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cde84cdc8f
* 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>
Workflows for Testing
The workflows are contained in .yml files and use the callable workflow method. Workflows can be triggered from PR, creation or merge, and on a scheduled timer. There are a few that only get triggered manually.
Scheduled Workflows
- daily-schedule.yml executes the daily-build.yml which first checks that there are changes
- tarball.yml to create a source.zip and source.tar.gz
- cygwin.yml to test on cygwin
- script.yml to test and report to my.cdash
- par-script.yml to test with released MPI and report to my.cdash
- par-source.yml to test with MPI default branch and report to my.cdash
- analysis.yml to test with LEAK and ADDRESS sanitizers and report to my.cdash
- ctest.yml to create signed binaries with commit hash in the name
- abi-report.yml to compare ABI to the last released binaries
- release-files.yml uploads new binaries to snapshots
- remove-files.yml remove previous binaries
- h5py.yml executes Python tests for h5py
- markdown-link-check.yml checks the links in markdown files
- scorecard.yml executes code-scanning and uploads to Github dashboard
- vfd.yml executes vfd-main.yml with combos of Release and Debug
- vfd-subfiling.yml configures, builds, and tests MPI with subfiling feature
- vol.yml calls the following workflows
- vol_rest.yml tests the REST VOL connector
- vol_ext_passthru.yml tests the external passthrough VOL connector
- vol_async.yml tests the asynchronous I/O VOL connector
- vol_cache.yml tests the cache VOL connector
- vol_adios2.yml tests the ADIOS2 VOL connector
- vol_log.yml tests the Log-based VOL connector
Manual Only Workflows
- publish-branch.yml publishes a local folder to the support.hdfgroup bucket
- publish-release.yml publishes release binaries to the support.hdfgroup bucket
- release.yml creates binaries for an official release or snapshot
- tarball.yml to create a source.zip and source.tar.gz
- ctest.yml to create signed binaries
- abi-report.yml to compare ABI to last released binaries
- maven-staging.yml to generate and test Maven artifacts with Java examples across all platforms
- maven-deploy.yml to deploy Maven artifacts to repositories
- release-files.yml uploads new binaries to releases page
- java-examples-maven-test.yml comprehensive Java examples testing with Maven artifacts
Triggered Workflows
- clang-format-check.yml runs clang-format and reports issues
- call-workflows.yml
- codespell.yml checks spelling
- cve.yml executes test_hdf5_cve.sh script
- hdfeos5.yml configures and builds HDF5 then tests HDF-EOS5
- linkchecker.yml verifies the links in generated doxygen files
- netcdf.yml configures and builds HDF5 then tests NetCDF
Workflows called by call-workflows.yml
- main-spc.yml configure, build, and test HDF5 with:
- API default v1_6
- API default v1_8
- API default v1_10
- API default v1_12
- API default v1_14
- API default v2_0
- using system zlib
- using zlibng
- using no filters
- in debug mode and -Werror compiler option
- in release mode and -Werror compiler option
- with minimum CMake Version 3.18
- main.yml configure, build, test, and package HDF5 on Ubuntu, macOS, and Windows
- main-static.yml configure, build, test static only HDF5 on Ubuntu, macOS, and Windows
- bintest.yml test binary packages created by main.yml
- main-par.yml configure, build, and test HDF5 with openmpi
- main-par-spc.yml configure, build, and test HDF5 with HDF5_ENABLE_WARNINGS_AS_ERRORS=ON
- intel.yml configure, build, and test HDF5 with Intel OneAPI on Linux and Windows
- nvhpc.yml configure, build, and test HDF5 with nvhpc
- aocc.yml configure, build, and test HDF5 with AOCC and OpenMPI
- testxpr.yml configure, build, and test HDF5 with HDF_TEST_EXPRESS=0
- julia.yml configure and build HDF5, then test Julia hdf5 source
- msys2.yml configure, build, and test HDF5 on mingw32, mingw64, ucrt64, clang64
- i386.yml configure, build, and test HDF5 on 32-bit Linux