* Enable data sieving for chunks that can't be cached
Fixed an issue that prevented use of a data sieve buffer for I/O on dataset
chunks when those chunks couldn't be cached by the library. This issue
could result in worst-case behavior of I/O on a single data element at a
time when chunks are non-contiguous with respect to memory layout.
Added a test to attempt to catch performance regressions in I/O on dataset
chunks that are non-contiguous with respect to memory layout
Updated the External File List logic to set the data sieve buffer size to
the smaller of the dataset size and the size set in the FAPL, similar to
the logic elsewhere in the library
* 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.
Removed code to set JAVA_HOME to a specific directory, which seemed to cause a conflict between the Java version used to compile and the runtime Java version.
It is considered best practice for cmake package configuration files to use "find_dependency" instead of "find_package".
This is because it can propagate flags properly, gives more clear error messages and is able to avoid duplicate dependency include issues.
This change fixes an issue I am seeing in some external cmake projects when including hdf5. As per issue report here https://github.com/HDFGroup/hdf5/issues/6107
* 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.
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
Setup:
Add JDK 21 setup using actions/setup-java@v5 in arm-main.yml for Windows 11 ARM.
CMake Configuration:
Enable Java build with -DHDF5_BUILD_JAVA=ON in arm-main.yml for Windows 11 ARM.
Fixed#5677
Corrects error return values from 0 to FAIL in H5Z__scaleoffset_decompress_one_byte(), H5Z__scaleoffset_decompress_one_atomic(), and H5Z__scaleoffset_decompress() in H5Zscaleoffset.c
A malformed file can cause the scale-offset filter to have too little input data causing a heap buffer overflow. Additional checks on the maximum buffer length are required during the decompression.
This PR fixes CVE-2025-2308.
A malformed file can trigger bit field type conversions that can (due to missing boundary checks in the conversion step) cause a heap buffer overflow. This PR adds a check on the defined conversion to ensure it does not read beyond the size of a single bit field element. Thus, H5T__bit_copy does not result in a buffer overflow. There are several other calls to H5T__bit_copy which might be subject to a similar issue.
This PR fixes CVE-2025-2309.
Fix zero-element read failure in H5D__virtual_read() and H5D__virtual_write() in H5Dvirtual.c by skipping H5S_SELECT_BOUNDS if nelmts is 0.
Add test_vds_empty_slice() in rtree.c to verify zero-element read behavior on virtual datasets with r-trees.
* 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)
jhendersonHDF
Scot BreitenfeldandClaude Sonnet 4.5
bmribler
efferre79
H. Joe Lee
Larry Knox
dependabot[bot]
malcolm-vivosa
christian-wojek
William Allen
Matt L
Gerd Heber
Neil Fortner