Add doxygen for high level modules to hdf5 1.12 (#1901)

* Add doxygen for high level modules to hdf5 1.12

* 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, 543 insertions, 0 deletions

diff --git a/hl/src/H5TBpublic.h b/hl/src/H5TBpublic.h
index 1750490..dc0e31a 100644
--- a/hl/src/H5TBpublic.h
+++ b/hl/src/H5TBpublic.h
@@ -18,6 +18,70 @@
 extern "C" {
 #endif
 
+/**\defgroup H5TB Table
+ *
+ * <em>Creating and manipulating HDF5 datasets intended to be
+ * interpreted as tables (H5TB)</em>
+ *
+ * The HDF5 Table API defines a standard storage for HDF5 datasets
+ * that are intended to be interpreted as tables. A table is defined
+ * as a collection of records whose values are stored in fixed-length
+ * fields. All records have the same structure, and all values in
+ * each field have the same data type.
+ *
+ * \note \Bold{Programming hints:}
+ * \note To use any of these functions or subroutines,
+ *       you must first include the relevant include file (C) or
+ *       module (Fortran) in your application.
+ * \note The following line includes the HDF5 Table package, H5TB,
+ *       in C applications:
+ *       \code #include "hdf5_hl.h" \endcode
+ * \note To include the H5TB module in Fortran applications specify:
+ *       \code use h5tb \endcode
+ *       Fortran applications must also include \ref H5open before
+ *       any HDF5 calls to initialize global variables and \ref H5close
+ *       after all HDF5 calls to close the Fortran interface.
+ *
+ * <table>
+ * <tr valign="top"><td style="border: none;">
+ *
+ * - Creation
+ *   - \ref H5TBmake_table
+ * - Storage
+ *   - \ref H5TBappend_records (No Fortran)
+ *   - \ref H5TBwrite_records (No Fortran)
+ *   - \ref H5TBwrite_fields_name
+ *   - \ref H5TBwrite_fields_index
+ *
+ * - Modification
+ *   - \ref H5TBdelete_record (No Fortran)
+ *   - \ref H5TBinsert_record (No Fortran)
+ *   - \ref H5TBadd_records_from (No Fortran)
+ *   - \ref H5TBcombine_tables (No Fortran)
+ *   - \ref H5TBinsert_field
+ *   - \ref H5TBdelete_field
+ *
+ * </td><td style="border: none;">
+ *
+ * - Retrieval
+ *   - \ref H5TBread_table
+ *   - \ref H5TBread_records (No Fortran)
+ *   - \ref H5TBread_fields_name
+ *   - \ref H5TBread_fields_index
+ *
+ * - Query
+ *   - \ref H5TBget_table_info
+ *   - \ref H5TBget_field_info
+ *
+ * - Query Table Attributes
+ *   - \ref H5TBAget_fill
+ *   - \ref H5TBAget_title
+ *
+ * </td></tr>
+ * </table>
+ *
+ */
+
 /*-------------------------------------------------------------------------
  *
  * Create functions
@@ -25,6 +89,38 @@ extern "C" {
  *-------------------------------------------------------------------------
  */
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5TB
+ *
+ * \brief Creates and writes a table
+ *
+ * \param[in] table_title   The title of the table
+ * \fg_loc_id
+ * \param[in] dset_name     The name of the dataset to create
+ * \param[in] nfields       The number of fields
+ * \param[in] nrecords      The number of records
+ * \param[in] type_size     The size in bytes of the structure
+ *                          associated with the table;
+ *                          This value is obtained with \c sizeof().
+ * \param[in] field_names   An array containing the names of
+ *                          the fields
+ * \param[in] field_offset  An array containing the offsets of
+ *                          the fields
+ * \param[in] field_types   An array containing the type of
+ *                          the fields
+ * \param[in] chunk_size    The chunk size
+ * \param[in] fill_data     Fill values data
+ * \param[in] compress      Flag that turns compression on or off
+ * \param[in] buf           Buffer with data to be written to the table
+ *
+ * \return \herr_t
+ *
+ * \details H5TBmake_table() creates and writes a dataset named
+ *          \p dset_name attached to the object specified by the
+ *          identifier loc_id.
+ *
+ */
 H5_HLDLL herr_t H5TBmake_table(const char *table_title, hid_t loc_id, const char *dset_name, hsize_t nfields,
                                hsize_t nrecords, size_t type_size, const char *field_names[],
                                const size_t *field_offset, const hid_t *field_types, hsize_t chunk_size,
@@ -37,17 +133,128 @@ H5_HLDLL herr_t H5TBmake_table(const char *table_title, hid_t loc_id, const char
  *-------------------------------------------------------------------------
  */
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5TB
+ *
+ * \brief Adds records to the end of the table
+ *
+ * \fg_loc_id
+ * \param[in] dset_name     The name of the dataset to overwrite
+ * \param[in] nrecords      The number of records to append
+ * \param[in] type_size     The size of the structure type,
+ *                          as calculated by \c sizeof().
+ * \param[in] field_offset  An array containing the offsets of
+ *                          the fields. These offsets can be
+ *                          calculated with the #HOFFSET macro
+ * \param[in] dst_sizes     An array containing the sizes of
+ *                          the fields
+ * \param[in] buf           Buffer with data
+ *
+ * \return \herr_t
+ *
+ * \details H5TBappend_records() adds records to the end of the table
+ *          named \p dset_name attached to the object specified by the
+ *          identifier \p loc_id. The dataset is extended to hold the
+ *          new records.
+ *
+ */
 H5_HLDLL herr_t H5TBappend_records(hid_t loc_id, const char *dset_name, hsize_t nrecords, size_t type_size,
                                    const size_t *field_offset, const size_t *dst_sizes, const void *buf);
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5TB
+ *
+ * \brief Overwrites records
+ *
+ * \fg_loc_id
+ * \param[in] dset_name    The name of the dataset to overwrite
+ * \param[in] start         The zero index record to start writing
+ * \param[in] nrecords      The number of records to write
+ * \param[in] type_size     The size of the structure type, as
+ *                          calculated by \c sizeof().
+ * \param[in] field_offset  An array containing the offsets of
+ *                          the fields.  These offsets can be
+ *                          calculated with the #HOFFSET macro
+ * \param[in] dst_sizes     An array containing the sizes of
+ *                          the fields
+ * \param[in] buf           Buffer with data
+ *
+ * \return \herr_t
+ *
+ * \details H5TBwrite_records() overwrites records starting at the zero
+ *          index position start of the table named \p dset_name attached
+ *          to the object specified by the identifier \p loc_id.
+ *
+ */
 H5_HLDLL herr_t H5TBwrite_records(hid_t loc_id, const char *dset_name, hsize_t start, hsize_t nrecords,
                                   size_t type_size, const size_t *field_offset, const size_t *dst_sizes,
                                   const void *buf);
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5TB
+ *
+ * \brief Overwrites fields
+ *
+ * \fg_loc_id
+ * \param[in] dset_name    The name of the dataset to overwrite
+ * \param[in] field_names   The names of the fields to write
+ * \param[in] start         The zero index record to start writing
+ * \param[in] nrecords      The number of records to write
+ * \param[in] type_size     The size of the structure type, as
+ *                          calculated by \c sizeof().
+ * \param[in] field_offset  An array containing the offsets of
+ *                          the fields.  These offsets can be
+ *                          calculated with the #HOFFSET macro
+ * \param[in] dst_sizes     An array containing the sizes of
+ *                          the fields
+ * \param[in] buf           Buffer with data
+ *
+ * \return \herr_t
+ *
+ * \details H5TBwrite_fields_name() overwrites one or several fields
+ *          specified by \p field_names with data in \p buf from a
+ *          dataset named \p dset_name attached to the object specified
+ *          by the identifier \p loc_id.
+ *
+ */
 H5_HLDLL herr_t H5TBwrite_fields_name(hid_t loc_id, const char *dset_name, const char *field_names,
                                       hsize_t start, hsize_t nrecords, size_t type_size,
                                       const size_t *field_offset, const size_t *dst_sizes, const void *buf);
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5TB
+ *
+ * \brief Overwrites fields
+ *
+ * \fg_loc_id
+ * \param[in] dset_name     The name of the dataset to overwrite
+ * \param[in] nfields       The number of fields to overwrite.
+ *                          This parameter is also the size of the
+ *                          \p field_index array.
+ * \param[in] field_index   The indexes of the fields to write
+ * \param[in] start         The zero based index record to start writing
+ * \param[in] nrecords      The number of records to write
+ * \param[in] type_size     The size of the structure type, as
+ *                          calculated by \c sizeof().
+ * \param[in] field_offset  An array containing the offsets of
+ *                          the fields.  These offsets can be
+ *                          calculated with the #HOFFSET macro
+ * \param[in] dst_sizes     An array containing the sizes of
+ *                          the fields
+ * \param[in] buf           Buffer with data
+ *
+ * \return \herr_t
+ *
+ * \details H5TBwrite_fields_index() overwrites one or several fields
+ *          specified by \p field_index with a buffer \p buf from a
+ *          dataset named \p dset_name attached to the object
+ *          specified by the identifier \p loc_id.
+ *
+ */
 H5_HLDLL herr_t H5TBwrite_fields_index(hid_t loc_id, const char *dset_name, hsize_t nfields,
                                        const int *field_index, hsize_t start, hsize_t nrecords,
                                        size_t type_size, const size_t *field_offset, const size_t *dst_sizes,
@@ -60,18 +267,128 @@ H5_HLDLL herr_t H5TBwrite_fields_index(hid_t loc_id, const char *dset_name, hsiz
  *-------------------------------------------------------------------------
  */
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5TB
+ *
+ * \brief Reads a table
+ *
+ * \fg_loc_id
+ * \param[in] dset_name    The name of the dataset to read
+ * \param[in] dst_size     The size of the structure type,
+ *                          as calculated by \c sizeof()
+ * \param[in] dst_offset    An array containing the offsets of
+ *                          the fields.  These offsets can be
+ *                          calculated with the #HOFFSET macro
+ * \param[in] dst_sizes     An array containing the sizes of
+ *                          the fields.  These sizes can be
+ *                          calculated with the sizeof() macro.
+ * \param[in] dst_buf       Buffer with data
+ *
+ * \return \herr_t
+ *
+ * \details H5TBread_table() reads a table named
+ *          \p dset_name attached to the object specified by
+ *          the identifier \p loc_id.
+ *
+ */
 H5_HLDLL herr_t H5TBread_table(hid_t loc_id, const char *dset_name, size_t dst_size, const size_t *dst_offset,
                                const size_t *dst_sizes, void *dst_buf);
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5TB
+ *
+ * \brief Reads one or several fields. The fields are identified by name.
+ *
+ * \fg_loc_id
+ * \param[in] dset_name    The name of the dataset to read
+ * \param[in] field_names   An array containing the names of the
+ *                          fields to read
+ * \param[in] start         The start record to read from
+ * \param[in] nrecords      The number of records to read
+ * \param[in] type_size     The size in bytes of the structure associated
+ *                          with the table
+ *                          (This value is obtained with \c sizeof().)
+ * \param[in] field_offset  An array containing the offsets of the fields
+ * \param[in] dst_sizes     An array containing the size in bytes of
+ *                          the fields
+ * \param[out] buf          Buffer with data
+ *
+ * \return \herr_t
+ *
+ * \details H5TBread_fields_name() reads the fields identified
+ *          by \p field_names from a dataset named \p dset_name
+ *          attached to the object specified by the identifier \p loc_id.
+ *
+ */
 H5_HLDLL herr_t H5TBread_fields_name(hid_t loc_id, const char *dset_name, const char *field_names,
                                      hsize_t start, hsize_t nrecords, size_t type_size,
                                      const size_t *field_offset, const size_t *dst_sizes, void *buf);
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5TB
+ *
+ *
+ * \brief Reads one or several fields. The fields are identified by index.
+ *
+ * \fg_loc_id
+ * \param[in] dset_name     The name of the dataset to read
+ * \param[in] nfields       The number of fields to read
+ *                          (This parameter is also the size of the
+ *                          \p field_index array.)
+ *                          fields to read
+ * \param[in] field_index   The indexes of the fields to read
+ * \param[in] start         The start record to read from
+ * \param[in] nrecords      The number of records to read
+ * \param[in] type_size     The size in bytes of the structure associated
+ *                          with the table
+ *                          (This value is obtained with \c sizeof())
+ * \param[in] field_offset  An array containing the offsets of the fields
+ * \param[in] dst_sizes     An array containing the size in bytes of
+ *                          the fields
+ * \param[out] buf          Buffer with data
+ *
+ * \return \herr_t
+ *
+ * \details H5TBread_fields_index() reads the fields identified
+ *          by \p field_index from a dataset named \p dset_name attached
+ *          to the object specified by the identifier \p loc_id.
+ *
+ */
 H5_HLDLL herr_t H5TBread_fields_index(hid_t loc_id, const char *dset_name, hsize_t nfields,
                                       const int *field_index, hsize_t start, hsize_t nrecords,
                                       size_t type_size, const size_t *field_offset, const size_t *dst_sizes,
                                       void *buf);
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5TB
+ *
+ *
+ * \brief Reads records
+ *
+ * \fg_loc_id
+ * \param[in] dset_name     The name of the dataset to read
+ * \param[in] start         The start record to read from
+ * \param[in] nrecords      The number of records to read
+ * \param[in] type_size     The size of the structure type,
+ *                          as calculated by \c sizeof()
+ * \param[in] dst_offset    An array containing the offsets of the
+ *                          fields.  These offsets can be calculated
+ *                          with the #HOFFSET macro
+ * \param[in] dst_sizes     An array containing the size in bytes of
+ *                          the fields
+ * \param[out] buf          Buffer with data
+ *
+ * \return \herr_t
+ *
+ * \details H5TBread_records() reads some records identified from a dataset
+ *          named \p dset_name attached to the object specified by the
+ *          identifier \p loc_id.
+ *
+ */
 H5_HLDLL herr_t H5TBread_records(hid_t loc_id, const char *dset_name, hsize_t start, hsize_t nrecords,
                                  size_t type_size, const size_t *dst_offset, const size_t *dst_sizes,
                                  void *buf);
@@ -83,8 +400,52 @@ H5_HLDLL herr_t H5TBread_records(hid_t loc_id, const char *dset_name, hsize_t st
  *-------------------------------------------------------------------------
  */
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5TB
+ *
+ *
+ * \brief Gets the table dimensions
+ *
+ * \fg_loc_id
+ * \param[in] dset_name     The name of the dataset to read
+ * \param[out] nfields      The number of fields
+ * \param[out] nrecords     The number of records
+ *
+ * \return \herr_t
+ *
+ * \details H5TBget_table_info() retrieves the table dimensions from a
+ *          dataset named \p dset_name attached to the object specified
+ *          by the identifier \p loc_id.
+ *
+ */
 H5_HLDLL herr_t H5TBget_table_info(hid_t loc_id, const char *dset_name, hsize_t *nfields, hsize_t *nrecords);
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5TB
+ *
+ *
+ * \brief Gets information about a table
+ *
+ * \fg_loc_id
+ * \param[in] dset_name         The name of the dataset to read
+ * \param[out] field_names      An array containing the names of the fields
+ * \param[out] field_sizes      An array containing the size of the fields
+ * \param[out] field_offsets    An array containing the offsets of the fields
+ * \param[out] type_size        The size of the HDF5 datatype associated
+ *                              with the table.  (More specifically,
+ *                              the size in bytes of the HDF5 compound
+ *                              datatype used to define a row, or record,
+ *                              in the table)
+ *
+ * \return \herr_t
+ *
+ * \details H5TBget_field_info() gets information about a dataset
+ *          named \p dset_name attached to the object specified
+ *          by the identifier \p loc_id.
+ *
+ */
 H5_HLDLL herr_t H5TBget_field_info(hid_t loc_id, const char *dset_name, char *field_names[],
                                    size_t *field_sizes, size_t *field_offsets, size_t *type_size);
 
@@ -95,21 +456,162 @@ H5_HLDLL herr_t H5TBget_field_info(hid_t loc_id, const char *dset_name, char *fi
  *-------------------------------------------------------------------------
  */
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5TB
+ *
+ *
+ * \brief Delete records
+ *
+ * \fg_loc_id
+ * \param[in] dset_name    The name of the dataset
+ * \param[in] start        The start record to delete from
+ * \param[in] nrecords     The number of records to delete
+ *
+ * \return \herr_t
+ *
+ * \details H5TBdelete_record() deletes nrecords number of records starting
+ *          from \p start from the middle of the table \p dset_name
+ *          ("pulling up" all the records after it).
+ *
+ */
 H5_HLDLL herr_t H5TBdelete_record(hid_t loc_id, const char *dset_name, hsize_t start, hsize_t nrecords);
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5TB
+ *
+ *
+ * \brief Insert records
+ *
+ * \fg_loc_id
+ * \param[in] dset_name     The name of the dataset
+ * \param[in] start         The position to insert
+ * \param[in] nrecords      The number of records to insert
+ * \param[in] dst_size      The size in bytes of the structure
+ *                          associated with the table
+ * \param[in] dst_offset    An array containing the offsets of the
+ *                          fields
+ * \param[in] dst_sizes     An array containing the size in bytes of
+ *                          the fields
+ * \param[in] buf           Buffer with data
+ *
+ * \return \herr_t
+ *
+ * \details H5TBinsert_record() inserts records into the middle of the table
+ *          ("pushing down" all the records after it)
+ *
+ */
 H5_HLDLL herr_t H5TBinsert_record(hid_t loc_id, const char *dset_name, hsize_t start, hsize_t nrecords,
                                   size_t dst_size, const size_t *dst_offset, const size_t *dst_sizes,
                                   void *buf);
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5TB
+ *
+ *
+ * \brief Add records from first table to second table
+ *
+ * \fg_loc_id
+ * \param[in] dset_name1    The name of the dataset to read the records
+ * \param[in] start1        The position to read the records from the
+ *                          first table
+ * \param[in] nrecords      The number of records to read from the first
+ *                          table
+ * \param[in] dset_name2    The name of the dataset to write the records
+ * \param[in] start2        The position to write the records on the
+ *                          second table
+ *
+ * \return \herr_t
+ *
+ * \details H5TBadd_records_from() adds records from a dataset named
+ *          \p dset_name1 to a dataset named \p dset_name2. Both tables
+ *          are attached to the object specified by the identifier loc_id.
+ *
+ */
 H5_HLDLL herr_t H5TBadd_records_from(hid_t loc_id, const char *dset_name1, hsize_t start1, hsize_t nrecords,
                                      const char *dset_name2, hsize_t start2);
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5TB
+ *
+ *
+ * \brief Combines records from two tables into a third
+ *
+ * \param[in] loc_id1       Identifier of the file or group in which
+ *                          the first table is located
+ * \param[in] dset_name1    The name of the first table to combine
+ * \param[in] loc_id2       Identifier of the file or group in which
+ *                          the second table is located
+ * \param[in] dset_name2    The name of the second table to combine
+ * \param[in] dset_name3    The name of the new table
+ *
+ * \return \herr_t
+ *
+ * \details H5TBcombine_tables() combines records from two datasets named
+ *          \p dset_name1 and \p dset_name2, to a new table named
+ *          \p dset_name3. These tables can be located on different files,
+ *          identified by \p loc_id1 and \p loc_id2 (identifiers obtained
+ *          with H5Fcreate()). They can also be located on the same file.
