Merge pull request #1045 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:1.10/master to 1.10/masterhdf5-1_10_2

* commit 'cc2eea14f6a6532a201dde13af13353d4d73fd92': (1014 commits)
  Commit release date changes.
  Fix typo in INSTALL_Cygwin.txt
  Update references and merge from 1_10
  Corrected email address
  Commit Barbara's INSTALL* file updates.
  Commit Elena's RELEASE.txt edits and Les'/Lori's README.txt revision.
  ommit Elena's RELEASE.txt edits and Les'/Lori's README.txt revision.
  Remove stray '/'.
  Add subdirectory for CMake-HDF5-1.10.2.zip.
  Correct name of hl compile script
  Add directory in release CMake...tar.gz file.
  Minor edits in RELEASE.txt. Set version for HDF5 1.10.2 release.
  release branch should not generate headers
  Switch default build mode to production. Set version to 1.10.2-pre2..
  HDFF5-1.10.2-pre1 releaseed. Add links for security bug fixes to RELEASE.txt.
  Fix VS2017 binary readme
  Couple fixes to the test routine for HDFFV-10425.
  Add test and release info for the fix to HDFFV-10425 test failure with H5DOwrite_chunk.
  Updated RELEASE.txt
  Remove known probelem that was fixed.
  ...

3 files changed, 209 insertions, 23 deletions

diff --git a/java/src/hdf/hdf5lib/CMakeLists.txt b/java/src/hdf/hdf5lib/CMakeLists.txt
index c856c04..9506fc1 100644
--- a/java/src/hdf/hdf5lib/CMakeLists.txt
+++ b/java/src/hdf/hdf5lib/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 3.2.2)
+cmake_minimum_required (VERSION 3.10)
 PROJECT (HDF5_JAVA_HDF_HDF5 Java)
 
 set (CMAKE_VERBOSE_MAKEFILE 1)
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index 1f0dd3a..7c1ff5b 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -214,7 +214,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
  * exception handlers to print out the HDF-5 error stack.
  * <hr>
  *
- * @version HDF5 1.10.1 <BR>
+ * @version HDF5 1.10.2 <BR>
  *          <b>See also: <a href ="./hdf.hdf5lib.HDFArray.html"> hdf.hdf5lib.HDFArray</a> </b><BR>
  *          <a href ="./hdf.hdf5lib.HDF5Constants.html"> hdf.hdf5lib.HDF5Constants</a><BR>
  *          <a href ="./hdf.hdf5lib.HDF5CDataTypes.html"> hdf.hdf5lib.HDF5CDataTypes</a><BR>
@@ -237,7 +237,7 @@ public class H5 implements java.io.Serializable {
      *
      * Make sure to update the versions number when a different library is used.
      */
-    public final static int LIB_VERSION[] = { 1, 10, 1 };
+    public final static int LIB_VERSION[] = { 1, 10, 2 };
 
     public final static String H5PATH_PROPERTY_KEY = "hdf.hdf5lib.H5.hdf5lib";
 
@@ -424,7 +424,7 @@ public class H5 implements java.io.Serializable {
     private synchronized static native int H5dont_atexit() throws HDF5LibraryException;
 
     /**
-     * Turn off error handling By default, the C library prints the error stack of the HDF-5 C library on stdout. This
+     * Turn off error handling. By default, the C library prints the error stack of the HDF-5 C library on stdout. This
      * behavior may be disabled by calling H5error_off().
      *
      * @return a non-negative value if successful
@@ -432,6 +432,12 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5error_off();
 
     /**
+     * Turn on error handling. By default, the C library prints the error stack of the HDF-5 C library on stdout. This
+     * behavior may be reenabled by calling H5error_on().
+     */
+    public synchronized static native void H5error_on();
+
+    /**
      * H5garbage_collect collects on all free-lists of all types.
      *
      * @return a non-negative value if successful
@@ -2893,7 +2899,8 @@ public class H5 implements java.io.Serializable {
      * @param file_id
      *            IN: Identifier of the target file.
      *
-     * @param mdc_logging_status, the status
+     * @param mdc_logging_status
+     *          the status
      *             mdc_logging_status[0] = is_enabled, whether logging is enabled
      *             mdc_logging_status[1] = is_currently_logging, whether events are currently being logged
      *
@@ -4450,7 +4457,7 @@ public class H5 implements java.io.Serializable {
     // //
     // ////////////////////////////////////////////////////////////
 
