Sync 1.14 branch with develop (#3923)

* Fix build error on freebsd (#3883)

Fixes:

checking for config freebsd12.1... no
checking for config freebsd... found
compiler '/home/svcpetsc/petsc-hash-pkgs/39f577/bin/mpicc' is GNU gcc-9.2.0
compiler '/home/svcpetsc/petsc-hash-pkgs/39f577/bin/mpif90' is GNU gfortran-9.2.0
stdout: .: cannot open ./config/classic-fflags: No such file or directory

* Correct CMake command and example packaging (#3888)

* Feat: Hashpin sensitive dependencies on GitHub Actions and enable Dependabot to update them monthly (#3892)

* feat: hashpin sensitive dependencies on GHAs

Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com>

* feat: enable dependabot for monthly updates on GHA

Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com>

---------

Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com>

* Some changes to portal links when they could be found on docs.hdfgroup.org, and changed the helpdesk link to help.hdfgroup.org (#3893)

* Updated some portal links to go directly to docs.hdfgroup. 

* Fixed some portal and help desk links

* Add variable option syncing for examples (#3885)

* Add period(.) at the end of the sentence for consistency. (#3897)

* Remove redundant backslash character from comment. (#3899)

* Disable doxygen as errors for netcdf (#3900)

* disable building doxygen for netcdf test

* Doc versions (#3903)

* Added missing \since tags to H5D.

* Committing clang-format changes

* Fixed H5T version info.

* Committing clang-format changes

* Added missing version info to H5E.

* Committing clang-format changes

* Added version info to H5F public APIs.

* Committing clang-format changes

* Added missing H5Z public API version info.

* Added missing version info to H5G public APIs

* Added missing version info to H5I public API.

* Added missing version info to H5 public APIs

* Committing clang-format changes

* Added missing version info to H5P public APIs

* Added missing version info to H5R public APIs

* Fix comment error.

* Committing clang-format changes

---------

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

* Change Trouble Shooting to Troubleshooting (#3905)

* Implement optimized support for vector I/O in Subfiling VFD (#3896)

Vector I/O requests are now processed within a single
set of I/O call batches, rather than each I/O vector
entry (tuple constructed from the types, addrs, sizes
and bufs arrays) being processed individually. This allows I/O to be
more efficiently parallelized among the I/O concentrator processes
during large I/O requests.

* Fixed some calculations and add test cases for issues spotted from review

* Removed a variable that was compensating for previous miscalculations

* Add 'warning density' computation to the warnhist script (#3910)

* Add 'warning density' computation to the warnhist script, along with several
cleanups to it.   Add "--enable-show-all-warnings" configure (and CMake)
option to disable compiler diagnostic suppression (and therefore show all the
otherwise suppressed compiler diagnostics), disabled by default.  Clean up
a buncn of misc. warnings.

Signed-off-by: Quincey Koziol <qkoziol@amazon.com>

* Added H5Fdelete_f with test (#3912)

* New Fortran Examples added (#3916)

* added subfiling example

* Added filtered writes with no selection example

* Version and space corrections.

* Restore H5_VERSION definition in configure.ac.

* renamed defined H5_VERS* to avoid conflicts (#3926)

1 files changed, 38 insertions, 1 deletions

diff --git a/src/H5Gpublic.h b/src/H5Gpublic.h
index cc04680..4c0e2de 100644
--- a/src/H5Gpublic.h
+++ b/src/H5Gpublic.h
@@ -214,6 +214,9 @@ H5_DLL hid_t H5Gopen2(hid_t loc_id, const char *name, hid_t gapl_id);
  * --------------------------------------------------------------------------
  * \ingroup ASYNC
  * \async_variant_of{H5Gopen}
+ *
+ * \since 1.12.0
+ *
  */
 #ifndef H5_DOXYGEN
 H5_DLL hid_t H5Gopen_async(const char *app_file, const char *app_func, unsigned app_line, hid_t loc_id,
@@ -273,6 +276,9 @@ H5_DLL herr_t H5Gget_info(hid_t loc_id, H5G_info_t *ginfo);
  * --------------------------------------------------------------------------
  * \ingroup ASYNC
  * \async_variant_of{H5Gget_info}
+ *
+ * \since 1.12.0
+ *
  */
 #ifndef H5_DOXYGEN
 H5_DLL herr_t H5Gget_info_async(const char *app_file, const char *app_func, unsigned app_line, hid_t loc_id,
@@ -317,6 +323,9 @@ H5_DLL herr_t H5Gget_info_by_name(hid_t loc_id, const char *name, H5G_info_t *gi
  * --------------------------------------------------------------------------
  * \ingroup ASYNC
  * \async_variant_of{H5Gget_info_by_name}
+ *
+ * \since 1.12.0
+ *
  */
 #ifndef H5_DOXYGEN
 H5_DLL herr_t H5Gget_info_by_name_async(const char *app_file, const char *app_func, unsigned app_line,
@@ -377,6 +386,9 @@ H5_DLL herr_t H5Gget_info_by_idx(hid_t loc_id, const char *group_name, H5_index_
  * --------------------------------------------------------------------------
  * \ingroup ASYNC
  * \async_variant_of{H5Gget_info_by_idx}
+ *
+ * \since 1.12.0
+ *
  */
 #ifndef H5_DOXYGEN
 H5_DLL herr_t H5Gget_info_by_idx_async(const char *app_file, const char *app_func, unsigned app_line,
@@ -468,6 +480,9 @@ H5_DLL herr_t H5Gclose(hid_t group_id);
  * --------------------------------------------------------------------------
  * \ingroup ASYNC
  * \async_variant_of{H5Gclose}
+ *
+ * \since 1.12.0
+ *
  */
 #ifndef H5_DOXYGEN
 H5_DLL herr_t H5Gclose_async(const char *app_file, const char *app_func, unsigned app_line, hid_t group_id,
@@ -683,6 +698,8 @@ H5_DLL hid_t H5Gopen1(hid_t loc_id, const char *name);
 
