* Skip some parallel example tests for small MPIEXEC_MAX_NUMPROCS values (#6224)
* chore: fix grammar (#6227)
* Split static targets into separate optional target [UPDATED] (#6216)
Build-tree exports can't diverge from install-tree exports — the export(EXPORT ...) reads directly from the install export sets. No manual list to keep in sync.
Removed 3 global variables (HDF5_STATIC_LIBRARIES_TO_EXPORT, HDF5_JAVA_LIBRARIES_TO_EXPORT, HDF5_UTILS_TO_EXPORT) and their ~21 set_global_variable calls across tool/utility files.
Fixed the static-only build bug in the PR where the base export set was guarded by BUILD_SHARED_LIBS, breaking tools export.
Removed redundant utils in export files — the PR was dumping tools into all three build-tree export files (java, static, shared). Now they correctly appear only in the base export.
* Apply filters to variable-length data (#6178)
Closes can_apply and set_local filter callbacks skipped for H5T_VARIABLE dtypes #5942. A more detailed explanation of the rationale for this PR is in the linked issue.
Mandatory filters can be now applied to variable-length data. This notably includes h5py object strings and NpyStrings.
Optional filters applied to variable-length data no longer skip can_apply and set_local, only to jump directly to filter. This fixes hdf5_blosc and HDF5_Blosc2, which rely on set_local. Note that all filters which have neither can_apply nor set_local have always worked fine with vlen data, as long as they were tagged as optional. Notable examples are deflate, lzf, bzip2 (from hdf5plugin), and lz4 (also from hdf5plugin).
Lossy filters, such as scale-offset, are and remain untested and most likely broken, as I expect them to treat the vlen metadata as numbers and corrupt it. The right place to ensure proper behaviour is their can_apply function, which however is broken (filters: can_apply does nothing for optional filters #6161).
* 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>
Update version to 2.1 and derive version information from H5public.h, removing h5vers script and updating CMake and Java configurations.
Versioning:
Update version to 2.1 in H5public.h.
Derive version strings in H5public.h using macros.
CMake:
Extract version from H5public.h in HDF5config.cmake and HDF5AsSubdirMacros.cmake.
Configure README.md and CHANGELOG.md using CMakeLists.txt.
Java:
Generate H5Version.java from H5public.h for version consistency.
Update H5.java to use H5Version for version constants.
Removals:
Delete bin/h5vers script, previously used for version management.
Add generate-index-html.sh script and update workflows to generate and upload index.html files for HDF5 releases, enhancing Maven package testing and deployment.
FFM build requires Java 25, Jextract 25.
Generates FFM bindings during configure.
JNI is default when the requirements are not met or can be forced.
Presets added for maven and FFM - JNI is default selection.
Enhanced Maven options will work with either JNI or FFM
New Workflows for testing and maven uploads.
Extensive documentation changes for java.
Change default file format to 1.8 across various tests and examples, updating file creation and access logic accordingly.
Behavior:
Default file format version changed to 1.8 in H5Pfapl.c.
Updated file creation and access to use 1.8 format in h5ex_g_compact.c and test_file_image.c.
Set earliest file format in multiple test files including cache_tagging.c, dtypes.c, and links.c.
Tests:
Modified expected output in tools/test/misc/expected/*.ls files to reflect new file format locations.
Adjusted test logic in test_file_image.c and cache_tagging.c to accommodate format changes.
Misc:
Added comments and TODOs for future format testing in test_file_image.c.
Minor variable renaming for clarity in test_file_image.c.
Behavior:
Modify HDF5UseFortran.cmake to handle cross-compilation by providing default KINDs and sizes when CMAKE_CROSSCOMPILING is true.
Default values for INTEGER and REAL KINDs and their sizes are set when cross-compiling.
Error messages are adjusted to reflect cross-compilation scenarios.
Logic:
Conditional checks added for CMAKE_CROSSCOMPILING to determine if default values should be used.
Default values include INTEGER KINDs {1,2,4,8,16} and REAL KINDs {4,8,10,16}.
Default sizes for native kinds are set to 4 for INTEGER and REAL, and 8 for DOUBLE PRECISION when cross-compiling.
Misc:
Adjustments to verbose messages to indicate when defaults are used during cross-compilation.
Renamed all HDF5 examples build options from H5EX_* to H5EXAMPLE_* to better distinguish them from library options when building examples alongside the library.
Updated all CMake files, including:
Main examples CMakeLists.txt files
CMake configuration files in config/ directory
CMake preset files
Updated documentation files to reflect new option names
* Remove hbool_t from the public API
This was previously removed from the source code, but the API calls
retained hbool_t in the public API calls. This commit removes
hbool_t from the public APIs.
hbool_t is retained as a typedef for bool in H5public.h so existing
code doesn't break.
This update systematically renames variables across 2.0+ CMake files in the HDF5Examples directory and configuration templates. The goal is to change variables from sounding like build "options" (e.g., HDF5_BUILD_TOOLS, HDF5_ENABLE_PARALLEL) to reflecting library "state" (e.g., what features the installed library provides).
Implemented missing --help/-h, -c, -echo and -shlib/-noshlib options
Added new -nohl option to avoid building and linking against
high-level HDF5 libraries if desired
Implemented adding of HDF5 installation library directory to rpath of
resulting executable/library and added new -norpath option to avoid
this behavior if desired
Added parsing of HDF5_USE_SHLIB environment variable to determine
whether to link against shared or static HDF5 libraries
Added parsing of HDF5_PKG_CONFIG_ARGS environment variable to separate
pkg-config-specific options from compiler-specific options and prevent
conflicts
Larry Knox
H. Joe Lee
Matt L
Allen Byrne
Neil Fortner
Dana Robinson
Aleksandar Jelenak
Harmen Stoppels