Merges from develop/1.14 (#3118)

* Fix release action that allows files to be uploaded.
Add autotools h5copy help test.
Update cmake tools.cmake file for clang-tidy.
CMake build is missing H5FDsubfiling.h
macros improved for configure output capture.
Remove obsolete files

* Revert parallel config with TS

* Fix doxygen warnings

10 files changed, 9 insertions, 214 deletions

diff --git a/java/src/hdf/hdf5lib/CMakeLists.txt b/java/src/hdf/hdf5lib/CMakeLists.txt
index 1afc8b0..1738bcf 100644
--- a/java/src/hdf/hdf5lib/CMakeLists.txt
+++ b/java/src/hdf/hdf5lib/CMakeLists.txt
@@ -101,7 +101,6 @@ set (HDF5_JAVADOC_HDF_HDF5_STRUCTS_SOURCES
 set (HDF5_JAVA_HDF_HDF5_SOURCES
     HDFArray.java
     HDF5Constants.java
-    HDF5GroupInfo.java
     HDFNativeData.java
     H5.java
 )
@@ -135,15 +134,3 @@ set_target_properties (${HDF5_JAVA_HDF5_LIB_TARGET} PROPERTIES FOLDER libraries/
 if (HDF5_ENABLE_FORMATTERS)
   clang_format (HDF5_JAVA_SRC_FORMAT ${HDF5_JAVA_HDF_HDF5_CALLBACKS_SOURCES} ${HDF5_JAVA_HDF_HDF5_EXCEPTIONS_SOURCES} ${HDF5_JAVA_HDF_HDF5_STRUCTS_SOURCES} ${HDF5_JAVA_HDF_HDF5_SOURCES})
 endif ()
-
-create_javadoc(hdf5_java_doc
-    FILES ${HDF5_JAVADOC_HDF_HDF5_CALLBACKS_SOURCES} ${HDF5_JAVADOC_HDF_HDF5_EXCEPTIONS_SOURCES} ${HDF5_JAVADOC_HDF_HDF5_STRUCTS_SOURCES} ${HDF5_JAVADOC_HDF_HDF5_SOURCES}
-    OVERVIEW ${HDF5_JAVA_HDF5_SRC_DIR}/overview.html
-    CLASSPATH ${CMAKE_JAVA_INCLUDE_PATH}
-    WINDOWTITLE "HDF5 Java"
-    DOCTITLE "<h1>HDF5 Java Wrapper</h1>"
-    INSTALLPATH ${HDF5_INSTALL_DOC_DIR}
-    AUTHOR TRUE
-    USE TRUE
-    VERSION TRUE
-)
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index bb42106..90c4575 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -228,7 +228,7 @@ import hdf.hdf5lib.structs.H5O_token_t;
  * which prints out the HDF5 error stack, as described in the HDF5 C API <i><b>@ref H5Eprint()</b>.</i> This
  * may be used by Java exception handlers to print out the HDF5 error stack. <hr>
  *
- * @version HDF5 1.10.10 <br />
+ * @version HDF5 1.12.3 <br />
  *          <b>See also: </b>
  *          @ref HDFARRAY hdf.hdf5lib.HDFArray<br />
  *          @ref HDF5CONST hdf.hdf5lib.HDF5Constants<br />
@@ -5082,8 +5082,8 @@ public class H5 implements java.io.Serializable {
      *
      * @param name
      *            IN: File name to check.
-     * @param file_id
-     *            IN: File identifier for a currently-open HDF5 file
+     * @param fapl_id
+     *            IN: File access property list identifier
      *
      * @return true if file is accessible, false if not.
      *
@@ -5092,7 +5092,7 @@ public class H5 implements java.io.Serializable {
      * @exception NullPointerException
      *            name is null.
      **/
-    public synchronized static native boolean H5Fis_accessible(String name, long file_id)
+    public synchronized static native boolean H5Fis_accessible(String name, long fapl_id)
         throws HDF5LibraryException, NullPointerException;
 
