Merges from develop/1.14 (#3118)

* Fix release action that allows files to be uploaded.
Add autotools h5copy help test.
Update cmake tools.cmake file for clang-tidy.
CMake build is missing H5FDsubfiling.h
macros improved for configure output capture.
Remove obsolete files

* Revert parallel config with TS

* Fix doxygen warnings

3 files changed, 38 insertions, 34 deletions

diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h
index 13a6d34..32d4f64 100644
--- a/src/H5Dpublic.h
+++ b/src/H5Dpublic.h
@@ -279,7 +279,7 @@ extern "C" {
  *
  *          \p loc_id may specify a file, group, dataset, named datatype,
  *          or attribute.  If an attribute, dataset, or named datatype is
- *          specified then the dataset will be created at the location
+ *          specified, then the dataset will be created at the location
  *          where the attribute, dataset, or named datatype is attached.
  *
  *          \p name may be either an absolute path in the file or a relative
@@ -290,7 +290,7 @@ extern "C" {
  *          file location where the dataset will be created, the datatype
  *          is copied and converted to a transient type.
  *
- *          The link creation property list, \p lcpl_id, governs creation
+ *          The link creation property list, \p lcpl_id, governs the creation
  *          of the link(s) by which the new dataset is accessed and the
  *          creation of any intermediate groups that may be missing.
  *
@@ -334,12 +334,12 @@ H5_DLL hid_t H5Dcreate2(hid_t loc_id, const char *name, hid_t type_id, hid_t spa
  *
  *          \p loc_id may specify a file, group, dataset, named datatype,
  *          or attribute.  If an attribute, dataset, or named datatype is
- *          specified then the dataset will be created at the location
+ *          specified, then the dataset will be created at the location
  *          where the attribute, dataset, or named datatype is attached.
  *
  *          The dataset’s datatype and dataspace are specified by
  *          \p type_id and \p space_id, respectively. These are the
- *          datatype and dataspace of the dataset as it will exist in
+ *          datatype and dataspace of the dataset as they will exist in
  *          the file, which may differ from the datatype and dataspace
  *          in application memory.
  *
@@ -668,7 +668,7 @@ H5_DLL herr_t H5Dget_chunk_info_by_coord(hid_t dset_id, const hsize_t *offset, u
  *          context \p op_data.
  *
  * \par Example
- * For each chunk, print the allocated chunk size (0 for un-allocated chunks).
+ * For each chunk, print the allocated chunk size (0 for unallocated chunks).
  * \snippet H5D_examples.c H5Dchunk_iter_cb
  * Iterate over all chunked datasets and chunks in a file.
  * \snippet H5D_examples.c H5Ovisit_cb
@@ -700,22 +700,22 @@ H5_DLL herr_t H5Dchunk_iter(hid_t dset_id, hid_t dxpl_id, H5D_chunk_iter_op_t cb
  *          specified by the index \p index. The chunk belongs to a set of
  *          chunks in the selection specified by \p fspace_id. If the queried
  *          chunk does not exist in the file, the size will be set to 0 and
- *          address to #HADDR_UNDEF. The value pointed to by filter_mask will
+ *          address to HADDR_UNDEF. The value pointed to by filter_mask will
  *          not be modified. \c NULL can be passed in for any \p out parameters.
  *
  *          \p chk_idx is the chunk index in the selection. The index value
  *          may have a value of 0 up to the number of chunks stored in
