Merge pull request InsightSoftwareConsortium#4940 from blowekamp/hdf5…

…_1.12.3

Hdf5 1.14.5

Modules/ThirdParty/HDF5/.gitattributes

@@ -2,3 +2,7 @@ src/itkhdf5/src/H5C.c        hooks-max-size=500000
 src/itkhdf5/src/H5Dchunk.c   hooks-max-size=500000
 src/itkhdf5/src/H5Shyper.c   hooks-max-size=600000
 src/itkhdf5/src/H5Tconv.c    hooks-max-size=500000
+src/itkhdf5/src/H5Ppublic.h  hooks-max-size=500000
+src/H5Odtype.c               no-lf-at-eof
+
+src/itkhdf5/src/itk_hdf5_mangle.h.in hooks-max-size=500000

Modules/ThirdParty/HDF5/CMakeLists.txt

@@ -7,17 +7,6 @@ set(ITKHDF5_THIRD_PARTY 1)
 # modified before reaching this point)
 set(BUILD_SHARED_LIBS ${ITK_BUILD_SHARED_LIBS})
 
-if (BUILD_SHARED_LIBS)
-   add_definitions(-DH5_BUILT_AS_DYNAMIC_LIB=1)
-   set(ONLY_SHARED_LIBS ON CACHE INTERNAL "Only build shared")
-else()
-   set(ONLY_SHARED_LIBS OFF CACHE INTERNAL "Only build static")
-endif()
-if(CMAKE_LINKER MATCHES "link.exe$")
-  # Suppress undefined public symbols warning
-  set(CMAKE_STATIC_LINKER_FLAGS "${CMAKE_STATIC_LINKER_FLAGS} /IGNORE:4221")
-endif()
-
 if(ITK_USE_SYSTEM_HDF5)
 
   if(HDF5_DIR)

Modules/ThirdParty/HDF5/UpdateFromUpstream.sh

@@ -8,20 +8,21 @@ readonly name="HDF5"
 readonly ownership="HDF5 Maintainers <[email protected]>"
 readonly subtree="Modules/ThirdParty/HDF5/src/itkhdf5"
 readonly repo="https://github.com/HDFGroup/hdf5.git"
-readonly tag="hdf5-1_12_1"
+readonly tag="hdf5_1.14.5"
 readonly shortlog=false
 readonly paths="
    ACKNOWLEDGMENTS
    CTestConfig.cmake
-   README.txt
+   README.md
    config/cmake
-   config/cmake_ext_mod
    config/clang-warnings
    config/gnu-warnings
    config/intel-warnings
    CMakeLists.txt
    CMakeInstallation.cmake
    CMakeFilters.cmake
+   CMakeVOL.cmake
+   CMakeTests.cmake
    COPYING
    src
    c++/CMakeLists.txt
@@ -40,7 +41,7 @@ extract_source () {
     sed -i.bak -e '1 s| /bin/sh|/bin/sh|' c++/src/h5c++.in config/cmake/libh5cc.in
     rm c++/src/h5c++.in.bak config/cmake/libh5cc.in.bak
     chmod a+x c++/src/h5c++.in config/cmake/libh5cc.in
-    chmod a-x README.txt
+    chmod a-x README.md
     chmod a-x config/cmake/CTestScript.cmake
     chmod a-x config/cmake/HDF5_Examples_options.cmake
     chmod a-x config/cmake/libhdf5.pc.in
@@ -62,6 +63,7 @@ extract_source () {
     find . -name Makefile.am -delete
     find . -name Makefile.in -delete
     find . -name "*.lnt" -delete
+    find . -name "*.icns" -delete
     echo "* -whitespace" > .gitattributes
     popd
 }

