gentoo resync : 20.03.2022

6 files changed, 7 insertions, 278 deletions

diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
index 9b3acc76b6cf..c26e4e5832f4 100644
--- a/sci-chemistry/openbabel/Manifest
+++ b/sci-chemistry/openbabel/Manifest
@@ -1,10 +1,6 @@
-AUX openbabel-2.4.1-gcc10.patch 2317 BLAKE2B a76a4ef8b7502f8a80ebb807d2874d77f2ef5f532fa7b71a398245b737d1d55387121f4c24fc7dda7df47ddac4ad16e9cd12076787bedf0f63872708e9516d99 SHA512 ea37e5c53360728455be3d819c29fc27aa10556451a437e05c71c6a5e2bd5e1cfb4c229ff0e67e6c8ae7554f08b7bb16ad4be9ace36991c9c9f2417574b373f2
-AUX openbabel-python.cmake 4402 BLAKE2B 36c325a26f9b23c3957db22110628a0a922ad02b6a7415fc197713d3df8f1703475bf2f2c53b546b7915466ce30b6b3c72c505ea72443dd23a17a7f9131f4f6e SHA512 a7bcdf90588930b05d11312429e735d3cc6a94053e67117bef6c1614932651abee7c4e082916482a9012622c0f29c3ba62dd7788b72aca6c88293660c7f2a3db
-DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6
 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-2.4.1-r2.ebuild 2178 BLAKE2B fd0d324a28dac54a6b67359b9250ab4331195eeb32c10de46d9d5d4e5c4bce44298eb0953eb06006823b7c6bdc5ab0b7f22b0b3334800e2f06d080a3e24fe311 SHA512 494acf7a358eb01a8bc77713da9135195013833c8bc993adad25221715238e53309719c0e42bdcd8ee076d35b26228946cfad5e08aab3259119db741c27ae5bd
-EBUILD openbabel-3.1.1_p20210225.ebuild 7237 BLAKE2B f0825a4ce1a6f2c504d8ea7b308cd5aa65e53be15055f92383e563cb38a5fb504d9bd2bcfd4c4b00e67673b2ca1e6ba85804f9fbd5d33a62ffa0f40369046282 SHA512 dec2f95380a9250941b743bffffca3fd83507137cd21daa87211327cc42ce8e7b77474c6d17b0b67a148832b81b44e1f245277226461c362e6a9809cbc6d5c3c
-EBUILD openbabel-9999.ebuild 7197 BLAKE2B 77bfe052690916bda80ba7d38993f38fb1bff632f27d7d7d352bff6eddabe38cda89fe0f5574a37744091c80e59f1b575fea5a00da9c5a60f594a6c94ea4f9f2 SHA512 79781c3bff2a795c85dc4ca99640ee52c59130ddfd49c8452473fd2cb544991759f3c76f3cb9afa5a9671ee91508706707e9e02d8a95668f544274f315e4be03
+EBUILD openbabel-3.1.1_p20210225.ebuild 7234 BLAKE2B 5ea580096819ba3df0b18fe713d04f7811d6c65016ca18492ee4a1deada357261580e87bae9fca8cf9a9eea8214ca0fd7f7ac22f1272cd8f2577dd88c207a44d SHA512 0323ef9d33b9efe318b59c2de88073c3c30c5d90f470f0e8426f9a7563595e1e5e7446130a72c1a747ea080df7ee9189e473e3fc3a5464b07efd2066ed1dac91
+EBUILD openbabel-9999.ebuild 7196 BLAKE2B 07a467606b08dfa7c4b81cb58b25afc37cb06330e8d0c5012896905a672c206c0690898950d1b9bca35ea5ddc5dc415516341fe5f3c2095db7b91f169b9300b9 SHA512 1c1214ad4eb0ec7128feedb5708f814d3910ab0c6adbdaa19b8e34c11968daa8d92efafa2685b69558f5b884f9c09f27f19d75db26a5e522c357081496f4f378
 MISC metadata.xml 862 BLAKE2B 56a35c050142f5a8939441d6a669986ad58321154f1a46fb78dcf6b861311bbb28d6f49507fff673519396533fbbfb8bf0214aa9dbdf1041ae7497c3287a3eb3 SHA512 7d289c49a91b4ae9a3910c6feb1014fa307ccc01b1e041e1aece7c8f135ac2eb1f5aae562dfd25d17e38d88c5747786a7406d6c09d10f74e80c08691599dec80
diff --git a/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc10.patch b/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc10.patch
deleted file mode 100644
index 88d8c2add64a..000000000000
--- a/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc10.patch
+++ /dev/null
@@ -1,62 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 2e66dd1..ef4f16b 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -1,16 +1,11 @@
- # Please ensure that any changes remain compliant with 2.4.8.
- if(NOT EMBED_OPENBABEL)
--  cmake_minimum_required(VERSION 2.4.8)
-+  cmake_minimum_required(VERSION 2.4.10)
- endif()
- 
- project(openbabel)