- *          the file that have a nonempty intersection with the file
- *          dataspace selection
+ *          the file that has a nonempty intersection with the file
+ *          dataspace selection.
  *
  *          \note As of 1.10.5, the dataspace intersection is not yet
- *          supported, hence, the index is of all the written chunks.
+ *          supported. Hence, the index is of all the written chunks.
  *
  *          \p fspace_id specifies the file dataspace selection.  It is
- *          intended to take #H5S_ALL for specifying the current selection.
+ *          intended to take #H5S_ALL to specify the current selection.
  *
  *          \note Please be aware that this function currently does not
- *          support non-trivial selections, thus \p fspace_id has no
+ *          support non-trivial selections; thus \p fspace_id has no
  *          effect. Also, the implementation does not handle the #H5S_ALL
  *          macro correctly.  As a workaround, an application can get
  *          the dataspace for the dataset using H5Dget_space() and pass that
@@ -735,7 +735,7 @@ H5_DLL herr_t H5Dget_chunk_info(hid_t dset_id, hid_t fspace_id, hsize_t chk_idx,
  *
  * \dset_id
  *
- * \return Returns the offset in bytes; otherwise, returns #HADDR_UNDEF,
+ * \return Returns the offset in bytes; otherwise, returns HADDR_UNDEF,
  *         a negative value.
  *
  * \details H5Dget_offset() returns the address in the file of
@@ -983,7 +983,7 @@ H5_DLL herr_t H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid
  *          the file. Only one chunk can be written with this function.
  *
  *          \p filters is a mask providing a record of which filters are
- *          used with the the chunk. The default value of the mask is
+ *          used with the chunk. The default value of the mask is
  *          zero (0), indicating that all enabled filters are applied. A
  *          filter is skipped if the bit corresponding to the filter’s
  *          position in the pipeline (0 ≤ position < 32) is turned on.
@@ -1102,6 +1102,8 @@ H5_DLL herr_t H5Dread_chunk(hid_t dset_id, hid_t dxpl_id, const hsize_t *offset,
  *            be restarted at the point of exit; a second H5Diterate()
  *            call will always restart at the beginning.
  *
+ * \warning   Modifying the selection of \p space_id during iteration
+ *            will lead to undefined behavior.
  *
  * \since 1.10.2
  *
@@ -1304,7 +1306,7 @@ H5_DLL herr_t H5Drefresh(hid_t dset_id);
  *          \p op and scatters it to the supplied buffer \p dst_buf in a
  *          manner similar to data being written to a dataset.
  *
- *          \p dst_space_id is a dataspace which defines the extent of \p
+ *          \p dst_space_id is a dataspace that defines the extent of \p
  *          dst_buf and the selection within it to scatter the data to.
  *
  *          \p type_id is the datatype of the data to be scattered in both
@@ -1361,7 +1363,7 @@ H5_DLL herr_t H5Dscatter(H5D_scatter_func_t op, void *op_data, hid_t type_id, hi
  *          enough to hold all the data if the callback function \p op is
  *          not provided.
  *
- *          \p op is a callback function which handles the gathered data.
+ *          \p op is a callback function that handles the gathered data.
  *          It is optional if \p dst_buf is large enough to hold all of the
  *          gathered data; required otherwise.
  *
@@ -1407,10 +1409,12 @@ H5_DLL herr_t H5Dgather(hid_t src_space_id, const void *src_buf, hid_t type_id,
  */
 H5_DLL herr_t H5Dclose(hid_t dset_id);
 
+/// \cond DEV
 /* Internal API routines */
 H5_DLL herr_t H5Ddebug(hid_t dset_id);
 H5_DLL herr_t H5Dformat_convert(hid_t dset_id);
 H5_DLL herr_t H5Dget_chunk_index_type(hid_t did, H5D_chunk_index_t *idx_type);
+/// \endcond
 
 /* Symbols defined for compatibility with previous versions of the HDF5 API.
  *
@@ -1489,10 +1493,10 @@ H5_DLL herr_t H5Dget_chunk_index_type(hid_t did, H5D_chunk_index_t *idx_type);
  *
  *          H5Dcreate() and H5Dcreate_anon() return a dataset identifier for
  *          success or a negative value for failure. The dataset identifier
- *          should eventually be closed by calling H5Dclose() to release
+ *          should eventually be closed by calling H5Dclose() to release the
  *          resources it uses.
  *
- *          See H5Dcreate_anon() for discussion of the differences between
+ *          See H5Dcreate_anon() for a discussion of the differences between
  *          H5Dcreate() and H5Dcreate_anon().
  *
  *          The HDF5 library provides flexible means of specifying a fill value,
@@ -1568,7 +1572,7 @@ H5_DLL hid_t H5Dopen1(hid_t loc_id, const char *name);
  *
  *          This function ensures that the dataset dimensions are of at least
  *          the sizes specified in size. The function H5Dset_extent() must be
- *          used if the dataset dimension sizes are are to be reduced.
+ *          used if the dataset dimension sizes are to be reduced.
  *
  * \version 1.8.0 Function deprecated in this release. Parameter size
  *                syntax changed to \Code{const hsize_t size[]} in this release.
@@ -1596,7 +1600,7 @@ H5_DLL herr_t H5Dextend(hid_t dset_id, const hsize_t size[]);
  *          The \p type_id must be the datatype stored in the buffer. The \p
  *          space_id describes the selection for the memory buffer to free the
  *          VL datatypes within. The \p dxpl_id is the dataset transfer property
- *          list which was used for the I/O transfer to create the buffer. And
+ *          list that was used for the I/O transfer to create the buffer. And
  *          \p buf is the pointer to the buffer to be reclaimed.
  *
  *          The VL structures (\ref hvl_t) in the user's buffer are modified to
diff --git a/src/H5Fpublic.h b/src/H5Fpublic.h
index 195495c..65b30b8 100644
--- a/src/H5Fpublic.h
+++ b/src/H5Fpublic.h
@@ -385,7 +385,7 @@ H5_DLL hid_t H5Fcreate(const char *filename, unsigned flags, hid_t fcpl_id, hid_
  *          opened.
  *
  *          The \p fapl_id parameter specifies the file access property list.
- *          Use of #H5P_DEFAULT specifies that default I/O access properties
+ *          The use of #H5P_DEFAULT specifies that default I/O access properties
  *          are to be used.
  *
  *          The \p flags parameter specifies whether the file will be opened in
@@ -495,7 +495,7 @@ H5_DLL hid_t H5Freopen(hid_t file_id);
  * \snippet H5F_examples.c flush
  *
  * \attention HDF5 does not possess full control over buffering. H5Fflush()
- *            flushes the internal HDF5 buffers then asks the operating system
+ *            flushes the internal HDF5 buffers and then asks the operating system
  *            (the OS) to flush the system buffers for the open files. After
  *            that, the OS is responsible for ensuring that the data is
  *            actually flushed to disk.
@@ -522,7 +522,7 @@ H5_DLL herr_t H5Fflush(hid_t object_id, H5F_scope_t scope);
  * \snippet H5F_examples.c minimal
  *
  * \note \Bold{Delayed close:} Note the following deviation from the
- *       above-described behavior. If H5Fclose() is called for a file but one
+ *       above-described behavior. If H5Fclose() is called for a file, but one
  *       or more objects within the file remain open, those objects will remain
  *       accessible until they are individually closed. Thus, if the dataset
  *       \c data_sample is open when H5Fclose() is called for the file
@@ -531,7 +531,7 @@ H5_DLL herr_t H5Fflush(hid_t object_id, H5F_scope_t scope);
  *       automatically closed once all objects in the file have been closed.\n
  *       Be warned, however, that there are circumstances where it is not
  *       possible to delay closing a file. For example, an MPI-IO file close is
- *       a collective call; all of the processes that opened the file must
+ *       a collective call; all of the processes that open the file must
  *       close it collectively. The file cannot be closed at some time in the
  *       future by each process in an independent fashion. Another example is
  *       that an application using an AFS token-based file access privilege may
@@ -1303,7 +1303,7 @@ H5_DLL herr_t H5Fstart_swmr_write(hid_t file_id);
  *          \snippet this H5F_sect_info_t_snip
  *
  *          This routine retrieves free-space section information for \p nsects
- *          sections or at most the maximum number of sections in the specified
+ *          sections or, at most, the maximum number of sections in the specified
  *          free-space manager. If the number of sections is not known, a
  *          preliminary H5Fget_free_sections() call can be made by setting \p
  *          sect_info to NULL and the total number of free-space sections for
@@ -1569,7 +1569,7 @@ H5_DLL herr_t H5Fget_page_buffering_stats(hid_t file_id, unsigned accesses[2], u
  * \brief Obtains information about a cache image if it exists
  *
  * \file_id
- * \param[out] image_addr Offset of the cache image if it exists, or #HADDR_UNDEF if it does not
+ * \param[out] image_addr Offset of the cache image if it exists, or HADDR_UNDEF if it does not
  * \param[out] image_size Length of the cache image if it exists, or 0 if it does not
  * \returns \herr_t
  *
@@ -1611,7 +1611,7 @@ H5_DLL herr_t H5Fget_mdc_image_info(hid_t file_id, haddr_t *image_addr, hsize_t
  *          file_id. This setting is used to inform the library to create
  *          minimized dataset object headers when \c TRUE.
  *
- *          The setting's value is returned in the boolean pointer minimize.
+ *          The setting's value is returned in the boolean pointer minimized.
  *
  * \since 1.10.5
  *
@@ -1810,7 +1810,7 @@ H5_DLL herr_t H5Fget_info1(hid_t obj_id, H5F_info1_t *file_info);
 /**
  * \ingroup H5F
  *
- * \brief Sets thelatest version of the library to be used for writing objects
+ * \brief Sets the latest version of the library to be used for writing objects
  *
  * \file_id
  * \param[in] latest_format Latest format flag
diff --git a/src/H5Rpublic.h b/src/H5Rpublic.h
index becbd15..5d2701c 100644
--- a/src/H5Rpublic.h
+++ b/src/H5Rpublic.h
@@ -75,7 +75,7 @@ typedef haddr_t hobj_ref_t;
 /**
  * Buffer to store heap ID and index
  *
- * This needs to be large enough to store largest #haddr_t in a worst case
+ * This needs to be large enough to store largest haddr_t in a worst case
  * machine (8 bytes currently) plus an int.
  *
  * \deprecated Dataset region reference type that is used with deprecated
@@ -259,7 +259,7 @@ H5_DLL herr_t H5Rdestroy(H5R_ref_t *ref_ptr);
  *          \snippet this H5R_type_t_snip
  *
  *          Note that #H5R_OBJECT1 and #H5R_DATASET_REGION1 can never be
- *          associated to an \ref H5R_ref_t reference and can therefore never be
+ *          associated with an \ref H5R_ref_t reference and can, therefore, never be
  *          returned through that function.
  *
  *          \ref H5R_ref_t is defined in H5Rpublic.h as:
@@ -302,7 +302,7 @@ H5_DLL htri_t H5Requal(const H5R_ref_t *ref1_ptr, const H5R_ref_t *ref2_ptr);
  * \return \herr_t
  *
  * \details H5Rcopy() creates a copy of an existing reference.
- *          \p src_ref_ptr points to the reference to copy and \p dst_ref_ptr is the
+ *          \p src_ref_ptr points to the reference to copy, and \p dst_ref_ptr is the
  *          pointer to the destination reference.
  *
  */
@@ -336,7 +336,7 @@ H5_DLL herr_t H5Rcopy(const H5R_ref_t *src_ref_ptr, H5R_ref_t *dst_ref_ptr);
  *
  *          The object opened with this function should be closed when it
  *          is no longer needed so that resource leaks will not develop. Use
- *          the appropriate close function such as H5Oclose() or H5Dclose()
+ *          the appropriate close function, such as H5Oclose() or H5Dclose()
  *          for datasets.
  *
  */
@@ -574,7 +574,7 @@ H5_DLL ssize_t H5Rget_attr_name(const H5R_ref_t *ref_ptr, char *name, size_t siz
  *
  *          A \Emph{reference type} is the type of reference, either an object
  *          reference or a dataset region reference. An \Emph{object reference}
- *          points to an HDF5 object while a \Emph{dataset region reference}
+ *          points to an HDF5 object, while a \Emph{dataset region reference}
  *          points to a defined region within a dataset.
  *
  *          The \Emph{referenced object} is the object the reference points
@@ -646,7 +646,7 @@ H5_DLL H5G_obj_t H5Rget_obj_type1(hid_t id, H5R_type_t ref_type, const void *ref
  *
  *          The object opened with this function should be closed when it is no
  *          longer needed so that resource leaks will not develop. Use the
- *          appropriate close function such as H5Oclose() or H5Dclose() for
+ *          appropriate close function, such as H5Oclose() or H5Dclose() for
  *          datasets.
  *
  * \version 1.10.0 Function H5Rdereference() renamed to H5Rdereference1() and
@@ -783,7 +783,7 @@ H5_DLL herr_t H5Rget_obj_type2(hid_t id, H5R_type_t ref_type, const void *ref, H
  *
  *          The object opened with this function should be closed when it is no
  *          longer needed so that resource leaks will not develop. Use the
- *          appropriate close function such as H5Oclose() or H5Dclose() for
+ *          appropriate close function, such as H5Oclose() or H5Dclose() for
  *          datasets.
  *
  * \since 1.10.0