Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)

* commit '0e34f0feaaeb6d2286f87f695f25fae45c070a42': (26 commits)
  HDFFV-10664 update reference file
  HDFFV-10664 update reference files
  HDFFV-10664 add missing function and check for restriction
  Remove "bad" statements at end of TEST_ERROR.     Formerly arguments to FAIL_PUTS_ERROR
  Add RELEASE.txt entry for HDFFV-10596.
  Add semicolon at end of TEST_ERROR() invocation for consistency.
  Uninstall should remove the libhdf5_hl_fortran links.
  Add symlinks named libhdf5_hl_fortran* to libhdf5hl_fortran in Makefile.am to match cmake install and the name pattern for other hl lib files.
  Change FAIL_PUTS_ERROR to TEST_ERROR.
  Cleaned up the parallel flush test and set t_pflush1 to always fail. Also set CMake to handle this.
  Update calls: H5Dcreate to H5Dcreate2, H5Acreate to H5Acreate2.
  Removed a comment.
  Fix comment
  Align H5Lcreate_ud behavior with documentation for NULL udata pointer
  Update toolchain comment
  Use c99 standard cmake variable
  Add PGI toolchain
  Correction based on code review.
  HDFFV-10664 add check for state before set call
  HDFFV-10546 refactor variable name
  ...

11 files changed, 311 insertions, 29 deletions

diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index e354207..51b0d38 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -3229,13 +3229,56 @@ public class H5 implements java.io.Serializable {
     public synchronized static native void H5Fget_mdc_logging_status(long file_id, boolean[] mdc_logging_status)
             throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Fget_dset_no_attrs_hint gets the file-level setting to create minimized dataset object headers.
+     *
+     * @param file_id
+     *            IN: Identifier of the target file.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native boolean H5Fget_dset_no_attrs_hint(long file_id)
+            throws HDF5LibraryException;
+
+
+    /**
+     * H5Fset_dset_no_attrs_hint sets the file-level setting to create minimized dataset object headers.
+     *
+     * @param file_id
+     *            IN: Identifier of the target file.
+     * @param minimize
+     *          the minimize hint setting
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native void H5Fset_dset_no_attrs_hint(long file_id, boolean minimize)
+            throws HDF5LibraryException;
+
+
+    /**
+     * H5Fset_libver_bounds sets a different low and high bounds while a file is open.
+     *
+     * @param file_id
+     *            IN: Identifier of the target file.
+     * @param low
+     *            IN: The earliest version of the library that will be used for writing objects
+     * @param high
+     *            IN: The latest version of the library that will be used for writing objects.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native void H5Fset_libver_bounds(long file_id, int low, int high)
+            throws HDF5LibraryException;
+
     // /////// unimplemented ////////
     //  herr_t H5Fget_eoa(hid_t file_id, haddr_t *eoa);
     //  herr_t H5Fincrement_filesize(hid_t file_id, hsize_t increment);
     // ssize_t H5Fget_file_image(hid_t file_id, void * buf_ptr, size_t buf_len);
     // herr_t H5Fget_metadata_read_retry_info(hid_t file_id, H5F_retry_info_t *info);
     // ssize_t H5Fget_free_sections(hid_t file_id, H5F_mem_t type, size_t nsects, H5F_sect_info_t *sect_info/*out*/);
-    //  herr_t H5Fset_libver_bounds(hid_t file_id, H5F_libver_t low, H5F_libver_t high);
     //  herr_t H5Fformat_convert(hid_t fid);
     //  herr_t H5Freset_page_buffering_stats(hid_t file_id);
     //  herr_t H5Fget_page_buffering_stats(hid_t file_id, unsigned accesses[2],
@@ -6922,8 +6965,6 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pset_fill_time(long plist_id, int fill_time) throws HDF5LibraryException,
     NullPointerException;
 
