* 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
Link checker can't access the acm url, hence will fail. The change in
this PR is a workaround to provide the url but prevent the link checker
from accessing it. Please do not add https://.
Fix issue where chunked datasets could get setup with an incorrect
chunking index type in parallel HDF5
Fix issue where metadata cache images with an undefined address
and size of 0 couldn't be properly decoded
Fix issue where a flag in H5Cimage.c wasn't getting set correctly
for release builds of the library, leading to incorrect error
checking when reconstructing metadata cache entries
During file creation, the direct I/O VFD only checked data alignment
requirements for writes and assumed they were the same for reads.
Checks are now performed separately for writes and reads. In order
to avoid EINVAL errors, the VFD is also now slightly more conservative
about when it tries to avoid performing extra work when data alignment
isn't required.
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.
Before this, error on install when using HDF5 via FetchContent
as CMAKE_SOURCE_DIR pointed to parent project
Co-authored-by: scivision <scivision@users.noreply.github.com>
* 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
* Add 2.1.0 CHANGELOG to HISTORY-2.X.md.
Set release default to draft.
* Updated CHANGELOG.md Executive Summary "Important" section similar to
that in HDF5 2.1.0 release.
* Generate "Extra libraries" in `libhdf5.settings` using a new variable `LINK_LIBS_SETTINGS` rather than `LINK_LIBS`
* Follow up to #6220
* Try to deal with Windows MSVC
* Re-write zlib/szip CMake logic for clarity
* Update external libaec, zlib-ng and zlib builds to not use patching process
* Add FindZLIBNG module to locate zlib-ng on system
* Rework HDF5 filter plugins support
Improve performance of H5Ovisit (and H5Ocopy, and functions that
retrieve and object name) by passing more information about the visited
object from the underlying H5G_visit routine to these callbacks.
Introduced an internal object callback for H5G_visit to facilitate this.
H5Ovisit1 and potentially H5Ovisit2 are still slow with deeply nested
groups due to the way these deprecated functions interact with the VOL
layer.
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.
Provided a link back to The HDF Group's consulting and contact us pages, added a link for the forum post reference, and added U.S. in the NSF acknowledgement text.
* 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
H. Joe Lee
Scot Breitenfeld
jhendersonHDF
vchoi-hdfgroup
bmribler
Aleksandar Jelenak
scivisionandscivision
Gerd Heber
Larry Knox
SY Wang
Neil Fortner
phfix
Alex Dutka
dependabot[bot]
Lori Cooper