Fix doxygen missing references (HDFGroup#5205)

qkoziol · Jan 6, 2025 · 67d074c · 67d074c
1 parent 85bef9d
commit 67d074c
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diff --git a/.gitattributes b/.gitattributes
@@ -204,7 +204,7 @@ java/src/hdf/hdf5lib/H5.java -text
 java/src/hdf/hdf5lib/HDF5Constants.java -text
 java/src/hdf/hdf5lib/HDFArray.java -text
 java/src/hdf/hdf5lib/HDFNativeData.java -text
-java/src/hdf/hdf5lib/callbacks/Callbacks.java -text
+java/src/hdf/hdf5lib/callbacks/H5Callbacks.java -text
 java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java -text
 java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java -text
 java/src/hdf/hdf5lib/callbacks/H5D_append_cb.java -text

diff --git a/doc/parallel-compression.md b/doc/parallel-compression.md
@@ -341,7 +341,7 @@ hid_t file_id = H5Fcreate("file.h5", H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
 [u6]: https://hdfgroup.github.io/hdf5/develop/group___d_c_p_l.html#ga4335bb45b35386daa837b4ff1b9cd4a4
 [u7]: https://hdfgroup.github.io/hdf5/develop/group___d_c_p_l.html#ga6bd822266b31f86551a9a1d79601b6a2
 [u8]: https://www.hdfgroup.org/2022/03/04/parallel-compression-improvements-in-hdf5-1-13-1/
-[u9]: https://support.hdfgroup.org/releases/hdf5/documentation/advanced_topics/chunking_in_hdf5.md
+[u9]: https://hdfgroup.github.io/hdf5/develop/chunking__in__hdf5_8dox.html
 [u10]: https://support.hdfgroup.org/releases/hdf5/documentation/hdf5_topics/HDF5ImprovingIOPerformanceCompressedDatasets.pdf
 [u11]: https://hdfgroup.github.io/hdf5/develop/group___f_a_p_l.html#gab99d5af749aeb3896fd9e3ceb273677a
 [u12]: https://hdfgroup.github.io/hdf5/develop/group___f_c_p_l.html#ga167ff65f392ca3b7f1933b1cee1b9f70

diff --git a/java/src/Makefile.am b/java/src/Makefile.am
@@ -41,7 +41,7 @@ CLASSPATH_ENV=CLASSPATH=.:$(top_srcdir)/java/lib/slf4j-api-2.0.6.jar:$$CLASSPATH
 AM_JAVACFLAGS = $(H5_JAVACFLAGS) -deprecation
 
 hdf5_java_JAVA =  \
-	${pkgpath}/callbacks/Callbacks.java \
+	${pkgpath}/callbacks/H5Callbacks.java \
 	${pkgpath}/callbacks/H5A_iterate_cb.java \
 	${pkgpath}/callbacks/H5A_iterate_t.java \
 	${pkgpath}/callbacks/H5D_append_cb.java \

diff --git a/java/src/hdf/hdf5lib/CMakeLists.txt b/java/src/hdf/hdf5lib/CMakeLists.txt
@@ -10,7 +10,7 @@ SET_GLOBAL_VARIABLE (HDF5_JAVA_SOURCE_PACKAGES
 )
 
 set (HDF5_JAVA_HDF_HDF5_CALLBACKS_SOURCES
-    callbacks/Callbacks.java
+    callbacks/H5Callbacks.java
     callbacks/H5A_iterate_cb.java
     callbacks/H5A_iterate_t.java
     callbacks/H5D_append_cb.java

diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
@@ -5348,7 +5348,7 @@ public synchronized static native void H5Fset_libver_bounds(long file_id, int lo
     //    herr_t H5Fget_mpi_atomicity(hid_t file_id, hbool_t *flag);
     // #endif /* H5_HAVE_PARALLEL */
 
-    // /**
+    // /*
     // * H5Fget_vfd_handle returns a pointer to the file handle from the
     // low-level file driver
     // * currently being used by the HDF5 library for file I/O.
@@ -5365,7 +5365,7 @@ public synchronized static native void H5Fset_libver_bounds(long file_id, int lo
     // H5Fget_vfd_handle(int file_id, int fapl)
     //             throws HDF5LibraryException;
 