Modules/ThirdParty/HDF5/src/CMakeLists.txt

@@ -5,7 +5,6 @@ set(HDF5_EXTERNALLY_CONFIGURED ON)
 # can not be skipped for installation.  Use the install COMPONENTS
 # features instead.
 set(HDF5_INSTALL_NO_DEVELOPMENT FALSE)
-set(HDF5_EXTERNAL_LIB_PREFIX "itk")
 set(HDF5_EXPORTED_TARGETS ${ITKHDF5-targets})
 set(HDF5_INSTALL_LIB_DIR ${ITKHDF5_INSTALL_LIBRARY_DIR})
 set(HDF5_INSTALL_BIN_DIR ${ITKHDF5_INSTALL_RUNTIME_DIR})
@@ -16,45 +15,26 @@ set(HDF5_ALLOW_EXTERNAL_SUPPORT OFF CACHE INTERNAL "Allow External Library Build
 set(HDF5_BUILD_CPP_LIB ON CACHE INTERNAL "Build HDF5 C++ Library")
 set(HDF5_BUILD_HL_LIB ON CACHE INTERNAL "Build High Level HDF5 Library")
 set(HDF5_DISABLE_COMPILER_WARNINGS OFF CACHE INTERNAL "Disable HDF5 warnings")
-set(HDF5_ENABLE_CODESTACK OFF CACHE INTERNAL "Enable the function stack tracing (for developer debugging).")
 set(HDF5_ENABLE_COVERAGE OFF CACHE INTERNAL "Enable code coverage for Libraries and Programs")
 set(HDF5_ENABLE_DEPRECATED_SYMBOLS ON CACHE INTERNAL "Enable deprecated public API symbols")
-set(HDF5_ENABLE_GPFS OFF CACHE INTERNAL "Enable GPFS hints for the MPI/POSIX file driver")
-set(HDF5_ENABLE_HSIZET ON CACHE INTERNAL "Enable datasets larger than memory")
-set(HDF5_ENABLE_LARGE_FILE ON CACHE INTERNAL "Enable support for large (64-bit) files on Linux.")
 set(HDF5_ENABLE_PARALLEL OFF CACHE INTERNAL "Enable parallel build (requires MPI)")
 set(HDF5_ENABLE_SZIP_SUPPORT OFF CACHE INTERNAL "Use SZip Filter")
-set(HDF5_ENABLE_THREADSAFE ON CACHE INTERNAL "Enable Threadsafety")
+set(HDF5_ENABLE_THREADSAFE OFF CACHE INTERNAL "Enable Threadsafety")
 set(HDF5_ENABLE_TRACE OFF CACHE INTERNAL "Enable API tracing capability")
 set(HDF5_ENABLE_USING_MEMCHECKER OFF CACHE INTERNAL "Indicate that a memory checker is used")
 set(HDF5_ENABLE_Z_LIB_SUPPORT ON CACHE INTERNAL "Enable HDF5 Zlib Filters")
-set(HDF5_Enable_Clear_File_Buffers ON CACHE INTERNAL "Securely clear file buffers before writing to file")
 set(HDF5_Enable_Instrument OFF CACHE INTERNAL "Instrument The library")
-set(HDF5_METADATA_TRACE_FILE OFF CACHE INTERNAL "Enable metadata trace file collection")
 set(HDF5_PACKAGE_EXTLIBS OFF CACHE INTERNAL "CPACK - include external libraries")
 set(HDF5_STRICT_FORMAT_CHECKS OFF CACHE INTERNAL "Whether to perform strict file format checks")
-set(HDF5_USE_16_API_DEFAULT OFF CACHE INTERNAL "Use the HDF5 1.6.x API by default")
