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Merge pull request #4940 from blowekamp/hdf5_1.12.3
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Hdf5 1.14.5
blowekamp authored Dec 17, 2024
2 parents 9a137fb + 5fea965 commit e3c3369
Showing 835 changed files with 180,475 additions and 131,666 deletions.
4 changes: 4 additions & 0 deletions Modules/ThirdParty/HDF5/.gitattributes
Original file line number Diff line number Diff line change
@@ -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
11 changes: 0 additions & 11 deletions Modules/ThirdParty/HDF5/CMakeLists.txt
Original file line number Diff line number Diff line change
@@ -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)
10 changes: 6 additions & 4 deletions Modules/ThirdParty/HDF5/UpdateFromUpstream.sh
Original file line number Diff line number Diff line change
@@ -8,20 +8,21 @@ readonly name="HDF5"
readonly ownership="HDF5 Maintainers <hdf5-maintainers@hdfgroup.org>"
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
}
66 changes: 37 additions & 29 deletions Modules/ThirdParty/HDF5/src/CMakeLists.txt
Original file line number Diff line number Diff line change
@@ -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)
67 changes: 40 additions & 27 deletions Modules/ThirdParty/HDF5/src/itkhdf5/.clang-format
Original file line number Diff line number Diff line change
@@ -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']
...

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