-    // Generic property list routines
+    // /////// Generic property list routines ///////
 
     /**
      * H5Pget_class_name retrieves the name of a generic property list class
@@ -4766,7 +4773,7 @@ public class H5 implements java.io.Serializable {
 
     public synchronized static native int H5Piterate(long plist, int[] idx, H5P_iterate_cb op, H5P_iterate_t op_data) throws HDF5LibraryException;
 
-    // Object creation property list (OCPL) routines
+    // /////// Object creation property list (OCPL) routines ///////
 
     /**
      * H5Pget_attr_phase_change retrieves attribute storage phase change thresholds.
@@ -5070,7 +5077,7 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pset_fletcher32(long plist) throws HDF5LibraryException,
     NullPointerException;
 
-    // File creation property list (FCPL) routines
+    // /////// File creation property list (FCPL) routines ///////
 
     /**
      * H5Pget_userblock retrieves the size of a user block in a file creation property list.
@@ -5479,7 +5486,7 @@ public class H5 implements java.io.Serializable {
            throws HDF5LibraryException, IllegalArgumentException;
 
 
-    // File access property list (FAPL) routines
+    // /////// File access property list (FAPL) routines ///////
 
     /**
      * H5Pget_alignment retrieves the current settings for alignment properties from a file access property list.
@@ -5811,7 +5818,8 @@ public class H5 implements java.io.Serializable {
      *
      * @param fapl_id
      *            IN: File access property list identifier
-     * @param mdc_log_options, the options
+     * @param mdc_log_options
+     *         the options
      *             mdc_logging_options[0] = is_enabled, whether logging is enabled
      *             mdc_logging_options[1] = start_on_access, whether the logging begins as soon as the file is opened or created
      *
@@ -5858,6 +5866,37 @@ public class H5 implements java.io.Serializable {
     public synchronized static native void H5Pset_metadata_read_attempts(long plist_id, long attempts)
             throws HDF5LibraryException;
 
+    /**
+     * H5Pget_evict_on_close retrieves the file access property list setting that determines whether an HDF5 object
+     * will be evicted from the library's metadata cache when it is closed.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     *
+     * @return indication if the object will be evicted on close.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native boolean H5Pget_evict_on_close(long fapl_id)
+            throws HDF5LibraryException;
+
+    /**
+     * H5Pset_evict_on_close controls the library's behavior of evicting metadata associated with a closed object.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param evict_on_close
+     *            IN: Whether the HDF5 object should be evicted on close.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native void H5Pset_evict_on_close(long fapl_id, boolean evict_on_close)
+            throws HDF5LibraryException;
+
     // Dataset creation property list (DCPL) routines //
 
     /**
@@ -6064,6 +6103,36 @@ public class H5 implements java.io.Serializable {
      **/
     public synchronized static native String H5Pget_virtual_dsetname(long dcpl_id, long index) throws HDF5LibraryException, IllegalArgumentException;
 