  * \version 1.8.0 Function deprecated in this release.
  *
+ * \since 1.0.0
+ *
  */
 H5_DLL herr_t H5Glink(hid_t cur_loc_id, H5G_link_t type, const char *cur_name, const char *new_name);
 /**
@@ -716,9 +733,11 @@ H5_DLL herr_t H5Glink(hid_t cur_loc_id, H5G_link_t type, const char *cur_name, c
  *          current_name is \Code{./foo}, \p new_name is \Code{./x/y/bar}, and a
  *          request is made for \Code{./x/y/bar}, then the actual object looked
  *          up is \Code{./x/y/./foo}.
-
+ *
  * \version 1.8.0 Function deprecated in this release.
  *
+ * \since 1.6.0
+ *
  */
 H5_DLL herr_t H5Glink2(hid_t cur_loc_id, const char *cur_name, H5G_link_t type, hid_t new_loc_id,
                        const char *new_name);
@@ -748,6 +767,8 @@ H5_DLL herr_t H5Glink2(hid_t cur_loc_id, const char *cur_name, H5G_link_t type,
  *
  * \version 1.8.0 Function deprecated in this release.
  *
+ * \since 1.0.0
+ *
  */
 H5_DLL herr_t H5Gmove(hid_t src_loc_id, const char *src_name, const char *dst_name);
 /**
@@ -779,6 +800,8 @@ H5_DLL herr_t H5Gmove(hid_t src_loc_id, const char *src_name, const char *dst_na
  *
  * \version 1.8.0 Function deprecated in this release.
  *
+ * \since 1.6.0
+ *
  */
 H5_DLL herr_t H5Gmove2(hid_t src_loc_id, const char *src_name, hid_t dst_loc_id, const char *dst_name);
 /**
@@ -820,6 +843,8 @@ H5_DLL herr_t H5Gmove2(hid_t src_loc_id, const char *src_name, hid_t dst_loc_id,
  *
  * \version 1.8.0 Function deprecated in this release.
  *
+ * \since 1.0.0
+ *
  */
 H5_DLL herr_t H5Gunlink(hid_t loc_id, const char *name);
 /**
@@ -858,6 +883,8 @@ H5_DLL herr_t H5Gunlink(hid_t loc_id, const char *name);
  *
  * \version 1.8.0 Function deprecated in this release.
  *
+ * \since 1.0.0
+ *
  */
 H5_DLL herr_t H5Gget_linkval(hid_t loc_id, const char *name, size_t size, char *buf /*out*/);
 /**
@@ -898,6 +925,8 @@ H5_DLL herr_t H5Gget_linkval(hid_t loc_id, const char *name, size_t size, char *
  *
  * \version 1.8.0 Function deprecated in this release.
  *
+ * \since 1.0.0
+ *
  */
 H5_DLL herr_t H5Gset_comment(hid_t loc_id, const char *name, const char *comment);
 /**
@@ -943,6 +972,8 @@ H5_DLL herr_t H5Gset_comment(hid_t loc_id, const char *name, const char *comment
  *
  * \version 1.8.0 Function deprecated in this release.
  *
+ * \since 1.0.0
+ *
  */
 H5_DLL int H5Gget_comment(hid_t loc_id, const char *name, size_t bufsize, char *buf);
 /**
@@ -1008,6 +1039,8 @@ H5_DLL int H5Gget_comment(hid_t loc_id, const char *name, size_t bufsize, char *
  *
  * \version 1.8.0 Function deprecated in this release.
  *
+ * \since 1.0.0
+ *
  */
 H5_DLL herr_t H5Giterate(hid_t loc_id, const char *name, int *idx, H5G_iterate_t op, void *op_data);
 /**
@@ -1029,6 +1062,8 @@ H5_DLL herr_t H5Giterate(hid_t loc_id, const char *name, int *idx, H5G_iterate_t
  *
  * \version 1.8.0 Function deprecated in this release.
  *
+ * \since 1.6.0
+ *
  */
 H5_DLL herr_t H5Gget_num_objs(hid_t loc_id, hsize_t *num_objs);
 /**
@@ -1086,6 +1121,8 @@ H5_DLL herr_t H5Gget_num_objs(hid_t loc_id, hsize_t *num_objs);
  * \version 1.6.1 Two new fields were added to the \ref H5G_stat_t struct in
  *                this release.
  *
+ * \since 1.0.0
+ *
  */
 H5_DLL herr_t H5Gget_objinfo(hid_t loc_id, const char *name, hbool_t follow_link,
                              H5G_stat_t *statbuf /*out*/);