-    // /**
+    // /*
     // * H5Fget_mdc_config loads the current metadata cache configuration into
     // * the instance of H5AC_cache_config_t pointed to by the config_ptr
     // parameter.
@@ -5382,7 +5382,7 @@ public synchronized static native void H5Fset_libver_bounds(long file_id, int lo
     // public synchronized static native void H5Fget_mdc_config(int file_id, H5AC_cache_config_t config_ptr)
     //             throws HDF5LibraryException, NullPointerException;
 
-    // /**
+    // /*
     // * H5Fset_mdc_config attempts to configure the file's metadata cache
     // according to the configuration supplied.
     // *
@@ -10028,7 +10028,7 @@ public synchronized static native String H5Pget_virtual_dsetname(long dcpl_id, l
         throws HDF5LibraryException, IllegalArgumentException;
 
     //    /////  unimplemented /////
-    //    /**
+    //    /*
     //     * H5Pget_vds_file_cache_size retrieves the size of the vds link open file cache.
     //     *
     //     * @param fapl_id
@@ -10043,7 +10043,7 @@ public synchronized static native String H5Pget_virtual_dsetname(long dcpl_id, l
     //    public synchronized static native int H5Pget_vds_file_cache_size(long fapl_id) throws
     //    HDF5LibraryException;
     //
-    //    /**
+    //    /*
     //     * H5Pset_vds_file_cache_size sets the number of files that can be held open in an vds link open
     //     * file cache.
     //     *
@@ -10075,10 +10075,9 @@ public synchronized static native String H5Pget_virtual_dsetname(long dcpl_id, l
      * @param size
      *            OUT: the offset value and the size of the external file data.
      *
-     *            <pre>
-     *      size[0] = offset // a location to return an offset value
-     *      size[1] = size // a location to return the size of
-     *                // the external file data.
+     * <pre>
+     *    size[0] = offset // a location to return an offset value
+     *    size[1] = size // a location to return the size of the external file data.
      * </pre>
      *
      * @return a non-negative value if successful
@@ -13929,7 +13928,7 @@ public synchronized static native boolean H5Tdetect_class(long type_id, int cls)
     public synchronized static native int H5Tencode(long obj_id, byte[] buf, long nalloc)
         throws HDF5LibraryException, NullPointerException;
 
-    // /**
+    // /*
     //  * @ingroup JH5T
     //  *
     //  * H5Tencode converts a data type description into binary form in a buffer.

diff --git a/java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java b/java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java
@@ -18,7 +18,7 @@
  * Information class for link callback for H5Aiterate.
  *
  */
-public interface H5A_iterate_cb extends Callbacks {
+public interface H5A_iterate_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

diff --git a/.../src/hdf/hdf5lib/callbacks/Callbacks.java → ...rc/hdf/hdf5lib/callbacks/H5Callbacks.java b/.../src/hdf/hdf5lib/callbacks/Callbacks.java → ...rc/hdf/hdf5lib/callbacks/H5Callbacks.java
@@ -13,11 +13,11 @@
 package hdf.hdf5lib.callbacks;
 
 /**
- * @page CALLBACKS HDF5 Java Callbacks Interface
+ * @page CALLBACKS HDF5 Java H5Callbacks Interface
  * All callback definitions must derive from this interface.  Any
  * derived interfaces must define a single public method  named "callback".
  * You are responsible for deregistering your callback (if necessary)
- * in its {@link Object#finalize} method.  If native code attempts to call
+ * in its Object finalize method.  If native code attempts to call
  * a callback which has been GC'd, you will likely crash the VM.  If
  * there is no method to deregister the callback (e.g. <code>atexit</code>
  * in the C library), you must ensure that you always keep a live reference
@@ -28,7 +28,7 @@
  * exceptions thrown will be passed to the default callback exception
  * handler.
  *
- * @defgroup JCALLBK HDF5 Library Java Callbacks
+ * @defgroup JCALLBK HDF5 Library Java H5Callbacks
  */
-public interface Callbacks {
+public interface H5Callbacks {
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5D_append_cb.java b/java/src/hdf/hdf5lib/callbacks/H5D_append_cb.java
@@ -16,7 +16,7 @@
  * Information class for link callback for H5Pset/get_append_flush.
  *
  */
-public interface H5D_append_cb extends Callbacks {
+public interface H5D_append_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

diff --git a/java/src/hdf/hdf5lib/callbacks/H5D_iterate_cb.java b/java/src/hdf/hdf5lib/callbacks/H5D_iterate_cb.java
@@ -16,7 +16,7 @@
  * Information class for link callback for H5Diterate.
  *
  */
-public interface H5D_iterate_cb extends Callbacks {
+public interface H5D_iterate_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