     /**
@@ -13773,7 +13773,7 @@ public class H5 implements java.io.Serializable {
     /**
      * @ingroup JH5T
      *
-     * H5Tcreate creates a new dataype of the specified class with the specified number of bytes.
+     * H5Tcreate creates a new datatype of the specified class with the specified number of bytes.
      *
      * @param tclass
      *            IN: Class of datatype to create.
@@ -15228,7 +15228,7 @@ public class H5 implements java.io.Serializable {
     /**
      * @ingroup JH5T
      *
-     * H5Tvlen_create creates a new variable-length (VL) dataype.
+     * H5Tvlen_create creates a new variable-length (VL) datatype.
      *
      * @param base_id
      *            IN: Identifier of parent datatype.
diff --git a/java/src/hdf/hdf5lib/HDF5GroupInfo.java b/java/src/hdf/hdf5lib/HDF5GroupInfo.java
deleted file mode 100644
index 50c7db0..0000000
--- a/java/src/hdf/hdf5lib/HDF5GroupInfo.java
+++ /dev/null
@@ -1,188 +0,0 @@
-/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
- * All rights reserved.                                                      *
- *                                                                           *
- * This file is part of HDF5.  The full HDF5 copyright notice, including     *
- * terms governing use, modification, and redistribution, is contained in    *
- * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://www.hdfgroup.org/licenses.               *
- * If you do not have access to either file, you may request a copy from     *
- * help@hdfgroup.org.                                                        *
- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
-
-package hdf.hdf5lib;
-
-/**
- * <p>
- * This class is a container for the information reported about an HDF5 Object
- * from the H5Gget_obj_info() method.
- * <p>
- * The fileno and objno fields contain four values which uniquely identify an
- * object among those HDF5 files which are open: if all four values are the same
- * between two objects, then the two objects are the same (provided both files
- * are still open). The nlink field is the number of hard links to the object or
- * zero when information is being returned about a symbolic link (symbolic links
- * do not have hard links but all other objects always have at least one). The
- * type field contains the type of the object, one of H5G_GROUP, H5G_DATASET, or
- * H5G_LINK. The mtime field contains the modification time. If information is
- * being returned about a symbolic link then linklen will be the length of the
- * link value (the name of the pointed-to object with the null terminator);
- * otherwise linklen will be zero. Other fields may be added to this structure
- * in the future.
- *
- * @deprecated  Not for public use. It is not used by the library.
- *    This class assumes that an object can contain four values which uniquely identify an
- *    object among those HDF5 files which are open. This is no longer valid in future
- *    HDF5 releases.
- */
-
-@Deprecated
-public class HDF5GroupInfo {
-    long[] fileno;
-    long[] objno;
-    int nlink;
-    int type;
-    long mtime;
-    int linklen;
-
-    /**
-     * Container for the information reported about an HDF5 Object
-     * from the H5Gget_obj_info() method
-     */
-    public HDF5GroupInfo()
-    {
-        fileno  = new long[2];
-        objno   = new long[2];
-        nlink   = -1;
-        type    = -1;
-        mtime   = 0;
-        linklen = 0;
-    }
-
-    /**
-     * Sets the HDF5 group information. Used by the JHI5.
-     *
-     * @param fn
-     *            File id number
-     * @param on
-     *            Object id number
-     * @param nl
-     *            Number of links
-     * @param t
-     *            Type of the object
-     * @param mt
-     *            Modification time
-     * @param len
-     *            Length of link
-     **/
-    public void setGroupInfo(long[] fn, long[] on, int nl, int t, long mt, int len)
-    {
-        fileno  = fn;
-        objno   = on;
-        nlink   = nl;
-        type    = t;
-        mtime   = mt;
-        linklen = len;
-    }
-
-    /** Resets all the group information to defaults. */
-    public void reset()
-    {
-        fileno[0] = 0;
-        fileno[1] = 0;
-        objno[0]  = 0;
-        objno[1]  = 0;
-        nlink     = -1;
-        type      = -1;
-        mtime     = 0;
-        linklen   = 0;
-    }
-
-    /**
-     * fileno accessors
-     * @return the file number if successful
-     */
-    public long[] getFileno() { return fileno; }
-
-    /**
-     * accessors
-     * @return the object number if successful
-     */
-    public long[] getObjno() { return objno; }
-
-    /**
-     * accessors
-     * @return type of group if successful
-     */
-    public int getType() { return type; }
-
-    /**
-     * accessors
-     * @return the number of links in the group if successful
-     */
-    public int getNlink() { return nlink; }
-
-    /**
-     * accessors
-     * @return the modified time value if successful
-     */
-    public long getMtime() { return mtime; }
-
-    /**
-     * accessors
-     * @return a length of link name if successful
-     */
-    public int getLinklen() { return linklen; }
-
-    /**
-     * The fileno and objno fields contain four values which uniquely identify
-     * an object among those HDF5 files.
-     */
-    @Override
-    public boolean equals(Object obj)
-    {
-        if (!(obj instanceof HDF5GroupInfo)) {
-            return false;
-        }
-
-        HDF5GroupInfo target = (HDF5GroupInfo)obj;
-        if ((fileno[0] == target.fileno[0]) && (fileno[1] == target.fileno[1]) &&
-            (objno[0] == target.objno[0]) && (objno[1] == target.objno[1])) {
-            return true;
-        }
-        else {
-            return false;
-        }
-    }
-
-    /**
-     * Returns the object id.
-     *
-     * @return the object id
-     */
-    public long getOID() { return objno[0]; }
-
-    /**
-     * /** Converts this object to a String representation.
-     *
-     * @return a string representation of this object
-     */
-    @Override
-    public String toString()
-    {
-        String fileStr = "fileno=null";
-        String objStr  = "objno=null";
-
-        if (fileno != null) {
-            fileStr = "fileno[0]=" + fileno[0] + ",fileno[1]=" + fileno[1];
-        }
-
-        if (objno != null) {
-            objStr = "objno[0]=" + objno[0] + ",objno[1]=" + objno[1];
-        }
-
-        return getClass().getName() + "[" + fileStr + "," + objStr + ",type=" + type + ",nlink=" + nlink +
-            ",mtime=" + mtime + ",linklen=" + linklen + "]";
-    }
-}
diff --git a/java/src/hdf/hdf5lib/HDFArray.java b/java/src/hdf/hdf5lib/HDFArray.java
index 28d5117..637a896 100644
--- a/java/src/hdf/hdf5lib/HDFArray.java
+++ b/java/src/hdf/hdf5lib/HDFArray.java
@@ -455,6 +455,7 @@ public class HDFArray {
                     new HDF5JavaException("HDFArray: unsupported Object type: " + ArrayDescriptor.NT);
                 throw(ex);
             }
+            break;
         } // end of statement for arrays of boxed objects
         default:
             HDF5JavaException ex =
@@ -527,6 +528,7 @@ public class HDFArray {
                             new HDF5JavaException("HDFArray: unsupported Object type: " + ArrayDescriptor.NT);
                         throw(ex);
                     }
+                    break;
                 } // end of statement for arrays of boxed numerics
                 } // end of switch statement for arrays of primitives
 