-    // /////// Dataset creation property list (DCPL) routines ///////
-
     /**
      * H5Pset_chunk_opts Sets the edge chunk option in a dataset creation property list.
      *
@@ -6952,6 +6993,36 @@ public class H5 implements java.io.Serializable {
      **/
     public synchronized static native int H5Pget_chunk_opts(long dcpl_id) throws HDF5LibraryException;
 
+    /**
+     * H5Pget_dset_no_attrs_hint accesses the flag for whether or not datasets created by the given dcpl
+     *     will be created with a "minimized" object header.
+     *
+     * @param dcpl_id
+     *            IN: Dataset creation property list
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native boolean H5Pget_dset_no_attrs_hint(long dcpl_id)
+            throws HDF5LibraryException;
+
+
+    /**
+     * H5Pset_dset_no_attrs_hint sets the dcpl to minimize (or explicitly to not minimized) dataset object
+     *     headers upon creation.
+     *
+     * @param dcpl_id
+     *            IN: Dataset creation property list
+     *
+     * @param minimize
+     *          the minimize hint setting
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native void H5Pset_dset_no_attrs_hint(long dcpl_id, boolean minimize)
+            throws HDF5LibraryException;
+
     // /////// Dataset access property list (DAPL) routines ///////
 
     /**
diff --git a/java/src/jni/h5fImp.c b/java/src/jni/h5fImp.c
index 248e654..80adffb 100644
--- a/java/src/jni/h5fImp.c
+++ b/java/src/jni/h5fImp.c
@@ -149,6 +149,9 @@ Java_hdf_hdf5lib_H5_H5Fis_1hdf5
     (JNIEnv *env, jclass clss, jstring name)
 {
     htri_t      bval = JNI_FALSE;
+#ifdef H5_NO_DEPRECATED_SYMBOLS
+    h5unimplemented(env, "H5Fis_hdf5:  not implemented");
+#else
     const char *fileName;
 
     PIN_JAVA_STRING(name, fileName);
@@ -162,7 +165,7 @@ Java_hdf_hdf5lib_H5_H5Fis_1hdf5
         else if (bval < 0)
             h5libraryError(env);
     }
-
+#endif
     return (jboolean)bval;
 } /* end Java_hdf_hdf5lib_H5_H5Fis_1hdf5 */
 
@@ -636,6 +639,66 @@ Java_hdf_hdf5lib_H5_H5Fget_1mdc_1logging_1status
     } /* end else */
 } /* end Java_hdf_hdf5lib_H5_H5Fget_1mdc_1logging_1status */
 
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Fset_dset_no_attrs_hint
+ * Signature: (JZ)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Fset_1dset_1no_1attrs_1hint
+(JNIEnv *env, jclass clss, jlong file_id, jboolean minimize)
+{
+    herr_t   retVal = -1;
+    hbool_t  minimize_val;
+
+    if (minimize == JNI_TRUE)
+        minimize_val = TRUE;
+    else
+        minimize_val = FALSE;
+
+    retVal = H5Fset_dset_no_attrs_hint((hid_t)file_id, (hbool_t)minimize_val);
+    if (retVal < 0)
+        h5libraryError(env);
+}
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Fget_dset_no_attrs_hint
+ * Signature: (J)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Fget_1dset_1no_1attrs_1hint
+(JNIEnv *env, jclass clss, jlong file_id)
+{
+    hbool_t    minimize = FALSE;
+    jboolean  bval = JNI_FALSE;
+
+    if (H5Fget_dset_no_attrs_hint((hid_t)file_id, (hbool_t *)&minimize) < 0) {
+        h5libraryError(env);
+    }
+    else {
+        if (minimize == TRUE)
+            bval =  JNI_TRUE;
+    } /* end else */
+
+    return bval;
+}
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Fset_libver_bounds
+ * Signature: (JII)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Fset_1libver_1bounds
+    (JNIEnv *env, jclass clss, jlong file_id, jint low, jint high)
+{
+    herr_t retVal = -1;
+
+    retVal = H5Fset_libver_bounds((hid_t)file_id, (H5F_libver_t)low, (H5F_libver_t)high);
+    if(retVal < 0)
+        h5libraryError(env);
+} /* end Java_hdf_hdf5lib_H5_H5Fset_1libver_1bounds */
 
