H5R Fortran wrappers and misc. H5R API/DOC updates #4446
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brtnfld
requested review from
derobins,
epourmal,
lrknox,
byrnHDF,
fortnern,
jhendersonHDF,
qkoziol,
vchoi-hdfgroup,
bmribler,
glennsong09 and
mattjala
as code owners
brtnfld
added
Merge - To 1.14
Priority - 0. Blocker ⛔
brtnfld
added
Component - C Library
src/H5Rpublic.h
Outdated
| @@ -524,7 +532,8 @@ H5_DLL herr_t H5Rget_obj_type3(H5R_ref_t *ref_ptr, hid_t rapl_id, H5O_type_t *ob | |||
| * application. If the length of the name, which determines | |||
| * the required value of size, is unknown, a preliminary | |||
| * H5Rget_file_name() call can be made. The return value of this | |||
| * call will be the size of the file name. That value can then be | |||
| * call will be the size of the file name (the size does not include | |||
| * the \p NULL terminator). That value can then be | |||
| * passed in for size in the second call to H5Rget_file_name(), | |||
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Maybe clarify here for each of these that the return value can't be directly passed in since it doesn't include the NUL terminator. I think some of the other docs say something similar to "that size + 1"
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Ok, I just copied the text from H5Rget_name. We also seem to mix "NULL" with \0 string in the docs. Some other functions don't call out if size includes this at all. Is there a particular description from another API that you prefer? It should probably mention when NULL is passed in as name.
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nvm, I think I found an example from H5P. Since this is a common case, I will create a doxygen ALIAS.
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added alias for doxygen.
byrnHDF
approved these changes
Apr 29, 2024
epourmal
approved these changes
May 1, 2024
lrknox
pushed a commit
to lrknox/hdf5
that referenced
this pull request
May 7, 2024
- 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.
lrknox
added a commit
that referenced
this pull request
May 7, 2024
* Split H5Tconv.c into modules by type (#4393) * Split H5Tconv.c into modules by type * Add new H5Tconv headers to list of private headers * Fix broken links in VOL API table (#4438) * Don't print thread ID when the library isn't multithreaded. (#4428) Corresponding changes to make error output for regression tests agnostic to thread setting. Signed-off-by: Quincey Koziol <[email protected]> * Start refactoring H5E code to avoid using IDs internally (#4427) * Add support for builtin_expect compiler hint (#4425) * Add support for __builtin_expect extension And H5_LIKELY / H5_UNLIKELY macros to wrap it Signed-off-by: Quincey Koziol <[email protected]> * Committing clang-format changes --------- Signed-off-by: Quincey Koziol <[email protected]> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * sanitizer flags need set before compiler flags (#4444) * Add navigate chapters and use release_docs in Learn Basics (#4441) * Fix for github issue #3790: infinite loop closing library (#4445) * 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. * H5R Fortran wrappers and misc. H5R API/DOC updates (#4446) - 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. * Fix heap-buffer-overflow in H5Fio.c (#4450) The buffer size for checksum was smaller than H5_SIZEOF_CHKSUM, causing an overflow while calculating the offset to the checksum in the buffer. A check was added so H5F_get_checksums would fail appropriately in all of its occurrences. Fix gh-4434 * Fix grammar in VOL guide (#4452) * Fix bug in MPI-IO VFD (#4456) Corrects incorrect usage of the vector_was_sorted parameter in H5FD__mpio_vector_build_types() * Bump the github-actions group with 3 updates (#4455) Bumps the github-actions group with 3 updates: [actions/download-artifact](https://github.com/actions/download-artifact), [peaceiris/actions-gh-pages](https://github.com/peaceiris/actions-gh-pages) and [github/codeql-action](https://github.com/github/codeql-action). Updates `actions/download-artifact` from 4.1.4 to 4.1.7 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](actions/download-artifact@c850b93...65a9edc) Updates `peaceiris/actions-gh-pages` from 3.9.3 to 4.0.0 - [Release notes](https://github.com/peaceiris/actions-gh-pages/releases) - [Changelog](https://github.com/peaceiris/actions-gh-pages/blob/main/CHANGELOG.md) - [Commits](peaceiris/actions-gh-pages@373f7f2...4f9cc66) Updates `github/codeql-action` from 3.24.9 to 3.25.3 - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@1b1aada...d39d31e) --- updated-dependencies: - dependency-name: actions/download-artifact dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions - dependency-name: peaceiris/actions-gh-pages dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-minor dependency-group: github-actions ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Fixed failures with xl compilers. (#4458) * type cast constant * fixed return types * Convert ERR test to use grep (#4451) * Convert ERR test to use grep * Eliminate use of .err files in CMake * Show error output if grep fails * Turn off cuda in NVHPC CI * Removed "function/code stack" debugging configure option (#4454) Easily replaced w/third-party tools, e.g. libbacktrace (https://github.com/ianlancetaylor/libbacktrace) * Clean up memory leaks in t_vfd (#4457) * Fixes and cleanup for ph5diff (#4460) * Fixes and cleanup for ph5diff Fixes concurrency issues in ph5diff that can cause interleaved output Fixes an issue where output can sometimes be dropped if it ended up in ph5diff's output overflow file Fixes an issue where MPI_Init is called after HDF5 has been initialized, preventing the library from setting up an MPI attribute to perform cleanup on MPI_Finalize Fixes an issue in config/cmake/runTest.cmake where the CMake logic would try to access an invalid list index if the number of lines in a test's output and reference files don't match * Add release note * Remove use of err files in autotools test scripts (#4461) * Fix typo in H5Rget_obj_type (#4463) Issue GH-1723 * Use ADD_H5_ERR_TEST to not compare output (#4464)
byrnHDF
pushed a commit
to byrnHDF/hdf5
that referenced
this pull request
May 14, 2024
- 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.
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Added missing newest reference 3 H5R APIs, fixed C H5R issue and added test and doc updates related to H5R.
Please take a look at Release.txt updates for details.