diff --git a/java/src/hdf/hdf5lib/callbacks/package-info.java b/java/src/hdf/hdf5lib/callbacks/package-info.java
index 5ef3fab..bf7bf3c 100644
--- a/java/src/hdf/hdf5lib/callbacks/package-info.java
+++ b/java/src/hdf/hdf5lib/callbacks/package-info.java
@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- *                                                                           *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
diff --git a/java/src/hdf/hdf5lib/exceptions/package-info.java b/java/src/hdf/hdf5lib/exceptions/package-info.java
index 2ac7806..784e57d 100644
--- a/java/src/hdf/hdf5lib/exceptions/package-info.java
+++ b/java/src/hdf/hdf5lib/exceptions/package-info.java
@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- *                                                                           *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
@@ -29,4 +28,4 @@
  * error code returned by the HDF5 library.
  *
  */
-package hdf.hdf5lib.exceptions;
\ No newline at end of file
+package hdf.hdf5lib.exceptions;
diff --git a/java/src/hdf/hdf5lib/package-info.java b/java/src/hdf/hdf5lib/package-info.java
index 7ae4df9..e742197 100644
--- a/java/src/hdf/hdf5lib/package-info.java
+++ b/java/src/hdf/hdf5lib/package-info.java
@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- *                                                                           *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
diff --git a/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java b/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java
index 181d681..9861334 100644
--- a/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java
@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- *                                                                           *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
diff --git a/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java b/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java
index 67c2463..62b2921 100644
--- a/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java
@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- *                                                                           *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
diff --git a/java/src/hdf/hdf5lib/structs/package-info.java b/java/src/hdf/hdf5lib/structs/package-info.java
index a3ec6cd..7bd3dee 100644
--- a/java/src/hdf/hdf5lib/structs/package-info.java
+++ b/java/src/hdf/hdf5lib/structs/package-info.java
@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- *                                                                           *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *