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hdf5_1_14
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Larry Knox a3545767b4 Sync develop changes April 22 - May 7 to hdf5_1_14 (#4465) 
* 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 <quincey@koziol.cc>

* 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 <quincey@koziol.cc>

* Committing clang-format changes

---------

Signed-off-by: Quincey Koziol <quincey@koziol.cc>
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](https://github.com/actions/download-artifact/compare/c850b930e6ba138125429b7e5c93fc707a7f8427...65a9edc5881444af0b9093a5e628f2fe47ea3b2e)

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](https://github.com/peaceiris/actions-gh-pages/compare/373f7f263a76c20808c831209c920827a82a2847...4f9cc6602d3f66b9c108549d475ec49e8ef4d45e)

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](https://github.com/github/codeql-action/compare/1b1aada464948af03b950897e5eb522f92603cc2...d39d31e687223d841ef683f52467bd88e9b21c14)

---
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] <support@github.com>
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)
2024-05-07 15:55:06 -05:00

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examples/h5_vds-exclim.c -text
examples/h5_vds-percival-unlim-maxmin.c -text
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examples/h5_vds-simpleIO.c -text
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fortran/src/H5_buildiface.F90 -text
fortran/src/H5config_f.inc.cmake -text
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fortran/test/H5_test_buildiface.F90 -text
hl/fortran/src/H5HL_buildiface.F90 -text
hl/fortran/src/hdf5_hl_fortrandll.def.in -text
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hl/tools/gif2h5/CMakeLists.txt -text
hl/tools/gif2h5/CMakeTests.cmake -text
hl/tools/gif2h5/testfiles/README -text
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java/examples/testfiles/examples.datasets.H5Ex_D_FillValue.txt -text
java/examples/testfiles/examples.datasets.H5Ex_D_Gzip.txt -text
java/examples/testfiles/examples.datasets.H5Ex_D_Hyperslab.txt -text
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java/examples/testfiles/examples.datasets.H5Ex_D_Szip.txt -text
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java/examples/testfiles/examples.groups.H5Ex_G_Visit.txt -text
java/examples/testfiles/examples.intro.H5_CreateAttribute.txt -text
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