Cherry-pick 12 develop branch PRs to hdf5_1_12 (#622)

* Snapshot version 1.12 release 1-3.  Update  version to 1.12.1-4.

* First cut of the H5 public API documentation. (#80)

* First cut of the H5 public API documentation.

* Added H5Z "bonus track."

* Applied Quincey's patch.

* Added the missing patches from Quincey's original patch.

* H5PL (complete) and basic H5VL API documentation.

* Added H5I API docs.

* Added H5L API docs.

* First installment from Elena's H5T batch.

* Second installment of Elena's H5T batch.

* Final installment of Elena's H5T batch.

* Full set of current H5F documentation. (#105)

* First cut of the H5 public API documentation.

* Added H5Z "bonus track."

* Applied Quincey's patch.

* Added the missing patches from Quincey's original patch.

* H5PL (complete) and basic H5VL API documentation.

* Added H5I API docs.

* Added H5L API docs.

* First installment from Elena's H5T batch.

* Second installment of Elena's H5T batch.

* Final installment of Elena's H5T batch.

* Migrated documentation for SWMR functions.

* Catching up on MDC functions.

* Integrated the H5F MDC function documentation.

* Added MDC and parallel H5F functions.

* Slightly updated main page.

* Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST.

* Doxygen - added (mostly) beginner functions (#112)

* Doxygen - added (mostly) beginner functions

* Removed duplicate H5Pset_szip function

* Add src/H5module.h to MANIFEST.

* close #195. (#196)

* Update HDF5PluginMacros.cmake

* Update HDF5PluginMacros.cmake

* Avoid aligned access for references by decoding into temporary buffer and then copying the result into the actual buffer.   Update test to be more thorough with using compound datatype fields everywhere. (#206)

* Modify temporary rpath for testing in java example scripts. (#230)

* Fix undefined left shifting of negative numbers (#338)

Undefined Bahavior Sanitizer errored here about left shifting negative numbers.

* Fixes various warnings noticed on Windows (#425)

* Fixes various warnings noticed on Windows

- Adds a prototype for our implementation of vasprintf
- Return type of H5_get_utf16_str() is now non-const
- Fixes possible uninitialized return type in Wremove_utf8
- Better isolation of fork() code in accum.c:test_swmr_write_big()
- Better isolation of non-zlib code in dsets.c:test_filter_delete()
- Removed unused variable in trefer.c:test_reference_cmpnd_obj()

* Fixes clang-format issues

* Applied clang-tidy readability-non-const-parameter warning fixes auto… (#429)

* Automatically applied clang-tidy readability-avoid-const-params-in-decls fixes

Removes useless const declarations.

* Fixed most readability-non-const-parameter warnings

These changes were made automatically by clang-tidy, but I manually reverted the changes related to the H5Z_func_t signature.

* Reformat source with clang v10.0.1.

Co-authored-by: Larry Knox <[email protected]>

* Added C++11 override keyword where appropriate (#433)

Added H5_OVERRIDE macro for compatibility with both C++11 and older.

* Various clang tidy warning fixes (#448)

* Fixed clang-tidy bugprone-reserved-identifier warnings

* Fixed clang-tidy bugprone-assert-side-effect warnings

* Fixed clang-tidy bugprone-copy-constructor-init warning

* Fixed clang-tidy readability-redundant-preprocessor warning

For error_test.c the removed code was already dead, because it was in the else of an `#if H5_USE_16_API` block.

Based on H5Location.h, I think p_get_ref_obj_type was meant to be in `#ifndef DOXYGEN_SHOULD_SKIP_THIS` and an `#endif` was missing.  Similarly, in the header, getObjTypeByIdx is only in H5_NO_DEPRECATED_SYMBOLS, not DOXYGEN_SHOULD_SKIP_THIS.

* Fixed clang-tidy readability-redundant-string-init warnings

* Fixed some clang-tidy performance-type-promotion-in-math-fn warnings

* Fixed clang-tidy performance-unnecessary-value-param warnings

* Reformat source with clang v10.0.1.

Co-authored-by: Larry Knox <[email protected]>

* Removed checks/workarounds for pre-C++89 compatibility (#449)

After 30+ years, just assume that the following exist:
- extension-less includes
- namespaces
- std::
- static_cast
- bool

* Fixed all clang-tidy bugprone-suspicious-string-compare warnings (#451)

* Fixed all clang-tidy bugprone-suspicious-string-compare warnings

This change was generated entirely by clang-tidy itself.

* Reformat code with clang v10.0.1.

Co-authored-by: Larry Knox <[email protected]>

* Remove 2 functions incorrectly merged from develop in a cherry-pick merge of PR #451.

* Minor parallel improvements (#519)

* Improve MPI error reporting, handled failed operations in parallel tests more nicely, and clean up MPI_Allreduce for determining whether to break collective I/O

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Clean up MPI-IO VFD tracing support (#520)

* Clean up tracing support

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Brings the native implementation of H5Fdelete() from Bitbucket (#524)

* Committing clang-format changes

* Brings the native VFD H5Fdelete() implementation from Bitbucket

Only brings the 'del' callbacks, not the 'open/close' scheme.

* Formatter changes

* Committing clang-format changes

* Fixes direct VFD callback name

* Removes UNUSED macro from family API call

* Adds barrier and rank 0 check to MPI-I/O VFD delete

* Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete"

This reverts commit 909765f.

* Revert "Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete""

This reverts commit 9b04bef.

* Adds a second barrier after the delete in MPI-I/O VFD

* Only delete files in the core VFD when the backing store flag is set

* Fixes string issues in multi VFD

Also, h5test.c cleanup code now uses H5Fdelete().

