I${openbabel_BINARY_DIR}/include -o ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp ${eigen_define} -outdir ${openbabel_SOURCE_DIR}/scripts/python/openbabel ${openbabel_SOURCE_DIR}/scripts/openbabel-python.i
-+	      COMMAND ${SWIG_EXECUTABLE} -python -c++ ${doxygen_switch} -small -O -templatereduce -naturalvar -I${PYTHON_INCLUDE_PATH} -I${openbabel_SOURCE_DIR}/include -I${openbabel_BINARY_DIR}/include -o ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp ${eigen_define} -outdir ${openbabel_SOURCE_DIR}/scripts/python/openbabel ${openbabel_SOURCE_DIR}/scripts/openbabel-python.i
-               MAIN_DEPENDENCY openbabel-python.i
-               VERBATIM
-               )
-@@ -84,6 +80,7 @@
-     configure_file(${openbabel_SOURCE_DIR}/scripts/python/openbabel/__init__.py.in
-                    ${openbabel_SOURCE_DIR}/scripts/python/openbabel/__init__.py)
-     add_library(bindings_python MODULE ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp)
-+    target_include_directories(bindings_python PRIVATE ${PYTHON_INCLUDE_PATH})
- 
-     if(APPLE)
-       # Don't link against Python library on Mac
diff --git a/sci-chemistry/openbabel/files/openbabel-python-r2.cmake b/sci-chemistry/openbabel/files/openbabel-python-r2.cmake
deleted file mode 100644
index a16970deb0b1..000000000000
--- a/sci-chemistry/openbabel/files/openbabel-python-r2.cmake
+++ /dev/null
@@ -1,103 +0,0 @@
-# The following is a cmake fragment taken from scripts/CMakeLists.txt and
-# edited for Gentoo python multibuild compatibility.
-
-if (DO_PYTHON_BINDINGS)
-	# Tags should be edited to reflect the active python implementation
-	set(EPYTHON @@EPYTHON@@)
-	set(PYTHON_INCLUDE_DIR @@PYTHON_INCLUDE_DIR@@)
-	set(PYTHON_LIBS @@PYTHON_LIBS@@)
-	set(PYTHON_SITEDIR @@PYTHON_SITEDIR@@)
-
-	add_custom_command(
-		OUTPUT ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py
-		COMMAND ${SWIG_EXECUTABLE} -python -c++ -small -O -templatereduce -naturalvar -I${PYTHON_INCLUDE_DIR} -I${CMAKE_SOURCE_DIR}/include -I${CMAKE_BINARY_DIR}/include -o ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp ${eigen_define} -outdir ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON} ${CMAKE_SOURCE_DIR}/scripts/openbabel-python.i
-		MAIN_DEPENDENCY openbabel-python.i
-		VERBATIM
-	)
-
-	configure_file(${CMAKE_SOURCE_DIR}/scripts/python/openbabel/__init__.py.in
-		${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/__init__.py)
-
-	add_library(bindings_python_${EPYTHON} MODULE ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp)
-    	target_include_directories(bindings_python_${EPYTHON} PRIVATE ${PYTHON_INCLUDE_DIR})
-	target_link_libraries(bindings_python_${EPYTHON} ${PYTHON_LIBS} ${BABEL_LIBRARY})
-
-	set_target_properties(bindings_python_${EPYTHON}
-		PROPERTIES
-		OUTPUT_NAME _openbabel
-		LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel
-		PREFIX ""
-		SUFFIX .so )
-
-	add_dependencies(bindings_python_${EPYTHON} openbabel)
-
-	install(TARGETS bindings_python_${EPYTHON}
-		LIBRARY DESTINATION ${PYTHON_SITEDIR}/openbabel
-		COMPONENT bindings_python)
-	install(FILES ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/__init__.py
-		DESTINATION ${PYTHON_SITEDIR}/openbabel
-		COMPONENT bindings_python)