 
 #ifdef __cplusplus
diff --git a/java/src/jni/h5fImp.h b/java/src/jni/h5fImp.h
index af0fa1d..fe253f9 100644
--- a/java/src/jni/h5fImp.h
+++ b/java/src/jni/h5fImp.h
@@ -255,6 +255,33 @@ JNIEXPORT void JNICALL
 Java_hdf_hdf5lib_H5_H5Fget_1mdc_1logging_1status
   (JNIEnv *, jclass, jlong, jbooleanArray);
 
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Fset_dset_no_attrs_hint
+ * Signature: (JZ)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Fset_1dset_1no_1attrs_1hint
+  (JNIEnv *, jclass, jlong, jboolean);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Fget_dset_no_attrs_hint
+ * Signature: (J)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Fget_1dset_1no_1attrs_1hint
+  (JNIEnv *, jclass, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Fset_libver_bounds
+ * Signature: (JII)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Fset_1libver_1bounds
+(JNIEnv *, jclass, jlong, jint, jint);
+
 #ifdef __cplusplus
 } /* end extern "C" */
 #endif /* __cplusplus */
diff --git a/java/src/jni/h5pImp.c b/java/src/jni/h5pImp.c
index 52008ce..19f9640 100644
--- a/java/src/jni/h5pImp.c
+++ b/java/src/jni/h5pImp.c
@@ -5946,6 +5946,51 @@ Java_hdf_hdf5lib_H5_H5Pget_1chunk_1opts
     return (jint)opts;
 } /* end Java_hdf_hdf5lib_H5_H5Pget_1chunk_1opts */
 
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_dset_no_attrs_hint
+ * Signature: (JZ)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1dset_1no_1attrs_1hint
+(JNIEnv *env, jclass clss, jlong dcpl_id, jboolean minimize)
+{
+    herr_t   retVal = -1;
+    hbool_t  minimize_val;
+
+    if (minimize == JNI_TRUE)
+        minimize_val = TRUE;
+    else
+        minimize_val = FALSE;
+
+    retVal = H5Pset_dset_no_attrs_hint((hid_t)dcpl_id, (hbool_t)minimize_val);
+    if (retVal < 0)
+        h5libraryError(env);
+}
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_dset_no_attrs_hint
+ * Signature: (J)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1dset_1no_1attrs_1hint
+(JNIEnv *env, jclass clss, jlong dcpl_id)
+{
+    hbool_t    minimize = FALSE;
+    jboolean  bval = JNI_FALSE;
+
+    if (H5Pget_dset_no_attrs_hint((hid_t)dcpl_id, (hbool_t *)&minimize) < 0) {
+        h5libraryError(env);
+    }
+    else {
+        if (minimize == TRUE)
+            bval =  JNI_TRUE;
+    } /* end else */
+
+    return bval;
+}
+
 #ifdef __cplusplus
 } /* end extern "C" */
 #endif /* __cplusplus */
diff --git a/java/src/jni/h5pImp.h b/java/src/jni/h5pImp.h
index 1d12e3d..0a603f7 100644
--- a/java/src/jni/h5pImp.h
+++ b/java/src/jni/h5pImp.h
@@ -1614,6 +1614,24 @@ JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_H5_H5Pget_1chunk_1opts
 (JNIEnv *, jclass, jlong);
 
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_dset_no_attrs_hint
+ * Signature: (JZ)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1dset_1no_1attrs_1hint
+  (JNIEnv *, jclass, jlong, jboolean);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_dset_no_attrs_hint
+ * Signature: (J)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1dset_1no_1attrs_1hint
+  (JNIEnv *, jclass, jlong);
+
 
 #ifdef __cplusplus
 } /* end extern "C" */
diff --git a/java/test/TestH5Dplist.java b/java/test/TestH5Dplist.java
index 406a1d3..1b5acfa 100644
--- a/java/test/TestH5Dplist.java
+++ b/java/test/TestH5Dplist.java
@@ -13,6 +13,7 @@
 
 package test;
 
