Transferred RM blocks in H5D and H5G to develop (#213)

4 files changed, 1598 insertions, 18 deletions

diff --git a/src/H5Dmodule.h b/src/H5Dmodule.h
index 178e50f..fd155b1 100644
--- a/src/H5Dmodule.h
+++ b/src/H5Dmodule.h
@@ -29,4 +29,15 @@
 #define H5_MY_PKG_ERR  H5E_DATASET
 #define H5_MY_PKG_INIT YES
 
+/**
+ * \defgroup H5D H5D
+ * \brief Group Interface
+ * \details The HDF5 Dataset Interface, H5D, provides a mechanism for managing
+ *          HDF5 datasets, including the transfer of data between memory and
+ *          disk and the description of dataset properties.
+ *
+ *          A Dataset is used by other HDF5 APIs, either by name or by a handle,
+ *          which is obtained by either creating or opening the dataset.
+ */
+
 #endif /* _H5Dmodule_H */
diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h
index 507f75b..00948f9 100644
--- a/src/H5Dpublic.h
+++ b/src/H5Dpublic.h
@@ -105,16 +105,22 @@ typedef enum H5D_vds_view_t {
 /* Callback for H5Pset_append_flush() in a dataset access property list */
 typedef herr_t (*H5D_append_cb_t)(hid_t dataset_id, hsize_t *cur_dims, void *op_data);
 
-/* Define the operator function pointer for H5Diterate() */
+/** Define the operator function pointer for H5Diterate() */
+//! [H5D_operator_t_snip]
 typedef herr_t (*H5D_operator_t)(void *elem, hid_t type_id, unsigned ndim, const hsize_t *point,
                                  void *operator_data);
+//! [H5D_operator_t_snip]
 
-/* Define the operator function pointer for H5Dscatter() */
+/** Define the operator function pointer for H5Dscatter() */
+//! [H5D_scatter_func_t_snip]
 typedef herr_t (*H5D_scatter_func_t)(const void **src_buf /*out*/, size_t *src_buf_bytes_used /*out*/,
                                      void *op_data);
+//! [H5D_scatter_func_t_snip]
 
-/* Define the operator function pointer for H5Dgather() */
+/** Define the operator function pointer for H5Dgather() */
+//! [H5D_gather_func_t_snip]
 typedef herr_t (*H5D_gather_func_t)(const void *dst_buf, size_t dst_buf_bytes_used, void *op_data);
+//! [H5D_gather_func_t_snip]
 
 /********************/
 /* Public Variables */
@@ -127,57 +133,1280 @@ typedef herr_t (*H5D_gather_func_t)(const void *dst_buf, size_t dst_buf_bytes_us
 extern "C" {
 #endif
 