-	install(FILES ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py
-		DESTINATION ${PYTHON_SITEDIR}/openbabel
-		COMPONENT bindings_python)
-	install(FILES ${CMAKE_SOURCE_DIR}/scripts/python/openbabel/pybel.py
-		DESTINATION ${PYTHON_SITEDIR}/openbabel
-		COMPONENT bindings_python)
-
-	if (ENABLE_TESTS)
-		# Make sure all module files are together in the same directory for testing
-		add_custom_command(TARGET bindings_python_${EPYTHON} POST_BUILD
-			COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/
-			COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/scripts/python/openbabel/pybel.py ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/)
-		set(TEST_SOURCE_DIR ${CMAKE_SOURCE_DIR}/test)
-		# define TESTDATADIR for tests that need input files
-		add_definitions(-DTESTDATADIR="${TEST_SOURCE_DIR}/files/")
-		# define FORMATDIR for location of format plugin binaries
-		set(FORMATDIR "${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/")
-		add_definitions(-DFORMATDIR="${FORMATDIR}/")
-		include_directories(${TEST_SOURCE_DIR})
-
-		# The macro is modified from cmake/modules/UsePythonTest.cmake
-		MACRO(ADD_PYTHON_TEST TESTNAME FILENAME)
-			GET_SOURCE_FILE_PROPERTY(loc ${FILENAME} LOCATION)
-			STRING(REGEX REPLACE ";" " " wo_semicolumn "${ARGN}")
-			FILE(WRITE ${CMAKE_BINARY_DIR}/test/${TESTNAME}.cmake
-"
-	MESSAGE(\"${PYTHONPATH}\")
-	EXECUTE_PROCESS(
-		COMMAND ${EPYTHON} ${loc} ${wo_semicolumn}
-		RESULT_VARIABLE import_res
-		OUTPUT_VARIABLE import_output
-		ERROR_VARIABLE  import_output
-	)
-
-	# Pass the output back to ctest
-	IF(import_output)
-		MESSAGE(\${import_output})
-	ENDIF(import_output)
-	IF(import_res)
-		MESSAGE(SEND_ERROR \${import_res})
-	ENDIF(import_res)
-"
-			)
-			ADD_TEST(${TESTNAME} ${CMAKE_COMMAND} -P ${CMAKE_BINARY_DIR}/test/${TESTNAME}.cmake)
-		ENDMACRO(ADD_PYTHON_TEST)
-
-		set(pybindtests
-			bindings
-			_pybel
-			example 
-			obconv_writers
-			cdjsonformat
-			pcjsonformat
-			roundtrip
-			)
-		foreach(pybindtest ${pybindtests})
-			ADD_PYTHON_TEST(pybindtest_${pybindtest}_${EPYTHON} ${TEST_SOURCE_DIR}/test${pybindtest}.py)
-			set_tests_properties(pybindtest_${pybindtest}_${EPYTHON} PROPERTIES
-				ENVIRONMENT "PYTHONPATH=${CMAKE_BINARY_DIR}/scripts/${EPYTHON}:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX};LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/scripts/${EPYTHON}:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}:\$ENV{LD_LIBRARY_PATH};BABEL_LIBDIR=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/;BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data"
-				FAIL_REGULAR_EXPRESSION "ERROR;FAIL;Test failed"
-			)
-		endforeach(pybindtest ${pybindtests})
-	endif (ENABLE_TESTS)
-endif(DO_PYTHON_BINDINGS)
diff --git a/sci-chemistry/openbabel/metadata.xml b/sci-chemistry/openbabel/metadata.xml
deleted file mode 100644
index a81d304be773..000000000000
--- a/sci-chemistry/openbabel/metadata.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<longdescription>
-		Open Babel is a chemical toolbox designed to speak the many languages of
-		chemical data. It's an open, collaborative project allowing anyone to
-		search, convert, analyze, or store data from molecular modeling, chemistry,
-		solid-state materials, biochemistry, or related areas.
