* Fix MPI Fortran configuration for HDF5Examples (#6206)
When building Fortran parallel examples without MPI wrappers, the
compiler couldn't find mpi.mod because MPI_Fortran_INCLUDE_DIRS
was not populated. This occurred because find_package(MPI) was only
called for C, not Fortran.
Added enable_language(Fortran) and find_package(MPI REQUIRED
COMPONENTS Fortran) to properly configure MPI for Fortran examples,
ensuring MPI include directories and libraries are correctly set.
* Adds RFCs to the RFC table (#6190)
* Added two RFCs to the RFC table
"Adding support for digitally signed plugins to HDF5"
" Write-Ahead log"
* Updated to use the ACM link
* Add HDF5 2.0.0 Library Migration Guide (#6183)
* Add HDF5 2.0.0 Library Migration Guide
* Revise HDF5 migration guide for version 2.0.0
Use 2.0.0 consistently.
* Clarify API changes in HDF5 2.0.0 Migration Guide
* Fixes the "multiple @param documentation sections" doxygen warnings (#6195)
Addresses the "multiple @ param documentation sections" warnings are caused by the interaction of three things:
1. MACRO_EXPANSION = YES with EXPAND_ONLY_PREDEF = NO in Doxyfile.in
2. Versioned API macros in H5version.h like:
\def documentation in APIVersions.dox like:
3. \def H5Tarray_create \api_vers_2{H5Tarray_create,H5Tarray_create1,H5Tarray_create2}
Because Doxygen expands all macros, it sees H5Tarray_create as an alias for H5Tarray_create1. It then associates documentation from both the \def block (for the macro) and the function's own doc block (with \param entries) with the same function — resulting in "multiple @ param documentation sections."
* Update Doxygen version from 1.16.0 to 1.16.1
Use Doxygen 1.16.1 for all platforms. This version includes the latest
bug fixes and improvements while maintaining compatibility with our
documentation format.
* Fix Windows Doxygen installation for version 1.16.1
Handle different Windows binary naming conventions across Doxygen versions:
- 1.16.1 uses: doxygen-VERSION.windows.x64.bin.zip
- 1.16.0 uses: doxygen-VERSION.x64.bin.zip
Try the newer naming convention first, then fall back to the older one
if the download fails. This ensures compatibility across versions.
* Use ssciwr/doxygen-install in setup-doxygen action
Replace direct installation of official Doxygen binaries with
ssciwr/doxygen-install action. This avoids Java documentation parsing
errors that occur with official binaries but not with distribution
builds.
The setup-doxygen action now serves as a thin wrapper around
ssciwr/doxygen-install@f13be16c83 (v1),
using commit hash for security and reproducibility.
* Remove redundant version specification from workflows
The setup-doxygen action already has a default version (1.16.1),
so explicit version specification in workflows is unnecessary.
This follows DRY principles and makes version updates simpler.
* Updates to #6205 (#6208)
* Fix MPI Fortran configuration for HDF5Examples (#6205)
When building Fortran parallel examples standalone without MPI
wrappers, the compiler cannot find mpi.mod because
MPI_Fortran_INCLUDE_DIRS is not populated.
* Use MPI::MPI_Fortran imported target instead of raw MPI variables
Replace manual MPI_Fortran_LIBRARIES, MPI_Fortran_LINK_FLAGS, and
MPI_Fortran_INCLUDE_DIRS usage with the MPI::MPI_Fortran imported
target, which transitively carries all include dirs, compile flags,
and link flags. This eliminates the CMAKE_Fortran_EXE_LINKER_FLAGS
hack and the manual target_include_directories in H5PAR.
* Update nvhpc version to 26.1 with CUDA version 13.1. (#6213)
# branches: [develop]
* Inherit Debug C build flags in Developer build mode (#6182)
* Bump the github-actions group across 1 directory with 11 updates (#6215)
* Bump the github-actions group across 1 directory with 11 updates
Bumps the github-actions group with 11 updates in the / directory:
| Package | From | To |
| --- | --- | --- |
| [actions/cache](https://github.com/actions/cache) | `5.0.1` | `5.0.3` |
| [lukka/get-cmake](https://github.com/lukka/get-cmake) | `4.2.1` | `4.2.3` |
| [softwareforgood/check-artifact-v4-existence](https://github.com/softwareforgood/check-artifact-v4-existence) | `0.3.0` | `0.4.1` |
| [github/codeql-action](https://github.com/github/codeql-action) | `3.31.9` | `4.32.2` |
| [azure/trusted-signing-action](https://github.com/azure/trusted-signing-action) | `0.5.11` | `1.1.0` |
| [cygwin/cygwin-install-action](https://github.com/cygwin/cygwin-install-action) | `7d2dc1e241644c3318bed9ec74115d1929baa681` | `2566376092c4e280f21131be027af3f5bb2420a4` |
| [aws-actions/configure-aws-credentials](https://github.com/aws-actions/configure-aws-credentials) | `5.1.1` | `6.0.0` |
| [vmactions/freebsd-vm](https://github.com/vmactions/freebsd-vm) | `1.3.4` | `1.4.2` |
| [vmactions/openbsd-vm](https://github.com/vmactions/openbsd-vm) | `1.3.1` | `1.3.5` |
| [mpi4py/setup-mpi](https://github.com/mpi4py/setup-mpi) | `1.4.1` | `1.4.2` |
| [actions/setup-python](https://github.com/actions/setup-python) | `6.1.0` | `6.2.0` |
vmactions/openbsd-vm@d6c29ce1b4 (`1.3.5`) failed to run ssh on the github runner. 271a1ba62300483cfc58345ff9f425f1349a2cab for v1.3.4 was used instead.
