Update java code with doxygen tags, add menu files. (#1972)

* Update java code with doxygen tags, add menu files.

* Add -Xdoclint:none to autotools javadoc command

* Committing clang-format changes

* Add fortran RM list descriptions

* delete empty file

* doc tag location changes

* Spelling corrections

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

17 files changed, 35 insertions, 77 deletions

diff --git a/src/H5Amodule.h b/src/H5Amodule.h
index cab56d4..e3bfe6f 100644
--- a/src/H5Amodule.h
+++ b/src/H5Amodule.h
@@ -375,7 +375,7 @@
  *
  * Previous Chapter \ref sec_dataspace - Next Chapter \ref sec_error
  *
- * \defgroup H5A H5A
+ * \defgroup H5A Attributes (H5A)
  *
  * An HDF5 attribute is a small metadata object describing the nature and/or intended usage of a primary data
  * object. A primary data object may be a dataset, group, or committed datatype.
diff --git a/src/H5Dmodule.h b/src/H5Dmodule.h
index 0eb7d68..4ad3709 100644
--- a/src/H5Dmodule.h
+++ b/src/H5Dmodule.h
@@ -2730,7 +2730,7 @@ allocated if necessary.
  *     // Define dataset datatype
  *     datatype = H5Tcopy(H5T_NATIVE_INT);
  *
- *     // Initiliaze data buffer
+ *     // Initialize data buffer
  *     for (i=0; i < NX; i++)
  *       for (j=0; j < NY; j++)
  *         orig_data[i][j] = rand() % 10000;
@@ -2851,7 +2851,7 @@ allocated if necessary.
  *     // Define dataset datatype
  *     datatype = H5Tcopy(H5T_NATIVE_FLOAT);
  *
- *     // Initiliaze data buffer
+ *     // Initialize data buffer
  *     for (i=0; i < NX; i++)
  *       for (j=0; j < NY; j++)
  *         orig_data[i][j] = (rand() % 10000) / 1000.0;
@@ -2983,7 +2983,7 @@ allocated if necessary.
  */
 
 /**
- * \defgroup H5D H5D
+ * \defgroup H5D Datasets (H5D)
  *
  * Use the functions in this module to manage HDF5 datasets, including the
  * transfer of data between memory and disk and the description of dataset
diff --git a/src/H5Emodule.h b/src/H5Emodule.h
index aeba66d..f2e6d44 100644
--- a/src/H5Emodule.h
+++ b/src/H5Emodule.h
@@ -580,7 +580,7 @@
  *
  * Previous Chapter \ref sec_attribute - Next Chapter \ref sec_plist
  *
- * \defgroup H5E H5E
+ * \defgroup H5E Error Handling (H5E)
  *
  * \internal The \c FUNC_ENTER macro clears the error stack whenever an
  *           interface function is entered. When an error is detected, an entry
diff --git a/src/H5Fmodule.h b/src/H5Fmodule.h
index 0aba5cd..523d6bf 100644
--- a/src/H5Fmodule.h
+++ b/src/H5Fmodule.h
@@ -1470,7 +1470,7 @@
  */
 
 /**
- * \defgroup H5F H5F
+ * \defgroup H5F Files (H5F)
  *
  * Use the functions in this module to manage HDF5 files.
  *
diff --git a/src/H5Gmodule.h b/src/H5Gmodule.h
index 13589fd..a112a40 100644
--- a/src/H5Gmodule.h
+++ b/src/H5Gmodule.h
@@ -951,7 +951,7 @@
  */
 
 /**
- * \defgroup H5G H5G
+ * \defgroup H5G Groups (H5G)
  *
  * Use the functions in this module to manage HDF5 groups.
  *
diff --git a/src/H5Imodule.h b/src/H5Imodule.h
index 024d8ab..1ad9f1b 100644
--- a/src/H5Imodule.h
+++ b/src/H5Imodule.h
@@ -30,7 +30,7 @@
 #define H5_MY_PKG_INIT NO
 