* Formatted source

* Rework fapl checks for MPI-I/O VFD delete callback

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Minor warning fixes in develop (#526)

* Committing clang-format changes

* Minor warning fixes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Removes implementation of my_strdup() from the multi VFD (#527)

* Committing clang-format changes

* Removes my_strdup() from the multi VFD

* Use strdup directly when memory sanity checks are off

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Removes dead H5ST package from the library (#528)

* Committing clang-format changes

* Removes the unused H5ST package from the library

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fix HDFFV-11232 (#530)

* fixed missed closing of a dataset

* fixed missed closing of a dataset

* fixed typo in error return

* Committing clang-format changes

* minor edits

* code format

* Committing clang-format changes

* code format

* minor edit

* added H5fortkit dependency for H5VLff.F90, HDFFV-11232

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fixes incorrect usage of H5I_BADID (#554)

* Committing clang-format changes

* Fixes incorrect use of H5I_BADID

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fixes a segfault when H5Pset_mdc_log_options is called multiple times on a fapl (#601)

* Committing clang-format changes

* Fixes a segfault when H5Pset_mdc_log_options() is called multiple times

An internal string is incorrectly freed when the API call is invoked
multiple times on a property list, which will usually cause a segfault
to occur. On the first call the log location is NULL so the problem
doesn't occur.

Fixes HDFFV-11239

* Fixes typos

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fix for a segfault when H5Pset_fapl_log is passed an invalid fapl ID (#607)

* Committing clang-format changes

* Fixes an issue where H5Pset_fapl_log sefaults when passed an invalid
fapl ID

This was due to a pointer-containing struct being memset after the first
internal API call. If the first call failed, the error condition would
check if the pointer was not NULL and then attempt to free it if not.
This would lead to the freeing of a wild pointer if an invalid fapl ID
were passed in.

This was fixed by reordering the memset and adding a test to ensure the
problem stays fixed.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fixes crashes when size_hint > UINT32_MAX is passed to H5Gcreate1 (#611)

* Committing clang-format changes

* Fixes incorrect size_hint handling in H5Gcreate1

* Updates the size hint type for group creation

* Updates the RELEASE.txt note

* Revert "Updates the RELEASE.txt note"

This reverts commit 3df386a.

* Reverts previous behavior to use a uint32_t struct field

* Updates RELEASE.txt

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Revert "Brings the native implementation of H5Fdelete() from Bitbucket (#524)"

This reverts commit 38d1b12.

Co-authored-by: Gerd Heber <[email protected]>
Co-authored-by: bljhdf <[email protected]>
Co-authored-by: H. Joe Lee <[email protected]>
Co-authored-by: Quincey Koziol <[email protected]>
Co-authored-by: Sean McBride <[email protected]>
Co-authored-by: Dana Robinson <[email protected]>
Co-authored-by: Quincey Koziol <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <[email protected]>

MANIFEST

@@ -1029,8 +1029,6 @@
 ./src/H5SMpkg.h
 ./src/H5SMprivate.h
 ./src/H5SMtest.c
-./src/H5ST.c
-./src/H5STprivate.h
 ./src/H5T.c
 ./src/H5Tarray.c
 ./src/H5Tbit.c
@@ -1343,7 +1341,6 @@
 ./test/ttsafe_cancel.c
 ./test/ttsafe_dcreate.c
 ./test/ttsafe_error.c
-./test/ttst.c
 ./test/tunicode.c
 ./test/tvlstr.c
 ./test/tvltypes.c

fortran/src/Makefile.am

@@ -155,7 +155,7 @@ H5Pff.lo:            $(srcdir)/H5Pff.F90 H5f90global.lo H5fortkit.lo
 H5Rff.lo:            $(srcdir)/H5Rff.F90 H5f90global.lo
 H5Sff.lo:            $(srcdir)/H5Sff.F90 H5f90global.lo
 H5Tff.lo:            $(srcdir)/H5Tff.F90 H5f90global.lo
-H5VLff.lo:           $(srcdir)/H5VLff.F90 H5f90global.lo
+H5VLff.lo:           $(srcdir)/H5VLff.F90 H5f90global.lo H5fortkit.lo
 H5Zff.lo:            $(srcdir)/H5Zff.F90 H5f90global.lo
 H5_gen.lo:           H5_gen.F90 H5f90global.lo H5Aff.lo H5Dff.lo H5Pff.lo
 HDF5.lo:             $(srcdir)/HDF5.F90 H5f90global.lo H5_ff.lo H5Aff.lo  \

hl/c++/src/H5PacketTable.h

@@ -35,7 +35,7 @@ class H5_HLCPPDLL PacketTable {
      */
     PacketTable()
     {
-        table_id = H5I_BADID;
+        table_id = H5I_INVALID_HID;
     }
 
     /* "Open" Constructor

hl/src/H5PT.c

@@ -29,7 +29,7 @@ static H5I_type_t H5PT_ptable_id_type = H5I_UNINIT;
 #define H5PT_HASH_TABLE_SIZE 64
 
 /* Packet Table private functions */
-static herr_t H5PT_free_id(void *id);
+static herr_t H5PT_free_id(void *id, void **_ctx);
 static herr_t H5PT_close(htbl_t *table);
 static herr_t H5PT_create_index(htbl_t *table_id);
 static herr_t H5PT_set_index(htbl_t *table_id, hsize_t pt_index);
@@ -402,7 +402,7 @@ H5PTopen(hid_t loc_id, const char *dset_name)
  *-------------------------------------------------------------------------
  */
 static herr_t
-H5PT_free_id(void *id)
+H5PT_free_id(void *id, void H5_ATTR_UNUSED **_ctx)
 {
     HDfree(id);
     return SUCCEED;