-	</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">openbabel</remote-id>
-		<remote-id type="github">openbabel/openbabel</remote-id>
-	</upstream>
-	<use>
-		<flag name="inchi">Build support for IUPAC International Chemical Identifier format</flag>
-		<flag name="json">Build support for JSON formats (ChemDoodle, PubChem, etc...)</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-chemistry/openbabel/openbabel-3.1.1_p20241221-r2.ebuild b/sci-chemistry/openbabel/openbabel-3.1.1_p20241221-r2.ebuild
deleted file mode 100644
index 1cc66e2c7a02..000000000000
--- a/sci-chemistry/openbabel/openbabel-3.1.1_p20241221-r2.ebuild
+++ /dev/null
@@ -1,238 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{13..14} )
-WX_GTK_VER=3.2-gtk3
-
-inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg
-
-DESCRIPTION="Interconverts file formats used in molecular modeling"
-HOMEPAGE="https://openbabel.org/ https://github.com/openbabel/openbabel/"
-
-if [[ "${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="889c350feb179b43aa43985799910149d4eaa2bc"
-		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"
-fi
-
-LICENSE="GPL-2"
-# See src/CMakeLists.txt for LIBRARY_VERSION
-SLOT="0/7.0.0"
-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 )"
-REQUIRED_USE="
-	python? ( ${PYTHON_REQUIRED_USE} )
-	test? ( inchi !minimal python? ( json png ) ${PYTHON_REQUIRED_USE} )
-"
-
-RDEPEND="
-	dev-cpp/eigen:=
-	virtual/zlib:=
-	inchi? ( sci-libs/inchi )
-	json? ( >=dev-libs/rapidjson-1.1.0 )
-	!minimal? (
-		dev-libs/libxml2:2=
-		png? ( x11-libs/cairo )
-	)
-	perl? ( dev-lang/perl:= )
-	python? ( ${PYTHON_DEPS} )
-	wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}=[X] )
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	dev-lang/perl
-	doc? (
-		app-text/doxygen
-		dev-texlive/texlive-latex
-	)
-	perl? ( dev-lang/swig )
-	python? ( dev-lang/swig )
-	test? ( dev-lang/python )
-"
-
-PATCHES=(
-	# Set include dir only for global implementation
-	"${FILESDIR}"/${PN}-3.1.1_p2024-fix_pybind.patch
-	# prevent installation of examples in /usr/bin
-	"${FILESDIR}"/${PN}-3.1.1_p2024-fix_examples.patch
-	# cmake4-compat
-	"${FILESDIR}"/${PN}-3.1.1_p2024-cmake4.patch
-)
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-gen_python_bindings() {
-	mkdir -p scripts/${EPYTHON} || die
-	# Appends to scripts/CMakeLists.txt, substituting the correct tags, for
-	# each valid python implementation,
-	cat "${FILESDIR}"/${PN}-python-r2.cmake | \
-		sed -e "s|@@EPYTHON@@|${EPYTHON}|" \
-			-e "s|@@PYTHON_INCLUDE_DIR@@|$(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
-
-	# Prevent bundled inchi as fallback
-	rm -r include/inchi || die
-
-	use python && python_foreach_impl gen_python_bindings
-}
-
-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=(
-		$(cmake_use_find_package png Cairo)
-		$(cmake_use_find_package wxwidgets wxWidgets)
-		-DCMAKE_SKIP_RPATH=ON
-		-DBUILD_DOCS=$(usex doc)
-		-DBUILD_EXAMPLES=$(usex examples)
-		-DBUILD_GUI=$(usex wxwidgets)
-		-DENABLE_OPENMP=$(usex openmp)
-		-DENABLE_TESTS=$(usex test)
-		-DMINIMAL_BUILD=$(usex minimal)
-		# All three required to comply w/ useflag and prevent bundled lib
-		-DOPENBABEL_USE_SYSTEM_INCHI=$(usex inchi)
-		-DADD_INCHI_FORMAT=$(usex inchi)
-		-DWITH_INCHI=$(usex inchi)
-		-DOPTIMIZE_NATIVE=OFF
-		-DPERL_BINDINGS=$(usex perl)
-		-DPYTHON_BINDINGS=$(usex python)
-		-DRUN_SWIG=$(use_bindings)
-		-DWITH_COORDGEN=false
-		-DWITH_JSON=$(usex json)
-		# MEAPARSER
-		-DCMAKE_DISABLE_FIND_PACKAGE_Boost=ON
-		-DWITH_MAEPARSER=false
-	)
-
-	if use perl; then
-		perl_set_version
-		mycmakeargs+=(
-			-DPERL_INSTDIR="${VENDOR_ARCH}"
-		)
-	fi
-
-	if use test; then
-		# Help cmake find the python interpreter when dev-lang/python-exec is built
-		# without native-symlinks support.