-set(HDF5_USE_FILTER_FLETCHER32 ON CACHE INTERNAL "Use the FLETCHER32 Filter")
-set(HDF5_USE_FILTER_NBIT ON CACHE INTERNAL "Use the NBIT Filter")
-set(HDF5_USE_FILTER_SCALEOFFSET ON CACHE INTERNAL "Use the SCALEOFFSET Filter")
-set(HDF5_USE_FILTER_SHUFFLE ON CACHE INTERNAL "Use the SHUFFLE Filter")
-set(HDF5_USE_H5DUMP_PACKED_BITS ON CACHE INTERNAL "Use the PACKED BITS feature in h5dump")
 set(HDF5_WANT_DATA_ACCURACY ON CACHE INTERNAL "IF data accuracy is guaranteed during data conversions")
 set(HDF5_WANT_DCONV_EXCEPTION ON CACHE INTERNAL "exception handling functions is checked during data conversions")
 set(HDF_LEGACY_NAMING ON CACHE INTERNAL "Use Legacy Names for Libraries and Programs")
 set(HDF5_BUILD_FRAMEWORKS OFF CACHE INTERNAL "TRUE to build as frameworks libraries, FALSE to build according to BUILD_SHARED_LIBS")
 set(HDF5_BUILD_WITH_INSTALL_NAME  OFF CACHE INTERNAL "Build with library install_name set to the installation path")
 set(HDF5_ENABLE_ALL_WARNINGS OFF CACHE INTERNAL "Enable all warnings")
 set(HDF5_ENABLE_DEBUG_APIS OFF CACHE INTERNAL "Turn on debugging in all packages")
-set(HDF5_ENABLE_DIRECT_VFD ON CACHE INTERNAL "Build the Direct I/O Virtual File Driver")
+set(HDF5_ENABLE_DIRECT_VFD OFF CACHE INTERNAL "Build the Direct I/O Virtual File Driver")
 set(HDF5_ENABLE_EMBEDDED_LIBINFO ON CACHE INTERNAL "embed library info into executables")
-set(HDF5_ENABLE_GROUPFIVE_WARNINGS OFF CACHE INTERNAL "Enable group five warnings")
-set(HDF5_ENABLE_GROUPFOUR_WARNINGS OFF CACHE INTERNAL "Enable group four warnings")
-set(HDF5_ENABLE_GROUPONE_WARNINGS OFF CACHE INTERNAL "Enable group one warnings")
-set(HDF5_ENABLE_GROUPSIX_WARNINGS OFF CACHE INTERNAL "Enable group six warnings")
-set(HDF5_ENABLE_GROUPTHREE_WARNINGS OFF CACHE INTERNAL "Enable group three warnings")
-set(HDF5_ENABLE_GROUPTWO_WARNINGS OFF CACHE INTERNAL "Enable group two warnings")
-set(HDF5_ENABLE_GROUPZERO_WARNINGS OFF CACHE INTERNAL "Enable group zero warnings")
 set(HDF5_GENERATE_HEADERS OFF CACHE INTERNAL "Rebuild Generated Files")
 set(HDF5_PACK_EXAMPLES OFF CACHE INTERNAL "Package the HDF5 Library Examples Compressed File")
 set(HDF5_NO_PACKAGES OFF CACHE INTERNAL "CPACK - Disable packaging")
@@ -64,17 +44,46 @@ set(HDF_TEST_EXPRESS OFF CACHE INTERNAL "Control testing framework (0-3)")
 set(BUILD_STATIC_EXECS OFF CACHE INTERNAL "Build Static Executables")
 set(BUILD_USER_DEFINED_LIBS OFF CACHE INTERNAL "Build user defined libs")
 