 /**
- * \defgroup H5I H5I
+ * \defgroup H5I Identifiers (H5I)
  *
  * Use the functions in this module to manage identifiers defined by the HDF5
  * library. See \ref H5IUD for user-defined identifiers and identifier
diff --git a/src/H5Lmodule.h b/src/H5Lmodule.h
index 47c8ad1..f61b891 100644
--- a/src/H5Lmodule.h
+++ b/src/H5Lmodule.h
@@ -30,7 +30,7 @@
 #define H5_MY_PKG_INIT YES
 
 /**
- * \defgroup H5L H5L
+ * \defgroup H5L Links (H5L)
  *
  * Use the functions in this module to manage HDF5 links and link types.
  *
diff --git a/src/H5Omodule.h b/src/H5Omodule.h
index 866e3b4..977861b 100644
--- a/src/H5Omodule.h
+++ b/src/H5Omodule.h
@@ -30,7 +30,7 @@
 #define H5_MY_PKG_INIT YES
 
 /**
- * \defgroup H5O H5O
+ * \defgroup H5O Objects (H5O)
  *
  * Use the functions in this module to manage HDF5 objects.
  *
diff --git a/src/H5PLmodule.h b/src/H5PLmodule.h
index 94cbf49..84d3583 100644
--- a/src/H5PLmodule.h
+++ b/src/H5PLmodule.h
@@ -28,7 +28,7 @@
 #define H5_MY_PKG_INIT YES
 
