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ESMTPS id 4Td1ZV0gPgzmyX; Sun, 18 Feb 2024 10:08:02 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.17.1/8.17.1) with ESMTP id 41IA82Ln085705; Sun, 18 Feb 2024 10:08:02 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 41IA82Sb085702; Sun, 18 Feb 2024 10:08:02 GMT (envelope-from git) Date: Sun, 18 Feb 2024 10:08:02 GMT Message-Id: <202402181008.41IA82Sb085702@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: 555deadfa394 - main - science/{,py-}gemmi: update 0.6.4 =?utf-8?Q?=E2=86=92?= 0.6.5 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 555deadfa394ed7671fc2630d230a37fe230c53c Auto-Submitted: auto-generated The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=555deadfa394ed7671fc2630d230a37fe230c53c commit 555deadfa394ed7671fc2630d230a37fe230c53c Author: Yuri Victorovich AuthorDate: 2024-02-18 10:05:59 +0000 Commit: Yuri Victorovich CommitDate: 2024-02-18 10:07:54 +0000 science/{,py-}gemmi: update 0.6.4 → 0.6.5 Reported by: portscout --- science/gemmi/Makefile | 2 +- science/gemmi/distinfo | 6 +- science/gemmi/pkg-plist | 4 +- science/py-gemmi/Makefile | 6 +- science/py-gemmi/distinfo | 6 +- science/py-gemmi/files/patch-CMakeLists.txt | 135 +++++++++++++++++++++------- science/py-gemmi/pkg-plist | 24 +++++ 7 files changed, 137 insertions(+), 46 deletions(-) diff --git a/science/gemmi/Makefile b/science/gemmi/Makefile index 69f3716cd296..21e999fe3441 100644 --- a/science/gemmi/Makefile +++ b/science/gemmi/Makefile @@ -1,6 +1,6 @@ PORTNAME= gemmi DISTVERSIONPREFIX= v -DISTVERSION= 0.6.4 +DISTVERSION= 0.6.5 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org diff --git a/science/gemmi/distinfo b/science/gemmi/distinfo index ef65e0e89e1e..79f0c73aea79 100644 --- a/science/gemmi/distinfo +++ b/science/gemmi/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1702577537 -SHA256 (project-gemmi-gemmi-v0.6.4_GH0.tar.gz) = 507eea6ea112e2b142cc3dfa7de20c25e9f34c76ef77ef3caabfaf94d3657cb3 -SIZE (project-gemmi-gemmi-v0.6.4_GH0.tar.gz) = 1778062 +TIMESTAMP = 1708245101 +SHA256 (project-gemmi-gemmi-v0.6.5_GH0.tar.gz) = 9159506a16e0d22bbeeefc4d34137099318307db1b2bebf06fb2ae501571b19c +SIZE (project-gemmi-gemmi-v0.6.5_GH0.tar.gz) = 1785842 diff --git a/science/gemmi/pkg-plist b/science/gemmi/pkg-plist index 9341c877ea8e..758fba0338fc 100644 --- a/science/gemmi/pkg-plist +++ b/science/gemmi/pkg-plist @@ -38,6 +38,7 @@ include/gemmi/fstream.hpp include/gemmi/grid.hpp include/gemmi/gz.hpp include/gemmi/input.hpp +include/gemmi/intensit.hpp include/gemmi/interop.hpp include/gemmi/it92.hpp include/gemmi/iterator.hpp @@ -45,7 +46,6 @@ include/gemmi/json.hpp include/gemmi/levmar.hpp include/gemmi/linkhunt.hpp include/gemmi/math.hpp -include/gemmi/merge.hpp include/gemmi/metadata.hpp include/gemmi/mmcif.hpp include/gemmi/mmcif_impl.hpp @@ -78,6 +78,7 @@ include/gemmi/select.hpp include/gemmi/seqalign.hpp include/gemmi/seqid.hpp include/gemmi/seqtools.hpp +include/gemmi/serialize.hpp