+set (SZIP_USE_EXTERNAL OFF CACHE INTERNAL "Use External Library Building for SZIP" )
+set (ZLIB_USE_EXTERNAL OFF CACHE INTERNAL "Use External Library Building for ZLIB" )
+set (HDF5_DIMENSION_SCALES_NEW_REF OFF CACHE INTERNAL "Use new-style references with dimension scale APIs" )
+set (HDF5_EXTERNAL_LIB_PREFIX "itk" CACHE INTERNAL "Use prefix for custom library naming.")
+set (HDF5_LIB_INFIX "" CACHE INTERNAL "Use infix for custom library naming.")
+set (HDF5_USE_GNU_DIRS OFF CACHE INTERNAL "TRUE to use GNU Coding Standard install directory variables, FALSE to use historical settings")
+set (HDF5_TEST_SERIAL OFF CACHE INTERNAL "Execute non-parallel tests" )
+
+set (HDF5_BUILD_DOC                   OFF CACHE INTERNAL "Build documentation")
+set (HDF5_ENABLE_MAP_API              OFF CACHE INTERNAL "Build the map API")
+set (HDF5_ENABLE_WARNINGS_AS_ERRORS   OFF CACHE INTERNAL "Interpret some warnings as errors")
+set (HDF5_MINGW_STATIC_GCC_LIBS       OFF CACHE INTERNAL "")
+set (HDF5_MSVC_NAMING_CONVENTION      OFF CACHE INTERNAL "Use MSVC Naming conventions for Shared Libraries")
+set (HDF5_ENABLE_PLUGIN_SUPPORT OFF CACHE INTERNAL "Enable PLUGIN Filters")
+
+set (HDF5_BUILD_STATIC_TOOLS OFF CACHE INTERNAL "Build Static Tools NOT Shared Tools")
+set (HDF5_ENABLE_MAP_API OFF CACHE INTERNAL "Build the map API")
+set (HDF5_ENABLE_NONSTANDARD_FEATURES ON CACHE INTERNAL "Enable support for non-standard programming language features")
+set (HDF5_ENABLE_SUBFILING_VFD OFF CACHE INTERNAL "Build Parallel HDF5 Subfiling VFD")
+set (HDF5_USE_LIBAEC_STATIC OFF CACHE INTERNAL "Use static AEC library" )
+set (HDF5_USE_ZLIB_NG OFF CACHE INTERNAL "Use zlib-ng library as zlib library" )
+set (HDF5_USE_ZLIB_STATIC OFF CACHE INTERNAL "Find static zlib library" )
+set (ALLOW_UNSUPPORTED OFF CACHE INTERNAL "Allow unsupported combinations of configure options")
+
+
+if (NOT BUILD_SHARED_LIBS)
+  set (BUILD_STATIC_LIBS ON CACHE INTERNAL "Build Static Libraries")
+endif()
+
 # Setup all necessary overrides for zlib so that HDF5 uses our
 # internally compiled zlib rather than any other version
 if(HDF5_ENABLE_Z_LIB_SUPPORT)
   # We must tell the main HDF5 library that it depends on our zlib
-  set(ZLIB_INCLUDE_DIRS "${ITKZLIB_INCLUDE_DIRS}")
-  set(ZLIB_LIBRARIES "${ITKZLIB_LIBRARIES}")
-  if(BUILD_SHARED_LIBS)
-    set(ZLIB_SHARED_LIBRARY ${ITKZLIB_LIBRARIES})
-  endif()
-  set(ZLIB_STATIC_LIBRARY ${ITKZLIB_LIBRARIES})
+  # see src/itkhdf5/CMakeLists.txt for detauls
+  set(H5_ZLIB_INCLUDE_DIRS "${ITKZLIB_INCLUDE_DIRS}")
+  set(H5_ZLIB_LIBRARIES "${ITKZLIB_LIBRARIES}")
+  set(HDF5_LIB_DEPENDENCIES ${ITKZLIB_LIBRARIES})
   set(H5_ZLIB_HEADER "itk_zlib.h")
+
+  set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${H5_ZLIB_LIBRARIES})
 endif()
 
