From 73aba9228d2967647629b40ae957719588c757d5 Mon Sep 17 00:00:00 2001 From: Thomas Kluyver Date: Thu, 15 Oct 2020 10:49:22 +0100 Subject: Note that the description for system errors may be used by h5py --- src/H5Eprivate.h | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/H5Eprivate.h b/src/H5Eprivate.h index 8f89201..bf733ea 100644 --- a/src/H5Eprivate.h +++ b/src/H5Eprivate.h @@ -114,12 +114,14 @@ typedef struct H5E_t H5E_t; #define HSYS_DONE_ERROR(majorcode, minorcode, retcode, str) \ { \ int myerrno = errno; \ + /* h5py may rely on the description format to get the errno - please try to avoid breaking it */ \ HDONE_ERROR(majorcode, minorcode, retcode, "%s, errno = %d, error message = '%s'", str, myerrno, \ HDstrerror(myerrno)); \ } #define HSYS_GOTO_ERROR(majorcode, minorcode, retcode, str) \ { \ int myerrno = errno; \ + /* h5py may rely on the description format to get the errno - please try to avoid breaking it */ \ HGOTO_ERROR(majorcode, minorcode, retcode, "%s, errno = %d, error message = '%s'", str, myerrno, \ HDstrerror(myerrno)); \ } -- cgit v0.12 From bb2ed7151b05b0a159a991bacc7c58d46f39d3c5 Mon Sep 17 00:00:00 2001 From: Thomas Kluyver Date: Thu, 15 Oct 2020 15:29:56 +0100 Subject: More general message about using description for errno --- src/H5Eprivate.h | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/src/H5Eprivate.h b/src/H5Eprivate.h index bf733ea..f3d3b6f 100644 --- a/src/H5Eprivate.h +++ b/src/H5Eprivate.h @@ -114,14 +114,18 @@ typedef struct H5E_t H5E_t; #define HSYS_DONE_ERROR(majorcode, minorcode, retcode, str) \ { \ int myerrno = errno; \ - /* h5py may rely on the description format to get the errno - please try to avoid breaking it */ \ + /* Other projects may rely on the description format to get the errno and any changes should be \ + * considered as an API change \ + */ \ HDONE_ERROR(majorcode, minorcode, retcode, "%s, errno = %d, error message = '%s'", str, myerrno, \ HDstrerror(myerrno)); \ } #define HSYS_GOTO_ERROR(majorcode, minorcode, retcode, str) \ { \ int myerrno = errno; \ - /* h5py may rely on the description format to get the errno - please try to avoid breaking it */ \ + /* Other projects may rely on the description format to get the errno and any changes should be \ + * considered as an API change \ + */ \ HGOTO_ERROR(majorcode, minorcode, retcode, "%s, errno = %d, error message = '%s'", str, myerrno, \ HDstrerror(myerrno)); \ } -- cgit v0.12 From 9bd2102b7747b255b570d428399151296baa17d1 Mon Sep 17 00:00:00 2001 From: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Fri, 16 Oct 2020 11:10:35 -0500 Subject: Update javadoc comments to reduce warnings (#41) --- java/src/hdf/hdf5lib/H5.java | 2806 ++++++++++++++++++-- java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java | 25 +- java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java | 4 + java/src/hdf/hdf5lib/callbacks/H5D_append_cb.java | 22 +- java/src/hdf/hdf5lib/callbacks/H5D_append_t.java | 4 + java/src/hdf/hdf5lib/callbacks/H5D_iterate_cb.java | 24 +- java/src/hdf/hdf5lib/callbacks/H5D_iterate_t.java | 4 + java/src/hdf/hdf5lib/callbacks/H5E_walk_cb.java | 22 +- java/src/hdf/hdf5lib/callbacks/H5E_walk_t.java | 4 + .../hdf5lib/callbacks/H5L_iterate_opdata_t.java | 4 + java/src/hdf/hdf5lib/callbacks/H5L_iterate_t.java | 25 +- .../hdf5lib/callbacks/H5O_iterate_opdata_t.java | 4 + java/src/hdf/hdf5lib/callbacks/H5O_iterate_t.java | 25 +- .../hdf5lib/callbacks/H5P_cls_close_func_cb.java | 21 +- .../hdf5lib/callbacks/H5P_cls_close_func_t.java | 4 + .../hdf5lib/callbacks/H5P_cls_copy_func_cb.java | 22 +- .../hdf/hdf5lib/callbacks/H5P_cls_copy_func_t.java | 4 + .../hdf5lib/callbacks/H5P_cls_create_func_cb.java | 21 +- .../hdf5lib/callbacks/H5P_cls_create_func_t.java | 4 + java/src/hdf/hdf5lib/callbacks/H5P_iterate_cb.java | 22 +- java/src/hdf/hdf5lib/callbacks/H5P_iterate_t.java | 4 + .../hdf5lib/callbacks/H5P_prp_close_func_cb.java | 22 +- .../hdf5lib/callbacks/H5P_prp_compare_func_cb.java | 22 +- .../hdf5lib/callbacks/H5P_prp_copy_func_cb.java | 22 +- .../hdf5lib/callbacks/H5P_prp_create_func_cb.java | 22 +- .../hdf5lib/callbacks/H5P_prp_delete_func_cb.java | 23 +- .../hdf/hdf5lib/callbacks/H5P_prp_get_func_cb.java | 23 +- .../hdf/hdf5lib/callbacks/H5P_prp_set_func_cb.java | 23 +- java/src/hdf/hdf5lib/exceptions/HDF5Exception.java | 3 + .../hdf5lib/exceptions/HDF5ReferenceException.java | 6 + .../hdf/hdf5lib/structs/H5AC_cache_config_t.java | 5 +- java/src/hdf/hdf5lib/structs/H5A_info_t.java | 5 +- java/src/hdf/hdf5lib/structs/H5E_error2_t.java | 5 +- java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java | 2 +- java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java | 2 +- java/src/hdf/hdf5lib/structs/H5F_info2_t.java | 5 +- java/src/hdf/hdf5lib/structs/H5G_info_t.java | 5 +- java/src/hdf/hdf5lib/structs/H5L_info_t.java | 5 +- java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java | 25 +- java/src/hdf/hdf5lib/structs/H5O_info_t.java | 5 +- .../src/hdf/hdf5lib/structs/H5O_native_info_t.java | 7 +- java/src/hdf/hdf5lib/structs/H5O_token_t.java | 5 +- java/src/hdf/hdf5lib/structs/H5_ih_info_t.java | 9 +- src/H5FDhdfs.c | 2 +- 44 files changed, 3097 insertions(+), 231 deletions(-) diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java index 1147e6c..f7d8dc4 100644 --- a/java/src/hdf/hdf5lib/H5.java +++ b/java/src/hdf/hdf5lib/H5.java @@ -241,10 +241,14 @@ public class H5 implements java.io.Serializable { */ public final static int LIB_VERSION[] = { 1, 13, 0 }; + /** + * add system property to load library by path + */ public final static String H5PATH_PROPERTY_KEY = "hdf.hdf5lib.H5.hdf5lib"; - // add