Add doxygen for high level modules. (#1839)

* Add doxygen for high level modules.

* Committing clang-format changes

* Correct spelling based on spelling check.

* Committing clang-format changes

Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

1 files changed, 199 insertions, 0 deletions

diff --git a/hl/src/H5DOpublic.h b/hl/src/H5DOpublic.h
index 88616a3..99358b3 100644
--- a/hl/src/H5DOpublic.h
+++ b/hl/src/H5DOpublic.h
@@ -18,6 +18,29 @@
 extern "C" {
 #endif
 
+/**\defgroup H5DO Optimizations
+ *
+ * <em>Bypassing default HDF5 behavior in order to optimize for specific
+ * use cases (H5DO)</em>
+ *
+ * HDF5 functions described is this section are implemented in the HDF5 High-level
+ * library as optimized functions. These functions generally require careful setup
+ * and testing as they enable an application to bypass portions of the HDF5
+ * library’s I/O pipeline for performance purposes.
+ *
+ * These functions are distributed in the standard HDF5 distribution and are
+ * available any time the HDF5 High-level library is available.
+ *
+ * - \ref H5DOappend
+ *    \n Appends data to a dataset along a specified dimension.
+ * - \ref H5DOread_chunk
+ *   \n Reads a raw data chunk directly from a dataset in a file into a buffer (DEPRECATED)
+ * - \ref H5DOwrite_chunk
+ *   \n  Writes a raw data chunk from a buffer directly to a dataset in a file (DEPRECATED)
+ * .
+ *
+ */
+
 /*-------------------------------------------------------------------------
  *
  * "Optimized dataset" routines.
@@ -25,6 +48,48 @@ extern "C" {
  *-------------------------------------------------------------------------
  */
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5DO
+ *
+ * \brief Appends data to a dataset along a specified dimension.
+ *
+ * \param[in] dset_id   Dataset identifier
+ * \param[in] dxpl_id   Dataset transfer property list identifier
+ * \param[in] axis      Dataset Dimension (0-based) for the append
+ * \param[in] extension Number of elements to append for the
+ *                      axis-th dimension
+ * \param[in] memtype   The memory datatype identifier
+ * \param[in] buf       Buffer with data for the append
+ *
+ * \return \herr_t
+ *
+ * \details The H5DOappend() routine extends a dataset by \p extension
+ *          number of elements along a dimension specified by a
+ *          dimension \p axis and writes \p buf of elements to the
+ *          dataset. Dimension \p axis is 0-based. Elements’ type
+ *          is described by \p memtype.
+ *
+ *          This routine combines calling H5Dset_extent(),
+ *          H5Sselect_hyperslab(), and H5Dwrite() into a single routine
+ *          that simplifies application development for the common case
+ *          of appending elements to an existing dataset.
+ *
+ *          For a multi-dimensional dataset, appending to one dimension
+ *          will write a contiguous hyperslab over the other dimensions.
+ *          For example, if a 3-D dataset has dimension sizes (3, 5, 8),
+ *          extending the 0th dimension (currently of size 3) by 3 will
+ *          append 3*5*8 = 120 elements (which must be pointed to by the
+ *          \p buffer parameter) to the dataset, making its final
+ *          dimension sizes (6, 5, 8).
+ *
+ *          If a dataset has more than one unlimited dimension, any of
+ *          those dimensions may be appended to, although only along
+ *          one dimension per call to H5DOappend().
+ *
+ * \since   1.10.0
+ *
+ */
 H5_HLDLL herr_t H5DOappend(hid_t dset_id, hid_t dxpl_id, unsigned axis, size_t extension, hid_t memtype,
                            const void *buf);
 
@@ -35,8 +100,142 @@ H5_HLDLL herr_t H5DOappend(hid_t dset_id, hid_t dxpl_id, unsigned axis, size_t e
 #ifndef H5_NO_DEPRECATED_SYMBOLS
 
