When using the '-s' (h5ls) or '-r' (h5dump) option to display 1-byte integer datasets and attributes as ASCII characters, a closing double-quote character for data values was dropped in some cases.
* Updated h5dump --xml
The location of the files HDF5-File.xsd and HDF5-File.dtd no longer exists, and
the files were added to the repo (PR #5490). Before the --xml is actually removed,
running the h5dump tests will fail. This PR updated h5dump and the expected output
to use the correct files' location and actually completed the ticket HELP-2668.
* Added missing expected files from the previous commit
* Fixed typo
* Made corrections per review feedbacks
* Committing clang-format changes
* Missing files from previous commit
* Use valid URL for xmlns
---------
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
feat: add optional digital signature verification for HDF5 filter plugins
Introduce an opt-in plugin signing and verification system that allows
HDF5 deployments to require cryptographically signed filter plugins before
loading them. Disabled by default (HDF5_REQUIRE_SIGNED_PLUGINS=OFF).
New tool: h5sign
- Signs plugin shared libraries by appending an RSA signature and a
14-byte footer (algo_id | sig_len | 8-byte magic | format_ver) to the
binary without modifying the original content.
- Supports SHA-512 (default), SHA-256, SHA-384, and their PSS variants
(-a/--algorithm flag).
- Detects already-signed plugins; --force strips the old signature and
re-signs.
- Security hardened: keeps the file descriptor open through hashing and
appending (no TOCTOU window), enforces a 2048-bit minimum RSA key size,
rolls back partial writes on failure, and rejects paths that are not
regular files.
Verification (H5PLsig.c)
- At plugin load time, reads the footer, validates the magic and format
version, then checks the RSA signature against all public keys found in
the KeyStore directory.
- File is hashed once; per-key verification operates on the pre-computed
digest (no redundant I/O for multi-key keystores).
- Plugins whose signature hash appears in revoked_signatures.txt are
rejected regardless of key validity.
- Runtime debug output via HDF5_DEBUG=pl.
KeyStore management
- Trusted public keys are PEM files in a directory specified by
HDF5_PLUGIN_KEYSTORE_DIR (build time) or HDF5_PLUGIN_KEYSTORE (env var).
- HDF5_LOCK_PLUGIN_KEYSTORE cmake option disables the env-var override for
security-hardened deployments.
Test infrastructure
- h5signverifytest: positive, negative, tamper, re-sign, and revocation
test cases.
- CTest fixture-based dependency graph (FIXTURES_SETUP/FIXTURES_REQUIRED)
replaces fragile DEPENDS chains so tests remain correct under -R filtering.
- Dedicated signed-plugins.yml CI workflow; full test suite scoped to
H5SIGN and H5PLUGIN-signature tests to avoid unrelated flaky failures.
- Cross-platform: Linux, macOS, and Windows (MSVC-compatible, BIO-based
OpenSSL I/O, HDsleep/HDsetenv portability wrappers).
Documentation: docs/PLUGIN_SIGNATURE_README.md covers usage, footer
format, revocation file format, FAQ, and troubleshooting.
Co-authored-by: Glenn Song <gsong@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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.
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
Adds predefined datatypes for FP8 data in E4M3 and E5M2 formats
Does not add support for any native FP8 types; datatype conversions are performed in software
Ensure proper closure of resources in gent_array1_big, gent_nested_compound_dt, and gent_intscalars in h5dumpgentest.c.
Add error handling and cleanup logic to prevent resource leaks.
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.
Add VOL tests for h5dump, update test generation logic, and modify test configurations.
Tests:
Add VOL tests for h5dump in CMakeTests.cmake and CMakeTestsXML.cmake.
Modify ADD_H5_TEST macro to support VOL-specific tests and filtering.
Add gent_tvms() function in h5dumpgentest.c and h5dumpgentest.h for generating test files.
Adds predefined datatypes for little- and big-endian bfloat16 data
Does not add support for any native bfloat16 types; datatype conversions are performed in software
Also adds missing float16 predefined types to fortran
The trefer_extR test depends upon this pair of files, but always uses the pre-generated ones checked into the repo. This adds a routine to generate them, which will soon be used by the h5dump VOL tests.
Adds workflow to build ROS3 VFD and optionally build aws-c-s3 library
from source or use package managers
Adds testing of ROS3 VFD with s3proxy and docker
Adds new H5Pset_fapl_ros3_endpoint()/H5Pget_fapl_ros3_endpoint() API
functions to set/get an alternative endpoint URL to use when opening
files with the ROS3 VFD
Cleans up warnings in tools and tests related to ROS3 VFD structure size
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
* Re-write ROS3 VFD S3 backend to use AWS' C S3 library
Replaces the ROS3 VFD's libcurl-based S3 backend with a new
backend which uses the aws-c-s3 library
Adds support for sourcing credentials from standard AWS
configuration files, environment variables, etc. with a
fallback to anonymous credentials when credentials can't be
found
Adds support for sourcing AWS region from standard AWS
configuration files and environment variables
Adds support for new environment variables HDF5_ROS3_VFD_DEBUG,
HDF5_ROS3_VFD_LOG_LEVEL and HDF5_ROS3_VFD_LOG_FILE for debugging
purposes
Replaces function to load testing credentials in the ros3.c and
s3comms.c tests with new function that delegates to the aws-c-s3
library for better compatibility with standard AWS configuration
files and environment variables
Adds support for s3:// object URIs
Adds HTTP User-Agent header in form of
'libhdf5/<hdf5_version> (vfd:ros3) libaws-c-s3'
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
* Add header files for tool gentest scripts
* Correct library type for core targets
* Use EXIT_SUCCESS/EXIT_FAILURE on script exit
* Remove h5clear from merged script
* Include gentest header
* Add udfilter files to h5copy gen func
* Add nerror returns to main generator functions
* Move defines to tool headers
* Add copyright header
Build test generator programs against shared libraries, if available,
by default. Otherwise, build them against static libraries. If
HDF5_BUILD_STATIC_TOOLS is set to ON, the tools test generator
programs will be built against static libraries even if shared
libraries are available.