-		python_setup
-		mycmakeargs+=(
-			-DPYTHON_EXECUTABLE="${PYTHON}"
-		)
-	fi
-
-	cmake_src_configure
-}
-
-src_test() {
-	local CMAKE_SKIP_TESTS=(
-		# https://github.com/openbabel/openbabel/issues/2766
-		test_align_{4,5}
-	)
-	! use wxwidgets && CMAKE_SKIP_TESTS+=(
-		test_tautomer_{22,27}
-	)
-
-	# Weird 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 ${x}
-	done
-
-	if use doc; then
-		cmake_src_install docs
-		docinto html/API
-		dodoc -r doc/API/html/.
-	fi
-
-	if use examples; then
-		# no compression since we want ready-to-run scripts
-		docompress -x /usr/share/doc/${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" ${PN}
-		newicon "${S}"/src/GUI/babel.xpm ${PN}.xpm
-	fi
-}
diff --git a/sci-chemistry/openbabel/openbabel-3.1.1_p20241221-r4.ebuild b/sci-chemistry/openbabel/openbabel-3.1.1_p20241221-r4.ebuild
deleted file mode 100644
index e9ea539cde58..000000000000
--- a/sci-chemistry/openbabel/openbabel-3.1.1_p20241221-r4.ebuild
+++ /dev/null
@@ -1,247 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-GENTOO_DEPEND_ON_PERL="no"
-PYTHON_COMPAT=( python3_{13..14} )
-WX_GTK_VER=3.2-gtk3
-
-inherit cmake desktop flag-o-matic perl-module python-r1 toolchain-funcs wxwidgets xdg
-
-DESCRIPTION="Interconverts file formats used in molecular modeling"
-HOMEPAGE="https://openbabel.org/ https://github.com/openbabel/openbabel/"
-
-if [[ "${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="889c350feb179b43aa43985799910149d4eaa2bc"
-		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"
-fi
-
-LICENSE="GPL-2"
-# See src/CMakeLists.txt for LIBRARY_VERSION
-SLOT="0/7.0.0"
-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 ${GENTOO_PERL_USESTRING}"
-RESTRICT="!test? ( test )"
-REQUIRED_USE="
-	python? ( ${PYTHON_REQUIRED_USE} )
-	test? ( inchi !minimal python? ( json png ) ${PYTHON_REQUIRED_USE} )
-"
-
-RDEPEND="
-	dev-cpp/eigen:=
-	virtual/zlib:=
-	inchi? ( sci-libs/inchi )
-	json? ( >=dev-libs/rapidjson-1.1.0 )
-	!minimal? (
-		dev-libs/libxml2:2=
-		png? ( x11-libs/cairo )
-	)
-	perl? (
-		${GENTOO_PERL_DEPSTRING}
-		dev-lang/perl:=
-	)
-	python? ( ${PYTHON_DEPS} )
-	wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}=[X] )
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	dev-lang/perl
-	doc? (
-		app-text/doxygen
-		dev-texlive/texlive-latex
-	)
-	perl? ( dev-lang/swig )
-	python? ( dev-lang/swig )
-	test? ( dev-lang/python )
-"
-
-PATCHES=(
-	# Set include dir only for global implementation
-	"${FILESDIR}"/${PN}-3.1.1_p2024-fix_pybind.patch
-	# prevent installation of examples in /usr/bin
-	"${FILESDIR}"/${PN}-3.1.1_p2024-fix_examples.patch
-	# cmake4-compat
-	"${FILESDIR}"/${PN}-3.1.1_p2024-cmake4.patch
-)
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-gen_python_bindings() {
-	mkdir -p scripts/${EPYTHON} || die
-	# Appends to scripts/CMakeLists.txt, substituting the correct tags, for
-	# each valid python implementation,
-	cat "${FILESDIR}"/${PN}-python-r2.cmake | \
-		sed -e "s|@@EPYTHON@@|${EPYTHON}|" \
-			-e "s|@@PYTHON_INCLUDE_DIR@@|$(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
-
-	# Prevent bundled inchi as fallback