system property to load library by name from library path, via - // System.loadLibrary() + /** + * add system property to load library by name from library path, via System.loadLibrary() + */ public final static String H5_LIBRARY_NAME_PROPERTY_KEY = "hdf.hdf5lib.H5.loadLibraryName"; private static String s_libraryName; private static boolean isLibraryLoaded = false; @@ -257,6 +261,9 @@ public class H5 implements java.io.Serializable { loadH5Lib(); } + /** + * load native library + */ public static void loadH5Lib() { // Make sure that the library is loaded only once if (isLibraryLoaded) @@ -468,6 +475,35 @@ public class H5 implements java.io.Serializable { **/ public synchronized static native int H5get_libversion(int[] libversion) throws HDF5LibraryException; + /** + * H5set_free_list_limits + * Sets limits on the different kinds of free lists. Setting a value + * of -1 for a limit means no limit of that type. These limits are global + * for the entire library. Each "global" limit only applies to free lists + * of that type, so if an application sets a limit of 1 MB on each of the + * global lists, up to 3 MB of total storage might be allocated (1MB on + * each of regular, array and block type lists). + * + * The settings for block free lists are duplicated to factory free lists. + * Factory free list limits cannot be set independently currently. + * + * @param reg_global_lim + * The limit on all "regular" free list memory used + * @param reg_list_lim + * The limit on memory used in each "regular" free list + * @param arr_global_lim + * The limit on all "array" free list memory used + * @param arr_list_lim + * The limit on memory used in each "array" free list + * @param blk_global_lim + * The limit on all "block" free list memory used + * @param blk_list_lim + * The limit on memory used in each "block" free list + * @return a non-negative value if successful, along with the version information. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + */ public synchronized static native int H5set_free_list_limits(int reg_global_lim, int reg_list_lim, int arr_global_lim, int arr_list_lim, int blk_global_lim, int blk_list_lim) throws HDF5LibraryException; @@ -1016,7 +1052,7 @@ public class H5 implements java.io.Serializable { /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with - * mem_type_id. The entire attribute is read into buf from the file. + * mem_type_id. The entire attribute is read into buffer from the file. * * @param attr_id * IN: Identifier of an attribute to read. @@ -1037,11 +1073,47 @@ public class H5 implements java.io.Serializable { public synchronized static native int H5Aread(long attr_id, long mem_type_id, byte[] obj, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Aread(long attr_id, long mem_type_id, byte[] buf) throws HDF5LibraryException, NullPointerException { return H5Aread(attr_id, mem_type_id, buf, true); } + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param obj + * Buffer to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Aread(long attr_id, long mem_type_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException { return H5Aread(attr_id, mem_type_id, obj, true); @@ -1141,170 +1213,486 @@ public class H5 implements java.io.Serializable { return status; } + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of double from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of double to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Aread_double(long attr_id, long mem_type_id, double[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of double from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of double to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Aread_double(long attr_id, long mem_type_id, double[] buf) throws HDF5LibraryException, NullPointerException { return H5Aread_double(attr_id, mem_type_id, buf, true); } + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of float from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of float to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Aread_float(long attr_id, long mem_type_id, float[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of float from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of float to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Aread_float(long attr_id, long mem_type_id, float[] buf) throws HDF5LibraryException, NullPointerException { return H5Aread_float(attr_id, mem_type_id, buf, true); } - public synchronized static native int H5Aread_int(long attr_id, long mem_type_id, int[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; - - public synchronized static int H5Aread_int(long attr_id, long mem_type_id, int[] buf) - throws HDF5LibraryException, NullPointerException - { - return H5Aread_int(attr_id, mem_type_id, buf, true); - } - - public synchronized static native int H5Aread_long(long attr_id, long mem_type_id, long[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; - - public synchronized static int H5Aread_long(long attr_id, long mem_type_id, long[] buf) - throws HDF5LibraryException, NullPointerException - { - return H5Aread_long(attr_id, mem_type_id, buf, true); - } - - public synchronized static native int H5Aread_reg_ref(long attr_id, long mem_type_id, String[] buf) - throws HDF5LibraryException, NullPointerException; - - public synchronized static native int H5Aread_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning) - throws HDF5LibraryException, NullPointerException; - - public synchronized static int H5Aread_short(long attr_id, long mem_type_id, short[] buf) - throws HDF5LibraryException, NullPointerException - { - return H5Aread_short(attr_id, mem_type_id, buf, true); - } - - public synchronized static native int H5AreadVL(long attr_id, long mem_type_id, Object[] buf) - throws HDF5LibraryException, NullPointerException; - - public synchronized static native int H5Aread_string(long attr_id, long mem_type_id, String[] buf) - throws HDF5LibraryException, NullPointerException; - - public synchronized static native int H5Aread_VLStrings(long attr_id, long mem_type_id, Object[] buf) - throws HDF5LibraryException, NullPointerException; - - public synchronized static native int H5AreadComplex(long attr_id, long mem_type_id, String[] buf) - throws HDF5LibraryException, NullPointerException; - /** - * H5Arename changes the name of attribute that is attached to the object specified by loc_id. The attribute named - * old_attr_name is renamed new_attr_name. + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of int from the file. * - * @param loc_id - * IN: Location or object identifier; may be dataset or group - * @param old_attr_name - * IN: Prior attribute name - * @param new_attr_name - * IN: New attribute name + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of int to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. * - * @return A non-negative value if successful; otherwise returns a negative value. + * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException - * - Name is null. + * - data buffer is null. **/ - public synchronized static native int H5Arename(long loc_id, String old_attr_name, String new_attr_name) + public synchronized static native int H5Aread_int(long attr_id, long mem_type_id, int[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; /** - * H5Arename_by_name changes the name of attribute that is attached to the object specified by loc_id and obj_name. - * The attribute named old_attr_name is renamed new_attr_name. + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of int from the file. * - * @param loc_id - * IN: Location or object identifier; may be dataset or group - * @param obj_name - * IN: Name of object, relative to location, whose attribute is to be renamed - * @param old_attr_name - * IN: Prior attribute name - * @param new_attr_name - * IN: New attribute name - * @param lapl_id - * IN: Link access property list + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of int to store data read from the file. * - * @return A non-negative value if successful; otherwise returns a negative value. + * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException - * - Name is null. + * - data buffer is null. **/ - public synchronized static native int H5Arename_by_name(long loc_id, String obj_name, String old_attr_name, - String new_attr_name, long lapl_id) throws HDF5LibraryException, NullPointerException; + public synchronized static int H5Aread_int(long attr_id, long mem_type_id, int[] buf) + throws HDF5LibraryException, NullPointerException + { + return H5Aread_int(attr_id, mem_type_id, buf, true); + } /** - * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with - * mem_type_id. The entire attribute is written from buf to the file. + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of long from the file. * * @param attr_id - * IN: Identifier of an attribute to write. + * IN: Identifier of an attribute to read. * @param mem_type_id * IN: Identifier of the attribute datatype (in memory). * @param buf - * IN: Buffer with data to be written to the file. + * Buffer of long to store data read from the file. * @param isCriticalPinning - * IN: request lock on data reference. + * request lock on data reference. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException - * - data is null. + * - data buffer is null. **/ - public synchronized static native int H5Awrite(long attr_id, long mem_type_id, byte[] buf, boolean isCriticalPinning) + public synchronized static native int H5Aread_long(long attr_id, long mem_type_id, long[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; - public synchronized static int H5Awrite(long attr_id, long mem_type_id, byte[] buf) + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of long from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of long to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ + public synchronized static int H5Aread_long(long attr_id, long mem_type_id, long[] buf) throws HDF5LibraryException, NullPointerException { - return H5Awrite(attr_id, mem_type_id, buf, true); - } - - public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj) - throws HDF5Exception, HDF5LibraryException, NullPointerException - { - return H5Awrite(attr_id, mem_type_id, obj, true); + return H5Aread_long(attr_id, mem_type_id, buf, true); } /** - * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with - * mem_type_id. The entire attribute is written from data object to the file. + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of String from the file. * * @param attr_id - * IN: Identifier of an attribute to write. + * IN: Identifier of an attribute to read. * @param mem_type_id * IN: Identifier of the attribute datatype (in memory). - * @param obj - * IN: Data object to be written. - * @param isCriticalPinning - * request lock on data reference. + * @param buf + * Buffer of String to store data read from the file. * * @return a non-negative value if successful * - * @exception HDF5Exception - * - Failure in the data conversion. * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException - * - data object is null + * - data buffer is null. **/ - public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj, boolean isCriticalPinning) + public synchronized static native