Addressed TODO documentation issues

doxygen/aliases

@@ -392,7 +392,7 @@ ALIASES += indexes="<table><tr><td>#H5_INDEX_NAME</td><td>Lexicographic order on
 ALIASES += link_types="<table><tr><td>#H5L_TYPE_HARD</td><td>Hard link</td></tr><tr><td>#H5L_TYPE_SOFT</td><td>Soft link</td></tr><tr><td>#H5L_TYPE_EXTERNAL</td><td>External link</td></tr><tr><td>#H5L_TYPE_ERROR</td><td>Error</td></tr></table>"
 ALIASES += mem_types="<table><tr><td>#H5FD_MEM_DEFAULT</td><td>The default file memory allocation type</td></tr><tr><td>#H5FD_MEM_SUPER</td><td>File memory allocated for Superblock</td></tr><tr><td>#H5FD_MEM_BTREE</td><td>File memory allocated for B-tree</td></tr><tr><td>#H5FD_MEM_DRAW</td><td>File memory allocated for raw data</td></tr><tr><td>#H5FD_MEM_GHEAP</td><td>File memory allocated for Global Heap</td></tr><tr><td>#H5FD_MEM_LHEAP</td><td>File memory allocated for Local Heap</td></tr><tr><td>#H5FD_MEM_OHDR</td><td>File memory allocated for Object Header</td></tr></table>"
 ALIASES += norm_type="<table><tr><td>#H5T_NORM_IMPLIED</td><td>0</td><td>MSB of mantissa is not stored, always 1</td></tr><tr><td>#H5T_NORM_MSBSET</td><td>1</td><td>MSB of mantissa is always 1</td></tr><tr><td>#H5T_NORM_NONE</td><td>2</td><td>Mantissa is not normalized</td></tr></table>"
-ALIASES += obj_types="<table><tr><td>#H5F_OBJ_FILE</td><td>Files only</td></tr><tr><td>#H5F_OBJ_DATASET</td><td>Datasets only</td></tr><tr><td>#H5F_OBJ_GROUP</td><td>Groups only</td></tr><tr><td>#H5F_OBJ_DATATYPE</td><td>Datatypes only. If \p file_id is #H5F_OBJ_ALL, this will count committed and transient datatypes. Otherwise, it will only count committed datatypes. </td></tr><tr><td>#H5F_OBJ_ATTR</td><td>Attributes only</td></tr><tr><td>#H5F_OBJ_ALL</td><td>All of the above</td></tr></tr><tr><td>#H5F_OBJ_LOCAL</td><td>Restrict search to objects opened through current file identifier.</td></tr></table> \attention #H5F_OBJ_LOCAL does not stand alone; it is effective only when used in combination with one or more of the preceding types. For example, #H5F_OBJ_DATASET | #H5F_OBJ_GROUP | #H5F_OBJ_LOCAL would count all datasets and groups opened through the current file identifier."
+ALIASES += obj_types="<table><tr><td>#H5F_OBJ_FILE</td><td>Files only</td></tr><tr><td>#H5F_OBJ_DATASET</td><td>Datasets only</td></tr><tr><td>#H5F_OBJ_GROUP</td><td>Groups only</td></tr><tr><td>#H5F_OBJ_DATATYPE</td><td>Datatypes only. If \p file_id is #H5F_OBJ_ALL, this will count committed and transient datatypes. Otherwise, it will only count committed datatypes. </td></tr><tr><td>#H5F_OBJ_ATTR</td><td>Attributes only</td></tr><tr><td>#H5F_OBJ_ALL</td><td>All of the above</td></tr><tr><td>#H5F_OBJ_LOCAL</td><td>Restrict search to objects opened through current file identifier.</td></tr></table> \attention #H5F_OBJ_LOCAL does not stand alone; it is effective only when used in combination with one or more of the preceding types. For example, #H5F_OBJ_DATASET | #H5F_OBJ_GROUP | #H5F_OBJ_LOCAL would count all datasets and groups opened through the current file identifier."
 ALIASES += orders="<table><tr><td>#H5_ITER_INC</td><td>Increasing order</td></tr><tr><td>#H5_ITER_DEC</td><td>Decreasing order</td></tr><tr><td>#H5_ITER_NATIVE</td><td>Fastest available order</td></tr></table>"
 ALIASES += padding_type="<table><tr><td>#H5T_PAD_ZERO</td><td>0</td><td>Set background to zeros</td></tr><tr><td>#H5T_PAD_ONE</td><td>1</td><td>Set background to ones</td></tr><tr><td>#H5T_PAD_BACKGROUND</td><td>2</td><td>Leave background alone</td></tr></table>"
 ALIASES += scopes="<table><tr><td>#H5F_SCOPE_GLOBAL</td><td>Flushes the entire virtual file</td></tr><tr><td>#H5F_SCOPE_LOCAL</td><td>Flushes only the specified file</td></tr></table>"