 /* Compatibility wrappers for functionality moved to H5D */
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5DO
+ *
+ * \brief Writes a raw data chunk from a buffer directly to a dataset in a file.
+ *
+ * \param[in] dset_id       Identifier for the dataset to write to
+ * \param[in] dxpl_id       Transfer property list identifier for
+ *                          this I/O operation
+ * \param[in] filters       Mask for identifying the filters in use
+ * \param[in] offset        Logical position of the chunk’s first element
+ *                          in the dataspace
+ * \param[in] data_size     Size of the actual data to be written in bytes
+ * \param[in] buf           Buffer containing data to be written to the chunk
+ *
+ * \return \herr_t
+ *
+ * \deprecated This function was deprecated in favor of the function
+ *             H5Dwrite_chunk() of HDF5-1.10.3.
+ *             The functionality of H5DOwrite_chunk() was moved
+ *             to H5Dwrite_chunk().
+ * \deprecated For compatibility, this API call has been left as a stub which
+ *             simply calls H5Dwrite_chunk(). New code should use H5Dwrite_chunk().
+ *
+ * \details The H5DOwrite_chunk() writes a raw data chunk as specified by its
+ *          logical \p offset in a chunked dataset \p dset_id from the application
+ *          memory buffer \p buf to the dataset in the file. Typically, the data
+ *          in \p buf is preprocessed in memory by a custom transformation, such as
+ *          compression. The chunk will bypass the library’s internal data
+ *          transfer pipeline, including filters, and will be written directly to the file.
+ *
+ *          \p dxpl_id is a data transfer property list identifier.
+ *
+ *          \p filters is a mask providing a record of which filters are used
+ *          with the chunk. The default value of the mask is zero (\c 0),
+ *          indicating that all enabled filters are applied. A filter is skipped
+ *          if the bit corresponding to the filter’s position in the pipeline
+ *          (<tt>0 ≤ position < 32</tt>) is turned on. This mask is saved
+ *          with the chunk in the file.
+ *
+ *          \p offset is an array specifying the logical position of the first
+ *          element of the chunk in the dataset’s dataspace. The length of the
+ *          offset array must equal the number of dimensions, or rank, of the
+ *          dataspace. The values in \p offset must not exceed the dimension limits
+ *          and must specify a point that falls on a dataset chunk boundary.
+ *
+ *          \p data_size is the size in bytes of the chunk, representing the number of
+ *          bytes to be read from the buffer \p buf. If the data chunk has been
+ *          precompressed, \p data_size should be the size of the compressed data.
+ *
+ *          \p buf is the memory buffer containing data to be written to the chunk in the file.
+ *
+ * \attention   Exercise caution when using H5DOread_chunk() and H5DOwrite_chunk(),
+ *              as they read and write data chunks directly in a file.
+ *              H5DOwrite_chunk() bypasses hyperslab selection, the conversion of data
+ *              from one datatype to another, and the filter pipeline to write the chunk.
+ *              Developers should have experience with these processes before
+ *              using this function. Please see
+ *              <a href="https://portal.hdfgroup.org/display/HDF5/Using+the+Direct+Chunk+Write+Function">
+ *              Using the Direct Chunk Write Function</a>
+ *              for more information.
+ *
+ * \note    H5DOread_chunk() and H5DOwrite_chunk() are not
+ *          supported under parallel and do not support variable length types.
+ *
+ * \par Example
+ * The following code illustrates the use of H5DOwrite_chunk to write
+ * an entire dataset, chunk by chunk:
+ * \snippet H5DO_examples.c H5DOwrite
+ *
+ * \version 1.10.3  Function deprecated in favor of H5Dwrite_chunk.
+ *
+ * \since   1.8.11
+ */
 H5_HLDLL herr_t H5DOwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *offset,
                                 size_t data_size, const void *buf);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5DO
+ *
+ * \brief Reads a raw data chunk directly from a dataset in a file into a buffer.
+ *
+ * \param[in] dset_id           Identifier for the dataset to be read
+ * \param[in] dxpl_id           Transfer property list identifier for
+ *                              this I/O operation
+ * \param[in] offset            Logical position of the chunk’s first
+                                element in the dataspace
+ * \param[in,out] filters       Mask for identifying the filters used
+ *                              with the chunk
+ * \param[in] buf               Buffer containing the chunk read from
+ *                              the dataset
+ *
+ * \return \herr_t
+ *
+ * \deprecated This function was deprecated in favor of the function
+ *             H5Dread_chunk() as of HDF5-1.10.3.
+ *             In HDF5 1.10.3, the functionality of H5DOread_chunk()
+ *             was moved to H5Dread_chunk().
+ * \deprecated For compatibility, this API call has been left as a stub which
+ *             simply calls H5Dread_chunk().  New code should use H5Dread_chunk().
+ *
+ * \details The H5DOread_chunk() reads a raw data chunk as specified
+ *          by its logical \p offset in a chunked dataset \p dset_id
+ *          from the dataset in the file into the application memory
+ *          buffer \p buf. The data in \p buf is read directly from the file
+ *          bypassing the library’s internal data transfer pipeline,
+ *          including filters.
+ *
+ *          \p dxpl_id is a data transfer property list identifier.
+ *
+ *          The mask \p filters indicates which filters are used with the
+ *          chunk when written. A zero value indicates that all enabled filters
+ *          are applied on the chunk. A filter is skipped if the bit corresponding
+ *          to the filter’s position in the pipeline
+ *          (<tt>0 ≤ position < 32</tt>) is turned on.
+ *
+ *          \p offset is an array specifying the logical position of the first
+ *          element of the chunk in the dataset’s dataspace. The length of the
+ *          offset array must equal the number of dimensions, or rank, of the
+ *          dataspace. The values in \p offset must not exceed the dimension
+ *          limits and must specify a point that falls on a dataset chunk boundary.
+ *
+ *          \p buf is the memory buffer containing the chunk read from the dataset
+ *          in the file.
+ *
+ * \par Example
+ * The following code illustrates the use of H5DOread_chunk()
+ * to read a chunk from a dataset:
+ * \snippet H5DO_examples.c H5DOread
+ *
+ * \version 1.10.3  Function deprecated in favor of H5Dread_chunk.
+ *
+ * \since   1.10.2, 1.8.19
+ */
 H5_HLDLL herr_t H5DOread_chunk(hid_t dset_id, hid_t dxpl_id, const hsize_t *offset, uint32_t *filters /*out*/,
                                void *buf /*out*/);