diff options
Diffstat (limited to 'science/py-gemmi')
| -rw-r--r-- | science/py-gemmi/Makefile | 7 | ||||
| -rw-r--r-- | science/py-gemmi/distinfo | 6 | ||||
| -rw-r--r-- | science/py-gemmi/files/patch-CMakeLists.txt | 26 | ||||
| -rw-r--r-- | science/py-gemmi/pkg-plist | 2 |
4 files changed, 21 insertions, 20 deletions
diff --git a/science/py-gemmi/Makefile b/science/py-gemmi/Makefile index 2aac5d8717f0..9e7f9f8d7544 100644 --- a/science/py-gemmi/Makefile +++ b/science/py-gemmi/Makefile @@ -1,12 +1,13 @@ PORTNAME= gemmi DISTVERSIONPREFIX= v -DISTVERSION= 0.7.1 +DISTVERSION= 0.7.3 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Macromolecular crystallography library and utilities -WWW= https://gemmi.readthedocs.io/en/latest/ +WWW= https://gemmi.readthedocs.io/en/latest/ \ + https://github.com/project-gemmi/gemmi LICENSE= MPL20 LICENSE_FILE= ${WRKSRC}/LICENSE.txt @@ -36,4 +37,6 @@ PLIST_SUB= VER=${PORTVERSION} do-test: @cd ${WRKSRC} && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m unittest discover -v tests/ +# tests as of 0.7.3: test 'test_syntax_error' fails with syntax error, see https://github.com/project-gemmi/gemmi/issues/384 + .include <bsd.port.mk> diff --git a/science/py-gemmi/distinfo b/science/py-gemmi/distinfo index 9050772d8cc8..b40d35b8cada 100644 --- a/science/py-gemmi/distinfo +++ b/science/py-gemmi/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1742885714 -SHA256 (project-gemmi-gemmi-v0.7.1_GH0.tar.gz) = 5d87c3e82ee159f5642d7c083a74e00ca9cc038ccf9be2522d7ae985f3377393 -SIZE (project-gemmi-gemmi-v0.7.1_GH0.tar.gz) = 1910265 +TIMESTAMP = 1753140186 +SHA256 (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = ed5e1d0665f27d623d877fa36f6c99a5de21310cc8715337ff9f6b545bd2e9d3 +SIZE (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = 1924234 diff --git a/science/py-gemmi/files/patch-CMakeLists.txt b/science/py-gemmi/files/patch-CMakeLists.txt index d75096e3228b..62637e7014cd 100644 --- a/science/py-gemmi/files/patch-CMakeLists.txt +++ b/science/py-gemmi/files/patch-CMakeLists.txt @@ -1,4 +1,4 @@ ---- CMakeLists.txt.orig 2025-03-24 16:35:30 UTC +--- CMakeLists.txt.orig 2025-07-05 13:51:16 UTC +++ CMakeLists.txt @@ -6,7 +6,7 @@ string(REGEX REPLACE ".+\"([0-9]+\.[0-9]+\.[0-9]+)(-de string(REGEX REPLACE ".+\"([0-9]+\.[0-9]+\.[0-9]+)(-dev)?\"" "\\1" @@ -27,7 +27,7 @@ -target_include_directories(gemmi_headers INTERFACE - "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>" - "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>") --target_compile_features(gemmi_headers INTERFACE cxx_std_17) +-target_compile_features(gemmi_headers INTERFACE cxx_std_14) -set_target_properties(gemmi_headers PROPERTIES EXPORT_NAME headers) - -add_library(gemmi_cpp @@ -37,7 +37,7 @@ - src/monlib.cpp src/mtz.cpp src/mtz2cif.cpp - src/pdb.cpp src/polyheur.cpp src/read_cif.cpp - src/resinfo.cpp src/riding_h.cpp -- src/select.cpp src/sprintf.cpp src/symmetry.cpp +- src/select.cpp src/sprintf.cpp src/dssp.cpp src/symmetry.cpp - src/to_json.cpp src/to_mmcif.cpp src/to_pdb.cpp src/topo.cpp - src/xds_ascii.cpp) -add_library(gemmi::gemmi_cpp ALIAS gemmi_cpp) @@ -98,8 +98,8 @@ target_include_directories(gemmi-${target} PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party") endfunction() -@@ -336,7 +274,7 @@ add_executable(gemmi::prog ALIAS gemmi_prog) - prog/xds2mtz.cpp +@@ -337,7 +275,7 @@ add_executable(gemmi::prog ALIAS gemmi_prog) + prog/wcn.cpp prog/xds2mtz.cpp $<TARGET_OBJECTS:options>) add_executable(gemmi::prog ALIAS gemmi_prog) -target_link_libraries(gemmi_prog PRIVATE gemmi_cpp) @@ -107,7 +107,7 @@ target_include_directories(gemmi_prog PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party") target_compile_definitions(gemmi_prog PRIVATE GEMMI_ALL_IN_ONE=1) set_target_properties(gemmi_prog PROPERTIES OUTPUT_NAME gemmi EXPORT_NAME prog) -@@ -376,7 +314,7 @@ target_compile_definitions(cpptest PRIVATE USE_STD_SNP +@@ -377,17 +315,17 @@ target_compile_definitions(cpptest PRIVATE USE_STD_SNP add_executable(cpptest EXCLUDE_FROM_ALL tests/main.cpp tests/cif.cpp tests/windowsh.cpp) target_compile_definitions(cpptest PRIVATE USE_STD_SNPRINTF=1) @@ -115,11 +115,9 @@ +target_link_libraries(cpptest PRIVATE gemmi) target_include_directories(cpptest PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party") - add_executable(hello EXCLUDE_FROM_ALL examples/hello.cpp) -@@ -384,11 +322,11 @@ add_executable(doc_example EXCLUDE_FROM_ALL add_executable(doc_example EXCLUDE_FROM_ALL docs/code/sym.cpp docs/code/elem.cpp docs/code/resinfo.cpp - docs/code/cell.cpp docs/code/mutate.cpp src/resinfo.cpp) + docs/code/cell.cpp docs/code/mutate.cpp) -target_link_libraries(doc_example PRIVATE gemmi_cpp) +target_link_libraries(doc_example PRIVATE gemmi) add_executable(doc_example2 EXCLUDE_FROM_ALL docs/code/cif_cc.cpp) @@ -130,7 +128,7 @@ # always compile these tests with assertions enabled if (CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU|Intel") -@@ -396,14 +334,14 @@ add_executable(test_disulf EXCLUDE_FROM_ALL tests/disu +@@ -395,14 +333,14 @@ add_executable(test_disulf EXCLUDE_FROM_ALL tests/disu endif() add_executable(test_disulf EXCLUDE_FROM_ALL tests/disulf.cpp) @@ -148,16 +146,16 @@ enable_testing() -@@ -440,7 +378,7 @@ if (benchmark_FOUND) +@@ -439,7 +377,7 @@ if (benchmark_FOUND) foreach(b stoi elem mod niggli pdb resinfo round sym writecif) add_executable(${b}-bm EXCLUDE_FROM_ALL benchmarks/${b}.cpp) - if (b MATCHES "elem|resinfo|pdb|writecif") + if (b MATCHES "elem|resinfo|pdb|sym|writecif") - target_link_libraries(${b}-bm PRIVATE gemmi_cpp) + target_link_libraries(${b}-bm PRIVATE gemmi) endif() target_link_libraries(${b}-bm PRIVATE gemmi_headers benchmark::benchmark) set_property(TARGET ${b}-bm PROPERTY RUNTIME_OUTPUT_DIRECTORY -@@ -481,11 +419,11 @@ if (USE_PYTHON) +@@ -480,11 +418,11 @@ if (USE_PYTHON) python/unitcell.cpp python/write.cpp) if (STANDALONE_PYTHON_MODULE) @@ -172,7 +170,7 @@ endif() set_property(TARGET gemmi_py PROPERTY OUTPUT_NAME gemmi_ext) if (CMAKE_CONFIGURATION_TYPES) -@@ -568,19 +506,19 @@ endif() +@@ -567,19 +505,19 @@ endif() install(TARGETS gemmi_prog EXPORT GemmiTargets) endif() diff --git a/science/py-gemmi/pkg-plist b/science/py-gemmi/pkg-plist index 7cf8db927729..9201705db9d6 100644 --- a/science/py-gemmi/pkg-plist +++ b/science/py-gemmi/pkg-plist @@ -7,7 +7,6 @@ %%PYTHON_SITELIBDIR%%/gemmi/examples/cif_i_sigi.py %%PYTHON_SITELIBDIR%%/gemmi/examples/col_order.py %%PYTHON_SITELIBDIR%%/gemmi/examples/from_json.py -%%PYTHON_SITELIBDIR%%/gemmi/examples/hello.py %%PYTHON_SITELIBDIR%%/gemmi/examples/long_geom.py %%PYTHON_SITELIBDIR%%/gemmi/examples/map2mtz.py %%PYTHON_SITELIBDIR%%/gemmi/examples/maskcheck.py @@ -22,6 +21,7 @@ %%PYTHON_SITELIBDIR%%/gemmi/examples/qq-plot.py %%PYTHON_SITELIBDIR%%/gemmi/examples/rama_gather.py %%PYTHON_SITELIBDIR%%/gemmi/examples/rama_plot.py +%%PYTHON_SITELIBDIR%%/gemmi/examples/read_cif.py %%PYTHON_SITELIBDIR%%/gemmi/examples/refln-stats.py %%PYTHON_SITELIBDIR%%/gemmi/examples/simple_search.py %%PYTHON_SITELIBDIR%%/gemmi/examples/sub_ccd.py |