doxygen/dox/CollectiveCalls.dox

@@ -930,7 +930,6 @@
         #H5Topen1 at Release 1.8.0.
       </td>
       </tr>
-    </td></tr>
     </table>
  *
  * \section sec_collective_calls_props Properties

doxygen/dox/CollectiveMetadataIO.dox

@@ -239,7 +239,6 @@
  *    <tr>
  *      <td>#H5Zunregister</td>
  *    </tr>
- *  </tbody>
  * </table>
  *
  * In addition, most deprecated functions fall into this category.

doxygen/dox/FileFormatDisc.dox

@@ -849,7 +849,7 @@ Symbol 0:
     <!-- Object Header Message Flags -->
       <td><em>Flags:</em> 0x01</td>
     <!-- Reserved -->
-      <tdcolspan="3"><em>Reserved:</em> 0</td>
+      <td colspan="3"><em>Reserved:</em> 0</td>
     </tr>
     <tr align="center">
     <!-- Type Class and Version -->

doxygen/dox/H5.format.1.0.dox

@@ -873,7 +873,7 @@ as an atomic object.
 <tr align=center>
   <td>Version</td>
   <td colspan=3>Reserved</td>
-</td>
+</tr>
 <tr align=center>
   <td colspan=4>Collection Size</td>
 </tr>

doxygen/dox/H5.format.1.1.dox

@@ -1107,7 +1107,7 @@ variable-length datatype elements, etc).
 <tr align=center>
   <td>Version</td>
   <td colspan=3>Reserved</td>
-</td>
+</tr>
 <tr align=center>
   <td colspan=4>Collection Size<sup>L</sup></td>
 </tr>

doxygen/dox/H5.format.3.0.dox

@@ -7995,7 +7995,6 @@ information for the virtual layout class as well as indexing information for the
         <tr>
           <td align="left"><i>Implicit index</i></td>
           <td align="left">Address of the array of dataset chunks.</td>
-        </td>
         </tr>
         <tr>
           <td align="left"><i>Fixed Array index</i></td>
@@ -8004,7 +8003,6 @@ information for the virtual layout class as well as indexing information for the
         <tr>
           <td align="left"><i>Extensible Array index</i></td>
           <td align="left">Address of the index.</td>
-        </td>
         </tr>
         <tr>
           <td align="left"><i>Version 2 B-tree index</i></td>
@@ -8111,6 +8109,7 @@ The following information exists only when the chunk is filtered. In other words
   <td>Min Pointers</td>
   <td>Min Elements</td>
 </tr>
+<tr>
   <td colspan="2">Page Bits</td>
   <td colspan="2" bgcolor="#DDDDDD"><em>This space inserted only to align table nicely</em></td>
 </tr>
@@ -8194,7 +8193,7 @@ The following information exists only when the chunk is filtered. In other words
   <th width="25%">byte</th>
   <th width="25%">byte</th>
   <th width="25%">byte</th>
-  <>byte</th>
+  <th>byte</th>
 </tr>
 <tr>
   <td colspan="4"><br />Address<sup>O</sup><br /><br /></td>
@@ -12465,7 +12464,6 @@ Reference Block stored in the global heap:
 </tr>
 <tr>
   <td colspan="4"><br />Dataspace Selection Information <em>(variable size)</em><br /><br /></td>
-</td>
 </tr>
 <tr>
   <td colspan="2">Length of Attribute Name </td>