 /**
- * \defgroup H5PL H5PL
+ * \defgroup H5PL Dynamically-loaded Plugins (H5PL)
  *
  * Use the functions in this module to manage the loading behavior of HDF5
  * plugins.
diff --git a/src/H5Pmodule.h b/src/H5Pmodule.h
index 7885782..0dd675a 100644
--- a/src/H5Pmodule.h
+++ b/src/H5Pmodule.h
@@ -882,7 +882,7 @@
  *
  * Previous Chapter \ref sec_error - Next Chapter \ref sec_addition
  *
- * \defgroup H5P H5P
+ * \defgroup H5P Property Lists (H5P)
  *
  * Use the functions in this module to manage HDF5 property lists and property
  * list classes. HDF5 property lists are the main vehicle to configure the
@@ -915,25 +915,25 @@
  * </table>
  *
  * \defgroup STRCPL String Creation Properties
- * \ingroup H5P
  * Currently, there are only two creation properties that you can use to control
  * the creation of HDF5 attributes and links. The first creation property, the
  * choice of a character encoding, applies to both attributes and links.
  * The second creation property applies to links only, and advises the library
  * to automatically create missing intermediate groups when creating new objects.
+ * \ingroup H5P
  *
  * \defgroup LCPL Link Creation Properties
- * \ingroup STRCPL
  * The first creation property, the choice of a character encoding, applies to
  * both attributes and links.
  * The second creation property applies to links only, and advises the library
  * to automatically create missing intermediate groups when creating new objects.
+ * \ingroup STRCPL
  *
  * @see STRCPL
  *
  * \defgroup ACPL Attribute Creation Properties
- * \ingroup STRCPL
  * The creation property, the choice of a character encoding, applies to attributes.
+ * \ingroup STRCPL
  *
  * @see STRCPL
  *
@@ -941,110 +941,68 @@
  * \ingroup H5P
  *
  * \defgroup DAPL Dataset Access Properties
- * \ingroup LAPL
  * Use dataset access properties to modify the default behavior of the HDF5
  * library when accessing datasets. The properties include adjusting the size
  * of the chunk cache, providing prefixes for external content and virtual
  * dataset file paths, and controlling flush behavior, etc. These properties
  * are \Emph{not} persisted with datasets, and can be adjusted at runtime before
  * a dataset is created or opened.
+ * \ingroup LAPL
  *
  * \defgroup DCPL Dataset Creation Properties
- * \ingroup OCPL
  * Use dataset creation properties to control aspects of dataset creation such
  * as fill time, storage layout, compression methods, etc.
  * Unlike dataset access and transfer properties, creation properties \Emph{are}
  * stored with the dataset, and cannot be changed once a dataset has been
  * created.
+ * \ingroup OCPL
  *
  * \defgroup DXPL Dataset Transfer Properties
- * \ingroup H5P
  * Use dataset transfer properties to customize certain aspects of reading
  * and writing datasets such as transformations, MPI-IO I/O mode, error
  * detection, etc. These properties are \Emph{not} persisted with datasets,
  * and can be adjusted at runtime before a dataset is read or written.
+ * \ingroup H5P
  *
  * \defgroup FAPL File Access Properties
- * \ingroup H5P
  * Use file access properties to modify the default behavior of the HDF5
  * library when accessing files. The properties include selecting a virtual
  * file driver (VFD), configuring the metadata cache (MDC), control
  * file locking, etc. These properties are \Emph{not} persisted with files, and
  * can be adjusted at runtime before a file is created or opened.
+ * \ingroup H5P
  *
  * \defgroup FCPL File Creation Properties
- * \ingroup GCPL
  * Use file creation properties to control aspects of file creation such
  * as setting a file space management strategy or creating a user block.
  * Unlike file access properties, creation properties \Emph{are}
  * stored with the file, and cannot be changed once a file has been
  * created.
+ * \ingroup GCPL
  *
  * \defgroup GAPL General Access Properties
- * \ingroup LAPL
  * The functions in this section can be applied to different kinds of property
  * lists.
+ * \ingroup LAPL
  *
  * \defgroup GCPL Group Creation Properties
- * \ingroup OCPL
  * Use group creation properties to control aspects of group creation such
  * as storage layout, compression, and link creation order tracking.
  * Unlike file access properties, creation properties \Emph{are}
  * stored with the group, and cannot be changed once a group has been
  * created.
+ * \ingroup OCPL
  *
  * \defgroup PLCR Property List Class Root
- * \ingroup H5P
- *
  * Use the functions in this module to manage HDF5 property lists.
- *
- * <table>
- * <tr><th>Create</th><th>Read</th></tr>
- * <tr valign="top">
- *   <td>
- *   \snippet{lineno} H5P_examples.c create
- *   </td>
- *   <td>
- *   \snippet{lineno} H5P_examples.c read
- *   </td>
- * <tr><th>Update</th><th>Delete</th></tr>
- * <tr valign="top">
- *   <td>
- *   \snippet{lineno} H5P_examples.c update
- *   </td>
- *   <td>
- *   \snippet{lineno} H5P_examples.c delete
- *   </td>
- * </tr>
- * </table>
- *
- * \defgroup PLCRA Property List Class Root (Advanced)
  * \ingroup H5P
  *
+ * \defgroup PLCRA Property List Class Root (Advanced)
  * You can create and customize user-defined property list classes using the
  * functions described below. Arbitrary user-defined properties can also
  * be inserted into existing property lists as so-called temporary properties.
+ * \ingroup H5P
  *
- * <table>
- * <tr><th>Create</th><th>Read</th></tr>
- *
- * <tr valign="top">
- *   <td>
- *   \snippet{lineno} H5P_examples.c create_class
- *   </td>
- *   <td>
- *   \snippet{lineno} H5P_examples.c read_class
- *   </td>
- * <tr><th>Update</th><th>Delete</th></tr>
- * <tr valign="top">
- *   <td>
- *   \snippet{lineno} H5P_examples.c update_class
- *   </td>
- *   <td>
- *   \snippet{lineno} H5P_examples.c delete_class
- *   </td>
- * </tr>
- * </table>
  *
  * \defgroup OCPL Object Creation Properties
  * \ingroup H5P
@@ -1053,19 +1011,19 @@
  * \ingroup H5P
  *
  * \defgroup FMPL File Mount Properties
+ * Empty property class.
  * \ingroup H5P
  *
- * Empty property class.
  *
  * \defgroup TCPL Datatype Creation Properties
+ * TCPL isn't supported yet.
  * \ingroup OCPL
  *
- * TCPL isn't supported yet.
  *
  * \defgroup TAPL Datatype Access Properties
+ * TAPL isn't supported yet.
  * \ingroup LAPL
  *
- * TAPL isn't supported yet.
  *
  *
  */
diff --git a/src/H5Ppublic.h b/src/H5Ppublic.h
index 017b636..2890a5a 100644
--- a/src/H5Ppublic.h
+++ b/src/H5Ppublic.h
@@ -765,7 +765,7 @@ H5_DLL htri_t H5Pexist(hid_t plist_id, const char *name);
  */
 H5_DLL herr_t H5Pget(hid_t plist_id, const char *name, void *value);
 /**
- *\ingroup PLCR
+ * \ingroup PLCR
  *
  * \brief Returns the property list class identifier for a property list
  *
diff --git a/src/H5Rmodule.h b/src/H5Rmodule.h
index d467ffe..c561058 100644
--- a/src/H5Rmodule.h
+++ b/src/H5Rmodule.h
@@ -26,7 +26,7 @@
 #define H5_MY_PKG_INIT YES
 