diff --git a/java/src/hdf/hdf5lib/callbacks/H5E_walk_cb.java b/java/src/hdf/hdf5lib/callbacks/H5E_walk_cb.java
@@ -18,7 +18,7 @@
  * Information class for link callback for H5Ewalk.
  *
  */
-public interface H5E_walk_cb extends Callbacks {
+public interface H5E_walk_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

diff --git a/java/src/hdf/hdf5lib/callbacks/H5L_iterate_t.java b/java/src/hdf/hdf5lib/callbacks/H5L_iterate_t.java
@@ -18,7 +18,7 @@
  * Information class for link callback for H5Lvisit/H5Lvisit_by_name.
  *
  */
-public interface H5L_iterate_t extends Callbacks {
+public interface H5L_iterate_t extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

diff --git a/java/src/hdf/hdf5lib/callbacks/H5O_iterate_t.java b/java/src/hdf/hdf5lib/callbacks/H5O_iterate_t.java
@@ -18,7 +18,7 @@
  * Information class for link callback for H5Ovisit/H5Ovisit_by_name.
  *
  */
-public interface H5O_iterate_t extends Callbacks {
+public interface H5O_iterate_t extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_cb.java
@@ -16,7 +16,7 @@
  * Information class for link callback for H5Pcreate_class.
  *
  */
-public interface H5P_cls_close_func_cb extends Callbacks {
+public interface H5P_cls_close_func_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_cb.java
@@ -16,7 +16,7 @@
  * Information class for link callback for H5Pcreate_class
  *
  */
-public interface H5P_cls_copy_func_cb extends Callbacks {
+public interface H5P_cls_copy_func_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_cb.java
@@ -16,7 +16,7 @@
  * Information class for link callback for H5Pcreate_class.
  *
  */
-public interface H5P_cls_create_func_cb extends Callbacks {
+public interface H5P_cls_create_func_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_iterate_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_iterate_cb.java
@@ -16,7 +16,7 @@
  * Information class for link callback for H5Piterate.
  *
  */
-public interface H5P_iterate_cb extends Callbacks {
+public interface H5P_iterate_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_close_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_close_func_cb.java
@@ -16,7 +16,7 @@
  * Information class for link callback for H5Pregister2.
  *
  */
-public interface H5P_prp_close_func_cb extends Callbacks {
+public interface H5P_prp_close_func_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_compare_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_compare_func_cb.java
@@ -16,7 +16,7 @@
  * Information class for link callback for H5Pregister2.
  *
  */
-public interface H5P_prp_compare_func_cb extends Callbacks {
+public interface H5P_prp_compare_func_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_copy_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_copy_func_cb.java
@@ -16,7 +16,7 @@
  * Information class for link callback for H5Pregister2.
  *
  */
-public interface H5P_prp_copy_func_cb extends Callbacks {
+public interface H5P_prp_copy_func_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_create_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_create_func_cb.java
@@ -16,7 +16,7 @@
  * Information class for link callback for H5Pregister2.
  *
  */
-public interface H5P_prp_create_func_cb extends Callbacks {
+public interface H5P_prp_create_func_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_delete_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_delete_func_cb.java
@@ -16,7 +16,7 @@
  * Information class for link callback for H5Pregister2.
  *
  */
-public interface H5P_prp_delete_func_cb extends Callbacks {
+public interface H5P_prp_delete_func_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_get_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_get_func_cb.java
@@ -16,7 +16,7 @@
  * Information class for link callback for H5Pregister2.
  *
  */
-public interface H5P_prp_get_func_cb extends Callbacks {
+public interface H5P_prp_get_func_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_set_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_set_func_cb.java
@@ -16,7 +16,7 @@
  * Information class for link callback for H5Pregister2.
  *
  */
-public interface H5P_prp_set_func_cb extends Callbacks {
+public interface H5P_prp_set_func_cb extends H5Callbacks {
     /**
      * @ingroup JCALLBK
      *

diff --git a/java/src/hdf/hdf5lib/callbacks/package-info.java b/java/src/hdf/hdf5lib/callbacks/package-info.java
@@ -11,8 +11,8 @@
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 /**
- * @page CALLBACKS_UG HDF5 Java Callbacks Interface
- * All callback definitions must derive from the Callbacks interface.  Any
+ * @page CALLBACKS_UG HDF5 Java H5Callbacks Interface
+ * All callback definitions must derive from the H5Callbacks interface.  Any
  * derived interfaces must define a single public method named "callback".
  * You are responsible for deregistering your callback (if necessary)
  * in its {@link Object#finalize} method.  If native code attempts to call

diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
@@ -537,7 +537,11 @@ Bug Fixes since HDF5-2.0.0 release
 
     Java Library
     ------------
-    -
+    - Renamed the Callbacks.java file to H5Callbacks.java
+
+      The Callbacks.java file was renamed to H5Callbacks.java to match the file
+      pattern used by doxygen. This change only affects the Java filenames and
+      does not change the classname or the package name.
 
