Adding metadata

6 files changed, 232 insertions, 253 deletions

diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
index 336f074b2917..ea27a18b1136 100644
--- a/sci-chemistry/openbabel/Manifest
+++ b/sci-chemistry/openbabel/Manifest
@@ -1 +1,2 @@
 DIST openbabel-3.1.1_p20241221.tar.gz 36864825 BLAKE2B 55e6fbdd5c50a557c40fd5ffaca41753f73175b2b4eea22abe5c2b0031363e3c133acf9a8daf5b1cb362a3adb6398204497af036b9a7ba3630c1d8ccbce0f9d3 SHA512 44340c3d08b22783cf6a702c192480869b73fef21104641feaf5cbcd51f693fd17bb05ad31a3520f330aa57733d6f4be707b3c1243b3010d6ceccca8974e732f
+DIST openbabel-3.2.0.tar.gz 37815471 BLAKE2B b94e4de7a190c8e3b63adcb1f50ad114eb14c30809c2e85f297872b243c4fb6a6001b86d705dc5276d92b74a5122d31a04f26db48547d56e35a6bfacbefac6b1 SHA512 0def0b8c6185ec648c41b32c9c2963329f764b57105efe895fa435fd2ee4878b70141b0ac9e80dddbc82e2ca95281955f612a21ba0dd5c0e7ef715061acf8234
diff --git a/sci-chemistry/openbabel/files/openbabel-3.2.0-cflags.patch b/sci-chemistry/openbabel/files/openbabel-3.2.0-cflags.patch
new file mode 100644
index 000000000000..099a01525fdd
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-3.2.0-cflags.patch
@@ -0,0 +1,11 @@
+# respect userflags
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -427,7 +427,6 @@ endif()
+ #define various build types
+ if(CMAKE_COMPILER_IS_GNUCXX)
+   set (CMAKE_CXX_FLAGS_RELEASE        "${CMAKE_CXX_FLAGS_RELEASE} -O3 -DNDEBUG")
+-  set (CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} -O2 -g")
+   set (CMAKE_CXX_FLAGS_DEBUG          "${CMAKE_CXX_FLAGS_DEBUG} -D_GLIBCXX_DEBUG -g3 -fno-inline")
+ endif()
+ 
diff --git a/sci-chemistry/openbabel/files/openbabel-3.2.0-system_inchi.patch b/sci-chemistry/openbabel/files/openbabel-3.2.0-system_inchi.patch
new file mode 100644
index 000000000000..1a2cdbc4dcfa
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-3.2.0-system_inchi.patch
@@ -0,0 +1,93 @@
+See PR pending https://github.com/openbabel/openbabel/pull/2969.patch
+fix headers with system InChI / various changes to handle InChI option
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -144,6 +144,7 @@ option(OPENBABEL_USE_SYSTEM_INCHI
+   "Use the system inchi library." OFF)
+ if(OPENBABEL_USE_SYSTEM_INCHI)
+   find_package(Inchi REQUIRED)
++  add_definitions(-DHAVE_SYSTEM_INCHI)
+   if (NOT INCHI_FOUND)
+     message(FATAL_ERROR "Inchi library not found.")
+   endif()
+--- a/include/openbabel/inchiformat.h
++++ b/include/openbabel/inchiformat.h
+@@ -21,8 +21,13 @@ GNU General Public License for more details.
+ #include <openbabel/obconversion.h>
+ #include <openbabel/obmolecformat.h>
+ 
++#ifdef HAVE_SYSTEM_INCHI
++#include <inchi_api.h>
++#define CURRENT_VER "unknown" // bcf_s.h is not packaged
++#else
+ #include "../inchi/inchi_api.h"
+ #include "../inchi/bcf_s.h"  // for CURRENT_VER
++#endif
+ #ifdef HAVE_SSTREAM
+ #include <sstream>
+ #else
+
+--- a/include/CMakeLists.txt
++++ b/include/CMakeLists.txt
+@@ -5,9 +5,13 @@ file(GLOB stereo_headers      openbabel/stereo/*.h)
+ file(GLOB depict_headers      openbabel/depict/*.h)
+ file(GLOB lbfgs_headers       LBFGS/*.h)
+ 
++if(WITH_INCHI)
+ if(NOT OPENBABEL_USE_SYSTEM_INCHI)
+ install(FILES inchi/inchi_api.h          DESTINATION include/inchi)
+ endif(NOT OPENBABEL_USE_SYSTEM_INCHI)
++else(WITH_INCHI)
++list(FILTER openbabel_headers      EXCLUDE REGEX ".*inchiformat\\.h$")
++endif(WITH_INCHI)
+ install(FILES chemdrawcdx.h        DESTINATION ${OB_INCLUDE_DIRS}/openbabel)
+ install(FILES ${openbabel_headers} DESTINATION ${OB_INCLUDE_DIRS}/openbabel)
+ install(FILES ${math_headers}      DESTINATION ${OB_INCLUDE_DIRS}/openbabel/math)