 /**
- * \defgroup H5R H5R
+ * \defgroup H5R References (H5R)
  *
  * Use the functions in this module to manage HDF5 references. Referents can
  * be HDF5 objects, attributes, and selections on datasets a.k.a. dataset
diff --git a/src/H5Smodule.h b/src/H5Smodule.h
index 5eeba33..9c6682e 100644
--- a/src/H5Smodule.h
+++ b/src/H5Smodule.h
@@ -727,7 +727,7 @@
  * \li 3. Define a second hyperslab selection, unioned with the first
  * \li 4. Get the destination dataspace
  * \li 5. Define one hyperslab selection for the destination
- * \li 6. Define a second hyperslab seletion, unioned with the first
+ * \li 6. Define a second hyperslab selection, unioned with the first
  * \li 7. Execute the data transfer (H5Dread or H5Dwrite) using the source and destination dataspaces
  *
  * The example below shows example code to create the selections for the source dataspace (the file). The
@@ -1516,7 +1516,7 @@
  */
 
 /**
- * \defgroup H5S H5S
+ * \defgroup H5S Dataspaces (H5S)
  *
  * Use the functions in this module to manage HDF5 dataspaces \Emph{and} selections.
  *
diff --git a/src/H5Tmodule.h b/src/H5Tmodule.h
index a2f6828..83f7467 100644
--- a/src/H5Tmodule.h
+++ b/src/H5Tmodule.h
@@ -3859,7 +3859,7 @@ filled according to the value of this property. The padding can be:
  */
 
 /**
- * \defgroup H5T H5T
+ * \defgroup H5T Datatypes (H5T)
  *
  * Use the functions in this module to manage HDF5 datatypes.
  *
diff --git a/src/H5Zmodule.h b/src/H5Zmodule.h
index c3ef881..b3a52fd 100644
--- a/src/H5Zmodule.h
+++ b/src/H5Zmodule.h
@@ -30,7 +30,7 @@
 #define H5_MY_PKG_INIT YES
 
 /**
- * \defgroup H5Z H5Z
+ * \defgroup H5Z Filters (H5Z)
  *
  * Use the functions in this module to manage HDF5 filters.
  *
diff --git a/src/H5module.h b/src/H5module.h
index 6fadec8..6668624 100644
--- a/src/H5module.h
+++ b/src/H5module.h
@@ -1428,7 +1428,7 @@
  */
 
 /**
- * \defgroup H5 H5
+ * \defgroup H5 Library General (H5)
  *
  * Use the functions in this module to manage the life cycle of HDF5 library
  * instances.
diff --git a/src/H5private.h b/src/H5private.h
index 0601e73..a94049f 100644
--- a/src/H5private.h
+++ b/src/H5private.h
@@ -1983,7 +1983,7 @@ typedef struct H5_api_struct {
 #define H5_FIRST_THREAD_INIT pthread_once(&H5TS_first_init_g, H5TS_pthread_first_thread_init);
 #endif
 
-/* Macros for threadsafe HDF-5 Phase I locks */
+/* Macros for threadsafe HDF5 Phase I locks */
 #define H5_API_LOCK   H5TS_mutex_lock(&H5_g.init_lock);
 #define H5_API_UNLOCK H5TS_mutex_unlock(&H5_g.init_lock);