* Various improvement in documentation and a decoding function
- Improves documentation on the type size when creating/accessing a compound datatype with no predefined struct (GH issue #5371)
- Provides better description of the min_meta_perc and min_raw_perc arguments in the H5Pset_page_buffer_size() (GH issue #5711)
- Adds error checkings to an internal decoding function
* Corrected the checks, the base address equals the end-of-file is valid.
* Skip for multi-file and split drivers when validating addresses against stored_eof
* Committing clang-format changes
* Remove incorrect name
* Fix typos
* Modified description of type_size arguments
* Used a more robust condition when checking EOF
* Corrected incorrect conflict resolving
* Update src/H5Fsuper_cache.c
Co-authored-by: Neil Fortner <fortnern@gmail.com>
* Update src/H5Fsuper_cache.c
Co-authored-by: Neil Fortner <fortnern@gmail.com>
* Committing clang-format changes
* Modified per feedbacks.
* Fix comparison per feedbacks
* Omit unused parameter name in a catch block
---------
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Neil Fortner <fortnern@gmail.com>
* Fix memory safety vulnerabilities in high-level and VFD code
H5FDstdio (src/H5FDstdio.c):
- Fix five error paths in H5FD_stdio_open() that called fclose(f) after
free(file): the correct resource to close is file->fp. Reorder to
fclose before free to match standard cleanup idiom and prevent file
descriptor leaks under memory-pressure failures.
H5VLnative (src/H5VLnative.c):
- Add assert(obj) and assert(file) to H5VL_native_get_file_struct() to
catch NULL-pointer programming errors early in debug builds.
H5LT (hl/src/H5LT.c):
- Add NULL check after strdup() in H5LTtext_to_dtype(); push H5E_NOSPACE
so the HDF5 error stack is populated on OOM.
- Fix H5Tclose(super) leak in H5T_ENUM, H5T_VLEN, H5T_ARRAY, H5T_COMPLEX
branches of H5LT_dtype_to_text(): super was only closed on the success
path; any failure between H5Tget_super and the final realloc_and_append
leaked the type ID. Super is now closed immediately after use.
- Refactor the repeated "get super-type text and append" pattern (four
near-identical ~15-line blocks) into static helper append_dtype_super_text().
Pushes H5E_NOSPACE on internal calloc failure.
- Rewrite realloc_and_append() doc comment to document the asymmetric
ownership contract (callee frees buf on realloc failure in
library-managed mode; no free in user-buf mode).
- Move the buf == NULL guard to before the _no_user_buf branch so both
modes short-circuit identically.
H5TB (hl/src/H5TB.c):
- Clarify H5TBget_field_info() else-branch comment: the two-branch copy
structure is an efficiency optimization (copy name_len+1 bytes rather
than HLTB_MAX_FIELD_LEN-1), not a backward-compatibility concern.
CHANGELOG (release_docs/CHANGELOG.md):
- Add entries for the stdio VFD leak fix, VOL NULL checks, and H5LT
memory-safety improvements.
* HL: add realloc_and_append invariant comments per fortnern review
Document the failure-path contract for realloc_and_append: buf is
passed by value so the caller's pointer is never written by the
function; failure is signaled solely through a NULL return; in
library-managed mode the underlying memory is freed on failure so
callers must not access the original pointer afterward.
Also annotate the point after a successful realloc where the
function can no longer fail.
* HL: reposition 'cannot fail' comment before buf assignment
The comment should mark the transition out of the failure zone —
after the only exit path (goto out), before buf = tmp_realloc.
Also drop the redundant else since the if body always exits.
* HL: fix nested comment syntax error in realloc_and_append Note
All #cmakedefine01 CMAKE_H5_* blocks used a five-line pattern:
#cmakedefine01 CMAKE_H5_HAVE_FOO
#if CMAKE_H5_HAVE_FOO == 0
#undef H5_HAVE_FOO
#else
#define H5_HAVE_FOO
#endif
This is exactly what #cmakedefine H5_HAVE_FOO does: it emits
#define H5_HAVE_FOO (no value) when the CMake variable is truthy and
/* #undef H5_HAVE_FOO */ when falsy. The CMAKE_H5_* intermediate
variables in fortran/src/CMakeLists.txt were only needed to feed these
blocks and are no longer required.
Replace all such blocks with #cmakedefine H5_HAVE_FOO, using the H5_*
variable directly. MPI_LOGICAL_KIND retains its value via
#cmakedefine H5_MPI_LOGICAL_KIND @H5_MPI_LOGICAL_KIND@.
This also fixes a real bug: H5_FORTRAN_C_BOOL_IS_UNIQUE was emitted as
#define H5_FORTRAN_C_BOOL_IS_UNIQUE 0 when C_BOOL and default LOGICAL
are the same kind (e.g. Apple PowerPC ABI). #ifdef only tests whether
a macro is defined, not its value, so the guard in H5_test_buildiface.F90
was always true and verify_c_bool was written into tf_gen.F90 regardless,
causing an "Ambiguous interfaces" build failure on that platform.