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -34,10 +34,15 @@ set(descriptors
+   descriptors/cmpdfilter.cpp
+   descriptors/groupcontrib.cpp
+   descriptors/filters.cpp
+-  descriptors/inchidescriptor.cpp
+   descriptors/smartsdescriptors.cpp
+ )
+ 
++if(WITH_INCHI)
++  set(descriptors ${descriptors}
++    descriptors/inchidescriptor.cpp
++  )
++endif()
++
+ set(fingerprints
+   fingerprints/finger2.cpp
+   fingerprints/finger3.cpp
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -142,15 +142,17 @@ endif()
+ option(WITH_INCHI   "Build inchi support" ON)
+ option(OPENBABEL_USE_SYSTEM_INCHI
+   "Use the system inchi library." OFF)
+-if(OPENBABEL_USE_SYSTEM_INCHI)
+-  find_package(Inchi REQUIRED)
+-  add_definitions(-DHAVE_SYSTEM_INCHI)
+-  if (NOT INCHI_FOUND)
+-    message(FATAL_ERROR "Inchi library not found.")
++if(WITH_INCHI)
++  if(OPENBABEL_USE_SYSTEM_INCHI)
++    find_package(Inchi REQUIRED)
++    add_definitions(-DHAVE_SYSTEM_INCHI)
++    if (NOT INCHI_FOUND)
++      message(FATAL_ERROR "Inchi library not found.")
++    endif()
++  else()
++    message(STATUS "Using included inchi library.")
++    set(INCHI_LIBRARY inchi)
+   endif()
+-else()
+-  message(STATUS "Using included inchi library.")
+-  set(INCHI_LIBRARY inchi)
+ endif()
+ 
+ if(WIN32)
diff --git a/sci-chemistry/openbabel/files/openbabel-python-3.2.cmake b/sci-chemistry/openbabel/files/openbabel-python-3.2.cmake
new file mode 100644
index 000000000000..5b1b275ec67c
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-python-3.2.cmake
@@ -0,0 +1,105 @@
+# The following is a cmake fragment taken from scripts/CMakeLists.txt and
+# and test/CMakeLists.txt edited for Gentoo python multibuild compatibility.
+# PYTHON_GENTOO_BINDINGS must be set instead of PYTHON_BINDINGS
+
+if (PYTHON_GENTOO_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
+			ketformat
+			cdjsonformat
+			pcjsonformat
+			#roundtrip #really long and heavy, could be >1500s
+			)
+		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 ${pybindtests})
+	endif (ENABLE_TESTS)
+endif(PYTHON_GENTOO_BINDINGS)
diff --git a/sci-chemistry/openbabel/openbabel-3.1.1_p20241221-r2.ebuild b/sci-chemistry/openbabel/openbabel-3.1.1_p20241221-r2.ebuild
deleted file mode 100644
index 1cc66e2c7a02..000000000000
--- a/sci-chemistry/openbabel/openbabel-3.1.1_p20241221-r2.ebuild
+++ /dev/null
@@ -1,238 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{13..14} )
-WX_GTK_VER=3.2-gtk3
-
-inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg
-
-DESCRIPTION="Interconverts file formats used in molecular modeling"
-HOMEPAGE="https://openbabel.org/ https://github.com/openbabel/openbabel/"
-
-if [[ "${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-9999.ebuild b/sci-chemistry/openbabel/openbabel-3.2.0.ebuild
index 780e60991924..0df337b4de62 100644
--- a/sci-chemistry/openbabel/openbabel-9999.ebuild
+++ b/sci-chemistry/openbabel/openbabel-3.2.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2025 Gentoo Authors
+# Copyright 1999-2026 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -16,9 +16,9 @@ if [[ "${PV}" == *9999* ]]; then
 	inherit git-r3
 	EGIT_REPO_URI="https://github.com/openbabel/${PN}.git"
 else
-	if [[ "${PV}" == *_p* ]]; then	# eg., openbabel-3.1.1_p20210325
+	if [[ "${PV}" == *_p* ]]; then
 		# Set to commit hash
-		OPENBABEL_COMMIT="889c350feb179b43aa43985799910149d4eaa2bc"
+		OPENBABEL_COMMIT=""
 		SRC_URI="https://github.com/${PN}/${PN}/archive/${OPENBABEL_COMMIT}.tar.gz -> ${P}.tar.gz"
 		S="${WORKDIR}/${PN}-${OPENBABEL_COMMIT}"
 	else
@@ -31,7 +31,7 @@ fi
 
 LICENSE="GPL-2"
 # See src/CMakeLists.txt for LIBRARY_VERSION
-SLOT="0/7.0.0"
+SLOT="0/8.0.0"
 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="
@@ -68,10 +68,12 @@ BDEPEND="
 "
 
 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
+	# fix headers for InChi
+	"${FILESDIR}"/${PN}-3.2.0-system_inchi.patch
+	# filter -O2
+	"${FILESDIR}"/${PN}-3.2.0-cflags.patch
 )
 
 pkg_pretend() {
@@ -86,7 +88,7 @@ gen_python_bindings() {
 	mkdir -p scripts/${EPYTHON} || die
 	# Appends to scripts/CMakeLists.txt, substituting the correct tags, for
 	# each valid python implementation,
-	cat "${FILESDIR}"/${PN}-python-r2.cmake | \
+	cat "${FILESDIR}"/${PN}-python-3.2.cmake | \
 		sed -e "s|@@EPYTHON@@|${EPYTHON}|" \
 			-e "s|@@PYTHON_INCLUDE_DIR@@|$(python_get_includedir)|" \
 			-e "s|@@PYTHON_LIBS@@|$(python_get_LIBS)|" \
@@ -134,7 +136,7 @@ src_configure() {
 		-DWITH_INCHI=$(usex inchi)
 		-DOPTIMIZE_NATIVE=OFF
 		-DPERL_BINDINGS=$(usex perl)
-		-DPYTHON_BINDINGS=$(usex python)
+		-DPYTHON_BINDINGS=OFF
 		-DRUN_SWIG=$(use_bindings)
 		-DWITH_COORDGEN=false
 		-DWITH_JSON=$(usex json)
@@ -150,12 +152,17 @@ src_configure() {
 		)
 	fi
 
+	if use python; then
+		mycmakeargs+=(
+			-DPYTHON_GENTOO_BINDINGS=ON
+		)
+	fi
+
 	if use test; then
-		# Help cmake find the python interpreter when dev-lang/python-exec is built
-		# without native-symlinks support.
+		# used for unittest
 		python_setup
 		mycmakeargs+=(
-			-DPYTHON_EXECUTABLE="${PYTHON}"
+			-DPython_EXECUTABLE="${PYTHON}"
 		)
 	fi
 
@@ -168,9 +175,9 @@ src_compile() {
 }
 
 src_test() {
-	local CMAKE_SKIP_TESTS=(
-		# https://github.com/openbabel/openbabel/issues/2766
-		test_align_{4,5}
+	local CMAKE_SKIP_TESTS=()
+	! use json && CMAKE_SKIP_TESTS+=(
+		test_ketformat*
 	)
 	! use wxwidgets && CMAKE_SKIP_TESTS+=(
 		test_tautomer_{22,27}
@@ -239,7 +246,7 @@ src_install() {
 	fi
 
 	if use wxwidgets; then
-		make_desktop_entry obgui "Open Babel" ${PN}
+		make_desktop_entry --eapi9 obgui -n "Open Babel" -i ${PN}
 		newicon "${S}"/src/GUI/babel.xpm ${PN}.xpm
 	fi
 }