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
@@ -211,4 +212,23 @@ public class TestH5Dplist {
       assertTrue("testH5Dset_extent - H5.H5Dread: ", extend_dset_data[4][8] == 99);
   }
 
+  @Test
+  public void testH5P_dset_no_attrs_hint() {
+      boolean ret_val_id = true;
+
+      _createPDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DATASET_CREATE);
+
+      try {
+          ret_val_id = H5.H5Pget_dset_no_attrs_hint(H5dcpl_id);
+          assertFalse("H5P_dset_no_attrs_hint", ret_val_id);
+          H5.H5Pset_dset_no_attrs_hint(H5dcpl_id, true);
+          ret_val_id = H5.H5Pget_dset_no_attrs_hint(H5dcpl_id);
+          assertTrue("H5P_dset_no_attrs_hint", ret_val_id);
+      }
+      catch (Throwable err) {
+          err.printStackTrace();
+          fail("H5P_dset_no_attrs_hint: " + err);
+      }
+  }
+
 }
diff --git a/java/test/TestH5Fbasic.java b/java/test/TestH5Fbasic.java
index a5afb6e..72a3c23 100644
--- a/java/test/TestH5Fbasic.java
+++ b/java/test/TestH5Fbasic.java
@@ -14,6 +14,7 @@
 package test;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
@@ -69,19 +70,6 @@ public class TestH5Fbasic {
     }
 
     @Test
-    public void testH5Fis_hdf5() {
-        boolean isH5 = false;
-
-        try {
-            isH5 = H5.H5Fis_hdf5(H5_FILE);
-        }
-        catch (Throwable err) {
-            fail("H5.H5Fis_hdf5 failed on " + H5_FILE + ": " + err);
-        }
-        assertTrue(isH5 == true);
-    }
-
-    @Test
     public void testH5Fis_accessible() {
         boolean isH5 = false;
 
@@ -328,4 +316,20 @@ public class TestH5Fbasic {
             fail("H5.H5Freset_mdc_hit_rate_stats: " + err);
         }
     }
+
+    @Test
+    public void testH5F_dset_no_attrs_hint() {
+        boolean ret_val_id = true;
+        try {
+            ret_val_id = H5.H5Fget_dset_no_attrs_hint(H5fid);
+            assertFalse("H5F_dset_no_attrs_hint", ret_val_id);
+            H5.H5Fset_dset_no_attrs_hint(H5fid, true);
+            ret_val_id = H5.H5Fget_dset_no_attrs_hint(H5fid);
+            assertTrue("H5F_dset_no_attrs_hint", ret_val_id);
+        }
+        catch (Throwable err) {
+            err.printStackTrace();
+            fail("H5F_dset_no_attrs_hint: " + err);
+        }
+    }
 }
diff --git a/java/test/TestH5Fparams.java b/java/test/TestH5Fparams.java
index 3d64aa9..40cbe4b 100644
--- a/java/test/TestH5Fparams.java
+++ b/java/test/TestH5Fparams.java
@@ -22,10 +22,12 @@ import java.io.File;
 
 import hdf.hdf5lib.H5;
 import hdf.hdf5lib.HDF5Constants;
+import hdf.hdf5lib.exceptions.HDF5FunctionArgumentException;
 import hdf.hdf5lib.structs.H5F_info2_t;
 
 import org.junit.After;
 import org.junit.Before;
+import org.junit.Ignore;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.TestName;
@@ -55,11 +57,6 @@ public class TestH5Fparams {
     }
 
     @Test(expected = NullPointerException.class)
-    public void testH5Fis_hdf5_null() throws Throwable {
-        H5.H5Fis_hdf5(null);
-    }
-
-    @Test(expected = NullPointerException.class)
     public void testH5Fis_accessible_null() throws Throwable {
         H5.H5Fis_accessible(null, -1);
     }
@@ -74,7 +71,7 @@ public class TestH5Fparams {
         H5.H5Funmount(-1, null);
     }
 