doxygen/dox/H5.format.4.0.dox

@@ -8165,7 +8165,6 @@ information for the virtual layout class as well as indexing information for the
         <tr>
           <td align="left"><i>Implicit index</i></td>
           <td align="left">Address of the array of dataset chunks.</td>
-        </td>
         </tr>
         <tr>
           <td align="left"><i>Fixed Array index</i></td>
@@ -8174,7 +8173,6 @@ information for the virtual layout class as well as indexing information for the
         <tr>
           <td align="left"><i>Extensible Array index</i></td>
           <td align="left">Address of the index.</td>
-        </td>
         </tr>
         <tr>
           <td align="left"><i>Version 2 B-tree index</i></td>
@@ -8281,6 +8279,7 @@ The following information exists only when the chunk is filtered. In other words
   <td>Min Pointers</td>
   <td>Min Elements</td>
 </tr>
+<tr>
   <td colspan="2">Page Bits</td>
   <td colspan="2" bgcolor="#DDDDDD"><em>This space inserted only to align table nicely</em></td>
 </tr>
@@ -8364,7 +8363,7 @@ The following information exists only when the chunk is filtered. In other words
   <th width="25%">byte</th>
   <th width="25%">byte</th>
   <th width="25%">byte</th>
-  <>byte</th>
+  <th>byte</th>
 </tr>
 <tr>
   <td colspan="4"><br />Address<sup>O</sup><br /><br /></td>
@@ -12710,7 +12709,6 @@ Reference Block stored in the global heap:
 </tr>
 <tr>
   <td colspan="4"><br />Dataspace Selection Information <em>(variable size)</em><br /><br /></td>
-</td>
 </tr>
 <tr>
   <td colspan="2">Length of Attribute Name </td>

doxygen/dox/UsersGuide.dox

@@ -113,6 +113,15 @@ Navigate back: \ref index "Main"
     </ul>
 \li \ref subsec_group_examples
 
+\ref sec_link
+\li \ref subsec_link_intro
+\li \ref subsec_link_types
+\li \ref subsec_link_create
+\li \ref subsec_link_ops
+\li \ref subsec_link_traverse
+\li \ref subsec_link_user
+\li \ref subsec_link_summary
+
 \ref sec_dataset
 \li \ref subsec_dataset_intro
 \li \ref subsec_dataset_function
@@ -228,6 +237,25 @@ Navigate back: \ref index "Main"
     </ul>
 \li \ref subsec_attribute_special
 
+\ref sec_object
+\li \ref subsec_object_intro
+\li \ref subsec_object_ops
+\li \ref subsec_object_visit
+\li \ref subsec_object_comments
+\li \ref subsec_object_refcount
+\li \ref subsec_object_cache
+\li \ref subsec_object_summary
+
+\ref sec_identifier
+\li \ref subsec_identifier_intro
+\li \ref subsec_identifier_types
+\li \ref subsec_identifier_refcount
+\li \ref subsec_identifier_valid
+\li \ref subsec_identifier_query
+\li \ref subsec_identifier_user
+\li \ref subsec_identifier_iteration
+\li \ref subsec_identifier_summary
+
 \ref sec_error
 \li \ref subsec_error_intro
 \li \ref subsec_error_program
@@ -266,6 +294,17 @@ Navigate back: \ref index "Main"
 \li \ref subsec_plist_resources
 \li \ref subsec_plist_notes
 
+\ref sec_vfd
+\li \ref subsec_vfd_intro
+\li \ref subsec_vfd_purpose
+\li \ref subsec_vfd_drivers
+\li \ref subsec_vfd_selection
+\li \ref subsec_vfd_custom
+\li \ref subsec_vfd_parallel
+\li \ref subsec_vfd_performance
+\li \ref subsec_vfd_query
+\li \ref subsec_vfd_summary
+
 \ref sec_vol
 \li \ref subsec_vol_intro
 \li \ref subsec_vol_abstract_layer
@@ -338,10 +377,24 @@ Navigate back: \ref index "Main"
 \li \ref subsec_async_intro
 
 \ref sec_map
+\li \ref subsec_map_intro
+\li \ref subsec_map_lifecycle
+\li \ref subsec_map_plist
+\li \ref subsec_map_datatypes
+\li \ref subsec_map_example
+\li \ref subsec_map_notes
 
 \ref sec_reference
 
-\ref sec_filter_plugins
+\ref sec_filter
+\li \ref subsec_filter_intro
+\li \ref subsec_filter_builtin
+\li \ref subsec_filter_usage
+\li \ref subsec_filter_pipeline
+\li \ref subsec_filter_custom
+\li \ref subsec_filter_query
+\li \ref subsec_filter_plugins
+\li \ref subsec_filter_summary
 
 \section sec_hl HDF5 High Level APIs
 \li \ref H5DO_UG

doxygen/dox/VFLTechNote.dox

@@ -521,7 +521,6 @@ The library makes many types of allocation requests:
 <td>#H5FD_MEM_DRAW</td><td>An allocation request for the raw data of a dataset.
 </td>
 </tr>
-</tr>
 <tr>
 <td>#H5FD_MEM_GHEAP</td><td>An allocation request for a global heap collection. Global
 heaps are used to store certain types of references such as dataset region references.