- set(CMAKE_MODULE_PATH ${openbabel_SOURCE_DIR}/cmake/modules)
- 
--# Allow loose loop constructs, i.e. no matching in if/else/endif or loops.
--# Note that this is true by default in CMake 2.6.0, but we currently only
--# require CMake 2.4.8 - remove this when the CMake requirement is bumped.
--set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS 1)
--
- if(COMMAND cmake_policy)
-   cmake_policy(SET CMP0003 NEW)
-   cmake_policy(SET CMP0005 OLD) # add_definitions need updating to set to NEW
-@@ -20,7 +15,6 @@ if(COMMAND cmake_policy)
- endif()
- 
- include (CheckCXXCompilerFlag)
--include (MacroEnsureVersion)
- 
- # Version numbering - should be bumped for each release
- # Note that for "beta" releases, we should start at x.90.0 -- we've
-@@ -238,16 +232,21 @@ check_type_size(clock_t CLOCK_T)
- 
- # Get the GCC version - from KDE4 cmake files
- if(CMAKE_COMPILER_IS_GNUCXX)
--  exec_program(${CMAKE_C_COMPILER} ARGS --version OUTPUT_VARIABLE _gcc_version_info)
--  string(REGEX MATCH "[345]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
--  # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the
--  # patch level, handle this here:
--  if (NOT _gcc_version)
--    string (REGEX REPLACE ".*\\(GCC\\).* ([34]\\.[0-9]) .*" "\\1.0" _gcc_version "${_gcc_version_info}")
--  endif ()
--  macro_ensure_version("4.0.0" "${_gcc_version}" GCC_IS_NEWER_THAN_4_0)
--  macro_ensure_version("4.1.0" "${_gcc_version}" GCC_IS_NEWER_THAN_4_1)
--  macro_ensure_version("4.2.0" "${_gcc_version}" GCC_IS_NEWER_THAN_4_2)
-+  if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.0.0))
-+    set(GCC_IS_NEWER_THAN_4_0 TRUE)
-+  else()
-+    set(GCC_IS_NEWER_THAN_4_0 FALSE)
-+  endif()
-+  if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.1.0))
-+    set(GCC_IS_NEWER_THAN_4_1 TRUE)
-+  else()
-+    set(GCC_IS_NEWER_THAN_4_1 FALSE)
-+  endif()
-+  if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.2.0))
-+    set(GCC_IS_NEWER_THAN_4_2 TRUE)
-+  else()
-+    set(GCC_IS_NEWER_THAN_4_2 FALSE)
-+  endif()
- endif()
- 
- if(UNIX)
diff --git a/sci-chemistry/openbabel/files/openbabel-python.cmake b/sci-chemistry/openbabel/files/openbabel-python.cmake
deleted file mode 100644
index 425b4656a9d2..000000000000
--- a/sci-chemistry/openbabel/files/openbabel-python.cmake
+++ /dev/null
@@ -1,104 +0,0 @@
-# The following is a cmake fragment taken from scripts/CMakeLists.txt and
-# edited for Gentoo python multibuild compatibility.
-
-if (PYTHON_BINDINGS)
-	# Tags should be edited to reflect the active python implementation
-	set(EPYTHON @@EPYTHON@@)
-	set(PYTHON_INCUDE_DIR @@PYTHON_INCUDE_DIR@@)
-	set(PYTHON_LIBS @@PYTHON_LIBS@@)
-	set(PYTHON_SITEDIR @@PYTHON_SITEDIR@@)
-
-	include_directories(${PYTHON_INCUDE_DIR})
-
-	add_custom_command(
-		OUTPUT ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py
-		COMMAND ${SWIG_EXECUTABLE} -python -c++ -small -O -templatereduce -naturalvar -I${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_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 ${pybindtests})
-	endif (ENABLE_TESTS)
-endif(PYTHON_BINDINGS)
diff --git a/sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild b/sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild
deleted file mode 100644
index 95161d26d6d6..000000000000
--- a/sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild
+++ /dev/null
@@ -1,101 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-WX_GTK_VER="3.0-gtk3"
-
-inherit cmake-utils desktop optfeature toolchain-funcs wxwidgets
-
