Date: Wed, 8 Mar 2023 11:41:49 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 224ec2aabb2b - main - =?utf-8?Q?science/py-gemmi:=20Update=200.5.8=20=E2=86=92=200.6.0?= Message-ID: <202303081141.328Bfnbm080980@gitrepo.freebsd.org>
next in thread | raw e-mail | index | archive | help
The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=224ec2aabb2bfa9e2c5d3ad4c594536ceb70b8f7 commit 224ec2aabb2bfa9e2c5d3ad4c594536ceb70b8f7 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2023-03-08 10:58:04 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2023-03-08 11:41:47 +0000 science/py-gemmi: Update 0.5.8 → 0.6.0 Reported by: portscout --- science/py-gemmi/Makefile | 10 +- science/py-gemmi/distinfo | 6 +- science/py-gemmi/files/patch-CMakeLists.txt | 202 +++++++++++++++++++++++----- science/py-gemmi/pkg-plist | 6 + 4 files changed, 186 insertions(+), 38 deletions(-) diff --git a/science/py-gemmi/Makefile b/science/py-gemmi/Makefile index 3c1a4fb91ca0..167af8a9ef98 100644 --- a/science/py-gemmi/Makefile +++ b/science/py-gemmi/Makefile @@ -1,6 +1,6 @@ PORTNAME= gemmi DISTVERSIONPREFIX= v -DISTVERSION= 0.5.8 +DISTVERSION= 0.6.0 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,17 +12,19 @@ LICENSE= MPL20 LICENSE_FILE= ${WRKSRC}/LICENSE.txt BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pip>0:devel/py-pip@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pybind11>0:devel/py-pybind11@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \ pybind11>=2.6:devel/pybind11 +LIB_DEPENDS= libgemmi_cpp.so:science/gemmi -USES= cmake compiler:c++17-lang python +USES= cmake compiler:c++20-lang localbase:ldflags python USE_PYTHON= flavors USE_GITHUB= yes GH_ACCOUNT= project-gemmi CMAKE_ON= USE_PYTHON - -PLIST_FILES= ${PYTHON_SITELIBDIR}/gemmi${PYTHON_EXT_SUFFIX}.so +CMAKE_ARGS= -DPython_EXECUTABLE=${PYTHON_CMD} TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} TEST_WRKSRC= ${BUILD_WRKSRC}/tests diff --git a/science/py-gemmi/distinfo b/science/py-gemmi/distinfo index 4a694c3cbfd2..78fe3395fb96 100644 --- a/science/py-gemmi/distinfo +++ b/science/py-gemmi/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1671964416 -SHA256 (project-gemmi-gemmi-v0.5.8_GH0.tar.gz) = b67c8f79d85c4fd6766ce5b0418c79f4cb54a62d9091de6d0a7c20bb6060070e -SIZE (project-gemmi-gemmi-v0.5.8_GH0.tar.gz) = 1695293 +TIMESTAMP = 1678255262 +SHA256 (project-gemmi-gemmi-v0.6.0_GH0.tar.gz) = 5f033dded4bf1f3d8fa88636d798aea70bfb2a2f0e209fd517b36d773f83588d +SIZE (project-gemmi-gemmi-v0.6.0_GH0.tar.gz) = 1737083 diff --git a/science/py-gemmi/files/patch-CMakeLists.txt b/science/py-gemmi/files/patch-CMakeLists.txt index 74cb0c82e534..aa925ae1bb93 100644 --- a/science/py-gemmi/files/patch-CMakeLists.txt +++ b/science/py-gemmi/files/patch-CMakeLists.txt @@ -1,46 +1,186 @@ ---- CMakeLists.txt.orig 2022-09-21 17:17:09 UTC +- workaround for https://github.com/project-gemmi/gemmi/issues/257 + +--- CMakeLists.txt.orig 2023-03-06 11:12:31 UTC +++ CMakeLists.txt -@@ -274,6 +274,7 @@ add_executable(gemmi-wcn EXCLUDE_FROM_ALL $<TARGET_OBJ - src/wcn.cpp $<TARGET_OBJECTS:input>) - support_gz(gemmi-wcn) - -+if (FALSE) - add_executable(program - src/align.cpp src/blobs.cpp - src/cif2mtz.cpp src/cif2json.cpp src/contact.cpp -@@ -290,15 +291,16 @@ add_executable(program - $<TARGET_OBJECTS:options>) - support_gz(program) - target_compile_definitions(program PRIVATE GEMMI_ALL_IN_ONE=1) --set_target_properties(program PROPERTIES OUTPUT_NAME gemmi) -+#set_target_properties(program PROPERTIES OUTPUT_NAME gemmi) +@@ -182,21 +182,23 @@ if (GEMMI_VERSION_INFO) + target_compile_definitions(options PRIVATE GEMMI_VERSION_INFO=${GEMMI_VERSION_INFO}) + endif() + +-add_library(gemmi_cpp +- src/crd.cpp src/mmcif.cpp src/mtz.cpp src/mtz2cif.cpp +- src/polyheur.cpp +- src/read_cif.cpp src/mmread_gz.cpp src/resinfo.cpp +- src/riding_h.cpp src/sprintf.cpp src/to_mmcif.cpp +- src/to_pdb.cpp src/monlib.cpp src/topo.cpp src/xds_ascii.cpp) +-set_property(TARGET gemmi_cpp PROPERTY POSITION_INDEPENDENT_CODE ON) ++#add_library(gemmi_cpp ++# src/crd.cpp src/mmcif.cpp src/mtz.cpp src/mtz2cif.cpp ++# src/polyheur.cpp ++# src/read_cif.cpp src/mmread_gz.cpp src/resinfo.cpp ++# src/riding_h.cpp src/sprintf.cpp src/to_mmcif.cpp ++# src/to_pdb.cpp src/monlib.cpp src/topo.cpp src/xds_ascii.cpp) ++#set_property(TARGET gemmi_cpp PROPERTY POSITION_INDEPENDENT_CODE ON) + #set_property(TARGET gemmi_cpp PROPERTY CXX_VISIBILITY_PRESET hidden) +-target_compile_definitions(gemmi_cpp PRIVATE GEMMI_BUILD) ++#target_compile_definitions(gemmi_cpp PRIVATE GEMMI_BUILD) + if (BUILD_SHARED_LIBS) +- target_compile_definitions(gemmi_cpp PUBLIC GEMMI_SHARED) ++ #target_compile_definitions(gemmi_cpp PUBLIC GEMMI_SHARED) + endif() +-support_gz(gemmi_cpp) ++#support_gz(gemmi_cpp) + ++find_package(gemmi REQUIRED) + ++ + # Gemmi subcommands compiled as individual binaries. + # Not built by default and used mostly for testing. + function(add_single_prog target) +@@ -204,7 +206,7 @@ function(add_single_prog target) + add_executable(gemmi-${target} EXCLUDE_FROM_ALL prog/${target}.cpp ${arg_ADD_SRC} + $<TARGET_OBJECTS:options>) + if (NOT arg_NOLIB) +- target_link_libraries(gemmi-${target} PRIVATE gemmi_cpp) ++ #target_link_libraries(gemmi-${target} PRIVATE gemmi_cpp) + endif() + if (arg_GZ) + support_gz(gemmi-${target}) +@@ -243,29 +245,29 @@ add_single_prog(wcn) + add_single_prog(xds2mtz GZ) + + # gemmi program with a number of subcommands +-add_executable(gemmi_prog +- prog/align.cpp prog/blobs.cpp +- prog/cif2mtz.cpp prog/cif2json.cpp prog/contact.cpp +- prog/contents.cpp prog/convert.cpp prog/fprime.cpp +- prog/grep.cpp prog/h.cpp prog/json2cif.cpp +- prog/main.cpp prog/map.cpp prog/map2sf.cpp +- prog/mapcoef.cpp prog/mask.cpp +- prog/merge.cpp prog/mondiff.cpp prog/mtz.cpp prog/mtz2cif.cpp +- prog/prep.cpp prog/reindex.cpp prog/residues.cpp prog/rmsz.cpp +- prog/sf2map.cpp prog/sfcalc.cpp prog/sg.cpp prog/tags.cpp +- prog/validate.cpp prog/validate_mon.cpp prog/wcn.cpp +- prog/xds2mtz.cpp +- $<TARGET_OBJECTS:options>) +-target_link_libraries(gemmi_prog PRIVATE gemmi_cpp) +-support_gz(gemmi_prog) +-target_compile_definitions(gemmi_prog PRIVATE GEMMI_ALL_IN_ONE=1) +-set_property(TARGET gemmi_prog PROPERTY OUTPUT_NAME gemmi) ++#add_executable(gemmi_prog ++# prog/align.cpp prog/blobs.cpp ++# prog/cif2mtz.cpp prog/cif2json.cpp prog/contact.cpp ++# prog/contents.cpp prog/convert.cpp prog/fprime.cpp ++# prog/grep.cpp prog/h.cpp prog/json2cif.cpp ++# prog/main.cpp prog/map.cpp prog/map2sf.cpp ++# prog/mapcoef.cpp prog/mask.cpp ++# prog/merge.cpp prog/mondiff.cpp prog/mtz.cpp prog/mtz2cif.cpp ++# prog/prep.cpp prog/reindex.cpp prog/residues.cpp prog/rmsz.cpp ++# prog/sf2map.cpp prog/sfcalc.cpp prog/sg.cpp prog/tags.cpp ++# prog/validate.cpp prog/validate_mon.cpp prog/wcn.cpp ++# prog/xds2mtz.cpp ++# $<TARGET_OBJECTS:options>) ++#target_link_libraries(gemmi_prog PRIVATE gemmi_cpp) ++#support_gz(gemmi_prog) ++#target_compile_definitions(gemmi_prog PRIVATE GEMMI_ALL_IN_ONE=1) ++#set_property(TARGET gemmi_prog PROPERTY OUTPUT_NAME gemmi) if (WIN32 AND USE_WMAIN) # _UNICODE=1 is now set globally -- #target_compile_definitions(program PRIVATE _UNICODE=1) -+ target_compile_definitions(program PRIVATE _UNICODE=1) + #target_compile_definitions(gemmi_prog PRIVATE _UNICODE=1) if(MINGW) # target_link_options were added in cmake 3.13 - set_target_properties(program PROPERTIES LINK_FLAGS "-municode") +- set_property(TARGET gemmi_prog PROPERTY LINK_FLAGS "-municode") ++ #set_property(TARGET gemmi_prog PROPERTY LINK_FLAGS "-municode") endif() endif() -+endif() - ### tests and examples ### +@@ -284,10 +286,10 @@ add_executable(doc_example EXCLUDE_FROM_ALL + docs/code/cell.cpp src/resinfo.cpp) + add_executable(doc_example2 EXCLUDE_FROM_ALL docs/code/cif_cc.cpp) + add_executable(doc_maybegz EXCLUDE_FROM_ALL docs/code/maybegz.cpp docs/code/mutate.cpp) +-target_link_libraries(doc_maybegz PRIVATE gemmi_cpp) ++target_link_libraries(doc_maybegz PRIVATE gemmi) + support_gz(doc_maybegz) + add_executable(doc_newmtz EXCLUDE_FROM_ALL docs/code/newmtz.cpp) +-target_link_libraries(doc_newmtz PRIVATE gemmi_cpp) ++target_link_libraries(doc_newmtz PRIVATE gemmi) + support_gz(doc_newmtz) -@@ -416,12 +418,12 @@ else() - message(STATUS "Skipping Python module. Add -D USE_PYTHON=1 to build it.") + # always compile these tests with assertions enabled +@@ -296,7 +298,7 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU|Intel") endif() --install(TARGETS program DESTINATION bin) --install(DIRECTORY include/gemmi DESTINATION include) -+#install(TARGETS program DESTINATION bin) -+#install(DIRECTORY include/gemmi DESTINATION include) - if (USE_PYTHON AND DEFINED PYTHON_INSTALL_DIR) - install(TARGETS py DESTINATION ${PYTHON_INSTALL_DIR}) -- install(DIRECTORY examples/ DESTINATION ${PYTHON_INSTALL_DIR}/gemmi-examples + add_executable(test_disulf EXCLUDE_FROM_ALL tests/disulf.cpp) +-target_link_libraries(test_disulf PRIVATE gemmi_cpp) ++target_link_libraries(test_disulf PRIVATE gemmi) + support_gz(test_disulf) + + # auth_label requires <experimental/filesystem> and -lstdc++fs +@@ -307,7 +309,7 @@ endif() + support_gz(auth_label) + + add_executable(check_conn EXCLUDE_FROM_ALL examples/check_conn.cpp) +-target_link_libraries(check_conn PRIVATE gemmi_cpp) ++target_link_libraries(check_conn PRIVATE gemmi) + + enable_testing() + +@@ -344,7 +346,7 @@ if (benchmark_FOUND) + foreach(b stoi elem mod niggli pdb resinfo round sym) + add_executable(${b}-bm EXCLUDE_FROM_ALL benchmarks/${b}.cpp) + if (b MATCHES "resinfo|pdb") +- target_link_libraries(${b}-bm PRIVATE gemmi_cpp) ++ target_link_libraries(${b}-bm PRIVATE gemmi) + endif() + target_link_libraries(${b}-bm PRIVATE benchmark::benchmark) + set_property(TARGET ${b}-bm PROPERTY RUNTIME_OUTPUT_DIRECTORY +@@ -372,8 +374,8 @@ if (USE_PYTHON) + python/mtz.cpp python/read.cpp python/recgrid.cpp + python/scaling.cpp python/search.cpp + python/sf.cpp python/sym.cpp python/topo.cpp python/refine.cpp +- python/unitcell.cpp python/write.cpp +- $<TARGET_OBJECTS:gemmi_cpp>) ++ python/unitcell.cpp python/write.cpp) ++ target_link_libraries(gemmi_py PRIVATE gemmi::gemmi_cpp) + set_property(TARGET gemmi_py PROPERTY OUTPUT_NAME gemmi) + if(CMAKE_CXX_FLAGS MATCHES "-Wshadow") + target_compile_options(gemmi_py PRIVATE "-Wno-shadow") +@@ -396,18 +398,18 @@ write_basic_package_version_file(gemmi-config-version. + COMPATIBILITY AnyNewerVersion) + + # In CMake 3.23 we'll be able to use FILE_SET to install the headers +-install(DIRECTORY include/gemmi DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}") ++#install(DIRECTORY include/gemmi DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}") + +-install(TARGETS gemmi_prog gemmi_cpp +- EXPORT GemmiTargets +- INCLUDES DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}") ++#install(TARGETS gemmi_prog gemmi_cpp ++# EXPORT GemmiTargets ++# INCLUDES DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}") + +-install(EXPORT GemmiTargets FILE gemmi-targets.cmake NAMESPACE gemmi:: +- DESTINATION "${GEMMI_INSTALL_CMAKEDIR}") +-install(FILES +- "${CMAKE_CURRENT_BINARY_DIR}/gemmi-config.cmake" +- "${CMAKE_CURRENT_BINARY_DIR}/gemmi-config-version.cmake" +- DESTINATION "${GEMMI_INSTALL_CMAKEDIR}") ++#install(EXPORT GemmiTargets FILE gemmi-targets.cmake NAMESPACE gemmi:: ++# DESTINATION "${GEMMI_INSTALL_CMAKEDIR}") ++#install(FILES ++# "${CMAKE_CURRENT_BINARY_DIR}/gemmi-config.cmake" ++# "${CMAKE_CURRENT_BINARY_DIR}/gemmi-config-version.cmake" ++# DESTINATION "${GEMMI_INSTALL_CMAKEDIR}") + + if (USE_PYTHON) + if (DEFINED PYTHON_INSTALL_DIR) +@@ -421,8 +423,8 @@ if (USE_PYTHON) + # and don't respect CMAKE_INSTALL_PREFIX. + # https://discourse.cmake.org/t/findpython3-how-to-specify-local-installation-directory-for-python-module/3580/5 + install(TARGETS gemmi_py DESTINATION "${Python_SITEARCH}") +- install(DIRECTORY examples/ DESTINATION "${Python_SITELIB}/gemmi-examples" - FILES_MATCHING PATTERN "*.py") -+ #install(DIRECTORY examples/ DESTINATION ${PYTHON_INSTALL_DIR}/gemmi-examples ++ #install(DIRECTORY examples/ DESTINATION "${Python_SITELIB}/gemmi-examples" + # FILES_MATCHING PATTERN "*.py") if (INSTALL_EGG_INFO) install(CODE - "execute_process(COMMAND \"${PYTHON_EXECUTABLE}\" setup.py install_egg_info --install-dir \"\$ENV{DESTDIR}${PYTHON_INSTALL_DIR}\" + "execute_process(COMMAND \"${Python_EXECUTABLE}\" setup.py install_egg_info --install-dir \"\$ENV{DESTDIR}${Python_SITELIB}\" diff --git a/science/py-gemmi/pkg-plist b/science/py-gemmi/pkg-plist new file mode 100644 index 000000000000..2ee4a839a8fb --- /dev/null +++ b/science/py-gemmi/pkg-plist @@ -0,0 +1,6 @@ +%%PYTHON_SITELIBDIR%%/gemmi-0.6.0-py%%PYTHON_VER%%.egg-info/PKG-INFO +%%PYTHON_SITELIBDIR%%/gemmi-0.6.0-py%%PYTHON_VER%%.egg-info/SOURCES.txt +%%PYTHON_SITELIBDIR%%/gemmi-0.6.0-py%%PYTHON_VER%%.egg-info/dependency_links.txt +%%PYTHON_SITELIBDIR%%/gemmi-0.6.0-py%%PYTHON_VER%%.egg-info/not-zip-safe +%%PYTHON_SITELIBDIR%%/gemmi-0.6.0-py%%PYTHON_VER%%.egg-info/top_level.txt +%%PYTHON_SITELIBDIR%%/gemmi%%PYTHON_EXT_SUFFIX%%.so
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?202303081141.328Bfnbm080980>