doxygen/dox/ViewTools2.dox

@@ -159,7 +159,7 @@ you will see a detailed usage statement with examples of modifying a filter. The
 numerous filters that you can apply to a dataset:
 <table>
 <tr>
-<th>Filter<th></th>Options</th>
+<th>Filter</th><th>Options</th>
 </tr>
 <tr>
 <td>GZIP compression (levels 1-9)

doxygen/dox/hdf5_1_8.dox

@@ -54,12 +54,13 @@ This section lists interface-level changes and other user-visible changes in beh
 \subsubsection subsubsec_rel_spec_18_change_22_new New and Changed Functions, Classes, Subroutines, Wrappers, and Macros
 <h4>In the C Interface (main library)</h4>
 The following are new C functions in this release:
-<table><thead><tr><th>Function</th><th>Description</th></tr></thead><tbody>
+<table>
+<tr><th>Function</th><th>Description</th></tr>
 <tr><td>#H5Pget_fapl_hdfs</td><td>Gets the information of the given Read-Only HDFS virtual file driver</td></tr>
 <tr><td>#H5Pget_fapl_ros3</td><td>Gets the information of the given Read-Only S3 virtual file driver</td></tr>
 <tr><td>#H5Pset_fapl_hdfs</td><td>Sets up Read-Only HDFS virtual file driver</td></tr>
 <tr><td>#H5Pset_fapl_ros3</td><td>Sets up Read-Only S3 virtual file driver</td></tr>
-</tbody></table>
+</table>
 
 <h4>In the C High Level Interface</h4>
 \li None.
@@ -225,13 +226,14 @@ The <code>\#ifdef VLPT_REMOVED</code> blocks have been removed from the packet t
 Changed shared library interface version numbers (soname)
 
 For HDF5 Release 1.8.17, the shared object version numbers have changed as follows.
-<table><thead><tr><th>Library</th><th>Release 1.8.16</th><th>Release 1.8.17</th><th>Reason for Change</th></tr></thead><tbody>
+<table>
+<tr><th>Library</th><th>Release 1.8.16</th><th>Release 1.8.17</th><th>Reason for Change</th></tr>
 <tr><td>HDF5 C Library</td><td>10.1.0</td><td>10.2.0</td><td>Added APIs</td></tr>
 <tr><td>HDF5 High-level C Library</td><td>10.0.2</td><td>10.1.0</td><td>Added APIs</td></tr>
 <tr><td>C++ Library</td><td>11.0.0</td><td>12.0.0</td><td>Changes in existing APIs</td></tr>
 <tr><td>High-level C++ Library</td><td>11.0.0</td><td>11.1.0</td><td>Added APIs</td></tr>
 <tr><td>All others</td><td>10.0.2</td><td>10.0.3</td><td>Code changes that did not result in interface changes</td></tr>
-</tbody></table>
+</table>
 
 <h4>Compatibility report for Release 1.8.17 versus Release 1.8.16</h4>
 The following interface compatibility report provides a full list of the changed symbols:
@@ -274,12 +276,13 @@ This function reports whether the linked version of the HDF5 Library was built w
     and #H5Pset_attr_creation_order/#H5Pget_attr_creation_order<br />
 
 The following wrappers were added to the class H5::ObjCreatPropList for the respective C functions:
-<table><thead><tr><th>C Function</th><th>C++ Wrapper</th></tr></thead><tbody>
+<table>
+<tr><th>C Function</th><th>C++ Wrapper</th></tr>
 <tr><td>#H5Pset_attr_phase_change</td><td>H5::ObjCreatPropList::setAttrPhaseChange</td></tr>
 <tr><td>#H5Pget_attr_phase_change</td><td>H5::ObjCreatPropList::getAttrPhaseChange</td></tr>
 <tr><td>#H5Pset_attr_creation_order</td><td>H5::ObjCreatPropList::setAttrCrtOrder</td></tr>
 <tr><td>#H5Pget_attr_creation_order</td><td>H5::ObjCreatPropList::getAttrCrtOrder</td></tr>
-</tbody></table>
+</table>
 
 <h4>Library Configuration</h4>
 \li Use of thread-safety with the HDF5 High-level Library has been declared unsupported in
@@ -316,12 +319,13 @@ changes specific to each wrapper library.
 
