commit: 3b032e0f3d0d837c2faf2051da6257844e7ced55 Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> AuthorDate: Mon Mar 7 15:32:02 2022 +0000 Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> CommitDate: Mon Mar 7 16:28:16 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3b032e0f
sci-chemistry/openbabel: Drop 2.4.1-r2 Bug: https://bugs.gentoo.org/834115 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org> sci-chemistry/openbabel/Manifest | 1 - .../openbabel/files/openbabel-2.4.1-gcc10.patch | 62 ------------ .../openbabel/files/openbabel-python.cmake | 104 --------------------- sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild | 101 -------------------- 4 files changed, 268 deletions(-) diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest index 11fe53f8f9de..a9d177301beb 100644 --- a/sci-chemistry/openbabel/Manifest +++ b/sci-chemistry/openbabel/Manifest @@ -1,4 +1,3 @@ -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 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 -}