int H5Aread_reg_ref(long attr_id, long mem_type_id, String[] buf) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of short from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of short to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ + public synchronized static native int H5Aread_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of shortfrom the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of short to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ + public synchronized static int H5Aread_short(long attr_id, long mem_type_id, short[] buf) + throws HDF5LibraryException, NullPointerException + { + return H5Aread_short(attr_id, mem_type_id, buf, true); + } + + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of variable-lenght from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of variable-lenght to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ + public synchronized static native int H5AreadVL(long attr_id, long mem_type_id, Object[] buf) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of String from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of String to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ + public synchronized static native int H5Aread_string(long attr_id, long mem_type_id, String[] buf) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of variable-lenght strings from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of variable-lenght strings to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ + public synchronized static native int H5Aread_VLStrings(long attr_id, long mem_type_id, Object[] buf) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of string from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of string to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ + public synchronized static native int H5AreadComplex(long attr_id, long mem_type_id, String[] buf) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Arename changes the name of attribute that is attached to the object specified by loc_id. The attribute named + * old_attr_name is renamed new_attr_name. + * + * @param loc_id + * IN: Location or object identifier; may be dataset or group + * @param old_attr_name + * IN: Prior attribute name + * @param new_attr_name + * IN: New attribute name + * + * @return A non-negative value if successful; otherwise returns a negative value. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - Name is null. + **/ + public synchronized static native int H5Arename(long loc_id, String old_attr_name, String new_attr_name) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Arename_by_name changes the name of attribute that is attached to the object specified by loc_id and obj_name. + * The attribute named old_attr_name is renamed new_attr_name. + * + * @param loc_id + * IN: Location or object identifier; may be dataset or group + * @param obj_name + * IN: Name of object, relative to location, whose attribute is to be renamed + * @param old_attr_name + * IN: Prior attribute name + * @param new_attr_name + * IN: New attribute name + * @param lapl_id + * IN: Link access property list + * + * @return A non-negative value if successful; otherwise returns a negative value. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - Name is null. + **/ + public synchronized static native int H5Arename_by_name(long loc_id, String obj_name, String old_attr_name, + String new_attr_name, long lapl_id) throws HDF5LibraryException, NullPointerException; + + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buf to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer with data to be written to the file. + * @param isCriticalPinning + * IN: request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ + public synchronized static native int H5Awrite(long attr_id, long mem_type_id, byte[] buf, boolean isCriticalPinning) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buf to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ + public synchronized static int H5Awrite(long attr_id, long mem_type_id, byte[] buf) + throws HDF5LibraryException, NullPointerException + { + return H5Awrite(attr_id, mem_type_id, buf, true); + } + + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buf to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param obj + * IN: Buffer with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ + public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj) + throws HDF5Exception, HDF5LibraryException, NullPointerException + { + return H5Awrite(attr_id, mem_type_id, obj, true); + } + + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from data object to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param obj + * IN: Data object to be written. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5Exception + * - Failure in the data conversion. + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data object is null + **/ + public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj, boolean isCriticalPinning) throws HDF5Exception, HDF5LibraryException, NullPointerException { int status = -1; @@ -1353,60 +1741,286 @@ public class H5 implements java.io.Serializable { return status; } + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of double to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of double with data to be written to the file. + * @param isCriticalPinning + * IN: request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static native int H5Awrite_double(long attr_id, long mem_type_id, double[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of double to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of