include/gemmi/sfcalc.hpp include/gemmi/small.hpp include/gemmi/smcif.hpp @@ -88,7 +89,6 @@ include/gemmi/stats.hpp include/gemmi/symmetry.hpp include/gemmi/third_party/fast_float.h include/gemmi/third_party/pocketfft_hdronly.h -include/gemmi/third_party/sajson.h include/gemmi/third_party/tao/LICENSE include/gemmi/third_party/tao/NOTES include/gemmi/third_party/tao/pegtl.hpp diff --git a/science/py-gemmi/Makefile b/science/py-gemmi/Makefile index 8016c411bbb4..0a157ec2f5ed 100644 --- a/science/py-gemmi/Makefile +++ b/science/py-gemmi/Makefile @@ -1,6 +1,6 @@ PORTNAME= gemmi DISTVERSIONPREFIX= v -DISTVERSION= 0.6.4 +DISTVERSION= 0.6.5 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -25,7 +25,7 @@ USE_GITHUB= yes GH_ACCOUNT= project-gemmi CMAKE_ON= USE_PYTHON -CMAKE_OFF= BUILD_GEMMI_PROGRAM +CMAKE_OFF= BUILD_GEMMI_PROGRAM STANDALONE_PYTHON_MODULE CMAKE_ARGS= -DPython_EXECUTABLE=${PYTHON_CMD} TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} @@ -33,7 +33,7 @@ TEST_WRKSRC= ${BUILD_WRKSRC}/tests PLIST_SUB= VER=${PORTVERSION} -do-test: # 1 test fails, see https://github.com/project-gemmi/gemmi/issues/291 +do-test: @cd ${WRKSRC} && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m unittest discover -v tests/ .include diff --git a/science/py-gemmi/distinfo b/science/py-gemmi/distinfo index d58701d3138c..7d7f29781493 100644 --- a/science/py-gemmi/distinfo +++ b/science/py-gemmi/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1702578897 -SHA256 (project-gemmi-gemmi-v0.6.4_GH0.tar.gz) = 507eea6ea112e2b142cc3dfa7de20c25e9f34c76ef77ef3caabfaf94d3657cb3 -SIZE (project-gemmi-gemmi-v0.6.4_GH0.tar.gz) = 1778062 +TIMESTAMP = 1708246407 +SHA256 (project-gemmi-gemmi-v0.6.5_GH0.tar.gz) = 9159506a16e0d22bbeeefc4d34137099318307db1b2bebf06fb2ae501571b19c +SIZE (project-gemmi-gemmi-v0.6.5_GH0.tar.gz) = 1785842 diff --git a/science/py-gemmi/files/patch-CMakeLists.txt b/science/py-gemmi/files/patch-CMakeLists.txt index 187f8b297ce4..15c6e8d7f824 100644 --- a/science/py-gemmi/files/patch-CMakeLists.txt +++ b/science/py-gemmi/files/patch-CMakeLists.txt @@ -1,6 +1,6 @@ ---- CMakeLists.txt.orig 2023-12-13 10:39:37 UTC +--- CMakeLists.txt.orig 2024-02-17 11:35:57 UTC +++ CMakeLists.txt -@@ -6,7 +6,7 @@ file(STRINGS "${CMAKE_CURRENT_SOURCE_DIR}/include/gemm +@@ -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" gemmi_version_str ${gemmi_version_line}) @@ -9,7 +9,16 @@ message(STATUS "Gemmi version ${PROJECT_VERSION}") include(GNUInstallDirs) # for CMAKE_INSTALL_LIBDIR, etc -@@ -176,37 +176,39 @@ endif() +@@ -18,6 +18,8 @@ endif() + #set(CMAKE_INSTALL_BINDIR "${SKBUILD_SCRIPTS_DIR}") + endif() + ++find_package(gemmi REQUIRED) ++ + option(BUILD_SHARED_LIBS "Build shared library" ON) + option(BUILD_GEMMI_PROGRAM "Build gemmi command-line program" ON) + option(INSTALL_DEV_FILES "Install C++ headers, cmake configs, static lib" ON) +@@ -192,67 +194,67 @@ endif() # target_link_libraries(fgemmi PRIVATE cgemmi) #endif() @@ -30,7 +39,7 @@ -add_library(gemmi_cpp - src/align.cpp src/assembly.cpp src/calculate.cpp src/crd.cpp -- src/ddl.cpp src/eig3.cpp +- src/ddl.cpp src/eig3.cpp src/gz.cpp src/intensit.cpp src/json.cpp - src/mmcif.cpp src/mmread_gz.cpp src/mtz.cpp src/mtz2cif.cpp - src/polyheur.cpp src/read_cif.cpp src/resinfo.cpp - src/riding_h.cpp src/sprintf.cpp src/to_mmcif.cpp @@ -39,7 +48,7 @@ -set_property(TARGET gemmi_cpp PROPERTY POSITION_INDEPENDENT_CODE ON) +#add_library(gemmi_cpp +# src/align.cpp src/assembly.cpp src/calculate.cpp src/crd.cpp -+# src/ddl.cpp src/eig3.cpp ++# src/ddl.cpp src/eig3.cpp src/gz.cpp src/intensit.cpp src/json.cpp +# src/mmcif.cpp src/mmread_gz.cpp src/mtz.cpp src/mtz2cif.cpp +# src/polyheur.cpp src/read_cif.cpp src/resinfo.cpp +# src/riding_h.cpp src/sprintf.cpp src/to_mmcif.cpp @@ -56,15 +65,71 @@ - target_compile_definitions(gemmi_cpp PUBLIC GEMMI_SHARED) -endif() -target_link_libraries(gemmi_cpp PUBLIC gemmi_headers) --support_gz(gemmi_cpp) +#if (BUILD_SHARED_LIBS) +# target_compile_definitions(gemmi_cpp PUBLIC GEMMI_SHARED) +#endif() +#target_link_libraries(gemmi_cpp PUBLIC gemmi_headers) -+#support_gz(gemmi_cpp) -+find_package(gemmi REQUIRED) -+ +-if (FETCH_ZLIB_NG) +- target_compile_definitions(gemmi_cpp PRIVATE USE_ZLIB_NG=1) +- target_link_libraries(gemmi_cpp PRIVATE zlib) +-elseif (ZLIB_NG_FOUND) +- target_compile_definitions(gemmi_cpp PRIVATE USE_ZLIB_NG=1) +- target_link_libraries(gemmi_cpp PRIVATE ZLIB_NG::ZLIB_NG) +-elseif (ZLIB_FOUND) +- target_link_libraries(gemmi_cpp PRIVATE ZLIB::ZLIB) +-else() +- target_sources(gemmi_cpp PRIVATE +- "third_party/zlib/adler32.c" +- "third_party/zlib/crc32.c" +- "third_party/zlib/gzlib.c" +- "third_party/zlib/gzread.c" +- "third_party/zlib/inflate.c" +- "third_party/zlib/inftrees.c" +- "third_party/zlib/inffast.c" +- "third_party/zlib/zutil.c") +- check_include_file(unistd.h has_unistd_h) +- target_compile_definitions(gemmi_cpp PRIVATE NO_GZCOMPRESS=1 DYNAMIC_CRC_TABLE=1) +- if (has_unistd_h) +- target_compile_definitions(gemmi_cpp PRIVATE Z_HAVE_UNISTD_H=1) +- endif() +- target_include_directories(gemmi_cpp PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party/zlib") +- if (CMAKE_CXX_COMPILER_ID MATCHES "MSVC") +- # /wd4267 - conversion from 'size_t' to 'unsigned int', possible loss of data +- target_compile_options(gemmi_cpp PRIVATE /wd4267) +- endif() +-endif() ++#if (FETCH_ZLIB_NG) ++# target_compile_definitions(gemmi_cpp PRIVATE USE_ZLIB_NG=1) ++# target_link_libraries(gemmi_cpp PRIVATE zlib) ++#elseif (ZLIB_NG_FOUND) ++# target_compile_definitions(gemmi_cpp PRIVATE USE_ZLIB_NG=1) ++# target_link_libraries(gemmi_cpp PRIVATE ZLIB_NG::ZLIB_NG) ++#elseif (ZLIB_FOUND) ++# target_link_libraries(gemmi_cpp PRIVATE ZLIB::ZLIB) ++#else() ++# target_sources(gemmi_cpp PRIVATE ++# "third_party/zlib/adler32.c" ++# "third_party/zlib/crc32.c" ++# "third_party/zlib/gzlib.c" ++# "third_party/zlib/gzread.c" ++# "third_party/zlib/inflate.c" ++# "third_party/zlib/inftrees.c" ++# "third_party/zlib/inffast.c" ++# "third_party/zlib/zutil.c") ++# check_include_file(unistd.h