- H5TB: strcmp replaces strncmp in H5TBfind_field so that field names
that are a prefix of a requested name (or vice-versa) are no longer
matched. HLTB_MAX_FIELD_LEN (255) is now public in H5TBpublic.h and
exposed to Fortran as HLTB_MAX_FIELD_LEN_F in H5TBff.F90.
H5TBget_field_info documents the buffer-size requirement and truncation
behaviour. H5TBget_field_info guards against overflow on long names.
- H5IM: H5IMis_image and H5IMis_palette refactored into a shared helper
(H5IM__class_attr_equals). The helper now reads both fixed-length and
variable-length CLASS string attributes, using H5Treclaim for VL memory.
strcmp replaces strncmp for exact-match semantics.
- H5DS: H5DSis_scale and H5DS_is_reserved both support variable-length
CLASS string attributes via H5Aget_space/H5Aread/H5Treclaim. The
fixed-length path retains the 16-byte size guard. strcmp is used
throughout for exact comparison.
- Tests: new test functions test_is_scale_class_prefix,
test_is_reserved_class_prefix, and test_class_prefix cover fixed-length
prefix/exact/wrong-value cases and variable-length string cases.
test_table.c adds write and read field-name prefix rejection cases and
boundary-length truncation verification. All malloc calls are NULL-checked.
- CHANGELOG updated with a summary of all fixes.
* 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
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.
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.
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
* 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 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
Change default file format to 1.8 across various tests and examples, updating file creation and access logic accordingly.
Behavior:
Default file format version changed to 1.8 in H5Pfapl.c.
Updated file creation and access to use 1.8 format in h5ex_g_compact.c and test_file_image.c.
Set earliest file format in multiple test files including cache_tagging.c, dtypes.c, and links.c.
Tests:
Modified expected output in tools/test/misc/expected/*.ls files to reflect new file format locations.
Adjusted test logic in test_file_image.c and cache_tagging.c to accommodate format changes.
Misc:
Added comments and TODOs for future format testing in test_file_image.c.
Minor variable renaming for clarity in test_file_image.c.
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.
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
* Remove hbool_t from the public API
This was previously removed from the source code, but the API calls
retained hbool_t in the public API calls. This commit removes
hbool_t from the public APIs.
hbool_t is retained as a typedef for bool in H5public.h so existing
code doesn't break.
Implemented missing --help/-h, -c, -echo and -shlib/-noshlib options
Added new -nohl option to avoid building and linking against
high-level HDF5 libraries if desired
Implemented adding of HDF5 installation library directory to rpath of
resulting executable/library and added new -norpath option to avoid
this behavior if desired
Added parsing of HDF5_USE_SHLIB environment variable to determine
whether to link against shared or static HDF5 libraries
Added parsing of HDF5_PKG_CONFIG_ARGS environment variable to separate
pkg-config-specific options from compiler-specific options and prevent
conflicts
* Refactor warning macros
Replaces the scheme in H5warnings.h with a more compiler-agnostic
one that relocates ifdef complexity to the warnings header file
and uses better naming.
---------
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Simplify H5api_adpt.h
This change also uses the shared markup (e.g., __declspec) in both
static and shared libraries as the shared markup is ignored when
building static libs.
* Renamed some API decorations
Some API decorations (used to hide __declspec on Windows, among other
things) have been renamed:
H5_DLLCPP(VAR) --> H5CPP_DLL(VAR)
H5_HLDLL(VAR) --> H5HL_DLL(VAR)
H5_HLCPPDLL(VAR) --> H5CPP_HL_DLL(VAR)
H5_FCDLL(VAR) --> H5FC_DLL(VAR)
H5_FCTESTDLL(VAR) --> H5FC_TEST_DLL(VAR)
HDF5_HL_F90CSTUBDLL(VAR) --> H5FC_HL_DLL(VAR)
The shared library decorations are also now used when building static
libraries (where they are meaningless and ignored).
* h5cc: Allow overriding the compilers written into the file
Add a set of `HDF5_H5CC_C_COMPILER`, `HDF5_H5CC_CXX_COMPILER`
and `HDF5_H5CC_Fortran_COMPILER` CMake variables that can be used to
override the compiler string written into `h5cc`, `h5c++`, etc. This is
particularly useful when e.g. using ccache during the build,
as the ccache path otherwise ends up in `h5cc`.
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.
The hash_size parameter of H5Iregister_type() hasn't been used since 1.8.
It's been removed and the API call has been versioned.
This PR also updates the make_vers script to handle v2.0.0.
Fixes#4344
Scot Breitenfeld
jhendersonHDF
Julien Schueller
efferre79
Allen Byrne
Dana Robinson
Matt L
Michał Górny
H. Joe Lee