+//    /////  unimplemented /////
+//    /**
+//     * H5Pget_vds_file_cache_size retrieves the size of the vds link open file cache.
+//     *
+//     * @param fapl_id
+//     *            IN: File access property list identifier
+//     *
+//     * @return VDS link open file cache size in number of files.
+//     *
+//     * @exception HDF5LibraryException
+//     *                - Error from the HDF-5 Library.
+//     *
+//     **/
+//    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.
+//     *
+//     * @param fapl_id
+//     *            IN: File access property list identifier
+//     * @param efc_size
+//     *            IN: VDS link open file cache size in number of files.
+//     *
+//     * @exception HDF5LibraryException
+//     *                - Error from the HDF-5 Library.
+//     *
+//     **/
+//    public synchronized static native void H5Pset_vds_file_cache_size(long fapl_id, int efc_size)
+//            throws HDF5LibraryException;
+
     /**
      * H5Pget_external returns information about an external file.
      *
@@ -6283,7 +6352,37 @@ 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 access property list (DAPL) routines //
+    // /////// Dataset creation property list (DCPL) routines ///////
+
+    /**
+     * H5Pset_chunk_opts Sets the edge chunk option in a dataset creation property list.
+     *
+     * @param dcpl_id
+     *            IN: Dataset creation property list identifier
+     * @param opts
+     *            IN: Edge chunk option flag. Valid values are:
+     *                H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS - filters are not applied to partial edge chunks.
+     *                0 - Disables option; partial edge chunks will be compressed.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library
+     **/
+    public synchronized static native void H5Pset_chunk_opts(long dcpl_id, int opts) throws HDF5LibraryException;
+
+    /**
+     * H5Pget_chunk_opts retrieves the edge chunk option setting stored in the dataset creation property list .
+     *
+     * @param dcpl_id
+     *            IN: Dataset creation property list
+
+     * @return The edge chunk option setting.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library
+     **/
+    public synchronized static native int H5Pget_chunk_opts(long dcpl_id) throws HDF5LibraryException;
+
+    // /////// Dataset access property list (DAPL) routines ///////
 
     /**
      * Retrieves the maximum possible number of elements in the meta data cache and the maximum possible number of bytes
@@ -6386,12 +6485,76 @@ public class H5 implements java.io.Serializable {
      **/
     public synchronized static native long H5Pget_virtual_printf_gap(long dapl_id) throws HDF5LibraryException;
 
+    /**
+     * H5Pget_virtual_prefix Retrieves prefix applied to virtual file paths.
+     *
+     * @param dapl_id
+     *            IN: Link access property list identifier
+     *
+     * @return the prefix to be applied to virtual file paths.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native String H5Pget_virtual_prefix(long dapl_id)
+            throws HDF5LibraryException;
+
+    /**
+     * H5Pset_virtual_prefix Sets prefix to be applied to virtual file paths.
+     *
+     * @param dapl_id
+     *            IN: Dataset access property list identifier
+     * @param prefix
+     *            IN: Prefix to be applied to virtual file paths
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - prefix is null.
+     *
+     **/
+    public synchronized static native void H5Pset_virtual_prefix(long dapl_id, String prefix)
+            throws HDF5LibraryException, NullPointerException;
+
+    /**
+     * H5Pget_efile_prefix Retrieves prefix applied to external file paths.
+     *
+     * @param dapl_id
+     *            IN: Link access property list identifier
+     *
+     * @return the prefix to be applied to external file paths.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native String H5Pget_efile_prefix(long dapl_id)
+            throws HDF5LibraryException;
+
+    /**
+     * H5Pset_efile_prefix Sets prefix to be applied to external file paths.
+     *
+     * @param dapl_id
+     *            IN: Dataset access property list identifier
+     * @param prefix
+     *            IN: Prefix to be applied to external file paths
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - prefix is null.
+     *
+     **/
+    public synchronized static native void H5Pset_efile_prefix(long dapl_id, String prefix)
+            throws HDF5LibraryException, NullPointerException;
+
     // public synchronized static native void H5Pset_append_flush(long plist_id, int ndims, long[] boundary, H5D_append_cb func, H5D_append_t udata) throws HDF5LibraryException;
 
     // public synchronized static native void H5Pget_append_flush(long plist_id, int dims, long[] boundary, H5D_append_cb func, H5D_append_t udata) throws HDF5LibraryException;
 
 
-    // Dataset xfer property list (DXPL) routines //
+    // /////// Dataset xfer property list (DXPL) routines ///////
 
     /**
      * H5Pget_data_transform retrieves the data transform expression previously set in the dataset transfer property
@@ -6542,7 +6705,7 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pset_hyper_vector_size(long dxpl_id, long vector_size)
             throws HDF5LibraryException, NullPointerException;
 
-    // Link creation property list (LCPL) routines //
+    // /////// Link creation property list (LCPL) routines ///////
 