-	rm -r include/inchi || die
-
-	use python && python_foreach_impl gen_python_bindings
-}
-
-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=(
-		$(cmake_use_find_package png Cairo)
-		$(cmake_use_find_package wxwidgets wxWidgets)
-		-DCMAKE_SKIP_RPATH=ON
-		-DBUILD_DOCS=$(usex doc)
-		-DBUILD_EXAMPLES=$(usex examples)
-		-DBUILD_GUI=$(usex wxwidgets)
-		-DENABLE_OPENMP=$(usex openmp)
-		-DENABLE_TESTS=$(usex test)
-		-DMINIMAL_BUILD=$(usex minimal)
-		# All three required to comply w/ useflag and prevent bundled lib
-		-DOPENBABEL_USE_SYSTEM_INCHI=$(usex inchi)
-		-DADD_INCHI_FORMAT=$(usex inchi)
-		-DWITH_INCHI=$(usex inchi)
-		-DOPTIMIZE_NATIVE=OFF
-		-DPERL_BINDINGS=$(usex perl)
-		-DPYTHON_BINDINGS=$(usex python)
-		-DRUN_SWIG=$(use_bindings)
-		-DWITH_COORDGEN=false
-		-DWITH_JSON=$(usex json)
-		# MEAPARSER
-		-DCMAKE_DISABLE_FIND_PACKAGE_Boost=ON
-		-DWITH_MAEPARSER=false
-	)
-
-	if use perl; then
-		perl_set_version
-		mycmakeargs+=(
-			-DPERL_INSTDIR="${VENDOR_ARCH}"
-		)
-	fi
-
-	if use test; then
-		# Help cmake find the python interpreter when dev-lang/python-exec is built
-		# without native-symlinks support.
-		python_setup
-		mycmakeargs+=(
-			-DPYTHON_EXECUTABLE="${PYTHON}"
-		)
-	fi
-
-	cmake_src_configure
-}
-
-src_compile() {
-	# Avoid perl-module_src_compile (bug #963096)
-	cmake_src_compile
-}
-
-src_test() {
-	local CMAKE_SKIP_TESTS=(
-		# https://github.com/openbabel/openbabel/issues/2766
-		test_align_{4,5}
-	)
-	! use wxwidgets && CMAKE_SKIP_TESTS+=(
-		test_tautomer_{22,27}
-	)
-
-	# Weird 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 ${x}
-	done
-
-	if use doc; then
-		cmake_src_install docs
-		docinto html/API
-		dodoc -r doc/API/html/.
-	fi
-
-	if use examples; then
-		# no compression since we want ready-to-run scripts
-		docompress -x /usr/share/doc/${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 --eapi9 obgui -n "Open Babel" -i ${PN}
-		newicon "${S}"/src/GUI/babel.xpm ${PN}.xpm
-	fi
-}
diff --git a/sci-chemistry/openbabel/openbabel-9999.ebuild b/sci-chemistry/openbabel/openbabel-9999.ebuild
deleted file mode 100644
index 780e60991924..000000000000
--- a/sci-chemistry/openbabel/openbabel-9999.ebuild
+++ /dev/null
@@ -1,245 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-GENTOO_DEPEND_ON_PERL="no"
-PYTHON_COMPAT=( python3_{13..14} )
-WX_GTK_VER=3.2-gtk3
-
-inherit cmake desktop flag-o-matic perl-module python-r1 toolchain-funcs wxwidgets xdg
-
-DESCRIPTION="Interconverts file formats used in molecular modeling"
-HOMEPAGE="https://openbabel.org/ https://github.com/openbabel/openbabel/"
-
-if [[ "${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="889c350feb179b43aa43985799910149d4eaa2bc"
-		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"
-fi
-
-LICENSE="GPL-2"
-# See src/CMakeLists.txt for LIBRARY_VERSION
-SLOT="0/7.0.0"
-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 ${GENTOO_PERL_USESTRING}"
-RESTRICT="!test? ( test )"
-REQUIRED_USE="
-	python? ( ${PYTHON_REQUIRED_USE} )
-	test? ( inchi !minimal python? ( json png ) ${PYTHON_REQUIRED_USE} )
-"
-
-RDEPEND="
-	dev-cpp/eigen:=