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Creates a new dataset and links it into the file
+ *
+ * \fgdta_loc_id
+ * \param[in] name      Name of the dataset to open
+ * \type_id
+ * \space_id
+ * \lcpl_id
+ * \dcpl_id
+ * \dapl_id
+ *
+ * \return \hid_t{dataset}
+ *
+ *
+ * \details H5Dcreate2() creates a new dataset named \p name at
+ *          the location specified by \p loc_id, and associates constant
+ *          and initial persistent properties with that dataset, including
+ *          the datatype \p dtype_id, the dataspace \p space_id, and
+ *          other properties as specified by the dataset creation property
+ *          list \p dcpl_id and the access property list \p dapl_id,
+ *          respectively. Once created, the dataset is opened for access.
+ *
+ *          \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
+ *          where the attribute, dataset, or named datatype is attached.
+ *
+ *          \p name may be either an absolute path in the file or a relative
+ *          path from \p loc_id naming the dataset.
+ *
+ *          \p dtype_id specifies the datatype of each data element as stored
+ *          in the file.  If \p dtype_id is either a fixed-length or
+ *          variable-length string, it is important to set the string length
+ *          when defining the datatype. String datatypes are derived from
+ *          #H5T_C_S1 (or #H5T_FORTRAN_S1 for Fortran codes), which defaults
+ *          to 1 character in size.
+ *
+ *          If \p dtype_id is a committed datatype, and if the file location
+ *          associated with the committed datatype is different from the
+ *          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
+ *          of the link(s) by which the new dataset is accessed and the
+ *          creation of any * intermediate groups that may be missing.
+ *
+ *          The datatype and dataspace properties and the dataset creation
+ *          and access property lists are attached to the dataset, so the
+ *          caller may derive new datatypes, dataspaces, and creation and
+ *          access properties from the old ones and reuse them in calls to
+ *          create additional datasets.  Once created, the dataset can be
+ *          read from or written to. Reading data from a datatset that was
+ *          not previously written, the HDF5 library will return default
+ *          or user-defined fill values.
+ *
+ *          To conserve and release resources, the dataset should be closed
+ *          when access is no longer required.
+ *
+ * \since 1.8.0
+ *
+ * \see H5Dopen2(), H5Dclose(), H5Tset_size()
+ *
+ */
 H5_DLL hid_t  H5Dcreate2(hid_t loc_id, const char *name, hid_t type_id, hid_t space_id, hid_t lcpl_id,
                          hid_t dcpl_id, hid_t dapl_id);
 H5_DLL hid_t  H5Dcreate_async(const char *app_file, const char *app_func, unsigned app_line, hid_t loc_id,
                               const char *name, hid_t type_id, hid_t space_id, hid_t lcpl_id, hid_t dcpl_id,
                               hid_t dapl_id, hid_t es_id);
-H5_DLL hid_t  H5Dcreate_anon(hid_t file_id, hid_t type_id, hid_t space_id, hid_t plist_id, hid_t dapl_id);
-H5_DLL hid_t  H5Dopen2(hid_t file_id, const char *name, hid_t dapl_id);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Creates a dataset in a file without linking it into the file
+ *        structure
+ *
+ * \fgdta_loc_id
+ * \type_id
+ * \space_id
+ * \dcpl_id
+ * \dapl_id
+ *
+ * \return \hid_t{dataset}
+ *
+ * \details H5Dcreate_anon() creates a dataset in the file specified
+ *          by \p loc_id.
+ *
+ *          \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
+ *          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
+ *          the file, which may differ from the datatype and dataspace
+ *          in application memory.
+ *
+ *          Dataset creation property list and dataset access creation
+ *          property list are specified by \p dcpl_id and \p dapl_id.
+ *
+ *          H5Dcreate_anon() returns a new dataset identifier. Using
+ *          this identifier, the new dataset must be linked into the
+ *          HDF5 file structure with H5Olink() or it will be deleted
+ *          from the file when the file is closed.
+ *
+ *          See H5Dcreate2() for further details and considerations on
+ *          the use of H5Dcreate2() and H5Dcreate_anon().
+ *
+ *          The differences between this function and H5Dcreate2() are
+ *          as follows:
+ *          \li H5Dcreate_anon() explicitly includes a dataset access property
+ *          list. H5Dcreate() always uses default dataset access properties.
+ *
+ *          \li H5Dcreate_anon() neither provides the new dataset’s name nor
+ *          links it into the HDF5 file structure; those actions must be
+ *          performed separately through a call to H5Olink(), which offers
+ *          greater control over linking.
+ *
+ *          A dataset created with this function should be closed with
+ *          H5Dclose() when the dataset is no longer needed so that resource
+ *          leaks will not develop.
+ *
+ * \since 1.8.0
+ *
+ * \see H5Olink(), H5Dcreate(), Using Identifiers
+ *
+ */
+H5_DLL hid_t  H5Dcreate_anon(hid_t loc_id, hid_t type_id, hid_t space_id, hid_t dcpl_id, hid_t dapl_id);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Creates a new dataset and links it into the file
+ *
+ * \fgdta_loc_id
+ * \param[in] name      Name of the dataset to open
+ * \dapl_id
+ *
+ * \return \hid_t{dataset}
+ *
+ * \details H5Dopen2() opens the existing dataset specified
+ *          by a location identifier and name, \p loc_id and \p name,
+ *          respectively.
+ *
+ *          \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 opened at the location
+ *          where the attribute, dataset, or named datatype is attached.
+ *
+ *          The dataset access property list, \p dapl_id, provides
+ *          information regarding access to the dataset.
+ *
+ *          To conserve and release resources, the dataset should be closed
+ *          when access is no longer required.
+ *
+ * \since 1.8.0
+ *
+ * \see H5Dcreate2(), H5Dclose()
+ *
+ */
+H5_DLL hid_t  H5Dopen2(hid_t loc_id, const char *name, hid_t dapl_id);
 H5_DLL hid_t  H5Dopen_async(const char *app_file, const char *app_func, unsigned app_line, hid_t loc_id,
                             const char *name, hid_t dapl_id, hid_t es_id);
+
+/**
+ * --------------------------------------------------------------------------
+ *\ingroup H5D
+ *
+ * \brief Returns an identifier for a copy of the dataspace for a dataset
+ *
+ * \dset_id
+ *
+ * \return \hid_t{dataspace}
+ *
+ * \details H5Dget_space() makes a copy of the dataspace of
+ *          the dataset specified by \p dset_id. The function returns an
+ *          identifier for the new copy of the dataspace.
+ *
+ *          A dataspace identifier returned from this function should
+ *          be released with H5Sclose() when the identifier is no longer
+ *          needed so that resource leaks will not occur.
+ *
+ * \see H5Sclose()
+ *
+ */
 H5_DLL hid_t  H5Dget_space(hid_t dset_id);
 H5_DLL hid_t  H5Dget_space_async(const char *app_file, const char *app_func, unsigned app_line, hid_t dset_id,
                                  hid_t es_id);
+
 H5_DLL herr_t H5Dget_space_status(hid_t dset_id, H5D_space_status_t *allocation);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Returns an identifier for a copy of the datatype for a dataset
+ *
+ * \dset_id
+ *
+ * \return \hid_t{datatype}
+ *
+ * \details H5Dget_type() returns an identifier of a copy of
+ *          the datatype for a dataset.
+ *
+ *          If a dataset has a named datatype, then an identifier to the
+ *          opened datatype is returned. Otherwise, the returned datatype
+ *          is read-only. If atomization of the datatype fails, then the
+ *          datatype is closed.
+ *
+ *          A datatype identifier returned from this function should be
+ *          released with H5Tclose() when the identifier is no longer
+ *          needed to prevent resource leaks.
+ *
+ * \note Datatype Identifiers
+ *
+ *          Please note that the datatype identifier is actually an object
+ *          identifier or a handle returned from opening the datatype. It
+ *          is not persistent and its value can be different from one HDF5
+ *          session to the next.
+ *
+ *          H5Tequal() can be used to compare datatypes.
+ *
+ *          HDF5 High Level APIs that may also be of interest are:
+ *
+ *          H5LTdtype_to_text() creates a text description of a
+ *          datatype.  H5LTtext_to_dtype() creates an HDF5 datatype
+ *          given a text description.
+ *
+ */
 H5_DLL hid_t  H5Dget_type(hid_t dset_id);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Returns an identifier for a copy of the dataset creation
+ *        property list for a dataset
+ *
+ * \dset_id
+ *
+ * \return \hid_t{dataset creation property list}
+ *
+ * \details H5Dget_create_plist() returns an identifier for
+ *          a copy of the dataset creation property list associated with
+ *          the dataset specified by \p dset_id.
+ *
+ *          The creation property list identifier should be released
+ *          with H5Pclose() to prevent resource leaks.
+ *
+ */
 H5_DLL hid_t  H5Dget_create_plist(hid_t dset_id);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Returns the dataset access property list associated with
+ *        a dataset
+ *
+ * \dset_id
+ *
+ * \return \hid_t{dataset access property list}
+ *
+ * \details H5Dget_access_plist() returns a copy of the
+ *          dataset access property list used to open the specified
+ *          dataset, \p dset_id. Modifications to the returned property
+ *          list will have no effect on the dataset it was retrieved from.
+ *
+ *          The chunk cache parameters in the returned property lists will
+ *          be those used by the dataset. If the properties in the file
+ *          access property list were used to determine the dataset's
+ *          chunk cache configuration, then those properties will be
+ *          present in the returned dataset access property list. If
+ *          the dataset does not use a chunked layout, then the chunk
+ *          cache properties will be set to the default. The chunk cache
+ *          properties in the returned list are considered to be “set”,
+ *          and any use of this list will override the corresponding
+ *          properties in the file’s file access property list.
+ *
+ *          All link access properties in the returned list will be set
+ *          to the default values.
+ *
+ *          The access property list identifier should be released with
+ *          H5Pclose() when the identifier is no longer needed so that
+ *          resource leaks will not develop.
+ *
+ * \since 1.8.3
+ *
+ */
 H5_DLL hid_t  H5Dget_access_plist(hid_t dset_id);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Returns the amount of storage allocated for a dataset
+ *
+ * \dset_id
+ *
+ * \return Returns the amount of storage space, in bytes, or 0 (zero).
+ *
+ * \details H5Dget_storage_size() returns the amount of storage,
+ *          in bytes, that is allocated in the file for the raw data of
+ *          the dataset specified by \p dset_id.
+ *
+ *          \note The amount of storage in this case is the storage
+ *          allocated in the written file, which will typically differ
+ *          from the space required to hold a dataset in working memory.
+ *
+ *          \li For contiguous datasets, the returned size equals the current
+ *          allocated size of the raw data.
+ *          \li For unfiltered chunked datasets, the returned size is the
+ *          number of allocated chunks times the chunk size.
+ *          \li For filtered chunked datasets, the returned size is the
+ *          space required to store the filtered data. For example, if a
+ *          compression filter is in use, H5Dget_storage_size() will return
+ *          the total space required to store the compressed chunks.
+ *
+ *          H5Dget_storage_size() reports only the space required to store
+ *          the data, not including that of any metadata.
+ *
+ * \attention H5Dget_storage_size() does not differentiate between 0 (zero),
+ *          the value returned for the storage size of a dataset
+ *          with no stored values, and 0 (zero), the value returned to
+ *          indicate an error.
+ *
+ *          \note Note that H5Dget_storage_size() is not generally an
+ *          appropriate function to use when determining the amount
+ *          of memory required to work with a dataset. In such
+ *          circumstances, you must determine the number of data
+ *          points in a dataset and the size of an individual data
+ *          element. H5Sget_simple_extent_npoints() and H5Tget_size()