-    @Test
+    @Ignore
     public void testH5Fis_hdf5_text() {
         File txtFile = null;
         boolean isH5 = false;
@@ -195,7 +192,7 @@ public class TestH5Fparams {
                         HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
             }
             catch (Throwable err) {
-                fail("H5.H5Fopen: " + err);
+                fail("H5.H5Fcreate: " + err);
             }
 
             try {
@@ -215,4 +212,42 @@ public class TestH5Fparams {
             try {H5.H5Fclose(fid);} catch (Exception ex) {}
         }
     }
+
+    @Ignore//(expected = HDF5FunctionArgumentException.class)
+    public void testH5Fset_libver_bounds_invalidlow() throws Throwable {
+        long fid = -1;
+
+        try {
+            try {
+                fid = H5.H5Fcreate("test.h5", HDF5Constants.H5F_ACC_TRUNC,
+                        HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+            }
+            catch (Throwable err) {
+                fail("H5.H5Fcreate: " + err);
+            }
+            H5.H5Fset_libver_bounds(fid, 5, HDF5Constants.H5F_LIBVER_LATEST);
+        }
+        finally {
+            try {H5.H5Fclose(fid);} catch (Exception ex) {}
+        }
+    }
+
+    @Ignore//(expected = HDF5FunctionArgumentException.class)
+    public void testH5Fset_libver_bounds_invalidhigh() throws Throwable {
+        long fid = -1;
+
+        try {
+            try {
+                fid = H5.H5Fcreate("test.h5", HDF5Constants.H5F_ACC_TRUNC,
+                        HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+            }
+            catch (Throwable err) {
+                fail("H5.H5Fcreate: " + err);
+            }
+            H5.H5Fset_libver_bounds(fid, HDF5Constants.H5F_LIBVER_V110, HDF5Constants.H5F_LIBVER_V110+1);
+        }
+        finally {
+            try {H5.H5Fclose(fid);} catch (Exception ex) {}
+        }
+    }
 }
diff --git a/java/test/testfiles/JUnit-TestH5Dplist.txt b/java/test/testfiles/JUnit-TestH5Dplist.txt
index 1dfbed1..64e924a 100644
--- a/java/test/testfiles/JUnit-TestH5Dplist.txt
+++ b/java/test/testfiles/JUnit-TestH5Dplist.txt
@@ -1,7 +1,8 @@
 JUnit version 4.11
+.testH5P_dset_no_attrs_hint
 .testH5Dset_extent
 
 Time:  XXXX
 
-OK (1 test)
+OK (2 tests)
 
diff --git a/java/test/testfiles/JUnit-TestH5Fbasic.txt b/java/test/testfiles/JUnit-TestH5Fbasic.txt
index 2654624..cd4e282 100644
--- a/java/test/testfiles/JUnit-TestH5Fbasic.txt
+++ b/java/test/testfiles/JUnit-TestH5Fbasic.txt
@@ -1,7 +1,7 @@
 JUnit version 4.11
 .testH5Fget_mdc_size
 .testH5Fget_mdc_hit_rate
-.testH5Fis_hdf5
+.testH5F_dset_no_attrs_hint
 .testH5Fget_freespace
 .testH5Fclose
 .testH5Fget_filesize
diff --git a/java/test/testfiles/JUnit-TestH5Fparams.txt b/java/test/testfiles/JUnit-TestH5Fparams.txt
index e91cbdc..91a8435 100644
--- a/java/test/testfiles/JUnit-TestH5Fparams.txt
+++ b/java/test/testfiles/JUnit-TestH5Fparams.txt
@@ -9,10 +9,8 @@ JUnit version 4.11
 .testH5Funmount_null
 .testH5Fclose_negative
 .testH5Fopen_null
-.testH5Fis_hdf5_null
-.testH5Fis_hdf5_text
 
 Time:  XXXX
 
-OK (12 tests)
+OK (10 tests)