* Fix error in H5Ddebug(). Add h5ls test cases.
* Committing clang-format changes
* Fix cmake (hopefully)
* Fix cmake again (hopefully)
* Fix issue with modification times showing up differently on different
systems. Add test case for v1 b-trees.
* Add cmake for new tests
* Add RELEASE.txt entry
---------
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Implement support for complex number datatypes
Adds the new datatype class H5T_COMPLEX
Adds the new API function H5Tcomplex_create which creates a complex
number datatype from an ID of a base floating-point datatype
Adds the new feature check macros H5_HAVE_COMPLEX_NUMBERS and
H5_HAVE_C99_COMPLEX_NUMBERS
Adds the new datatype size macros H5_SIZEOF_FLOAT_COMPLEX,
H5_SIZEOF_DOUBLE_COMPLEX and H5_SIZEOF_LONG_DOUBLE_COMPLEX
Adds the new datatype ID macros H5T_NATIVE_FLOAT_COMPLEX,
H5T_NATIVE_DOUBLE_COMPLEX, H5T_NATIVE_LDOUBLE_COMPLEX,
H5T_CPLX_IEEE_F16LE, H5T_CPLX_IEEE_F16BE,
H5T_CPLX_IEEE_F32LE, H5T_CPLX_IEEE_F32BE,
H5T_CPLX_IEEE_F64LE and H5T_CPLX_IEEE_F64BE
Adds hard and soft datatype conversion paths between complex number
datatypes and all the integer and floating-point datatypes, as well as
between other complex number datatypes
Adds a special conversion path between complex number datatypes and
array or compound datatypes where the in-memory layout of data is the
same between the datatypes and data can be converted directly
Adds support for complex number datatypes to the h5dump, h5ls and
h5diff/ph5diff tools. Allows h5dump '-m' option to change floating-point
printing format for float complex and double complex datatypes, as well
as long double complex if it has the same size as double complex
Adds minimal support to the h5watch and h5import tools
Adds support for the predefined complex number datatypes and
H5Tcomplex_create function to the Java wrappers. Also adds initial,
untested support to the JNI for future use with HDFView
Adds support for just the H5T_COMPLEX datatype class to the Fortran
wrappers
Adds support for the predefined complex number datatypes and
H5Tcomplex_create function to the high level library H5LT interface
for use with the H5LTtext_to_dtype and H5LTdtype_to_text functions
Changes some usages of "complex" in the library since it conflicts with
the "complex" keyword from the complex.h header. Also changes various
usages of the word "complex" throughout the library to distinguish
compound datatypes from complex datatypes.
gcc 14 identifies likely places where the sizeof() call is used
for the first parameter to calloc(). This PR fixes the remaining
places in the library where this occurs and reworks a few other
allocations to be more uniform.
This is where most people will expect to find license information. The
COPYING_LBNL_HDF5 file has also been renamed to LICENSE_LBNL_HDF5.
The licenses are unchanged.
* Fix for github issue #3790: infinite loop closing library
Cause of the problem:
When h5dump tries to open the user provided test file, the metadata cache will
call the "get_final_load_size" callback to find out the actual size of the
the root object header. The callback function will call
H5O__prefix_deserialize() to allocate space for the object header
data structure (via H5FL_CALLOC) and to deserialize the object header prefix
in order to find the actual size of the object header.
The metadata cache will then check whether the actual size obtained
will exceed the file's EOA.
Since the actual size obtained from the test file exceeds the EOA,
the metadata cache throws an error and return.
However, the oh structure that was allocated in H5O__prefix_deserialize()
was not freed and hence causing the problem described in this issue.
Fix:
1) Deallocate the oh structure after obtaining and saving the needed
information in udata which will be used later on in the "verify_chksum" callback.
2) Deserialize the object header prefix in the "object header's
"deserialize" callback regardless. The original coding intends to keep the
deserialized prefix so that the object header's "deserialize" callback
does not need to deserialize the prefix again if the object header is coming
through the "get_final_load_size" callback.
jhendersonHDF
scivisionandscivision
Julien Schueller
Matt L
Allen Byrne
Aleksandar Jelenak
Neil Fortnerandgithub-actions
Dana Robinson
vchoi-hdfgroup