Hdf5 1 12 merge cmake ninja and java refs (#698)

* OESS-98 fix tools test for plugins

* sync fork

* Merge of changes from dev

* Move problem option to bottom of the list until fixed

* HDFFV-11106 - fix parsing optional args

* HDFFV-11106 add note

* grammer fix

* Whitespace after clang formatting

* Undo format version 11 changes

* Update check to working version

* Merge workflow and minor changes from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge serval small changes from dev

* fix typo

* Minor non-space formatting changes

* GH #386 copyright corrections for java folder

* revert because logic requires false return

* Merges from develop

#358 patches from vtk
#361 fix header guard spelling

* Remove case statement for H5I_EVENTSET

* Correct call with versioning

* Remove tabs

* Double underscore change

* Merges from develop

#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
Remove more underscores from header guards

* Merge #380 from develop

* Correct date entry

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

* Some Javadoc warning fixes

* Committing clang-format changes

* Updated javadoc fixes

* HDFFV-11228/9 merges from develop

* remove obsolete debug comment

* Fix conflict

* HDFFV-11229 merge changes from develop

* HDFFV-11229 merge second compare from develop

* HDFFV-11229 fix reference file

* HDFFV-11229 update autotools test script for two ref files

* HDFFV-11229 merge dev changes for long double display in tools

* Committing clang-format changes

* Update with changes from develop

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

Update pkgconfig scripts for parallel builds.
Fix install COPYING file reference.
Remove unused round defines.
Change CMake default setting of BUILD_CPP to off.

* Whitespace changes

* Rework CMake add_custom to use the BYPRODUCTS argument

* Revert CMake configure checks for round defines

* With VS 2015 minimum strdup is supported

* Doxygen comments merged from develop

* doxygen build updates

* Correct version string for map functions

* TRILAB-227 and tools debug merge from develop

* TRILAB-227 Enable test

* Quote subset args

* Use MATCHES in compiler id compare, merge from dev

* Revert test enable

* Add file to list

* doxygen version errors

* if blocks needed for build modes

* Update list of test platforms

* Issue #669 remove version from pkgcfg filename

* remove version from h5cc script

* Merge CMake and java refs from dev

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

3 files changed, 42 insertions, 9 deletions

diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index acae1ae..a90b1f4 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -10726,7 +10726,18 @@ public class H5 implements java.io.Serializable {
      * @exception IllegalArgumentException
      *                - an input array is invalid.
      **/
-    public synchronized static native long H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id)
+    public static long H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException {
+        long id = _H5Ropen_object(ref_ptr, rapl_id, oapl_id);
+        if (id > 0) {
+            log.trace("OPEN_IDS: H5Ropen_object add {}", id);
+            OPEN_IDS.add(id);
+            log.trace("OPEN_IDS: {}", OPEN_IDS.size());
+        }
+        return id;
+    }
+
+    private synchronized static native long _H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id)
             throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
 
     /**
@@ -10754,7 +10765,18 @@ public class H5 implements java.io.Serializable {
      * @exception IllegalArgumentException
      *                - an input array is invalid.
      **/
-    public synchronized static native long H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id)
+    public static long H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException {
+        long id = _H5Ropen_region(ref_ptr, rapl_id, oapl_id);
+        if (id > 0) {
+            log.trace("OPEN_IDS: H5Ropen_region add {}", id);
+            OPEN_IDS.add(id);
+            log.trace("OPEN_IDS: {}", OPEN_IDS.size());
+        }
+        return id;
+    }
+
+    private synchronized static native long _H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id)
             throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
 
     /**
@@ -10782,7 +10804,18 @@ public class H5 implements java.io.Serializable {
      * @exception IllegalArgumentException
      *                - an input array is invalid.
      **/
-    public synchronized static native long H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id)
+    public static long H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException {
+        long id = _H5Ropen_attr(ref_ptr, rapl_id, aapl_id);
+        if (id > 0) {
+            log.trace("OPEN_IDS: H5Ropen_attr add {}", id);
+            OPEN_IDS.add(id);
+            log.trace("OPEN_IDS: {}", OPEN_IDS.size());
+        }
+        return id;
+    }
+
+    private synchronized static native long _H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id)
             throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
 
     // Get type //
diff --git a/java/src/jni/h5rImp.c b/java/src/jni/h5rImp.c
index c08f5de..9fe0701 100644
--- a/java/src/jni/h5rImp.c
+++ b/java/src/jni/h5rImp.c
@@ -336,7 +336,7 @@ done:
  * Signature: ([BJJ)J
  */
 JNIEXPORT jlong JNICALL
-Java_hdf_hdf5lib_H5_H5Ropen_1object(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong oapl_id)
+Java_hdf_hdf5lib_H5__1H5Ropen_1object(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong oapl_id)
 {
     jboolean isCopy;
     jbyte *  refBuf = NULL;
@@ -371,7 +371,7 @@ done:
  * Signature: ([BJJ)J
  */
 JNIEXPORT jlong JNICALL
-Java_hdf_hdf5lib_H5_H5Ropen_1region(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong oapl_id)
+Java_hdf_hdf5lib_H5__1H5Ropen_1region(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong oapl_id)
 {
     jboolean isCopy;
     jbyte *  refBuf = NULL;
@@ -406,7 +406,7 @@ done:
  * Signature: ([BJJ)J
  */
 JNIEXPORT jlong JNICALL
-Java_hdf_hdf5lib_H5_H5Ropen_1attr(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong aapl_id)
+Java_hdf_hdf5lib_H5__1H5Ropen_1attr(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong aapl_id)
 {
     jboolean isCopy;
     jbyte *  refBuf = NULL;
diff --git a/java/src/jni/h5rImp.h b/java/src/jni/h5rImp.h
index cdfdd8e..ffd7737 100644
--- a/java/src/jni/h5rImp.h
+++ b/java/src/jni/h5rImp.h
@@ -78,21 +78,21 @@ JNIEXPORT jbyteArray JNICALL Java_hdf_hdf5lib_H5_H5Rcopy(JNIEnv *, jclass, jbyte
  * Method:    H5Ropen_object
  * Signature: ([BJJ)J
  */
-JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Ropen_1object(JNIEnv *, jclass, jbyteArray, jlong, jlong);
+JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Ropen_1object(JNIEnv *, jclass, jbyteArray, jlong, jlong);
 
 /*
  * Class:     hdf_hdf5lib_H5
  * Method:    H5Ropen_region
  * Signature: ([BJJ)J
  */
-JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Ropen_1region(JNIEnv *, jclass, jbyteArray, jlong, jlong);
+JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Ropen_1region(JNIEnv *, jclass, jbyteArray, jlong, jlong);
 
 /*
  * Class:     hdf_hdf5lib_H5
  * Method:    H5Ropen_attr
  * Signature: ([BJJ)J
  */
-JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Ropen_1attr(JNIEnv *, jclass, jbyteArray, jlong, jlong);
+JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Ropen_1attr(JNIEnv *, jclass, jbyteArray, jlong, jlong);
 
 /*
  * Class:     hdf_hdf5lib_H5