+ *          can be used to get that information.
+ *
+ */
 H5_DLL hsize_t H5Dget_storage_size(hid_t dset_id);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Returns the amount of storage allocated within the file for a
+ * raw data chunk in a dataset
+ *
+ * \dset_id
+ * \param[in]  offset   Logical offset in the dataset for the chunk to query
+ * \param[out] chunk_bytes The size in bytes for the chunk
+ *
+ * \return \herr_t
+ *
+ * \details H5Dget_chunk_storage_size() returns the size in bytes
+ *          allocated in the file for a raw data chunk as specified by
+ *          its logical \p offset in the dataset \p dset_id. The size is
+ *          returned in \p chunk_nbytes. It is the size of the compressed
+ *          data if the chunk is filtered and the size may be zero if no
+ *          storage is allocated yet for the dataset.
+ *
+ * \since 1.10.2
+ *
+ */
 H5_DLL herr_t  H5Dget_chunk_storage_size(hid_t dset_id, const hsize_t *offset, hsize_t *chunk_bytes);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Retrieves number of chunks that have nonempty intersection with a
+ *        specified selection
+ *
+ * \dset_id
+ * \param[in]  fspace_id   File dataspace selection identifier
+ * \param[out] nchunks     Number of chunks in the selection
+ *
+ * \return \herr_t
+ *
+ * \details H5Dget_num_chunks() retrieves the number of chunks
+ *          nchunks in a set of selected elements specified by \p fspace_id
+ *          for a dataset specified by the identifier \p dset_id. If \p
+ *          fspace_id is #H5S_ALL, the function will retrieve the total
+ *          number of chunks stored for the dataset.
+ *
+ *          \p fspace_id specifies the file dataspace selection.  It is
+ *          intended to take #H5S_ALL for specifying the current selection.
+ *
+ *          \note Please be aware that this function currently does not
+ *          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, application can get
+ *          the dataspace for the dataset using H5Dget_space() and pass that
+ *          in for \p fspace_id.  This will be fixed in coming releases.
+ *
+ * \since 1.10.5
+ *
+ */
 H5_DLL herr_t  H5Dget_num_chunks(hid_t dset_id, hid_t fspace_id, hsize_t *nchunks);
-H5_DLL herr_t  H5Dget_chunk_info_by_coord(hid_t dset_id, const hsize_t *coord, unsigned *filter_mask,
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Retrieves information about a chunk specified by its coordinates
+ *
+ * \dset_id
+ * \param[in]  offset      Logical position of the chunk’s first element
+ * \param[out] filter_mask Indicating filters used with the chunk when written
+ * \param[out] addr        Chunk address in the file
+ * \param[out] size        Chunk size in bytes, 0 if chunk doesn’t exist
+ *
+ * \return \herr_t
+ *
+ * \details H5Dget_chunk_info_by_coord() retrieves the \p filter_mask, \p size,
+ *          and \p addr for a chunk in the dataset specified by \p dset_id,
+ *          using the coordinates specified by \p offset.
+ *
+ *          If the queried chunk does not exist in the file, \p size will
+ *          be set to 0, \p addr to #HADDR_UNDEF, and the buffer \p
+ *          filter_mask will not be modified.
+ *
+ *          \p offset is a pointer to a one-dimensional array with a size
+ *          equal to the dataset’s rank. Each element is the logical
+ *          position of the chunk’s first element in a dimension.
+ *
+ * \since 1.10.5
+ *
+ */
+H5_DLL herr_t  H5Dget_chunk_info_by_coord(hid_t dset_id, const hsize_t *offset, unsigned *filter_mask,
                                           haddr_t *addr, hsize_t *size);
-H5_DLL herr_t  H5Dget_chunk_info(hid_t dset_id, hid_t fspace_id, hsize_t chk_idx, hsize_t *coord,
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Retrieves information about a chunk specified by its index
+ *
+ * \dset_id
+ * \param[in]  fspace_id File dataspace selection identifier (See Note below)
+ * \param[in]  chk_idx   Index of the chunk
+ * \param[out] offset    Logical position of the chunk’s first element
+ * \param[out] filter_mask Indicating filters used with the chunk when written
+ * \param[out] addr      Chunk address in the file
+ * \param[out] size      Chunk size in bytes, 0 if chunk doesn’t exist
+ *
+ * \return \herr_t
+ *
+ * \details H5Dget_chunk_info() retrieves the offset coordinates
+ *          offset, filter mask filter_mask, size size and address addr for
+ *          the dataset specified by the identifier dset_id and the chunk
+ *          specified by the index index. The chunk belongs to a set of
+ *          chunks in the selection specified by 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
+ *          not be modified. NULL can be passed in for any \p out parameters.
+ *
+ *          \p chk_idx is the chunk index in the selection. 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
+ *
+ *          \note As of 1.10.5, the dataspace intersection is not yet
+ *          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.
+ *
+ *          \note Please be aware that this function currently does not
+ *          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, application can get
+ *          the dataspace for the dataset using H5Dget_space() and pass that
+ *          in for \p fspace_id.  This will be fixed in coming releases.
+ *
+ * \since 1.10.5
+ *
+ */
+H5_DLL herr_t  H5Dget_chunk_info(hid_t dset_id, hid_t fspace_id, hsize_t chk_idx, hsize_t *offset,
                                  unsigned *filter_mask, haddr_t *addr, hsize_t *size);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Returns dataset address in file
+ *
+ * \dset_id
+ *
+ * \return Returns the offset in bytes; otherwise, returns #HADDR_UNDEF,
+ *         a negative value.
+ *
+ * \details H5Dget_offset() returns the address in the file of
+ *          the dataset, \p dset_id. That address is expressed as the
+ *          offset in bytes from the beginning of the file.
+ *
+ * \since 1.6.0
+ *
+ */
 H5_DLL haddr_t H5Dget_offset(hid_t dset_id);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Reads raw data from a dataset into a provided buffer
+ *
+ * \dset_id                 Identifier of the dataset to read from
+ * \param[in] mem_type_id   Identifier of the memory datatype
+ * \param[in] mem_space_id  Identifier of the memory dataspace
+ * \param[in] file_space_id Identifier of the dataset's dataspace in the file
+ * \param[in] dxpl_id       Identifier of a transfer property list
+ * \param[out] buf          Buffer to receive data read from file
+ *
+ * \return \herr_t
+ *
+ * \details H5Dread() reads a dataset, specified by its identifier
+ *          \p dset_id, from the file into an application memory buffer \p
+ *          buf. Data transfer properties are defined by the argument \p
+ *          dxpl_id. The memory datatype of the (partial) dataset
+ *          is identified by the identifier \p mem_type_id. The part
+ *          of the dataset to read is defined by \p mem_space_id and \p
+ *          file_space_id.
+ *
+ *          \p file_space_id is used to specify only the selection within
+ *          the file dataset's dataspace. Any dataspace specified in \p
+ *          file_space_id is ignored by the library and the dataset's
+ *          dataspace is always used. \p file_space_id can be the constant
+ *          #H5S_ALL, which indicates that the entire file dataspace,
+ *          as defined by the current dimensions of the dataset, is to
+ *          be selected.
+ *
+ *          \p mem_space_id is used to specify both the memory dataspace
+ *          and the selection within that dataspace. \p mem_space_id can
+ *          be the constant #H5S_ALL, in which case the file dataspace is
+ *          used for the memory dataspace and the selection defined with \p
+ *          file_space_id is used for the selection within that dataspace.
+ *
+ *          If raw data storage space has not been allocated for the dataset
+ *          and a fill value has been defined, the returned buffer \p buf
+ *          is filled with the fill value.
+ *
+ *          The behavior of the library for the various combinations of
+ *          valid dataspace identifiers and #H5S_ALL for the \p mem_space_id
+ *          and the \p file_space_id parameters is described below:
+ *
+ *          <table>
+ *            <tr>
+ *              <th>mem_space_id</th>
+ *              <th>file_space_id</th>
+ *              <th>Behavior</th>
+ *            </tr>
+ *            <tr>
+ *              <td>valid dataspace ID</td>
+ *              <td>valid dataspace ID</td>
+ *              <td>\p mem_space_id specifies the memory dataspace and the
+ *                  selection within it. \p file_space_id specifies the
+ *                  selection within the file dataset's dataspace.</td>
+ *            </tr>
+ *            <tr>
+ *              <td>#H5S_ALL</td>
+ *              <td>valid dataspace ID</td>
+ *              <td>The file dataset's dataspace is used for the memory
+ *                  dataspace and the selection specified with \p file_space_id
+ *                  specifies the selection within it. The combination of the
+ *                  file dataset's dataspace and the selection from
+ *                  \p file_space_id is used for memory also.</td>
+ *            </tr>
+ *            <tr>
+ *              <td>valid dataspace ID</td>
+ *              <td>#H5S_ALL</td>
+ *              <td>\p mem_space_id specifies the memory dataspace and the
+ *                  selection within it. The selection within the file
+ *                  dataset's dataspace is set to the "all" selection.</td>
+ *            </tr>
+ *            <tr>
+ *              <td>#H5S_ALL</td>
+ *              <td>#H5S_ALL</td>
+ *              <td>The file dataset's dataspace is used for the memory
+ *                  dataspace and the selection within the memory dataspace
+ *                  is set to the "all" selection. The selection within the
+ *                  file dataset's dataspace is set to the "all" selection.</td>
+ *            </tr>
+ *          </table>
+ *
+ * \details Setting an #H5S_ALL selection indicates that the entire
+ *          dataspace, as defined by the current dimensions of a dataspace,
+ *          will be selected. The number of elements selected in the memory
+ *          dataspace must match the number of elements selected in the
+ *          file dataspace.
+ *
+ *          \p dxpl_id can be the constant #H5P_DEFAULT, in which case the
+ *          default data transfer properties are used.
+ *
+ */
 H5_DLL herr_t  H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id,
-                       hid_t plist_id, void *buf /*out*/);
+                       hid_t dxpl_id, void *buf /*out*/);
+
 H5_DLL herr_t  H5Dread_async(const char *app_file, const char *app_func, unsigned app_line, hid_t dset_id,
-                             hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t plist_id,
+                             hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t dxpl_id,
                              void *buf /*out*/, hid_t es_id);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Writes raw data from a buffer to a dataset
+ *
+ * \param[in] dset_id        Identifier of the dataset to read from
+ * \param[in] mem_type_id    Identifier of the memory datatype
+ * \param[in] mem_space_id   Identifier of the memory dataspace
+ * \param[in] file_space_id  Identifier of the dataset's dataspace in the file
+ * \dxpl_id
+ * \param[out] buf           Buffer with data to be written to the file
+ *
+ * \return \herr_t
+ *
+ * \details H5Dwrite() writes a (partial) dataset, specified by
+ *          its identifier \p dset_id, from the application memory buffer \p
+ *          buf into the file. Data transfer properties are defined by the
+ *          argument \p dxpl_id. The memory datatype of the (partial)
+ *          dataset is identified by the identifier \p mem_type_id. The
+ *          part of the dataset to write is defined by \p mem_space_id
+ *          and \p file_space_id.
+ *
+ *          If \p mem_type_id is either a fixed-length or variable-length
+ *          string, it is important to set the string length when defining
+ *          the datatype. String datatypes are derived from #H5T_C_S1
+ *          (or #H5T_FORTRAN_S1 for Fortran codes), which defaults
+ *          to 1 character in size. See H5Tset_size() and Creating
+ *          variable-length string datatypes.
+ *
+ *          \p file_space_id is used to specify only the selection within
+ *          the file dataset's dataspace. Any dataspace specified in \p
+ *          file_space_id is ignored by the library and the dataset's
+ *          dataspace is always used. \p file_space_id can be the constant
+ *          #H5S_ALL, which indicates that the entire file dataspace,
+ *          as defined by the current dimensions of the dataset, is to
+ *          be selected.
+ *
+ *          \p mem_space_id is used to specify both the memory dataspace
+ *          and the selection within that dataspace. mem_space_id can be
+ *          the constant #H5S_ALL, in which case the file dataspace is
+ *          used for the memory dataspace and the selection defined with \p
+ *          file_space_id is used for the selection within that dataspace.
+ *
+ *          The behavior of the library for the various combinations of
+ *          valid dataspace IDs and #H5S_ALL for the mem_space_id and
+ *          thefile_space_id parameters is described below:
+ *
+ *          <table>
+ *          <tr><th>\c mem_space_id</th>
+ *          <th>\c file_space_id</th>
+ *          <th>Behavior</th></tr>
+ *          <tr><td>valid dataspace ID</td>
+ *              <td>valid dataspace ID</td>
+ *              <td>\p mem_space_id specifies the memory dataspace and the
+ *                  selection within it. \p file_space_id specifies the
+ *                  selection within the file dataset's dataspace.</td></tr>
+ *          <tr><td>#H5S_ALL</td>
+ *              <td>valid dataspace ID</td>
+ *              <td>The file dataset's dataspace is used for the memory
+ *                  dataspace and the selection specified with \p file_space_id
+ *                  specifies the selection within it. The combination of the
+ *                  file dataset's dataspace and the selection from \p
+ *                  file_space_id is used for memory also. valid dataspace
+ *                  ID</td></tr>
+ *          <tr><td>valid dataspace ID</td>
+ *              <td>#H5S_ALL</td>
+ *              <td>\p mem_space_id specifies the memory dataspace and the
+ *                  selection within it. The selection within the file
+ *                  dataset's dataspace is set to "all" selection.</td></tr>
+ *          <tr><td>#H5S_ALL</td>
+ *              <td>#H5S_ALL</td>
+ *              <td>The file dataset's dataspace is used for the memory
+ *                  dataspace and the selection within the memory dataspace is
+ *                  set to the "all" selection. The selection within the file
+ *                  dataset's dataspace is set to the "all"
+ *                  selection.</td></tr>
+ *          </table>
+ *          Setting an "all" selection indicates that the entire dataspace,
+ *          as defined by the current dimensions of a dataspace, will
+ *          be selected. The number of elements selected in the memory
+ *          dataspace must match the number of elements selected in the
+ *          file dataspace.
+ *
+ *          \p dxpl_id can be the constant #H5P_DEFAULT, in which
+ *          case the default data transfer properties are used.
+ *
+ *          Writing to a dataset will fail if the HDF5 file was not opened
+ *          with write access permissions.
+ *
+ *          If the dataset's space allocation time is set to
+ *          #H5D_ALLOC_TIME_LATE or #H5D_ALLOC_TIME_INCR and the space for
+ *          the dataset has not yet been allocated, that space is allocated
+ *          when the first raw data is written to the dataset. Unused space
+ *          in the dataset will be written with fill values at the same
+ *          time if the dataset's fill time is set to #H5D_FILL_TIME_IFSET
+ *          or #H5D_FILL_TIME_ALLOC.
+ *
+ * \attention If a dataset's storage layout is 'compact', care must be
+ *          taken when writing data to the dataset in parallel. A compact
+ *          dataset's raw data is cached in memory and may be flushed
+ *          to the file from any of the parallel processes, so parallel
+ *          applications should always attempt to write identical data to
+ *          the dataset from all processes.
+ *
+ * \see H5Pset_fill_time(), H5Pset_alloc_time()
+ *
+ */
 H5_DLL herr_t  H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id,
-                        hid_t plist_id, const void *buf);
+                        hid_t dxpl_id, const void *buf);
+
 H5_DLL herr_t  H5Dwrite_async(const char *app_file, const char *app_func, unsigned app_line, hid_t dset_id,
-                              hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t plist_id,
+                              hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t dxpl_id,
                               const void *buf, hid_t es_id);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Writes a raw data chunk from a buffer directly to a dataset in a file
+ *
+ * \dset_id
+ * \dxpl_id
+ * \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
+ *
+ * \details H5Dwrite_chunk() writes a raw data chunk as specified
+ *          by its logical offset \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. Only one chunk can be written with this function.
+ *
+ *          H5Dwrite_chunk() replaces the now deprecated H5DOwrite_chunk()
+ *          function, which was located in the high level optimization
+ *          library. The parameters and behavior are identical to the
+ *          original.
+ *
+ *          \p filters is a mask providing a record of which filters are
+ *          used with the 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.
+ *          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 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 H5Dread_chunk() and
+ *          H5Dwrite_chunk(), as they read and write data chunks directly
+ *          in a file. H5Dwrite_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
+ *          Using the Direct Chunk Write Function for more information.
+ *
+ * \note    H5Dread_chunk() and H5Dwrite_chunk() are not supported under
+ *          parallel and do not support variable length types.
+ *
+ * \since 1.10.2
+ *
+ */
 H5_DLL herr_t  H5Dwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *offset,
                               size_t data_size, const void *buf);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Reads a raw data chunk directly from a dataset in a file into
+ * a buffer
+ *
+ * \dset_id
+ * \dxpl_id
+ * \param[in]  offset   Logical position of the chunk’s first element in the
+ *                      dataspace
+ * \param[in,out]  filters  Mask for identifying the filters in use
+ * \param[out]  buf     Buffer containing data to be written to the chunk
+ *
+ * \return \herr_t
+ *
+ * \details H5Dread_chunk() reads a raw data chunk as specified by
+ *          its logical offset \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 offset is an array specifying the logical position of the
+ *          first element of the chunk in the dataset’s dataspace. The
+ *          length of the \p 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.
+ *
+ *          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
+ *          (0 ≤ position < 32) is turned on.
+ *
+ *          \p buf is the memory buffer containing the chunk read from
+ *          the dataset in the file.
+ *
+ * \attention Exercise caution when using H5Dread_chunk() and
+ *          H5Dwrite_chunk(), as they read and write data chunks directly
+ *          in a file. H5Dwrite_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
+ *          Using the Direct Chunk Write Function for more information.
+ *
+ * \note H5Dread_chunk() and H5Dwrite_chunk() are not supported under
+ *          parallel and do not support variable length types.
+ *
+ * \since 1.10.2
+ *
+ */
 H5_DLL herr_t  H5Dread_chunk(hid_t dset_id, hid_t dxpl_id, const hsize_t *offset, uint32_t *filters,
                              void *buf);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Iterates over all selected elements in a dataspace
+ *
+ * \param[in,out] buf Buffer containing the elements to iterate over
+ * \type_id
+ * \space_id
+ * \param[in] op Function pointer
+ * \param[in,out] operator_data User-defined data
+ *
+ * \return \success{The return value of the first operator that returns
+ *                  non-zero, or zero if all members were processed with no
+ *                  operator returning non-zero.}
+ * \return \failure{Negative if an error occurs in the library, or the negative
+ *                  value returned by one of the operators.}
+ *
+ * \details H5Diterate() iterates over all the data elements
+ *          in the memory buffer \p buf, executing the callback function
+ *          \p op once for each such data element.
+ *
+ *          The prototype of the callback function \p op is as follows
+ *          (as defined in the source code file H5Lpublic.h):
+ *          \snippet this H5D_operator_t_snip
+ *          The parameters of this callback function are:
+ *
+ *          <table>
+ *          <tr><td>\c elem</td>
+ *              <td><tt>[in,out]</tt></td>
+ *              <td>Pointer to the memory buffer containing the current
+ *                  data element</td></tr>
+ *          <tr><td>\c type_id</td>
+ *              <td><tt>[in]</tt></td>
+ *              <td>Datatype identifier of the elements stored in elem</td></tr>
+ *          <tr><td>\c ndim</td>
+ *              <td><tt>[in]</tt></td>
+ *              <td>Number of dimensions for the point array</td></tr>
+ *          <tr><td>\c point</td>
+ *              <td><tt>[in]</tt></td>
+ *              <td>Array containing the location of the element within
+ *                  the original dataspace</td></tr>
+ *          <tr><td>\c operator_data</td>
+ *              <td><tt>[in,out]</tt></td>
+ *              <td>Pointer to any user-defined data associated with the
+ *                  operation</td></tr>
+ *          </table>
+ *
+ *          The possible return values from the callback function, and
+ *          the effect ofeach,are as follows:
+ *
+ *          \li Zero causes the iterator to continue, returning zero
+ *          when all data elements have been processed.
+ *          \li A positive value causes the iterator to immediately
+ *          return that positive value, indicating short-circuit success.
+ *          \li A negative value causes the iterator to immediately return
+ *          that value, indicating failure.
+ *
+ *          The \p operator_data parameter is a user-defined pointer to
+ *          the data required to process dataset elements in the course
+ *          of the iteration. If operator needs to pass data back to the
+ *          application, such data can be returned in this same buffer. This
+ *          pointer is passed back to each step of the iteration in the
+ *          operator callback function’s operator_data parameter.
+ *
+ *          Unlike other HDF5 iterators, this iteration operation cannot
+ *          be restarted at the point of exit; a second H5Diterate()
+ *          call will always restart at the beginning.
+ *
+ *
+ * \since 1.10.2
+ *
+ */
 H5_DLL herr_t  H5Diterate(void *buf, hid_t type_id, hid_t space_id, H5D_operator_t op, void *operator_data);
-H5_DLL herr_t  H5Dvlen_get_buf_size(hid_t dataset_id, hid_t type_id, hid_t space_id, hsize_t *size);
-H5_DLL herr_t  H5Dfill(const void *fill, hid_t fill_type, void *buf, hid_t buf_type, hid_t space);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Determines the number of bytes required to store variable-length
+ *        (VL) data
+ *
+ * \dset_id
+ * \type_id
+ * \space_id
+ * \param[out] size Size in bytes of the memory buffer required to store
+ *        the VL data
+ *
+ * \return \herr_t
+ *
+ * \details H5Dvlen_get_buf_size() determines the number of bytes
+ *          required to store the VL data from the dataset, using \p
+ *          space_id for the selection in the dataset on disk and the \p
+ *          type_id for the memory representation of the VL data in memory.
+ *          \p size is returned with the number of bytes required to store
+ *          the VL data in memory.
+ *
+ * \since 1.10.2
+ *
+ */
+H5_DLL herr_t  H5Dvlen_get_buf_size(hid_t dset_id, hid_t type_id, hid_t space_id, hsize_t *size);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Fills dataspace elements with a fill value in a memory buffer
+ *
+ * \param[in] fill          Pointer to the fill value to be used
+ * \param[in] fill_type_id  Fill value datatype identifier
+ * \param[in,out] buf       Pointer to the memory buffer containing the
+ *                          selection to be filled
+ * \param[in] buf_type_id   Datatype of dataspace elements to be filled
+ * \space_id
+ *
+ * \return \herr_t
+ *
+ * \details H5Dfill() fills the dataspace selection in memory, \p space_id,
+ *          with the fill value specified in \p fill. If \p fill is NULL,
+ *          a fill value of 0 (zero) is used.
+ *
+ *          \p fill_type_id specifies the datatype of the fill value.
+ *          \p buf specifies the buffer in which the dataspace elements
+ *          will be written.
+ *          \p buf_type_id specifies the datatype of those data elements.
+ *
+ * \note Note that if the fill value datatype differs from the memory
+ *          buffer datatype, the fill value will be converted to the memory
+ *          buffer datatype before filling the selection.
+ *
+ * \note Applications sometimes write data only to portions of an
+ *          allocated dataset. It is often useful in such cases to fill
+ *          the unused space with a known fill value. See the following
+ *          function for more information:
+ *          - H5Pset_fill_value()
+ *          - H5Pget_fill_value()
+ *          - H5Pfill_value_defined()
+ *          - H5Pset_fill_time()
+ *          - H5Pget_fill_time()
+ *          - H5Pcreate()
+ *          - H5Pcreate_anon()
+ *
+ */
+H5_DLL herr_t  H5Dfill(const void *fill, hid_t fill_type_id, void *buf, hid_t buf_type_id, hid_t space_id);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Changes the sizes of a dataset’s dimensions
+ *
+ * \dset_id
+ * \param[in] size[]   Array containing the new magnitude of each dimension
+ *                     of the dataset
+ *
+ * \return \herr_t
+ *
+ * \details H5Dset_extent() sets the current dimensions of the
+ *          chunked dataset \p dset_id to the sizes specified in size.
+ *
+ *          \p size is a 1-dimensional array with n elements, where \p n is
+ *          the rank of the dataset’s current dataspace.
+ *
+ *          This function can be applied to the following datasets:
+ *          - A chunked dataset with unlimited dimensions
+ *          - A chunked dataset with fixed dimensions if the new dimension
+ *          sizes are less than the maximum sizes set with maxdims (see
+ *          H5Screate_simple())
+ *          - An external dataset with unlimited dimensions
+ *          - An external dataset with fixed dimensions if the new dimension
+ *          sizes are less than the maximum sizes set with \p maxdims
+ *
+ *          Note that external datasets are always contiguous and can be
+ *          extended only along the first dimension.
+ *
+ *          Space on disk is immediately allocated for the new dataset extent if
+ *          the dataset’s space allocation time is set to #H5D_ALLOC_TIME_EARLY.
+ *
+ *          Fill values will be written to the dataset in either of the
+ *          following situations, but not otherwise:
+ *
+ *          - If the dataset’s fill time is set to #H5D_FILL_TIME_IFSET and a
+ *            fill value is defined (see H5Pset_fill_time() and
+ *            H5Pset_fill_value())
+ *          - If the dataset’s fill time is set to #H5D_FILL_TIME_ALLOC
+ *            (see H5Pset_alloc_time())
+ *
+ *          \note
+ *          \li If the sizes specified in \p size array are smaller than
+ *          the dataset’s current dimension sizes, H5Dset_extent() will reduce
+ *          the dataset’s dimension sizes to the specified values. It is the
+ *          user application’s responsibility to ensure that valuable data is
+ *          not lost as H5Dset_extent() does not check.
+ *
+ *          \li Except for external datasets, H5Dset_extent() is for use with
+ *          chunked datasets only, not contiguous datasets.
+ *
+ *          \li A call to H5Dset_extent() affects the dataspace of a dataset.
+ *          If a dataspace handle was opened for a dataset prior to a call to
+ *          H5Dset_extent() then that dataspace handle will no longer reflect
+ *          the correct dataspace extent of the dataset. H5Dget_space() must
+ *          be called (after closing the previous handle) to obtain the current
+ *          dataspace extent.
+ *
+ * \since 1.8.0
+ *
+ */
 H5_DLL herr_t  H5Dset_extent(hid_t dset_id, const hsize_t size[]);
 H5_DLL herr_t  H5Dset_extent_async(const char *app_file, const char *app_func, unsigned app_line,
                                    hid_t dset_id, const hsize_t size[], hid_t es_id);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Flushes all buffers associated with a dataset to disk
+ *
+ * \dset_id
+ *
+ * \return \herr_t
+ *
+ * \details H5Dflush() causes all buffers associated with a
+ *          dataset to be immediately flushed to disk without removing
+ *          the data from the cache.
+ *
+ *          \note HDF5 does not possess full control over buffering.
+ *          H5Dflush() 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.
+ *
+ */
 H5_DLL herr_t  H5Dflush(hid_t dset_id);
+
 H5_DLL herr_t  H5Dwait(hid_t dset_id);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Refreshes all buffers associated with a dataset
+ *
+ * \dset_id
+ *
+ * \return \herr_t
+ *
+ * \details H5Drefresh() causes all buffers associated with a
+ *          dataset to be cleared and immediately re-loaded with updated
+ *          contents from disk.
+ *
+ *          This function essentially closes the dataset, evicts all
+ *          metadata associated with it from the cache, and then re-opens
+ *          the dataset. The reopened dataset is automatically re-registered
+ *          with the same identifier.
+ *
+ * \since 1.10.2
+ *
+ */
 H5_DLL herr_t  H5Drefresh(hid_t dset_id);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Scatters data into a selection within a memory buffer
+ *
+ * \param[in]  op       Callback function which provides data to be scattered
+ * \param[in]  op_data  User-defined pointer to data required by op
+ * \param[in]  type_id  Identifier for the datatype describing the data in
+ *                      both the source and destination buffers
+ * \param[in]  dst_space_id    Identifier for the dataspace for destination
+ * \param[out] dst_buf  Destination buffer which the data will be scattered to
+ *
+ * \return \herr_t
+ *
+ * \details H5Dscatter() retrieves data from the supplied callback
+ *          \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
+ *          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
+ *          the source and destination buffers.
+ *
+ *          \p dst_buf must be at least as large as the number of elements
+ *          in the extent of \p dst_space_id times the size in bytes of
+ *          \p type_id.
+ *
+ *          To retrieve the data to be scattered, H5Dscatter() repeatedly
+ *          calls \p op, which should return a valid source buffer, until
+ *          enough data to fill the selection has been retrieved. The
+ *          prototype of the callback function \p op is as follows (as
+ *          defined in the source code file H5Dpublic.h):
+ *          \snippet this H5D_scatter_func_t_snip
+ *          The parameters of this callback function are described below:
+ *
+ *          <table>
+ *          <tr><td>\c src_buf</td>
+ *              <td><tt>[out]</tt></td>
+ *              <td>Pointer to the buffer holding the next set of elements to
+ *                  scatter. On entry, the value of where \c src_buf points to
+ *                  is undefined. The callback function should set \c src_buf
+ *                  to point to the next set of elements.</td></tr>
+ *          <tr><td>\c src_buf_bytes_used</td>
+ *              <td><tt>[out]</tt></td>
+ *              <td>Pointer to the number of valid bytes in \c src_buf. On
+ *                  entry, the value where \c src_buf_bytes_used points to is
+ *                  undefined. The callback function should set
+ *                  \c src_buf_bytes_used to the of valid bytes in \c src_buf.
+ *                  This number must be a multiple of the datatype size.
+ *                  </td></tr>
+ *          <tr><td>\c op_data</td>
+ *              <td><tt>[in,out]</tt></td>
+ *              <td>User-defined pointer to data required by the callback
+ *                  function. A pass-through of the \c op_data pointer provided
+ *                  with the H5Dscatter() function call.</td></tr>
+ *          </table>
+ *
+ *          The callback function should always return at least one
+ *          element in \p src_buf, and must not return more elements
+ *          than are remaining to be scattered. This function will be
+ *          repeatedly called until all elements to be scattered have
+ *          been returned. The callback function should return zero (0)
+ *          to indicate success, and a negative value to indicate failure.
+ *
+ * \since 1.10.2
+ *
+ */
 H5_DLL herr_t  H5Dscatter(H5D_scatter_func_t op, void *op_data, hid_t type_id, hid_t dst_space_id,
                           void *dst_buf);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Gathers data from a selection within a memory buffer
+ * raw data chunk in a dataset
+ *
+ * \param[in]  src_space_id  Dataspace identifier for the source buffer
+ * \param[in]  src_buf   Source buffer which the data will be gathered from
+ * \param[in]  type_id   Datatype identifier for the source
+ * \param[in]  dst_buf_size   Size in bytes of \p dst_buf
+ * \param[out] dst_buf   Destination buffer for the gathered data
+ * \param[in]  op   Callback function which handles the gathered data
+ * \param[in]  op_data   User-defined pointer to data required by \p op
+ *
+ * \return \herr_t
+ *
+ * \details H5Dgather() retrieves data from a selection within the supplied
+ *          buffer src_buf and passes it to the supplied callback function
+ *          \p op in a contiguous form.
+ *
+ *          The dataspace \p src_space_id describes both the dimensions of
+ *          the source buffer and the selection within the source buffer
+ *          to gather data from.
+ *
+ *          \p src_buf must be at least the size of the gathered data, that
+ *          is, the number of elements in the extent of \p src_space_id
+ *          times the size in bytes of \p type_id.
+ *
+ *          The datatype \p type_id describes the data in both the source
+ *          and destination buffers. This information is used to calculate
+ *          the element size.
+ *
+ *          The data is gathered into \p dst_buf, which needs to be large
+ *          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.
+ *          It is optional if \p dst_buf is large enough to hold all of the
+ *          gathered data; required otherwise.
+ *
+ *          If no callback function is provided, H5Dgather() simply gathers
+ *          the data into \p dst_buf and returns. If a callback function is
+ *          provided, H5Dgather() repeatedly gathers up to \p dst_buf_size
+ *          bytes to process the serialized data. The prototype of the
+ *          callback function \p op is as follows (as defined in the source
+ *          code file H5Dpublic.h):
+ *          \snippet this H5D_gather_func_t_snip
+ *          The parameters of this callback function are described in the
+ *          table below.
+ *          <table>
+ *          <tr><td>\c dst_buf</td>
+ *              <td>Pointer to the destination buffer which has been filled
+ *                  with the next set of elements gathered. This will always be
+ *                  identical to the \p dst_buf passed to H5Dgather().</td></tr>
+ *          <tr><td>\c dst_buf_bytes_used</td>
+ *              <td>Pointer to the number of valid bytes in \p dst_buf.
+ *                  This number must be a multiple of the datatype
+ *                  size.</td></tr>
+ *          <tr><td>\c op_data</td>
+ *              <td>User-defined pointer to data required by the callback
+ *                  function; a pass-through of the \p op_data pointer
+ *                  provided with the H5Dgather() function call.</td></tr>
+ *          </table>
+ *          The callback function should process, store, or otherwise,
+ *          make use of the data returned in \p dst_buf before it returns,
+ *          because the buffer will be overwritten unless it is the last
+ *          call to the callback. This function will be repeatedly called
+ *          until all gathered elements have been passed to the callback
+ *          in \p dst_buf. The callback function should return zero (0)
+ *          to indicate success, and a negative value to indicate failure.
+ *
+ * \since 1.10.2
+ *
+ */
 H5_DLL herr_t  H5Dgather(hid_t src_space_id, const void *src_buf, hid_t type_id, size_t dst_buf_size,
                          void *dst_buf, H5D_gather_func_t op, void *op_data);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Closes the specified dataset
+ *
+ * \dset_id
+ *
+ * \return \herr_t
+ *
+ * \details H5Dclose() ends access to a dataset specified by \p dset_id
+ *          and releases resources used by it.
+ *
+ * \attention Further use of a released dataset identifier is illegal; a
+ *          function using such an identifier will generate an error.
+ *
+ * \since 1.8.0
+ *
+ * \see H5Dcreate2(), H5Dopen2()
+ *
+ */
 H5_DLL herr_t  H5Dclose(hid_t dset_id);
 H5_DLL herr_t  H5Dclose_async(const char *app_file, const char *app_func, unsigned app_line, hid_t dset_id,
                               hid_t es_id);
@@ -236,10 +1465,10 @@ H5_DLL herr_t H5Dget_chunk_index_type(hid_t did, H5D_chunk_index_t *idx_type);
 /* Typedefs */
 
