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Update hdf5 1.12.1 to 1.12.3 #4653

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Update hdf5 1.12.1 to 1.12.3 #4653

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4e15f8b
ENH: updated HDF5 1.12.1 to 1.12.3
seanm May 6, 2024
3f96eed
HDF5 2023-11-06 (106fb569)
Nov 7, 2023
b021190
Merge branch 'upstream-HDF5' into hdf5-1.12.3
seanm May 7, 2024
3012756
COMP: restore default disabled hdf5 + zlib
seanm May 9, 2024
f6a87ec
COMP: added more HDF5 symbols for mangling
seanm May 9, 2024
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5 changes: 2 additions & 3 deletions Modules/ThirdParty/HDF5/UpdateFromUpstream.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -8,14 +8,13 @@ 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_12_3"
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
Expand Down
32 changes: 18 additions & 14 deletions Modules/ThirdParty/HDF5/src/itkhdf5/.clang-format
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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 # Update $max_trace_macro_line_len in bin/trace also
IndentWidth: 4
---
Language: Cpp
#llvm11: AlignConsecutiveBitFields: false
AlignConsecutiveDeclarations: true
AlignConsecutiveMacros: true
Expand All @@ -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)/'
Expand All @@ -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"
Expand Down Expand Up @@ -92,5 +93,8 @@ StatementMacros:
#llvm11: WhitespaceSensitiveMacros:
#llvm11: - STRINGIZE
#llvm11: - PP_STRINGIZE
---
Language: Java
BreakAfterJavaFieldAnnotations: true
JavaImportGroups: ['java', 'hdf', 'hdf.hdf5lib', 'org']
...

181 changes: 99 additions & 82 deletions Modules/ThirdParty/HDF5/src/itkhdf5/CMakeFilters.cmake
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Original file line number Diff line number Diff line change
Expand Up @@ -9,25 +9,43 @@
# If you do not have access to either file, you may request a copy from
# [email protected].
#
if (FALSE) # XXX(kitware): avoid this showing up in VTK's cache file
option (USE_LIBAEC "Use AEC library as SZip Filter" OFF)
if (FALSE) # XXX(kitware): avoid this showing up in ITK's cache file
option (USE_LIBAEC_STATIC "Use static AEC library " OFF)
else ()
set (USE_LIBAEC OFF)
set (USE_LIBAEC_STATIC OFF)
endif ()
option (ZLIB_USE_EXTERNAL "Use External Library Building for ZLIB" OFF)
option (SZIP_USE_EXTERNAL "Use External Library Building for SZIP" OFF)

if (NOT ZLIB_USE_LOCALCONTENT)
set (ZLIB_URL ${ZLIB_TGZ_ORIGPATH}/${ZLIB_TGZ_NAME})
else ()
set (ZLIB_URL ${TGZPATH}/${ZLIB_TGZ_NAME})
endif ()
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "Filter ZLIB file is ${ZLIB_URL}")
endif ()

if (NOT LIBAEC_USE_LOCALCONTENT)
set (SZIP_URL ${LIBAEC_TGZ_ORIGPATH}/${LIBAEC_TGZ_NAME})
else ()
set (SZIP_URL ${TGZPATH}/${LIBAEC_TGZ_NAME})
endif ()
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "Filter SZIP file is ${SZIP_URL}")
endif ()

if (FALSE) # XXX(kitware): Hardcode settings.
include (ExternalProject)
include (FetchContent)

#option (HDF5_ALLOW_EXTERNAL_SUPPORT "Allow External Library Building (NO GIT TGZ)" "NO")
set (HDF5_ALLOW_EXTERNAL_SUPPORT "NO" CACHE STRING "Allow External Library Building (NO GIT TGZ)")
set_property (CACHE HDF5_ALLOW_EXTERNAL_SUPPORT PROPERTY STRINGS NO GIT TGZ)
else ()
set(HDF5_ALLOW_EXTERNAL_SUPPORT NO)
endif ()
if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ")
option (ZLIB_USE_EXTERNAL "Use External Library Building for ZLIB" 1)
option (SZIP_USE_EXTERNAL "Use External Library Building for SZIP" 1)
set (ZLIB_USE_EXTERNAL ON CACHE BOOL "Use External Library Building for ZLIB" FORCE)
set (SZIP_USE_EXTERNAL ON CACHE BOOL "Use External Library Building for SZIP" FORCE)
if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT")
set (ZLIB_URL ${ZLIB_GIT_URL} CACHE STRING "Path to zlib git repository")
set (ZLIB_BRANCH ${ZLIB_GIT_BRANCH})
Expand All @@ -37,26 +55,27 @@ if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MAT
if (NOT TGZPATH)
set (TGZPATH ${HDF5_SOURCE_DIR})
endif ()
set (ZLIB_URL ${TGZPATH}/${ZLIB_TGZ_NAME})
if (NOT EXISTS "${ZLIB_URL}")
set (HDF5_ENABLE_Z_LIB_SUPPORT OFF CACHE BOOL "" FORCE)
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "Filter ZLIB file ${ZLIB_URL} not found")
if (ZLIB_USE_LOCALCONTENT)
if (NOT EXISTS "${ZLIB_URL}")
set (HDF5_ENABLE_Z_LIB_SUPPORT OFF CACHE BOOL "" FORCE)
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "Filter ZLIB file ${ZLIB_URL} not found")
endif ()
endif ()
endif ()
set (SZIP_URL ${TGZPATH}/${SZIP_TGZ_NAME})
if (USE_LIBAEC)
set (SZIP_URL ${TGZPATH}/${SZAEC_TGZ_NAME})
endif ()
if (NOT EXISTS "${SZIP_URL}")
set (HDF5_ENABLE_SZIP_SUPPORT OFF CACHE BOOL "" FORCE)
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "Filter SZIP file ${SZIP_URL} not found")
if (LIBAEC_USE_LOCALCONTENT)
if (NOT EXISTS "${SZIP_URL}")
set (HDF5_ENABLE_SZIP_SUPPORT OFF CACHE BOOL "" FORCE)
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "Filter SZIP file ${SZIP_URL} not found")
endif ()
endif ()
endif ()
else ()
set (ZLIB_USE_EXTERNAL 0)
set (SZIP_USE_EXTERNAL 0)
set (HDF5_ENABLE_Z_LIB_SUPPORT OFF CACHE BOOL "" FORCE)
set (ZLIB_USE_EXTERNAL OFF CACHE BOOL "Use External Library Building for ZLIB")
set (HDF5_ENABLE_SZIP_SUPPORT OFF CACHE BOOL "" FORCE)
set (SZIP_USE_EXTERNAL OFF CACHE BOOL "Use External Library Building for SZIP")
endif ()
endif ()

Expand All @@ -67,36 +86,28 @@ if (FALSE) # XXX(kitware): Hardcode settings.
option (HDF5_ENABLE_Z_LIB_SUPPORT "Enable Zlib Filters" OFF)
else ()
set(HDF5_ENABLE_Z_LIB_SUPPORT ON)
mark_as_advanced (HDF5_ENABLE_Z_LIB_SUPPORT)
endif ()
if (HDF5_ENABLE_Z_LIB_SUPPORT)
if (NOT H5_ZLIB_HEADER)
if (NOT ZLIB_USE_EXTERNAL)
find_package (ZLIB NAMES ${ZLIB_PACKAGE_NAME}${HDF_PACKAGE_EXT} COMPONENTS static shared)
if (NOT ZLIB_FOUND)
find_package (ZLIB) # Legacy find
if (ZLIB_FOUND)
set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${ZLIB_LIBRARIES})
endif ()
endif ()
endif ()
if (ZLIB_FOUND)
set (H5_HAVE_FILTER_DEFLATE 1)
set (H5_HAVE_ZLIB_H 1)
set (H5_HAVE_LIBZ 1)
set (H5_ZLIB_HEADER "zlib.h")
set (ZLIB_INCLUDE_DIR_GEN ${ZLIB_INCLUDE_DIR})
set (ZLIB_INCLUDE_DIRS ${ZLIB_INCLUDE_DIRS} ${ZLIB_INCLUDE_DIR})
if (ZLIB_FOUND)
set (H5_ZLIB_HEADER "zlib.h")
set (ZLIB_INCLUDE_DIR_GEN ${ZLIB_INCLUDE_DIR})
set (ZLIB_INCLUDE_DIRS ${ZLIB_INCLUDE_DIRS} ${ZLIB_INCLUDE_DIR})
set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${ZLIB_LIBRARIES})
endif ()
else ()
if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ")
EXTERNAL_ZLIB_LIBRARY (${HDF5_ALLOW_EXTERNAL_SUPPORT})
set (H5_HAVE_FILTER_DEFLATE 1)
set (H5_HAVE_ZLIB_H 1)
set (H5_HAVE_LIBZ 1)
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "Filter ZLIB is built")
message (VERBOSE "Filter HDF5_ZLIB is built")
endif ()
else ()
message (FATAL_ERROR " ZLib is Required for ZLib support in HDF5")
set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${ZLIB_STATIC_LIBRARY})
endif ()
endif ()
else ()
Expand All @@ -105,13 +116,20 @@ if (HDF5_ENABLE_Z_LIB_SUPPORT)
set (H5_HAVE_ZLIB_H 1)
set (H5_HAVE_LIBZ 1)
endif ()
if (H5_HAVE_FILTER_DEFLATE)
set (EXTERNAL_FILTERS "${EXTERNAL_FILTERS} DEFLATE")
endif ()
set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${ZLIB_STATIC_LIBRARY})
INCLUDE_DIRECTORIES (${ZLIB_INCLUDE_DIRS})
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "Filter ZLIB is ON")
if (ZLIB_FOUND)
set (H5_HAVE_FILTER_DEFLATE 1)
set (H5_HAVE_ZLIB_H 1)
set (H5_HAVE_LIBZ 1)
if (H5_HAVE_FILTER_DEFLATE)
set (EXTERNAL_FILTERS "${EXTERNAL_FILTERS} DEFLATE")
endif ()
INCLUDE_DIRECTORIES (${ZLIB_INCLUDE_DIRS})
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "Filter HDF5_ZLIB is ON")
endif ()
else ()
set (HDF5_ENABLE_Z_LIB_SUPPORT OFF CACHE BOOL "" FORCE)
message (WARNING " ZLib support in HDF5 was enabled but not found")
endif ()
endif ()

Expand All @@ -121,54 +139,53 @@ endif ()
if (FALSE) # XXX(kitware): no need for szip support.
option (HDF5_ENABLE_SZIP_SUPPORT "Use SZip Filter" OFF)
if (HDF5_ENABLE_SZIP_SUPPORT)
option (HDF5_ENABLE_SZIP_ENCODING "Use SZip Encoding" OFF)
option (HDF5_ENABLE_SZIP_ENCODING "Use SZip Encoding" ON)
if (NOT SZIP_USE_EXTERNAL)
find_package (SZIP NAMES ${SZIP_PACKAGE_NAME}${HDF_PACKAGE_EXT} COMPONENTS static shared)
set(SZIP_FOUND FALSE)
set(libaec_USE_STATIC_LIBS ${USE_LIBAEC_STATIC})
find_package (libaec 1.0.5 CONFIG)
if (SZIP_FOUND)
set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${SZIP_LIBRARIES})
endif ()
if (NOT SZIP_FOUND)
find_package (SZIP) # Legacy find
if (SZIP_FOUND)
set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${SZIP_LIBRARIES})
find_package (SZIP NAMES ${LIBAEC_PACKAGE_NAME}${HDF_PACKAGE_EXT} COMPONENTS static shared)
if (NOT SZIP_FOUND)
find_package (SZIP) # Legacy find
endif ()
endif ()
endif ()
if (SZIP_FOUND)
set (H5_HAVE_FILTER_SZIP 1)
set (H5_HAVE_SZLIB_H 1)
set (H5_HAVE_LIBSZ 1)
set (SZIP_INCLUDE_DIR_GEN ${SZIP_INCLUDE_DIR})
set (SZIP_INCLUDE_DIRS ${SZIP_INCLUDE_DIRS} ${SZIP_INCLUDE_DIR})
if (SZIP_FOUND)
set (SZIP_INCLUDE_DIR_GEN ${SZIP_INCLUDE_DIR})
set (SZIP_INCLUDE_DIRS ${SZIP_INCLUDE_DIRS} ${SZIP_INCLUDE_DIR})
set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${SZIP_LIBRARIES})
endif ()
else ()
if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ")
EXTERNAL_SZIP_LIBRARY (${HDF5_ALLOW_EXTERNAL_SUPPORT} ${HDF5_ENABLE_SZIP_ENCODING})
set (H5_HAVE_FILTER_SZIP 1)
set (H5_HAVE_SZLIB_H 1)
set (H5_HAVE_LIBSZ 1)
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "Filter SZIP is built")
message (VERBOSE "... with library AEC")
endif ()
if (USE_LIBAEC)
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "... with library AEC")
endif ()
set (SZ_PACKAGE_NAME ${LIBAEC_PACKAGE_NAME})
else ()
set (SZ_PACKAGE_NAME ${SZIP_PACKAGE_NAME})
endif ()
else ()
message (FATAL_ERROR "SZIP is Required for SZIP support in HDF5")
set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${SZIP_STATIC_LIBRARY})
endif ()
endif ()
set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${SZIP_STATIC_LIBRARY})
INCLUDE_DIRECTORIES (${SZIP_INCLUDE_DIRS})
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "Filter SZIP is ON")
endif ()
if (H5_HAVE_FILTER_SZIP)
set (EXTERNAL_FILTERS "${EXTERNAL_FILTERS} DECODE")
endif ()
if (HDF5_ENABLE_SZIP_ENCODING)
set (H5_HAVE_SZIP_ENCODER 1)
set (EXTERNAL_FILTERS "${EXTERNAL_FILTERS} ENCODE")
if (SZIP_FOUND)
set (H5_HAVE_FILTER_SZIP 1)
set (H5_HAVE_SZLIB_H 1)
set (H5_HAVE_LIBSZ 1)
INCLUDE_DIRECTORIES (${SZIP_INCLUDE_DIRS})
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
message (VERBOSE "Filter SZIP is ON")
endif ()
if (H5_HAVE_FILTER_SZIP)
set (EXTERNAL_FILTERS "${EXTERNAL_FILTERS} DECODE")
endif ()
if (HDF5_ENABLE_SZIP_ENCODING)
set (H5_HAVE_SZIP_ENCODER 1)
set (EXTERNAL_FILTERS "${EXTERNAL_FILTERS} ENCODE")
endif ()
else ()
set (HDF5_ENABLE_SZIP_SUPPORT OFF CACHE BOOL "" FORCE)
message (WARNING "SZIP support in HDF5 was enabled but not found")
endif ()
endif ()
endif ()
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