 <h4>Changed shared library interface version numbers (soname)</h4>
 For HDF5 Release 1.8.16, the shared object version numbers have changed as follows.
-<table><thead><tr><th>Library</th><th>Release 1.8.15</th><th>Release 1.8.16</th><th>Reason for Change</th></tr></thead><tbody>
+<table>
+<tr><th>Library</th><th>Release 1.8.15</th><th>Release 1.8.16</th><th>Reason for Change</th></tr>
 <tr><td>HDF5 Library</td><td>10.0.1</td><td>10.1.0</td><td>Added APIs</td></tr>
 <tr><td>C++ Library</td><td>10.0.1</td><td>11.0.0</td><td>Changes in existing APIs</td></tr>
 <tr><td>High-level C++ Library</td><td>10.0.1</td><td>11.0.0</td><td>Changes in existing APIs</td></tr>
 <tr><td>All others</td><td>10.0.1</td><td>10.0.2</td><td>Code changes that did not result in interface changes</td></tr>
-</tbody></table>
+</table>
 
 <h4>Compatibility report for Release 1.8.16 versus Release 1.8.15</h4>
 The following interface compatibility report provides a full list of the changed symbols:

doxygen/examples/tables/predefinedDatatypes.dox

@@ -254,7 +254,6 @@
 <td>#H5T_C_S1</td>
 <td>String datatype in C (size defined in bytes rather than in bits)</td>
 </tr>
-</tr>
 <tr>
 <td>#H5T_FORTRAN_S1</td>
 <td>String datatype in Fortran (as defined for the HDF5 C library)</td>

hl/src/H5DOpublic.h

@@ -22,6 +22,13 @@ extern "C" {
  * Navigate back: \ref index "Main" / \ref UG
  * <hr>
  *
+ * \section sec_hldo_intro Introduction
+ *
+ * The HDF5 Dataset Optimization (H5DO) interface provides high-performance functions for specialized
+ * dataset I/O operations that bypass standard HDF5 processing layers when appropriate.
+ *
+ * @see H5DO Reference Manual
+ *
  * Since version 1.10.3 these functions are deprecated in favor of #H5Dwrite_chunk and #H5Dread_chunk.
  *
  * \section sec_hldo_direct_chunk Direct Chunk Write Function

hl/src/H5DSpublic.h

@@ -526,15 +526,11 @@ extern "C" {
  *
  * These relationships are represented in the file by attributes of the Dataset D and the Dimension
  * Scale Datasets. Figure 5 shows the values that are stored for the DIMENSION_LIST attribute of
- * Dataset D. This
- * <table>
- * <tr>
- * <td>
+ * Dataset D.
+ *
  * \image html UML_Attribute.jpg "The UML model for an HDF5 attribute"
- * </td>
- * </tr>
- * </table>
- * attribute is a one-dimensional array with the HDF5 datatype variable length
+ *
+ * This attribute is a one-dimensional array with the HDF5 datatype variable length
  * #H5T_STD_REF_OBJ. Each row of the array is zero or more object references for Dimension Scale datasets.
  *
  * Table 6 shows the DIMENSION_LABELLIST for Dataset D. This is a one dimensional array with some empty
@@ -559,30 +555,11 @@ extern "C" {
  * an item from the table, because the entries at both ends of the association must be updated
  * at the same time.
  *
- * <table>
- * <tr>
- * <td>
  * \image html H5DS_fig3.png "Figure 3. Example dataset and scales."
- * </td>
- * </tr>
- * </table>
  *
- * <table>
- * <tr>
- * <td>
  * \image html H5DS_fig4.png "Figure 4. Example labels, names, and attached scales."
- * </td>
- * </tr>
- * </table>
  *
- * <table>
- * <tr>
- * <td>
- * \image html H5DS_fig5.png "Figure 5. The table of dimension references, stored as an attribute of the
- * Dataset."
- * </td>
- * </tr>
- * </table>
+ * \image html H5DS_fig5.png "Figure 5. The table of dimension references."
  *
  * <table><caption>Table 6. The table of dimension labels.</caption>
  * <tr>
@@ -750,10 +727,12 @@ extern "C" {
  *    3. For each scale, detach the Dimension Scale S from dimension j of Dataset D with H5DSdetach_scale
  *    4. Delete the Dataset, with H5Gunlink.
  *
- * \subsection subsec_dim_scales_api_func Programming API: H5DS
- *  @see H5DS Reference Manual
+ * \subsection subsec_dim_scales_ops Dimension Scale Operations
  *
- * @todo Under Construction
+ * Attach dimension scales to datasets using #H5DSattach_scale and detach with #H5DSdetach_scale.
+ * Set and retrieve dimension scale names with #H5DSset_scale and #H5DSget_scale_name. Query
+ * if a dataset is a dimension scale with #H5DSis_scale and check attachments with #H5DSis_attached.
+ * Iterate through scales with #H5DSiterate_scales.
  *
  * Previous Chapter \ref sec_hldo_direct_chunk - Next Chapter \ref sec_hl_images
  *