 /* Function prototypes */
-H5_DLL hid_t  H5Dcreate1(hid_t file_id, const char *name, hid_t type_id, hid_t space_id, hid_t dcpl_id);
-H5_DLL hid_t  H5Dopen1(hid_t file_id, const char *name);
+H5_DLL hid_t  H5Dcreate1(hid_t loc_id, const char *name, hid_t type_id, hid_t space_id, hid_t dcpl_id);
+H5_DLL hid_t  H5Dopen1(hid_t loc_id, const char *name);
 H5_DLL herr_t H5Dextend(hid_t dset_id, const hsize_t size[]);
-H5_DLL herr_t H5Dvlen_reclaim(hid_t type_id, hid_t space_id, hid_t plist_id, void *buf);
+H5_DLL herr_t H5Dvlen_reclaim(hid_t type_id, hid_t space_id, hid_t dxpl_id, void *buf);
 
 #endif /* H5_NO_DEPRECATED_SYMBOLS */
 
diff --git a/src/H5Gmodule.h b/src/H5Gmodule.h
index 5f06405..ed617ec 100644
--- a/src/H5Gmodule.h
+++ b/src/H5Gmodule.h
@@ -29,4 +29,11 @@
 #define H5_MY_PKG_ERR  H5E_SYM
 #define H5_MY_PKG_INIT YES
 