* Fix issue with some Subfiling VFD test files not getting deleted (#6212)
* CMake: Fix Fortran cross-compilation support
Refactor the cross-compilation infrastructure to rely on the standard
CMAKE_CROSSCOMPILING_EMULATOR variable instead of the custom
CROSSCOMPILING_PATH environment hack.
Key changes:
- Removed `ENVIRONMENT "${CROSSCOMPILING_PATH}"` from all test definitions.
- Updated custom commands (e.g., H5match_types, H5_gen) to invoke the
emulator explicitly when cross-compiling.
- Updated ConfigureChecks.cmake and HDF5UseFortran.cmake to enable
`try_run` checks when an emulator is defined.
- Added config/toolchain/mingw-w64-x86-64-wine.sh wrapper to automatically
locate MinGW runtime libraries (like libgfortran) for Wine execution.
- Cleaned up toolchain files to remove hardcoded emulator paths, deferring
configuration to the build environment.
* Add Doxygen setup that results in missing Doygen documentation. (#6217)
* Added setup-doxygen action in ctest.yml Ubuntu gcc workflow.
* Also added actions/checkout for setup-doxygen.
* Fixes link checker failure (#6219)
Removed https:// as a workaround to avoid error by the link checker.
* Remove force-setting of ZLIB_USE_EXTERNAL / SZIP_USE_EXTERNAL (#6222)
Removes the force-setting of ZLIB_USE_EXTERNAL and SZIP_USE_EXTERNAL to
ON when HDF5_ALLOW_EXTERNAL_SUPPORT is GIT or TGZ so that zlib and
szip can be independently built from the system or externally as desired
* Truncate Subfiling VFD's stub file when truncating subfiles (#6210)
Ensure that the Subfiling VFD's stub file gets truncated when subfiles are
being truncated to avoid a potentially unreadable file when the EOF doesn't
match the stored EOF value
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Add CMake function to extract pkg-config info from libraries (#6220)
* Consistent extension for C++ (#6214)
Except for this file, all use cpp instead of cxx. No obvious reason why
the same file types should have different extensions.
* Enable Windows ARM64 CTest CI for release binaries (#6177)
* ci: add Windows ARM64 MSVC CTest job
* ci: add MSYS2 clangarm64 build on Windows ARM64
* cmake: add MSVC ARM64 presets for Windows
* zlib: fix MSVC static library flags for ARM64 builds
* Renamed .hxx file to .h and updated the #include for it.
* Committing clang-format changes
---------
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
Co-authored-by: Gerd Heber <gheber@hdfgroup.org>
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Julien Schueller <schueller@phimeca.com>
Co-authored-by: Martin Diehl <mail@martin-diehl.net>
Co-authored-by: Harish RS <harish.rajaselvan@multicorewareinc.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Adds predefined datatypes for FP6 data in E2M3 and E3M2 formats
Does not add support for any native FP6 types; datatype conversions are performed in software
Adds predefined datatypes for FP8 data in E4M3 and E5M2 formats
Does not add support for any native FP8 types; datatype conversions are performed in software
Adds predefined datatypes for little- and big-endian bfloat16 data
Does not add support for any native bfloat16 types; datatype conversions are performed in software
Also adds missing float16 predefined types to fortran
Makes testing parameters specified with AddTest non-const again when
passed to test functions. This allows test functions to update their
parameters during execution and is particularly useful for tests
which use those parameters to accumulate statistics, error counts,
etc. without resorting to global variables.
* Implement support for complex number datatypes
Adds the new datatype class H5T_COMPLEX
Adds the new API function H5Tcomplex_create which creates a complex
number datatype from an ID of a base floating-point datatype
Adds the new feature check macros H5_HAVE_COMPLEX_NUMBERS and
H5_HAVE_C99_COMPLEX_NUMBERS
Adds the new datatype size macros H5_SIZEOF_FLOAT_COMPLEX,
H5_SIZEOF_DOUBLE_COMPLEX and H5_SIZEOF_LONG_DOUBLE_COMPLEX
Adds the new datatype ID macros H5T_NATIVE_FLOAT_COMPLEX,
H5T_NATIVE_DOUBLE_COMPLEX, H5T_NATIVE_LDOUBLE_COMPLEX,
H5T_CPLX_IEEE_F16LE, H5T_CPLX_IEEE_F16BE,
H5T_CPLX_IEEE_F32LE, H5T_CPLX_IEEE_F32BE,
H5T_CPLX_IEEE_F64LE and H5T_CPLX_IEEE_F64BE
Adds hard and soft datatype conversion paths between complex number
datatypes and all the integer and floating-point datatypes, as well as
between other complex number datatypes
Adds a special conversion path between complex number datatypes and
array or compound datatypes where the in-memory layout of data is the
same between the datatypes and data can be converted directly
Adds support for complex number datatypes to the h5dump, h5ls and
h5diff/ph5diff tools. Allows h5dump '-m' option to change floating-point
printing format for float complex and double complex datatypes, as well
as long double complex if it has the same size as double complex
Adds minimal support to the h5watch and h5import tools
Adds support for the predefined complex number datatypes and
H5Tcomplex_create function to the Java wrappers. Also adds initial,
untested support to the JNI for future use with HDFView
Adds support for just the H5T_COMPLEX datatype class to the Fortran
wrappers
Adds support for the predefined complex number datatypes and
H5Tcomplex_create function to the high level library H5LT interface
for use with the H5LTtext_to_dtype and H5LTdtype_to_text functions
Changes some usages of "complex" in the library since it conflicts with
the "complex" keyword from the complex.h header. Also changes various
usages of the word "complex" throughout the library to distinguish
compound datatypes from complex datatypes.
This is where most people will expect to find license information. The
COPYING_LBNL_HDF5 file has also been renamed to LICENSE_LBNL_HDF5.
The licenses are unchanged.
* Reworked cleaning up test files, only removing test files if present to account for skipped tests
* changed to using H5Fis_accessible
* update to full use of remove_test_file
Fixed some conversion issues with Clang due to problematic undefined
behavior when casting a negative floating-point value to an integer
Fixed a bug in the library's software integer to floating-point
conversion function where a user's conversion exception function
returning H5T_CONV_UNHANDLED in the case of overflows would result in
incorrect data after conversion
Added configure checks for functions and macros related to _Float16
usage since some compilers expose the datatype but not the functions or
macros
Fixed a dt_arith test failure when H5_WANT_DCONV_EXCEPTION isn't defined
Fixed a few warnings from not explicitly casting some _Float16 variables
upwards
- Close/reopen file and file objects to prevent cache from being used instead of actual I/O.
- Moved vlen io test datasets under the dset container group instead of the root group
- Moved the PASSED() invocation to after individual test cleanup in case an error occurs during H5Treclaim
* Fix issue with HDF5_VOL_ALLOW_EXTERNAL CMake variable
* Add initial API test workflow
* Initialize parallel testing with MPI_THREAD_MULTIPLE when testing API
* Add CMake variable to allow specifying a VOL connector's package name
* Remove call to MPI_Init in serial API tests
While previously necessary, it now interferes with VOL connectors that
may need to be initialized with MPI_THREAD_MULTIPLE
* HDF5 API test updates
Removed test duplication from bringing API tests
back into the library from external VOL tests
repo
Synced changes between API tests and library's
tests
Updated API tests CMake code to directly use and
install testhdf5, testphdf5, etc. instead of
creating duplicate binaries
Added new h5_using_native_vol() test function to
determine whether the VOL connector being used
is (or the VOL connector stack being used resolves
to) the native VOL connector
* Remove duplicate variable
* Strip HD prefix from string/char C API calls
* HD(f)(put|get)(s|c)
* HDstr*
* HDv*printf
* HD(s)(print|scan)f
* HDperror
But NOT:
* HDstrcase*
* HDvasprintf
* HDstrtok_r
* HDstrndup
As those are not C99 and have portability work-around
implementations. They will be handled later.
* Fix th5_system.c screwup
* Fixed extra semi warning by adjusting alternative macro definitions
* Find-replace H5E_END_TRY; -> H5E_END_TRY
* Made H5Epush_goto a do-while loop, fixed indentation
* Made GOTOERROR and ERRMSG do-while loops
* Made Hgoto_error and Hgoto_done do-while loops
* Made vrfy_cint_type and vrfy_ctype do-while loops
* Made TEST_TYPE_CONTIG and others do-while loops
* Removed extraneous semi-colons
* Committing clang-format changes
---------
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update files to skip list and ignore_words_list for codespell to not
check files generated by autotools. Autotools generate misspellings
that can't be fixed in HDF5 code.
Allen Byrne
Matt L
Dana Robinson
Sean McBride
Lori Cooper