* Consolidate documentation under doc/ directory
Move user-facing guides from release_docs/ and doxygen/ into a single
doc/ root. release_docs/ now holds only release artifacts (changelogs,
history, release process, maintainer info).
- git mv release_docs/INSTALL*.md, USING_*.md, README_HPC.md,
BuildSystemNotes.md, AutotoolsToCMakeOptions.md,
HDF5_Library_2.0.0_Migration_Guide.md → doc/
- git mv doxygen/ → doc/doxygen/
- Update CMakeLists.txt: HDF5_DOXYGEN_DIR and add_subdirectory path
- Update CMakeInstallation.cmake: all install paths for moved files
- Update bin/make_vers: hardcoded doxygen/ path substitution
- Update doc/doxygen/CMakeLists.txt: EXAMPLES_DIRECTORY and comments
- Update README.md, CONTRIBUTING.md, SECURITY.md, config/README.md,
release_docs/RELEASE_PROCESS.md: links to moved files
- Update doxygen .dox files: release_docs/ URLs for moved guides
- Rewrite release_docs/README.md for narrowed scope
* Add HDF5_DOCS_DIR variable for doc/ root path
Introduce HDF5_DOCS_DIR = \${HDF5_SOURCE_DIR}/doc so that
CMakeInstallation.cmake and future callers reference the doc/
directory symbolically rather than by hardcoded path.
HDF5_DOXYGEN_DIR is now derived from HDF5_DOCS_DIR.
* fixed assignment of size in the wrapper
* Call H5DSget_label directly from Fortran wrapper
Replace the intermediate C wrapper h5dsget_label_c with a direct
bind(c) call to H5DSget_label from H5DSget_label_f. This eliminates
the malloc/free of a temporary buffer and the associated failure path
where size was incorrectly set when H5DSget_label failed. The Fortran
wrapper now handles the C-to-Fortran string conversion (equivalent to
HD5packFstring) by blank-padding the buffer from the returned label
length to the end.
* Remove unused h5dsget_label_c C wrapper
Replace all strcpy calls copying into fixed-size path buffers with snprintf to prevent buffer overflows. Also simplify the path prefix check and the empty-string initialization.
Fixes 6 critical CodeQL cpp/unbounded-write alerts.
* Updated SECURITY.md to meet OSSF Badge Standard
* Disable CodeQL on MD file changes
* Updated version support policy
* Suppress non-constant format string CodeQL alerts
Exclude cpp/non-constant-format and cpp/uncontrolled-format-string
rules. All flagged uses are intentional format-string-as-template
patterns for family file naming (%d) and configurable output
formatting (%g), not security vulnerabilities.
* Add justification comments for CodeQL exclusions
* Harden CI workflows: pin actions to SHAs and apply least-privilege permissions
- Pin all third-party actions to commit SHAs in codeql.yml and arm-main.yml
- Add top-level permissions: contents: read to codeql.yml and markdown-link-check.yml
- Move contents: write from top-level to job-level in daily-schedule.yml
* Exclude non-security CodeQL rules and tainted-format-string false positives
- Add cpp/tainted-format-string to exclusions (same justification as
existing format string rules: bounded snprintf with app-controlled formats)
- Exclude code style rules with no security severity: cpp/long-switch,
cpp/guarded-free, cpp/commented-out-code, cpp/use-of-goto
- These 350+ alerts are structural C patterns inherent to HDF5, not vulnerabilities
* Add OpenSSF Best Practices badge to README.md
Optimize Doxygen build process by skipping rebuilds when input files are unchanged, using timestamp checks in CMake configuration.
Behavior:
Skip Doxygen build if input files unchanged using timestamp check in CMakeLists.txt, hl/src/CMakeLists.txt, and src/CMakeLists.txt.
Introduces stamp files (hdf5lib_doc.stamp, hdf5hllib_doc.stamp) to track changes.
Documentation:
add_custom_command and add_custom_target used to manage Doxygen builds.
Shared Doxygen content inputs defined in top-level CMakeLists.txt for reuse.
Misc:
Reorder add_subdirectory(src) in CMakeLists.txt for visibility of Doxygen variables.
* Update release progress badges to use Priority-based categorization
- Replace "Release Blockers"/"Release Must Do" with "Critical Priority"/"High Priority"
- Switch issue filtering from Release gating field to Priority field (P0 - Critical/P1 - High)
- Remove "Nice to Have" badge from workflow and README
- Add failure step: on workflow error, update both badge gist files to bright
purple (BF00FF) with "FAILURE" message
- Version auto-detected from src/H5public.h for milestone filtering
* Fix stale class docstring: release blocker -> priority issue
Intel's icx compiler defines _WIN32 (with underscore) but not WIN32,
causing unistd.h and other POSIX headers to be incorrectly included
on Windows builds.
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.
* 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.
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.
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.
Scope Safety: Refactored parse_hdf5_version from a Macro to a Function to prevent variable namespace pollution.
Implemented a helper macro (_parse_version_component) to handle repetitive regex logic, significantly reducing code size and complexity.
Updated HDF5config.cmake to calculate paths dynamically using REALPATH relative to CMAKE_CURRENT_LIST_FILE, fixing issues with symlinks and execution context.
Decoupled the parsing logic from scope promotion; the helper now parses to a local variable, and the function explicitly handles the PARENT_SCOPE assignment.
* Fix Release Progress badges and workflow
- Fix update-progress.py to output blocker/mustdo counts in correct format
The workflow expects blocker_done=, blocker_total=, mustdo_done=, mustdo_total=
output lines but the script was only outputting human-readable format
- Update README badge links to point to project view 24 instead of base project
This fixes the workflow failures where BLOCKER_DONE and the related environment
variables were not being set, causing badge updates to fail.