+ *          In this case one uses the same identifier for both parameters
+ *          \p loc_id1 and \p loc_id2. If two files are used, the third
+ *          table is written in the first file.
+ *
+ */
 H5_HLDLL herr_t H5TBcombine_tables(hid_t loc_id1, const char *dset_name1, hid_t loc_id2,
                                    const char *dset_name2, const char *dset_name3);
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5TB
+ *
+ *
+ * \brief Insert a new field into a table
+ *
+ * \fg_loc_id
+ * \param[in] dset_name     The name of the table
+ * \param[in] field_name    The name of the field to insert
+ * \param[in] field_type    The data type of the field
+ * \param[in] position      The zero based index position where to
+ *                          insert the field
+ * \param[in] fill_data     Fill value data for the field. This parameter
+ *                          can be NULL
+ * \param[in] buf           Buffer with data
+ *
+ * \return \herr_t
+ *
+ * \details H5TBinsert_field() inserts a new field named \p field_name into
+ *          the table \p dset_name. Note: this function requires the table
+ *          to be re-created and rewritten in its entirety, and this can result
+ *          in some unused space in the file, and can also take a great deal of
+ *          time if the table is large.
+ *
+ */
 H5_HLDLL herr_t H5TBinsert_field(hid_t loc_id, const char *dset_name, const char *field_name,
                                  hid_t field_type, hsize_t position, const void *fill_data, const void *buf);
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5TB
+ *
+ *
+ * \brief Deletes a field from a table
+ *
+ * \fg_loc_id
+ * \param[in] dset_name     The name of the table
+ * \param[in] field_name    The name of the field to delete
+ *
+ * \return \herr_t
+ *
+ * \details H5TBdelete_field() deletes a field named \p field_name from the
+ *          table \p dset_name. Note: this function requires the table to be
+ *          re-created and rewritten in its entirety, and this can result in
+ *          some unused space in the file, and can also take a great deal of
+ *          time if the table is large.
+ *
+ */
 H5_HLDLL herr_t H5TBdelete_field(hid_t loc_id, const char *dset_name, const char *field_name);
 
 /*-------------------------------------------------------------------------
@@ -119,8 +621,49 @@ H5_HLDLL herr_t H5TBdelete_field(hid_t loc_id, const char *dset_name, const char
  *-------------------------------------------------------------------------
  */
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5TB
+ *
+ *
+ * \brief Reads a table's title
+ *
+ * \fg_loc_id
+ * \param[out] table_title  Buffer for title name
+ *
+ * \return \herr_t
+ *
+ * \details H5TBget_title() returns the title of the table identified
+ *          by \p loc_id in a buffer \p table_title.
+ *
+ */
 H5_HLDLL herr_t H5TBAget_title(hid_t loc_id, char *table_title);
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5TB
+ *
+ *
+ * \brief Reads the table attribute fill values
+ *
+ * \fg_loc_id
+ * \param[in] dset_name Name of table
+ * \param[in] dset_id   Table identifier
+ * \param[out] dst_buf Buffer of fill values for table fields
+ *
+ * \return
+ * \return A return value of 1 indicates that a fill value is present.
+ * \return A return value of 0 indicates a fill value is not present.
+ * \return A return value <0 indicates an error.
+ *
+ * \details H5TBget_fill() reads the table attribute fill values into
+ *          the buffer \p dst_buf for the table specified by \p dset_id
+ *          and \p dset_name located in \p loc_id.
+ *
+ * \par Example
+ * \include H5TBAget_fill.c
+ *
+ */
 H5_HLDLL htri_t H5TBAget_fill(hid_t loc_id, const char *dset_name, hid_t dset_id, unsigned char *dst_buf);
 
 #ifdef __cplusplus