Date: Sat, 7 Sep 2024 06:25:08 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: 122e253d6b17 - main - science/{,py-}gemmi: update 0.6.6 =?utf-8?Q?=E2=86=92?= 0.6.7
Message-ID: <202409070625.4876P8IA019995@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=122e253d6b179d61591fd168edf111c12fe5539b commit 122e253d6b179d61591fd168edf111c12fe5539b Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2024-09-07 05:26:00 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2024-09-07 06:24:52 +0000 science/{,py-}gemmi: update 0.6.6 → 0.6.7 Reported by: portscout --- science/gemmi/Makefile | 2 +- science/gemmi/distinfo | 6 +- science/gemmi/pkg-plist | 1 - science/py-gemmi/Makefile | 4 +- science/py-gemmi/distinfo | 6 +- science/py-gemmi/files/patch-CMakeLists.txt | 90 +++++++---------------------- 6 files changed, 30 insertions(+), 79 deletions(-) diff --git a/science/gemmi/Makefile b/science/gemmi/Makefile index a52e1099ff3a..38ba4f45c227 100644 --- a/science/gemmi/Makefile +++ b/science/gemmi/Makefile @@ -1,6 +1,6 @@ PORTNAME= gemmi DISTVERSIONPREFIX= v -DISTVERSION= 0.6.6 +DISTVERSION= 0.6.7 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org diff --git a/science/gemmi/distinfo b/science/gemmi/distinfo index c318b2645757..16fd0521e1d4 100644 --- a/science/gemmi/distinfo +++ b/science/gemmi/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1716957697 -SHA256 (project-gemmi-gemmi-v0.6.6_GH0.tar.gz) = 722369495f7374bb938d14da2c3a9f8444b753e2d9536cf097c161a53dbbae19 -SIZE (project-gemmi-gemmi-v0.6.6_GH0.tar.gz) = 1819188 +TIMESTAMP = 1725684236 +SHA256 (project-gemmi-gemmi-v0.6.7_GH0.tar.gz) = f3dd7c3aac0b01f0338ff5034c11be0e7b23639f018c8d6b1db7cc9d77a8dee9 +SIZE (project-gemmi-gemmi-v0.6.7_GH0.tar.gz) = 1833549 diff --git a/science/gemmi/pkg-plist b/science/gemmi/pkg-plist index c910ac13e611..4f43aefef81f 100644 --- a/science/gemmi/pkg-plist +++ b/science/gemmi/pkg-plist @@ -70,7 +70,6 @@ include/gemmi/read_map.hpp include/gemmi/recgrid.hpp include/gemmi/reciproc.hpp include/gemmi/refln.hpp -include/gemmi/remarks.hpp include/gemmi/resinfo.hpp include/gemmi/riding_h.hpp include/gemmi/scaling.hpp diff --git a/science/py-gemmi/Makefile b/science/py-gemmi/Makefile index 89b60d4aa7b1..53bdd5038597 100644 --- a/science/py-gemmi/Makefile +++ b/science/py-gemmi/Makefile @@ -1,6 +1,6 @@ PORTNAME= gemmi DISTVERSIONPREFIX= v -DISTVERSION= 0.6.6 +DISTVERSION= 0.6.7 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -18,7 +18,7 @@ BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pip>0:devel/py-pip@${PY_FLAVOR} \ LIB_DEPENDS= libgemmi_cpp.so:science/gemmi TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}biopython>0:biology/py-biopython@${PY_FLAVOR} -USES= cmake compiler:c++20-lang localbase:ldflags python +USES= cmake compiler:c++17-lang localbase:ldflags python USE_PYTHON= flavors USE_GITHUB= yes diff --git a/science/py-gemmi/distinfo b/science/py-gemmi/distinfo index 0b7ff31c6841..57a82e02e696 100644 --- a/science/py-gemmi/distinfo +++ b/science/py-gemmi/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1716960965 -SHA256 (project-gemmi-gemmi-v0.6.6_GH0.tar.gz) = 722369495f7374bb938d14da2c3a9f8444b753e2d9536cf097c161a53dbbae19 -SIZE (project-gemmi-gemmi-v0.6.6_GH0.tar.gz) = 1819188 +TIMESTAMP = 1725686168 +SHA256 (project-gemmi-gemmi-v0.6.7_GH0.tar.gz) = f3dd7c3aac0b01f0338ff5034c11be0e7b23639f018c8d6b1db7cc9d77a8dee9 +SIZE (project-gemmi-gemmi-v0.6.7_GH0.tar.gz) = 1833549 diff --git a/science/py-gemmi/files/patch-CMakeLists.txt b/science/py-gemmi/files/patch-CMakeLists.txt index 15c6e8d7f824..9446f2ca1c13 100644 --- a/science/py-gemmi/files/patch-CMakeLists.txt +++ b/science/py-gemmi/files/patch-CMakeLists.txt @@ -1,4 +1,4 @@ ---- CMakeLists.txt.orig 2024-02-17 11:35:57 UTC +--- CMakeLists.txt.orig 2024-09-06 14:24:17 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" @@ -18,7 +18,7 @@ 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() +@@ -200,71 +202,9 @@ endif() # target_link_libraries(fgemmi PRIVATE cgemmi) #endif() @@ -29,47 +29,29 @@ - "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>") -target_compile_features(gemmi_headers INTERFACE cxx_std_11) -set_target_properties(gemmi_headers PROPERTIES EXPORT_NAME headers) -+#add_library(gemmi_headers INTERFACE) -+#add_library(gemmi::headers ALIAS gemmi_headers) -+#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_11) -+#set_target_properties(gemmi_headers PROPERTIES EXPORT_NAME headers) - +- -add_library(gemmi_cpp - src/align.cpp src/assembly.cpp src/calculate.cpp src/crd.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 +- src/pdb.cpp src/polyheur.cpp src/read_cif.cpp src/read_map.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) -add_library(gemmi::gemmi_cpp ALIAS gemmi_cpp) -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/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 -+# src/to_pdb.cpp src/monlib.cpp src/topo.cpp src/xds_ascii.cpp) -+#add_library(gemmi::gemmi_cpp ALIAS gemmi_cpp) -+#set_property(TARGET gemmi_cpp PROPERTY POSITION_INDEPENDENT_CODE ON) - #set_property(TARGET gemmi_cpp PROPERTY CXX_VISIBILITY_PRESET hidden) +-#set_property(TARGET gemmi_cpp PROPERTY CXX_VISIBILITY_PRESET hidden) -target_compile_definitions(gemmi_cpp PRIVATE GEMMI_BUILD) -target_include_directories(gemmi_cpp PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party") -+#target_compile_definitions(gemmi_cpp PRIVATE GEMMI_BUILD) -+#target_include_directories(gemmi_cpp PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party") - +- -if (BUILD_SHARED_LIBS) - target_compile_definitions(gemmi_cpp PUBLIC GEMMI_SHARED) +- if (ADD_SOVERSION) +- set_target_properties(gemmi_cpp PROPERTIES VERSION ${PROJECT_VERSION} +- SOVERSION "0") +- endif() -endif() -target_link_libraries(gemmi_cpp PUBLIC gemmi_headers) -+#if (BUILD_SHARED_LIBS) -+# target_compile_definitions(gemmi_cpp PUBLIC GEMMI_SHARED) -+#endif() -+#target_link_libraries(gemmi_cpp PUBLIC gemmi_headers) - +- -if (FETCH_ZLIB_NG) - target_compile_definitions(gemmi_cpp PRIVATE USE_ZLIB_NG=1) - target_link_libraries(gemmi_cpp PRIVATE zlib) @@ -99,46 +81,16 @@ - target_compile_options(gemmi_cpp PRIVATE /wd4267) - endif() -endif() -+#if (FETCH_ZLIB_NG) -+# target_compile_definitions(gemmi_cpp PRIVATE USE_ZLIB_NG=1) -+# target_link_libraries(gemmi_cpp PRIVATE zlib) -+#elseif (ZLIB_NG_FOUND) -+# target_compile_definitions(gemmi_cpp PRIVATE USE_ZLIB_NG=1) -+# target_link_libraries(gemmi_cpp PRIVATE ZLIB_NG::ZLIB_NG) -+#elseif (ZLIB_FOUND) -+# target_link_libraries(gemmi_cpp PRIVATE ZLIB::ZLIB) -+#else() -+# target_sources(gemmi_cpp PRIVATE -+# "third_party/zlib/adler32.c" -+# "third_party/zlib/crc32.c" -+# "third_party/zlib/gzlib.c" -+# "third_party/zlib/gzread.c" -+# "third_party/zlib/inflate.c" -+# "third_party/zlib/inftrees.c" -+# "third_party/zlib/inffast.c" -+# "third_party/zlib/zutil.c") -+# check_include_file(unistd.h has_unistd_h) -+# target_compile_definitions(gemmi PRIVATE NO_GZCOMPRESS=1 DYNAMIC_CRC_TABLE=1) -+# if (has_unistd_h) -+# target_compile_definitions(gemmi PRIVATE Z_HAVE_UNISTD_H=1) -+# endif() -+# target_include_directories(gemmi PRIVATE "${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) -target_link_libraries(options PUBLIC gemmi_headers) -+#target_link_libraries(options PUBLIC gemmi_headers) 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}) -@@ -264,11 +266,11 @@ function(add_single_prog target) +@@ -276,11 +216,11 @@ 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} $<TARGET_OBJECTS:options>) @@ -155,7 +107,7 @@ target_include_directories(gemmi-${target} PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party") endfunction() -@@ -322,7 +324,7 @@ add_executable(gemmi::prog ALIAS gemmi_prog) +@@ -334,7 +274,7 @@ add_executable(gemmi::prog ALIAS gemmi_prog) prog/xds2mtz.cpp $<TARGET_OBJECTS:options>) add_executable(gemmi::prog ALIAS gemmi_prog) @@ -164,7 +116,7 @@ target_include_directories(gemmi_prog PRIVATE "${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) -@@ -374,9 +376,9 @@ add_executable(doc_maybegz EXCLUDE_FROM_ALL docs/code/ +@@ -386,9 +326,9 @@ 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) @@ -176,7 +128,7 @@ # always compile these tests with assertions enabled if (CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU|Intel") -@@ -384,14 +386,14 @@ add_executable(test_disulf EXCLUDE_FROM_ALL tests/disu +@@ -396,14 +336,14 @@ add_executable(test_disulf EXCLUDE_FROM_ALL tests/disu endif() add_executable(test_disulf EXCLUDE_FROM_ALL tests/disulf.cpp) @@ -194,7 +146,7 @@ enable_testing() -@@ -428,7 +430,7 @@ if (benchmark_FOUND) +@@ -440,7 +380,7 @@ 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") @@ -203,7 +155,7 @@ endif() target_link_libraries(${b}-bm PRIVATE gemmi_headers benchmark::benchmark) set_property(TARGET ${b}-bm PROPERTY RUNTIME_OUTPUT_DIRECTORY -@@ -466,11 +468,11 @@ if (USE_PYTHON) +@@ -482,11 +422,11 @@ if (USE_PYTHON) python/sf.cpp python/sym.cpp python/topo.cpp python/unitcell.cpp python/write.cpp) if (STANDALONE_PYTHON_MODULE) @@ -218,7 +170,7 @@ endif() set_property(TARGET gemmi_py PROPERTY OUTPUT_NAME gemmi) if(CMAKE_CXX_FLAGS MATCHES "-Wshadow") -@@ -518,19 +520,19 @@ endif() +@@ -541,19 +481,19 @@ endif() install(TARGETS gemmi_prog EXPORT GemmiTargets) endif()
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