 
     Configuration

diff --git a/release_docs/RELEASE_PROCESS.md b/release_docs/RELEASE_PROCESS.md
@@ -197,7 +197,7 @@ For more information on the HDF5 versioning and backward and forward compatibili
     - Change 'HDF5 target bucket directory' to 'vX_Y/vX_Y_Z'
     - Press "Run Workflow"
 
-### 10. Add the contents of the RELEASE.txt file in the release code to the HISTORY-<branch> file in the **support** branch, just below the introductory lines at the top of the HISTORY file.
+### 10. Add the contents of the RELEASE.txt file in the release code to the HISTORY-X_Y file in the **support** branch, just below the introductory lines at the top of the HISTORY file.
 
 ### 11. Conduct Release Retrospective (Release Manager)
 1. Schedule time and solicit comments from retrospective
@@ -216,5 +216,5 @@ For more information on the HDF5 versioning and backward and forward compatibili
 [u11]: https://github.com/HDFGroup/hdf5/blob/develop/src/CMakeLists.txt
 [u12]: https://github.com/HDFGroup/hdf5/blob/develop/configure.ac
 [u13]: https://hdfgroup.github.io/hdf5/develop/api-compat-macros.html
-[u14]: https://github.com/HDFGroup/hdf5/releases/tag/snapshot-2.0.0
+[u14]: https://github.com/HDFGroup/hdf5/releases/tag/snapshot-1.14
 [u15]: https://github.com/HDFGroup/hdf5/releases/tag/snapshot
diff --git a/src/H5FDmodule.h b/src/H5FDmodule.h
@@ -25,5 +25,9 @@
 #define H5_MY_PKG      H5FD
 #define H5_MY_PKG_ERR  H5E_VFL
 #define H5_MY_PKG_INIT YES
+/**
+ * \defgroup H5VFD Virtual File Driver Features
+ *
+ */
 
 #endif /* H5FDmodule_H */
diff --git a/src/H5FDonion.h b/src/H5FDonion.h
@@ -162,7 +162,7 @@ H5_DLL herr_t H5Pset_fapl_onion(hid_t fapl_id, const H5FD_onion_fapl_info_t *fa)
 
 /**
  * --------------------------------------------------------------------------
- * \ingroup H5FD
+ * \ingroup H5VFD
  *
  * \brief get the number of revisions
  *

diff --git a/src/H5FDpublic.h b/src/H5FDpublic.h
@@ -418,7 +418,7 @@ extern "C" {
 /* Function prototypes */
 
 /**
- * \ingroup H5FD
+ * \ingroup H5VFD
  *
  * \brief Allows querying a VFD ID for features before the file is opened
  *

diff --git a/src/H5Pmodule.h b/src/H5Pmodule.h
@@ -1114,6 +1114,10 @@
  * TAPL isn't supported yet.
  *
  *
+ * \defgroup MAPL VOL Data Mapping Properties
+ * \ingroup H5P
+ * Empty property class.
+ *
  *
  */
 

diff --git a/src/H5Tmodule.h b/src/H5Tmodule.h
@@ -4087,6 +4087,8 @@ filled according to the value of this property. The padding can be:
  * \ingroup H5T
  * \defgroup ATOM Atomic Datatypes
  * \ingroup H5T
+ * \defgroup COMPLEX Complex Datatypes
+ * \ingroup H5T
  * \defgroup CONV Conversion Function
  * \ingroup H5T
  * \defgroup OPAQUE Opaque Datatypes

diff --git a/src/H5Zmodule.h b/src/H5Zmodule.h
@@ -130,6 +130,8 @@
  * \ingroup H5ZPRE
  * \defgroup SZIP Szip Filter
  * \ingroup H5ZPRE
+ * \defgroup NBIT N-bit Filter
+ * \ingroup H5ZPRE
  *
  */