     /**
      * H5Pget_create_intermediate_group determines whether property is set to enable creating missing intermediate
@@ -6577,7 +6740,7 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pset_create_intermediate_group(long lcpl_id, boolean crt_intermed_group)
             throws HDF5LibraryException;
 
-    // Group creation property list (GCPL) routines //
+    // /////// Group creation property list (GCPL) routines ///////
 
     /**
      * H5Pget_local_heap_size_hint Retrieves the anticipated size of the local heap for original-style groups.
@@ -6734,14 +6897,14 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pset_link_creation_order(long gcpl_id, int crt_order_flags)
             throws HDF5LibraryException;
 
-    // String creation property list (STRCPL) routines //
+    // /////// String creation property list (STRCPL) routines ///////
 
     public synchronized static native int H5Pget_char_encoding(long plist_id) throws HDF5LibraryException;
 
     public synchronized static native void H5Pset_char_encoding(long plist_id, int encoding)
             throws HDF5LibraryException;
 
-    // Link access property list (LAPL) routines //
+    // /////// Link access property list (LAPL) routines ///////
 
     /**
      * H5Pget_nlinks retrieves the maximum number of soft or user-defined link traversals allowed, nlinks, before the
@@ -6894,7 +7057,7 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pset_elink_acc_flags(long lapl_id, int flags) throws HDF5LibraryException,
     IllegalArgumentException;
 
-    // Object copy property list (OCPYPL) routines //
+    // /////// Object copy property list (OCPYPL) routines ///////
 
     /**
      * H5Pget_copy_object retrieves the properties to be used when an object is copied.
@@ -6925,7 +7088,7 @@ public class H5 implements java.io.Serializable {
     public synchronized static native void H5Pset_copy_object(long ocp_plist_id, int copy_options)
             throws HDF5LibraryException;
 
-    // Other/Older property list routines //
+    // /////// Other/Older property list routines ///////
 
     /**
      * H5Pget_version retrieves the version information of various objects for a file creation property list.
@@ -6953,7 +7116,7 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pget_version(long plist, int[] version_info) throws HDF5LibraryException,
     NullPointerException, IllegalArgumentException;
 
-    // file drivers property list routines //
+    // /////// file drivers property list routines ///////
 
     public synchronized static native void H5Pget_fapl_core(long fapl_id, long[] increment, boolean[] backing_store)
             throws HDF5LibraryException, NullPointerException;
@@ -7100,20 +7263,28 @@ public class H5 implements java.io.Serializable {
     // File creation property list (FCPL) routines //
 
     // File access property list (FAPL) routines //
-    // herr_t H5Pset_driver( hid_t plist_id, hid_t new_driver_id, const void *new_driver_info )
-    // const void *H5Pget_driver_info( hid_t plist_id )
-    // herr_t H5Pget_multi_type ( hid_t fapl_id, H5FD_mem_t *type )
-    // herr_t H5Pset_multi_type ( hid_t fapl_id, H5FD_mem_t type )
+    // herr_t H5Pset_driver(hid_t plist_id, hid_t new_driver_id, const void *new_driver_info)
+    // const void *H5Pget_driver_info(hid_t plist_id)
+    // herr_t H5Pget_multi_type(hid_t fapl_id, H5FD_mem_t *type)
+    // herr_t H5Pset_multi_type(hid_t fapl_id, H5FD_mem_t type)
     // herr_t H5Pget_file_image(hid_t fapl_id, void **buf_ptr_ptr, size_t *buf_len_ptr);
     // herr_t H5Pset_file_image(hid_t fapl_id, void *buf_ptr, size_t buf_len);
     // herr_t H5Pget_file_image_callbacks(hid_t fapl_id, H5FD_file_image_callbacks_t *callbacks_ptr);
     // herr_t H5Pset_file_image_callbacks(hid_t fapl_id, H5FD_file_image_callbacks_t *callbacks_ptr);
     // herr_t H5Pset_core_write_tracking(hid_t fapl_id, hbool_t is_enabled, size_t page_size);
     // herr_t H5Pget_core_write_tracking(hid_t fapl_id, hbool_t *is_enabled, size_t *page_size);
+    // herr_t H5Pset_all_coll_metadata_ops(hid_t accpl_id, hbool_t is_collective);
+    // herr_t H5Pset_coll_metadata_write(hid_t fapl_id, hbool_t is_collective);
+    // herr_t H5Pget_coll_metadata_write(hid_t fapl_id, hbool_t *is_collective);
+    // herr_t H5Pget_page_buffer_size(hid_t fapl_id, size_t *buf_size, unsigned *min_meta_perc, unsigned *min_raw_perc);
+    // herr_t H5Pset_object_flush_cb (hid_t fapl_id, H5F_flush_cb_t func, void *user_data);
+    // herr_t H5Pget_object_flush_cb (hid_t fapl_id, H5F_flush_cb_t *func, void **user_data);
 