The badges were pointing to old unmaintained gists under user X.
Updated to use the gist automatically maintained by the Release Progress
workflow (gist ID: 0ad2eabb63b28eb90d69f5e5b2c1496f).
The workflow now successfully updates these badges every 4 hours with
current release blocker and must-do progress.
The script now auto-detects the HDF5 version from src/H5public.h and
filters release blockers/must-do items by milestone matching that version.
Changes:
- Added get_hdf5_version_from_header() to read version from H5public.h
- Updated GraphQL query to fetch milestone information from issues
- Added milestone filtering logic to only count items for the target release
- Made validation more lenient when using milestone filter (allows 0/0)
- Added MILESTONE_FILTER environment variable for manual override
For develop branch with version 2.1.0 in H5public.h, this will now only
count items with milestone containing "2.1" (e.g., "2.1.0", "HDF5 2.1").
* Add version number to badge labels
The badges now display the version (e.g., "2.1 Release Blockers" instead
of just "Release Blockers") when filtering by milestone.
Changes:
- Python script outputs version to GitHub Actions
- Workflow passes version to badge generation script
- Badge script includes version in label if available
- Labels show "X.Y Release Blockers" / "X.Y Release Must Do"
The three badges now track:
1. Release Blockers - Critical issues that must be resolved
2. Release Must Do - Important items for the release
3. Release Nice to Have - Optional improvements for the release
All three badges show version prefix (e.g., "2.1") and support 0/0
display when no items exist for a milestone.
---------
Co-authored-by: Claude Sonnet 4.5 <noreply@anthropic.com>
- Fix update-progress.py to output blocker/mustdo counts in correct format
The workflow expects blocker_done=, blocker_total=, mustdo_done=, mustdo_total=
output lines but the script was only outputting human-readable format
- Update README badge links to point to project view 24 instead of base project
This fixes the workflow failures where BLOCKER_DONE and related environment
variables were not being set, causing badge updates to fail.
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.
* switched from always verbose ctest output to ONLY on test failures
* Windows and macOS builds will skip clang-format check before building documentation
* resolved Doxygen warnings by adding H5G_link_t=H5L_type_t to the DOXYGEN_PREDEFINED list, by adding the macro definition, Doxygen now knows to treat H5G_link_t as H5L_type_
Adds CodeQL workflow for C/C++ analysis with scheduled, manual, and branch-specific triggers, including dependency setup, HDF5 configuration, and SARIF handling.
* fixes the GitHub Actions CPack failure on macOS
* Disables Spotlight indexing which can interfere with disk image operations
* Implements retry logic (waits 5 seconds and retries once if CPack fails)
* Add Fortran wrappers for H5Fstart_swmr_write, H5Dflush, and H5P{set,get}_append_flush
* corrected C doxygen docs for H5Pget_append_flush, clarified Fortran
Adds H5FDsubfiling_get_file_mapping() API to map logical HDF5 files to physical subfiles, with Fortran support and comprehensive testing.
Adds H5FDsubfiling_get_file_mapping() in H5FDsubfiling.c to retrieve subfile paths for a logical HDF5 file.
Updates Fortran interface in H5VFDff.F90 to include h5fdsubfiling_get_file_mapping_f().
Updates h5fuse.in to support a list of subfiles for processing with a new -l option.
* Fixed the link checker error where table headers
contained (\# of rows) and (\# of columns) with escaped hash symbols that Doxygen was
incorrectly interpreting as malformed links.
This PR implements an automated release progress monitoring system for the HDF5 project. The changes add a dynamic badge to the README that tracks completion of release-blocking issues from GitHub Project #39, addressing issue #5742. The implementation consists of three components:
- Python script (update-progress.py) that uses GitHub's GraphQL API to query project items, filter for 'Release_Blocker' items, and calculate completion percentage
- GitHub Actions workflow (update-progress.yml) that runs the script every 24 hours, generates badge data, and publishes it via GitHub Gist
- README updates that remove tentative release language and add the new progress badge with color-coded status indicators
The system replaces static release information with real-time progress tracking, providing better transparency into HDF5's feature-driven release process. The badge displays progress percentages with green (90%+), yellow (60-79%), orange (40-59%), and red (<40%) color coding.
* updated the complex datatype information and examples for F2003, HELP-2755
* updated derived types for Fortran 2003, uses doxygen awesome tabs feature
* 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
* point to HDFGroup repository
* updated checkout locations
* Fix incorrect and dead documentation link in
release_docs/RELEASE_PROCESS.md.
---------
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
- Add Fortran H5R APIs:
h5rcreate_attr_f, h5rcreate_object_f, h5rcreate_region_f,
h5ropen_attr_f, h5ropen_object_f, h5ropen_region_f,
h5rget_file_name_f, h5rget_attr_name_f, h5rget_obj_name_f,
h5rcopy_f, h5requal_f, h5rdestroy_f, h5rget_type_f
- Fixed function H5Requal actually to compare the reference pointers
Fixed an issue with H5Requal always returning true because the
function was only comparing the ref2_ptr to itself.
* changed to if string contains instead
* return status of VFDs in libhdf5.settings
* use *_ENABLE_* settings instead to report the state
* added map state
* updated resetting status if cmake option fails
* addressed issue wit promoted integers and reals
* fixed h5fcreate_f
* added option to use mpi_f08
* change the kind of logical in the parallel tests
* addressed missing return value from callback
Scot Breitenfeld