-DESCRIPTION="Interconverts file formats used in molecular modeling"
-HOMEPAGE="http://openbabel.org/wiki/Main_Page"
-SRC_URI="
-	mirror://sourceforge/openbabel/${P}.tar.gz
-	https://openbabel.org/docs/dev/_static/babel130.png -> ${PN}.png
-"
-
-# See src/CMakeLists.txt for LIBRARY_VERSION
-SLOT="0/5.0.0"
-LICENSE="GPL-2"
-KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux ~ppc-macos"
-IUSE="doc openmp test wxwidgets"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
-	dev-cpp/eigen:3
-	dev-libs/libxml2:2
-	sci-libs/inchi
-	sys-libs/zlib
-	wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] )
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	>=dev-util/cmake-2.4.10
-	doc? ( app-doc/doxygen )
-"
-
-DOCS=( AUTHORS NEWS.md README.md THANKS doc/dioxin.{inc,mol2} doc/README.{dioxin.pov,povray} )
-
-PATCHES=(
-	"${FILESDIR}"/${P}-gcc10.patch
-)
-
-pkg_setup() {
-	if use openmp; then
-		if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then
-			ewarn "OpenMP is not available in your current selected gcc"
-			die "need openmp capable gcc"
-		fi
-		FORTRAN_NEED_OPENMP=1
-	fi
-}
-
-src_prepare() {
-	sed \
-		-e '/__GNUC__/s:== 4:>= 4:g' \
-		-i include/openbabel/shared_ptr.h || die
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	use wxwidgets && setup-wxwidgets
-	local mycmakeargs=(
-		-DOPENBABEL_USE_SYSTEM_INCHI=ON
-		-DENABLE_OPENMP=$(usex openmp)
-		-DBUILD_GUI=$(usex wxwidgets)
-	)
-
-	cmake-utils_src_configure
-}
-
-src_install() {
-	docinto html
-	dodoc doc/{*.html,*.png}
-	if use doc ; then
-		docinto html/API
-		dodoc -r doc/API/html/*
-	fi
-
-	make_desktop_entry obgui "Open Babel" "${PN}"
-	doicon "${DISTDIR}/${PN}.png"
-
-	cmake-utils_src_install
-}
-
-src_test() {
-	local mycmakeargs=(
-		-DOPENBABEL_USE_SYSTEM_INCHI=ON
-		-DPYTHON_EXECUTABLE=false
-		-DOPENMP=$(usex openmp)
-		-DBUILD_GUI=$(usex wxwidgets)
-		-DTESTS=$(usex test)
-	)
-
-	cmake-utils_src_configure
-	cmake-utils_src_compile
-	cmake-utils_src_test -E py
-}
-
-pkg_postinst() {
-	optfeature "perl support" sci-chemistry/openbabel-perl
-	optfeature "python support" sci-chemistry/openbabel-python
-}
diff --git a/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild b/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild
index 67ac61c1741b..97dfa6e9a236 100644
--- a/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild
+++ b/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -25,7 +25,7 @@ else
 		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"
+	KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux ~ppc-macos"
 fi
 
 SRC_URI="${SRC_URI}
@@ -181,7 +181,7 @@ src_configure() {
 	)
 
 	if use test; then
-		# Help cmake find the python interpreter when dev-lang/python-exec is built 
+		# Help cmake find the python interpreter when dev-lang/python-exec is built
 		# without native-symlinks support.
 		python_setup
 		mycmakeargs+=( -DPYTHON_EXECUTABLE="${PYTHON}" )
diff --git a/sci-chemistry/openbabel/openbabel-9999.ebuild b/sci-chemistry/openbabel/openbabel-9999.ebuild
index baf793cb651c..2c73801d2362 100644
--- a/sci-chemistry/openbabel/openbabel-9999.ebuild
+++ b/sci-chemistry/openbabel/openbabel-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -181,7 +181,7 @@ src_configure() {
 	)
 
 	if use test; then
-		# Help cmake find the python interpreter when dev-lang/python-exec is built 
+		# Help cmake find the python interpreter when dev-lang/python-exec is built
 		# without native-symlinks support.
 		python_setup
 		mycmakeargs+=( -DPYTHON_EXECUTABLE="${PYTHON}" )