     // Dataset creation property list (DCPL) routines //
 
     // Dataset access property list (DAPL) routines //
+    // herr_t H5Pset_append_flush (hid_t dapl_id, int ndims, const hsize_t boundary[], H5D_append_cb_t func, void *user_data);
+    // herr_t H5Pget_append_flush(hid_t dapl_id, int ndims, hsize_t boundary[], H5D_append_cb_t *func, void **user_data)
 
     // Dataset xfer property list (DXPL) routines //
     // herr_t H5Pset_buffer(hid_t plist_id, size_t size, void *tconv, void *bkg);
diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java
index 8a3d6c8..eb4055d 100644
--- a/java/src/hdf/hdf5lib/HDF5Constants.java
+++ b/java/src/hdf/hdf5lib/HDF5Constants.java
@@ -88,6 +88,7 @@ public class HDF5Constants {
     public static final int H5D_VDS_ERROR = H5D_VDS_ERROR();
     public static final int H5D_VDS_FIRST_MISSING = H5D_VDS_FIRST_MISSING();
     public static final int H5D_VDS_LAST_AVAILABLE = H5D_VDS_LAST_AVAILABLE();
+    public static final int H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS = H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS();
 
     public static final int H5E_MAJOR = H5E_MAJOR();
     public static final int H5E_MINOR = H5E_MINOR();
@@ -205,7 +206,11 @@ public class HDF5Constants {
     public static final int H5F_CLOSE_SEMI = H5F_CLOSE_SEMI();
     public static final int H5F_CLOSE_STRONG = H5F_CLOSE_STRONG();
     public static final int H5F_CLOSE_WEAK = H5F_CLOSE_WEAK();
+    public static final int H5F_LIBVER_ERROR = H5F_LIBVER_ERROR();
     public static final int H5F_LIBVER_EARLIEST = H5F_LIBVER_EARLIEST();
+    public static final int H5F_LIBVER_V18 = H5F_LIBVER_V18();
+    public static final int H5F_LIBVER_V110 = H5F_LIBVER_V110();
+    public static final int H5F_LIBVER_NBOUNDS = H5F_LIBVER_NBOUNDS();
     public static final int H5F_LIBVER_LATEST = H5F_LIBVER_LATEST();
     public static final int H5F_OBJ_ALL = H5F_OBJ_ALL();
     public static final int H5F_OBJ_ATTR = H5F_OBJ_ATTR();
@@ -768,6 +773,8 @@ public class HDF5Constants {
 
     private static native final int H5D_VDS_LAST_AVAILABLE();
 
+    private static native final int H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS();
+
     private static native final long H5E_ALIGNMENT();
 
     private static native final long H5E_ALREADYEXISTS();
@@ -996,8 +1003,16 @@ public class HDF5Constants {
 
     private static native final int H5F_CLOSE_WEAK();
 
+    private static native final int H5F_LIBVER_ERROR();
+
     private static native final int H5F_LIBVER_EARLIEST();
 
+    private static native final int H5F_LIBVER_V18();
+
+    private static native final int H5F_LIBVER_V110();
+
+    private static native final int H5F_LIBVER_NBOUNDS();
+
     private static native final int H5F_LIBVER_LATEST();
 
     private static native final int H5F_OBJ_ALL();