has_unistd_h) ++# target_compile_definitions(gemmi PRIVATE NO_GZCOMPRESS=1 DYNAMIC_CRC_TABLE=1) ++# if (has_unistd_h) ++# target_compile_definitions(gemmi PRIVATE Z_HAVE_UNISTD_H=1) ++# endif() ++# target_include_directories(gemmi PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party/zlib") ++# if (CMAKE_CXX_COMPILER_ID MATCHES "MSVC") ++# # /wd4267 - conversion from 'size_t' to 'unsigned int', possible loss of data ++# target_compile_options(gemmi PRIVATE /wd4267) ++# endif() ++#endif() + + ### programs from prog/ ### add_library(options OBJECT prog/options.cpp) @@ -73,8 +138,8 @@ target_include_directories(options PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}/third_party") if (GEMMI_VERSION_INFO) target_compile_definitions(options PRIVATE GEMMI_VERSION_INFO=${GEMMI_VERSION_INFO}) -@@ -218,11 +220,11 @@ function(add_single_prog target) - cmake_parse_arguments(arg "NOLIB;GZ" "ADD_SRC" "" ${ARGN}) +@@ -264,11 +266,11 @@ function(add_single_prog target) + cmake_parse_arguments(arg "NOLIB" "ADD_SRC" "" ${ARGN}) add_executable(gemmi-${target} EXCLUDE_FROM_ALL prog/${target}.cpp ${arg_ADD_SRC} $) - if (arg_NOLIB) @@ -85,44 +150,43 @@ + #if (arg_NOLIB) + # target_link_libraries(gemmi-${target} PRIVATE gemmi_headers) + #else() -+ # target_link_libraries(gemmi-${target} PRIVATE gemmi_cpp) ++ # target_link_libraries(gemmi-${target} PRIVATE gemmi) + #endif() target_include_directories(gemmi-${target} PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party") - if (arg_GZ) -@@ -279,7 +281,7 @@ add_executable(gemmi_prog + endfunction() +@@ -322,7 +324,7 @@ add_executable(gemmi::prog ALIAS gemmi_prog) prog/xds2mtz.cpp $) add_executable(gemmi::prog ALIAS gemmi_prog) -target_link_libraries(gemmi_prog PRIVATE gemmi_cpp) -+target_link_libraries(gemmi_prog PRIVATE gemmi) - support_gz(gemmi_prog) ++target_link_libraries(gemmi_prog PRIVATE gemmi::gemmi_cpp) target_include_directories(gemmi_prog PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party") target_compile_definitions(gemmi_prog PRIVATE GEMMI_ALL_IN_ONE=1) -@@ -324,10 +326,10 @@ target_link_libraries(doc_example PRIVATE gemmi_header + set_target_properties(gemmi_prog PROPERTIES OUTPUT_NAME gemmi EXPORT_NAME prog) +@@ -374,9 +376,9 @@ add_executable(doc_maybegz EXCLUDE_FROM_ALL docs/code/ add_executable(doc_example2 EXCLUDE_FROM_ALL docs/code/cif_cc.cpp) target_link_libraries(doc_example2 PRIVATE gemmi_headers) 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) # always compile these tests with assertions enabled -@@ -336,7 +338,7 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU|Intel") + if (CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU|Intel") +@@ -384,14 +386,14 @@ add_executable(test_disulf EXCLUDE_FROM_ALL tests/disu endif() 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 and -lstdc++fs -@@ -348,7 +350,7 @@ endif() - support_gz(auth_label) + add_executable(auth_label EXCLUDE_FROM_ALL examples/auth_label.cpp) +-target_link_libraries(auth_label PRIVATE gemmi_cpp) ++target_link_libraries(auth_label PRIVATE gemmi) add_executable(check_conn EXCLUDE_FROM_ALL examples/check_conn.cpp) -target_link_libraries(check_conn PRIVATE gemmi_cpp) @@ -130,7 +194,7 @@ enable_testing() -@@ -385,7 +387,7 @@ if (benchmark_FOUND) +@@ -428,7 +430,7 @@ 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 "resinfo|pdb|writecif") @@ -139,19 +203,22 @@ endif() target_link_libraries(${b}-bm PRIVATE gemmi_headers benchmark::benchmark) set_property(TARGET ${b}-bm PROPERTY RUNTIME_OUTPUT_DIRECTORY -@@ -421,9 +423,8 @@ if (USE_PYTHON) - python/mtz.cpp python/read.cpp python/recgrid.cpp - python/scaling.cpp python/search.cpp +@@ -466,11 +468,11 @@ if (USE_PYTHON) python/sf.cpp python/sym.cpp python/topo.cpp -- python/unitcell.cpp python/write.cpp -- $) -- target_link_libraries(gemmi_py PRIVATE gemmi_headers) -+ python/unitcell.cpp python/write.cpp) -+ target_link_libraries(gemmi_py PRIVATE gemmi::gemmi_cpp) + python/unitcell.cpp python/write.cpp) + if (STANDALONE_PYTHON_MODULE) +- target_sources(gemmi_py PRIVATE $) +- get_target_property(_gemmi_cpp_libs gemmi_cpp LINK_LIBRARIES) ++ target_sources(gemmi_py PRIVATE gemmi::gemmi_cpp) ++ get_target_property(_gemmi_cpp_libs gemmi::gemmi_cpp LINK_LIBRARIES) + set_property(TARGET gemmi_py APPEND PROPERTY LINK_LIBRARIES ${_gemmi_cpp_libs}) + else() +- target_link_libraries(gemmi_py PRIVATE gemmi_cpp) ++ target_link_libraries(gemmi_py PRIVATE gemmi::gemmi_cpp) + endif() set_property(TARGET gemmi_py PROPERTY OUTPUT_NAME gemmi) if(CMAKE_CXX_FLAGS MATCHES "-Wshadow") - target_compile_options(gemmi_py PRIVATE "-Wno-shadow") -@@ -450,19 +451,19 @@ if (BUILD_GEMMI_PROGRAM) +@@ -518,19 +520,19 @@ endif() install(TARGETS gemmi_prog EXPORT GemmiTargets) endif() diff --git a/science/py-gemmi/pkg-plist b/science/py-gemmi/pkg-plist index 59aab86c27c8..9a35f7adf261 100644 --- a/science/py-gemmi/pkg-plist +++ b/science/py-gemmi/pkg-plist @@ -1 +1,25 @@ %%PYTHON_SITELIBDIR%%/gemmi%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON_SITELIBDIR%%/gemmi/examples/aafreq.py +%%PYTHON_SITELIBDIR%%/gemmi/examples/ccd_gi.py +%%PYTHON_SITELIBDIR%%/gemmi/examples/ccd_subgraph.py +%%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 +%%PYTHON_SITELIBDIR%%/gemmi/examples/maskdiff.py +%%PYTHON_SITELIBDIR%%/gemmi/examples/matthews.py +%%PYTHON_SITELIBDIR%%/gemmi/examples/merge_mtz_mmcif.py +%%PYTHON_SITELIBDIR%%/gemmi/examples/monomers.py +%%PYTHON_SITELIBDIR%%/gemmi/examples/mtrix_iso.py +%%PYTHON_SITELIBDIR%%/gemmi/examples/mtz_i_sigi.py +%%PYTHON_SITELIBDIR%%/gemmi/examples/multiproc.py +%%PYTHON_SITELIBDIR%%/gemmi/examples/patterson_slice.py +%%PYTHON_SITELIBDIR%%/gemmi/examples/rama_gather.py +%%PYTHON_SITELIBDIR%%/gemmi/examples/rama_plot.py +%%PYTHON_SITELIBDIR%%/gemmi/examples/refln-stats.py +%%PYTHON_SITELIBDIR%%/gemmi/examples/simple_search.py +%%PYTHON_SITELIBDIR%%/gemmi/examples/sub_ccd.py +%%PYTHON_SITELIBDIR%%/gemmi/examples/weight.py