-	virtual/zlib:=
-	inchi? ( sci-libs/inchi )
-	json? ( >=dev-libs/rapidjson-1.1.0 )
-	!minimal? (
-		dev-libs/libxml2:2=
-		png? ( x11-libs/cairo )
-	)
-	perl? (
-		${GENTOO_PERL_DEPSTRING}
-		dev-lang/perl:=
-	)
-	python? ( ${PYTHON_DEPS} )
-	wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}=[X] )
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	dev-lang/perl
-	doc? (
-		app-text/doxygen
-		dev-texlive/texlive-latex
-	)
-	perl? ( dev-lang/swig )
-	python? ( dev-lang/swig )
-	test? ( dev-lang/python )
-"
-
-PATCHES=(
-	# Set include dir only for global implementation
-	"${FILESDIR}"/${PN}-3.1.1_p2024-fix_pybind.patch
-	# prevent installation of examples in /usr/bin
-	"${FILESDIR}"/${PN}-3.1.1_p2024-fix_examples.patch
-)
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-gen_python_bindings() {
-	mkdir -p scripts/${EPYTHON} || die
-	# Appends to scripts/CMakeLists.txt, substituting the correct tags, for
-	# each valid python implementation,
-	cat "${FILESDIR}"/${PN}-python-r2.cmake | \
-		sed -e "s|@@EPYTHON@@|${EPYTHON}|" \
-			-e "s|@@PYTHON_INCLUDE_DIR@@|$(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
-
-	# Prevent bundled inchi as fallback
-	rm -r include/inchi || die
-
-	use python && python_foreach_impl gen_python_bindings
-}
-
-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=(
-		$(cmake_use_find_package png Cairo)
-		$(cmake_use_find_package wxwidgets wxWidgets)
-		-DCMAKE_SKIP_RPATH=ON
-		-DBUILD_DOCS=$(usex doc)
-		-DBUILD_EXAMPLES=$(usex examples)
-		-DBUILD_GUI=$(usex wxwidgets)
-		-DENABLE_OPENMP=$(usex openmp)
-		-DENABLE_TESTS=$(usex test)
-		-DMINIMAL_BUILD=$(usex minimal)
-		# All three required to comply w/ useflag and prevent bundled lib
-		-DOPENBABEL_USE_SYSTEM_INCHI=$(usex inchi)
-		-DADD_INCHI_FORMAT=$(usex inchi)
-		-DWITH_INCHI=$(usex inchi)
-		-DOPTIMIZE_NATIVE=OFF
-		-DPERL_BINDINGS=$(usex perl)
-		-DPYTHON_BINDINGS=$(usex python)
-		-DRUN_SWIG=$(use_bindings)
-		-DWITH_COORDGEN=false
-		-DWITH_JSON=$(usex json)
-		# MEAPARSER
-		-DCMAKE_DISABLE_FIND_PACKAGE_Boost=ON
-		-DWITH_MAEPARSER=false
-	)
-
-	if use perl; then
-		perl_set_version
-		mycmakeargs+=(
-			-DPERL_INSTDIR="${VENDOR_ARCH}"
-		)
-	fi
-
-	if use test; then
-		# Help cmake find the python interpreter when dev-lang/python-exec is built
-		# without native-symlinks support.
-		python_setup
-		mycmakeargs+=(
-			-DPYTHON_EXECUTABLE="${PYTHON}"
-		)
-	fi
-
-	cmake_src_configure
-}
-
-src_compile() {
-	# Avoid perl-module_src_compile (bug #963096)
-	cmake_src_compile
-}
-
-src_test() {
-	local CMAKE_SKIP_TESTS=(
-		# https://github.com/openbabel/openbabel/issues/2766
-		test_align_{4,5}
-	)
-	! use wxwidgets && CMAKE_SKIP_TESTS+=(
-		test_tautomer_{22,27}
-	)
-
-	# Weird 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 ${x}
-	done
-
-	if use doc; then
-		cmake_src_install docs
-		docinto html/API
-		dodoc -r doc/API/html/.
-	fi
-
-	if use examples; then
-		# no compression since we want ready-to-run scripts
-		docompress -x /usr/share/doc/${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" ${PN}
-		newicon "${S}"/src/GUI/babel.xpm ${PN}.xpm
-	fi
-}