+/**
+ * \defgroup H5G H5G
+ * \brief Group Interface
+ * \details The HDF5 Group Interface, H5G, provides a mechanism for managing
+ *          HDF5 groups and their members, which are other HDF5 objects.
+ */
+
 #endif /* _H5Gmodule_H */
diff --git a/src/H5Gpublic.h b/src/H5Gpublic.h
index f209c3d..e46bef6 100644
--- a/src/H5Gpublic.h
+++ b/src/H5Gpublic.h
@@ -51,12 +51,15 @@ typedef enum H5G_storage_type_t {
 } H5G_storage_type_t;
 
 /* Information struct for group (for H5Gget_info/H5Gget_info_by_name/H5Gget_info_by_idx) */
+//! [H5G_info_t_snip]
 typedef struct H5G_info_t {
     H5G_storage_type_t storage_type; /* Type of storage for links in group */
     hsize_t            nlinks;       /* Number of links in group */
     int64_t            max_corder;   /* Current max. creation order value for group */
     hbool_t            mounted;      /* Whether group has a file mounted on it */
 } H5G_info_t;
+//! [H5G_info_t_snip]
+
 
 /********************/
 /* Public Variables */
@@ -69,29 +72,355 @@ typedef struct H5G_info_t {
 extern "C" {
 #endif
 