 add_subdirectory(itkhdf5)
@@ -91,7 +100,6 @@ mark_as_advanced(HDF5_USE_18_API_DEFAULT)
 mark_as_advanced(HDF5_USE_FILE_LOCKING)
 mark_as_advanced(HDF5_USE_PREGEN)
 mark_as_advanced(USE_LIBAEC)
-unset(ALLOW_UNSUPPORTED CACHE)
 
 if(BUILD_SHARED_LIBS)
   set(target_extension -shared)

Modules/ThirdParty/HDF5/src/itkhdf5/.clang-format

@@ -1,7 +1,20 @@
 ---
-Language:        Cpp
 BasedOnStyle:  LLVM
 AlignConsecutiveAssignments: true
+BraceWrapping:
+  AfterFunction:   true
+  #llvm10-11: AfterControlStatement: false - Never
+  BeforeCatch:     true
+  BeforeElse:      true
+  #llvm11:   BeforeLambdaBody: false
+  #llvm11:   BeforeWhile:     false
+BreakBeforeBraces: Stroustrup
+BreakAfterJavaFieldAnnotations: true
+BreakStringLiterals: true
+ColumnLimit:     110
+IndentWidth:     4
+---
+Language:        Cpp
 #llvm11: AlignConsecutiveBitFields: false
 AlignConsecutiveDeclarations: true
 AlignConsecutiveMacros: true
@@ -22,17 +35,6 @@ AlwaysBreakAfterReturnType: AllDefinitions
 #  - H5_ATTR_CONST
 #  - H5_ATTR_PURE
 #  - H5_ATTR_FALLTHROUGH
-BraceWrapping:
-  AfterFunction:   true
-  #llvm10-11: AfterControlStatement: false - Never
-  BeforeCatch:     true
-  BeforeElse:      true
-  #llvm11:   BeforeLambdaBody: false
-  #llvm11:   BeforeWhile:     false
-BreakBeforeBraces: Stroustrup
-BreakAfterJavaFieldAnnotations: true
-BreakStringLiterals: true
-ColumnLimit:     110    # Update $max_trace_macro_line_len in bin/trace also
 ForEachMacros: ['ALL_MEMBERS', 'UNIQUE_MEMBERS']
 IncludeCategories:
   - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
@@ -55,7 +57,6 @@ IndentCaseLabels: true
 #llvm11: IndentCaseBlocks: false
 IndentGotoLabels: false
 #llvm11: IndentExternBlock: AfterExternBlock
-IndentWidth:     4
 #llvm11: InsertTrailingCommas: None
 MacroBlockBegin: "^BEGIN_FUNC"
 MacroBlockEnd: "^END_FUNC"
@@ -64,33 +65,45 @@ ObjCBlockIndentWidth: 4
 ReflowComments:  true
 SortIncludes:    false
 StatementMacros:
+  - CATCH
+  - END_MEMBERS
   - FUNC_ENTER_API
-  - FUNC_LEAVE_API
+  - FUNC_ENTER_API_NAMECHECK_ONLY
+  - FUNC_ENTER_NOAPI
+  - FUNC_ENTER_NOAPI_NOERR
+  - FUNC_ENTER_NOAPI_NOINIT
   - FUNC_ENTER_NOAPI_NOINIT_NOERR
+  - FUNC_ENTER_PACKAGE
+  - FUNC_LEAVE_API
+  - FUNC_LEAVE_API_NAMECHECK_ONLY
   - FUNC_LEAVE_NOAPI
+  - FUNC_LEAVE_NOAPI_NOFS
+  - H5E_END_TRY
+  - H5E_PRINTF
+  - H5E_THROW
   - H5_BEGIN_TAG
-  - HGOTO_DONE_TAG
   - H5_END_TAG
-  - HSYS_DONE_ERROR
-  - HSYS_GOTO_ERROR
-  - HDONE_ERROR
-  - HERROR
+  - H5_GCC_DIAG_OFF
+  - H5_GCC_DIAG_ON
+  - H5_CLANG_DIAG_OFF
+  - H5_CLANG_DIAG_ON
+  - H5_GCC_CLANG_DIAG_OFF
+  - H5_GCC_CLANG_DIAG_ON
   - H5_LEAVE
-  - H5E_PRINTF
-  - H5E_THROW
   - HGOTO_DONE
-  - HGOTO_ERROR
-  - HMPI_ERROR
   - HMPI_DONE_ERROR
+  - HMPI_ERROR
   - HMPI_GOTO_ERROR
-  - H5_GCC_DIAG_OFF
-  - H5_GCC_DIAG_ON
-  - CATCH
+  - HSYS_DONE_ERROR
+  - HSYS_GOTO_ERROR
 #llvm10: TypenameMacros:
 #llvm10:   - STACK_OF
 #llvm10:   - LIST
 #llvm11: WhitespaceSensitiveMacros:
 #llvm11:   - STRINGIZE
 #llvm11:   - PP_STRINGIZE
+---
+Language:      Java
+BreakAfterJavaFieldAnnotations: true
+JavaImportGroups: ['java', 'hdf', 'hdf.hdf5lib', 'org']
 ...
-