+/**
+ *-------------------------------------------------------------------------
+ * \ingroup H5G
+ *
+ * \brief Creates a new group and links it into the file
+ *
+ * \fgdta_loc_id
+ * \param[in] name      Name of the group to create
+ * \lcpl_id
+ * \gcpl_id
+ * \gapl_id
+ *
+ * \return \hid_t{group}
+ *
+ * \details H5Gcreate2() creates a new group in a file. After a
+ *          group has been created, links to datasets and to other groups
+ *          can be added.
+ *
+ *          The \p loc_id and \p name parameters specify where the group
+ *          is located. \p loc_id may be a file, group, dataset, named
+ *          datatype or attribute in the file. If an attribute, dataset,
+ *          or named datatype is specified for \p loc_id then the group
+ *          will be created at the location where the attribute, dataset,
+ *          or named datatype is attached. \p name is the link to the group;
+ *          \p name may be either an absolute path in the file (the links
+ *          from the root group to the new group) or a relative path from
+ *          \p loc_id (the link(s) from the group specified by \p loc_id
+ *          to the new group).
+ *
+ *          \p lcpl_id, \p gcpl_id, and \p gapl_id are property list
+ *          identifiers. These property lists govern how the link to the
+ *          group is created, how the group is created, and how the group
+ *          can be accessed in the future, respectively. #H5P_DEFAULT can
+ *          be passed in if the default properties are appropriate for
+ *          these property lists. Currently, there are no APIs for the
+ *          group access property list; use #H5P_DEFAULT.
+ *
+ *          The group identifier should be closed by H5Gclose() when access
+ *          is no longer required to prevent resource leaks.
+ *
+ * \since 1.8.0
+ *
+ * \see H5Gopen2(), H5Gclose()
+ *
+ */
 H5_DLL hid_t  H5Gcreate2(hid_t loc_id, const char *name, hid_t lcpl_id, hid_t gcpl_id, hid_t gapl_id);
 H5_DLL hid_t  H5Gcreate_async(const char *app_file, const char *app_func, unsigned app_line, hid_t loc_id,
                               const char *name, hid_t lcpl_id, hid_t gcpl_id, hid_t gapl_id, hid_t es_id);
+
+/**
+ *-------------------------------------------------------------------------
+ * \ingroup H5G
+ *
+ * \brief Creates a new empty group without linking it into the file structure
+ *
+ * \fgdta_loc_id
+ * \gcpl_id
+ * \gapl_id
+ *
+ * \return \hid_t{group}
+ *
+ * \details H5Gcreate_anon() creates a new empty group in the file
+ *          specified by \p loc_id. With default settings, H5Gcreate_anon()
+ *          provides similar functionality to that provided by
+ *          H5Gcreate1(), with the differences described in the list below.
+ *
+ *          The new group’s creation and access properties are specified
+ *          in \p gcpl_id and \p gapl_id, respectively.
+ *
+ *          H5Gcreate_anon() returns a new group identifier. This identifier
+ *          must be linked into the HDF5 file structure with H5Olink()
+ *          or it will be deleted from the file when the file is closed.
+ *
+ *          The differences between this function and H5Gcreate1() are
+ *          as follows:
+ *
+ *          \li H5Gcreate1() does not provide for the use of custom property
+ *              lists; H5Gcreate1() always uses default properties.
+ *          \li H5Gcreate_anon() neither provides the new group’s name
+ *              nor links it into the HDF5 file structure; those actions
+ *              must be performed separately through a call to H5Olink(),
+ *              which offers greater control over linking.
+ *          \li H5Gcreate_anon() does not directly provide a hint mechanism
+ *              for the group’s heap size. Comparable information can be
+ *              included in the group creation property list \p gcpl_id through
+ *              a H5Pset_local_heap_size_hint() call.
+ *
+ *          A group created with this function should be closed with
+ *          H5Gclose() when the group is no longer needed so that resource
+ *          leaks will not develop.
+ *
+ * \see H5Olink(), H5Dcreate(), Using Identifiers
+ *
+ * \since 1.8.0
+ *
+ */
 H5_DLL hid_t  H5Gcreate_anon(hid_t loc_id, hid_t gcpl_id, hid_t gapl_id);
+
+/**
+ *-------------------------------------------------------------------------
+ * \ingroup H5G
+ *
+ * \brief Opens an existing group in a file
+ *
+ * \fgdta_loc_id
+ * \param[in] name      Name of the group to open
+ * \gapl_id
+ *
+ * \return \hid_t{group}
+ *
+ * \details H5Gopen2() opens an existing group, \p name, at the location
+ *          specified by \p loc_id.
+ *
+ *          With default settings, H5Gopen2() provides similar functionality
+ *          to that provided by H5Gopen(). The only difference is that
+ *          H5Gopen2() can provide a group access property list, \p gapl_id.
+ *
+ *          H5Gopen2() returns a group identifier for the group that was
+ *          opened. This group identifier should be released by H5Gclose()
+ *          when it is no longer needed to prevent resource leaks.
+ *
+ * \since 1.8.0
+ *
+ * \see H5Gcreate2(), H5Gclose()
+ *
+ */
 H5_DLL hid_t  H5Gopen2(hid_t loc_id, const char *name, hid_t gapl_id);
 H5_DLL hid_t  H5Gopen_async(const char *app_file, const char *app_func, unsigned app_line, hid_t loc_id,
                             const char *name, hid_t gapl_id, hid_t es_id);
+
+/**
+ *-------------------------------------------------------------------------
+ * \ingroup H5G
+ *
+ * \brief Gets a group creation property list identifier
+ *
+ * \group_id
+ *
+ * \return \hid_t{creation property list}
+ *
+ * \details H5Gget_create_plist() returns an identifier for the group creation
+ *          property list associated with the group specified by \p group_id.
+ *
+ *          The creation property list identifier should be released with
+ *          H5Gclose() to prevent resource leaks.
+ *
+ * \since 1.8.0
+ *
+ * \see H5Gcreate2(), H5Gclose()
+ *
+ */
 H5_DLL hid_t  H5Gget_create_plist(hid_t group_id);
+
+/**
+ *-------------------------------------------------------------------------
+ * \ingroup H5G
+ *
+ * \brief Retrieves information about a group
+ *
+ * \fgdta_loc_id
+ * \param[out] ginfo Struct in which group information is returned
+ *
+ * \return \hid_t{group}
+ *
+ * \details H5Gget_info() retrieves information about the group at location
+ *          specified by \p loc_id. The information is returned in the \p ginfo.
+ *
+ *          \p ginfo is an H5G_info_t struct and is defined (in H5Gpublic.h)
+ *          as follows:
+ *
+ * \snippet this H5G_info_t_snip
+ * Possible values of \p storage_type are:
+ * \storage_type
+ *
+ * \since 1.8.0
+ *
+ * \see H5Gcreate2(), H5Gclose()
+ *
+ */
 H5_DLL herr_t H5Gget_info(hid_t loc_id, H5G_info_t *ginfo);
+
 H5_DLL herr_t H5Gget_info_async(const char *app_file, const char *app_func, unsigned app_line, hid_t loc_id,
                                 H5G_info_t *group_info /*out*/, hid_t es_id);
+
+/**
+ *-------------------------------------------------------------------------
+ * \ingroup H5G
+ *
+ * \brief Retrieves information about a group by its name
+ *
+ * \fgdta_loc_id
+ * \param[in] name      Name of the group to query
+ * \param[out] ginfo Struct in which group information is returned
+ * \lapl_id
+ *
+ * \return \herr_t
+ *
+ * \details H5Gget_info_by_name() retrieves information about the group \p name
+ *          at location specified by \p loc_id. The information is returned in
+ *          the \p ginfo struct.
+ *
+ *          If \p loc_id specifies the group for which information is queried,
+ *          then the group's \p name can be a dot (.).
+ *
+ *          \p ginfo is an H5G_info_t struct and is defined (in H5Gpublic.h)
+ *          as follows:
+ *
+ * \snippet this H5G_info_t_snip
+ * Possible values of \p storage_type are:
+ * \storage_type
+ *
+ * \since 1.8.0
+ *
+ * \see H5Gcreate2(), H5Gclose()
+ *
+ */
 H5_DLL herr_t H5Gget_info_by_name(hid_t loc_id, const char *name, H5G_info_t *ginfo, hid_t lapl_id);
 H5_DLL herr_t H5Gget_info_by_name_async(const char *app_file, const char *app_func, unsigned app_line,
                                         hid_t loc_id, const char *name, H5G_info_t *group_info /*out*/,
                                         hid_t lapl_id, hid_t es_id);
+
+/**
+ *-------------------------------------------------------------------------
+ * \ingroup H5G
+ *
+ * \brief Retrieves information about a group, according to the group’s
+ *        position within an index
+ *
+ * \fgdta_loc_id
+ * \param[in] group_name Name of the group to query
+ * \param[in] idx_type   Transient index identifying object
+ * \param[in] order      Transient index identifying object
+ * \param[in] n          Position in the index of the group to query
+ * \param[out] ginfo     Struct in which group information is returned
+ * \lapl_id
+ *
+ * \return Returns
+ *      \li The size of the object name if successful, or
+ *      \li 0 if no name is associated with the group identifier, or
+ *      \li negative value, if failure occurred
+ *
+ * \details H5Gget_info_by_idx() retrieves the same information
+ *          about a group as retrieved by the function H5Gget_info(),
+ *          but the means of identifying the group differs; the group is
+ *          identified by position in an index rather than by name.
+ *
+ *          \p loc_id and \p group_name specify the group containing
+ *          the group for which information is sought. The groups in \p
+ *          group_name are indexed by \p idx_type; the group for which
+ *          information is retrieved is identified in that index by index
+ *          order, \p order, and index position, \p n.
+ *
+ *          If \p loc_id specifies the group containing the group for
+ *          which information is queried, \p group_name can be a dot (.).
+ *
+ *          Valid values for \p index_type are as follows:
+ * \indexes
+ *          The order in which the index is to be examined, as specified
+ *          by \p order, can be one of the following:
+ * \orders
+ *
+ * \since 1.8.0
+ *
+ * \see H5Gcreate2(), H5Gclose()
+ *
+ */
 H5_DLL herr_t H5Gget_info_by_idx(hid_t loc_id, const char *group_name, H5_index_t idx_type,
                                  H5_iter_order_t order, hsize_t n, H5G_info_t *ginfo, hid_t lapl_id);
 H5_DLL herr_t H5Gget_info_by_idx_async(const char *app_file, const char *app_func, unsigned app_line,
                                        hid_t loc_id, const char *group_name, H5_index_t idx_type,
                                        H5_iter_order_t order, hsize_t n, H5G_info_t *group_info /*out*/,
                                        hid_t lapl_id, hid_t es_id);
+
+/**
+ *-------------------------------------------------------------------------
+ * \ingroup H5G
+ *
+ * \brief Flushes all buffers associated with a group to disk
+ *
+ * \group_id
+ *
+ * \return \herr_t
+ *
+ * \details H5Gflush() causes all buffers associated with a group to be
+ *          immediately flushed to disk without removing the data from
+ *          the cache.
+ *
+ * \attention
+ *          HDF5 does not possess full control over buffering. H5G_FLUSH
+ *          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.
+ *
+ * \since 1.8.0
+ *
+ * \see H5Gcreate2(), H5Gclose()
+ *
+ */
 H5_DLL herr_t H5Gflush(hid_t group_id);
+
+/**
+ *-------------------------------------------------------------------------
+ * \ingroup H5G
+ *
+ * \brief Refreshes all buffers associated with a group
+ *
+ * \group_id
+ *
+ * \return \herr_t
+ *
+ * \details H5Grefresh() causes all buffers associated with a group to be
+ *          cleared and immediately re-loaded with updated contents from disk.
+ *
+ *          This function essentially closes the group, evicts all
+ *          metadata associated with it from the cache, and then re-opens
+ *          the group. The reopened group is automatically re-registered
+ *          with the same identifier.
+ *
+ * \since 1.8.0
+ *
+ * \see H5Gcreate2(), H5Gclose()
+ *
+ */
 H5_DLL herr_t H5Grefresh(hid_t group_id);
+
+/**
+ *-------------------------------------------------------------------------
+ * \ingroup H5G
+ *
+ * \brief Closes the specified group
+ *
+ * \group_id
+ *
+ * \return \herr_t
+ *
+ * \details H5Gclose() releases resources used by a group which was
+ *          opened by H5Gcreate() or H5Gopen().  After closing a group,
+ *          \p group_id cannot be used again until another H5Gcreate()
+ *          or H5Gopen() is called on it.
+ *
+ *          Failure to release a group with this call will result in
+ *          resource leaks.
+ *
+ * \since 1.0.0
+ *
+ * \version 1.4.0 Fortran function introduced in this release
+ *
+ */
 H5_DLL herr_t H5Gclose(hid_t group_id);
 H5_DLL herr_t H5Gclose_async(const char *app_file, const char *app_func, unsigned app_line, hid_t group_id,
                              hid_t es_id);
@@ -160,10 +489,13 @@ typedef enum H5G_obj_t {
     H5G_RESERVED_7    /* Reserved for future use	*/
 } H5G_obj_t;
 
-/* Prototype for H5Giterate() operator */
+/** Define the operator function pointer for for H5Giterate() */
+//! [H5G_iterate_t_snip]
 typedef herr_t (*H5G_iterate_t)(hid_t group, const char *name, void *op_data);
+//! [H5G_iterate_t_snip]
 
-/* Information about an object */
+/** Information about an object */
+//! [H5G_stat_t_snip]
 typedef struct H5G_stat_t {
     unsigned long fileno[2]; /*file number			*/
     unsigned long objno[2];  /*object number			*/
@@ -173,6 +505,7 @@ typedef struct H5G_stat_t {
     size_t        linklen;   /*symbolic link value length	*/
     H5O_stat_t    ohdr;      /* Object header information    */
 } H5G_stat_t;
+//! [H5G_stat_t_snip]
 
 /* Function prototypes */
 H5_DLL hid_t     H5Gcreate1(hid_t loc_id, const char *name, size_t size_hint);