double with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static int H5Awrite_double(long attr_id, long mem_type_id, double[] buf) throws HDF5LibraryException, NullPointerException { return H5Awrite_double(attr_id, mem_type_id, buf, true); } + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of float to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of float with data to be written to the file. + * @param isCriticalPinning + * IN: request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static native int H5Awrite_float(long attr_id, long mem_type_id, float[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of float to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of float with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static int H5Awrite_float(long attr_id, long mem_type_id, float[] buf) throws HDF5LibraryException, NullPointerException { return H5Awrite_float(attr_id, mem_type_id, buf, true); } + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of int to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of int with data to be written to the file. + * @param isCriticalPinning + * IN: request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static native int H5Awrite_int(long attr_id, long mem_type_id, int[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of int to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of int with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static int H5Awrite_int(long attr_id, long mem_type_id, int[] buf) throws HDF5LibraryException, NullPointerException { return H5Awrite_int(attr_id, mem_type_id, buf, true); } + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of long to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of long with data to be written to the file. + * @param isCriticalPinning + * IN: request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static native int H5Awrite_long(long attr_id, long mem_type_id, long[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of long to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of long with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static int H5Awrite_long(long attr_id, long mem_type_id, long[] buf) throws HDF5LibraryException, NullPointerException { return H5Awrite_long(attr_id, mem_type_id, buf, true); } + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of short to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of short with data to be written to the file. + * @param isCriticalPinning + * IN: request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static native int H5Awrite_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of short to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of short with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static int H5Awrite_short(long attr_id, long mem_type_id, short[] buf) throws HDF5LibraryException, NullPointerException { return H5Awrite_short(attr_id, mem_type_id, buf, true); } + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of string to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of string with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static native int H5Awrite_string(long attr_id, long mem_type_id, String[] buf) throws HDF5LibraryException, NullPointerException; + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of variable-lenght to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of variable-lenght with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static native int H5AwriteVL(long attr_id, long mem_type_id, Object[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Awrite_VLStrings writes a variable length String dataset, specified by its identifier attr_id, from - * the application memory buffer buf into the file. + * the application memory buffer buffer of variable-lenght strings into the file. * * ---- contributed by Rosetta Biosoftware * @@ -1415,7 +2029,7 @@ public class H5 implements java.io.Serializable { * @param mem_type_id * Identifier of the memory datatype. * @param buf - * Buffer with data to be written to the file. + * Buffer of variable-lenght strings with data to be written to the file. * * @return a non-negative value if successful * @@ -1889,8 +2503,68 @@ public class H5 implements java.io.Serializable { * * @see public static int H5Dopen(int loc_id, String name, int dapl_id) **/ - private synchronized static native long _H5Dopen2(long loc_id, String name, long dapl_id) - throws HDF5LibraryException, NullPointerException; + private synchronized static native long _H5Dopen2(long loc_id, String name, long dapl_id) + throws HDF5LibraryException, NullPointerException; + + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer buf. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param obj + * Buffer to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ + public synchronized static native int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, + long file_space_id, long xfer_plist_id, byte[] obj, boolean isCriticalPinning) throws HDF5LibraryException, + NullPointerException; + + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer buf. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ + public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, + long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException + { + return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); + } /** * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application @@ -1908,8 +2582,6 @@ public class H5 implements java.io.Serializable { * Identifier of a transfer property list for this I/O operation. * @param obj * Buffer to store data read from the file. - * @param isCriticalPinning - * request lock on data reference. * * @return a non-negative value if successful * @@ -1918,16 +2590,6 @@ public class H5 implements java.io.Serializable { * @exception NullPointerException * - data buffer is null. **/ - public synchronized static native int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, byte[] obj, boolean isCriticalPinning) throws HDF5LibraryException, - NullPointerException; - - public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, - long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException - { - return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); - } - public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException { @@ -2043,65 +2705,411 @@ public class H5 implements java.io.Serializable { return status; } + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of type double. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of type double to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Dread_double(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, double[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of type double. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of double to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Dread_double(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of float. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of float to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Dread_float(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, float[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of float. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of float to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Dread_float(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of int. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of int to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Dread_int(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, int[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of int. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of int to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Dread_int(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of long. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of long to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Dread_long(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, long[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of long. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of long to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Dread_long(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of string. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of string to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Dread_reg_ref(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of short. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of short to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Dread_short(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, short[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of short. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of short to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Dread_short(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of variable-lenght. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of variable-lenght to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5DreadVL(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of string. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of string to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Dread_string(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of variable-lenght strings. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of variable-lenght strings to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Dread_VLStrings(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException; @@ -2170,7 +3178,7 @@ public class H5 implements java.io.Serializable { /** * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer - * buf into the file. + * into the file. * * @param dataset_id * Identifier of the dataset read from. @@ -2198,12 +3206,60 @@ public class H5 implements java.io.Serializable { long file_space_id, long xfer_plist_id, byte[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param obj + * Buffer with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException { @@ -2299,59 +3355,357 @@ public class H5 implements java.io.Serializable { return status; } + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of double with data to be written to the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static native int H5Dwrite_double(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, double[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of double with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static int H5Dwrite_double(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of float with data to be written to the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static native int H5Dwrite_float(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, float[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of float with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static int H5Dwrite_float(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of int with data to be written to the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static native int H5Dwrite_int(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, int[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of int with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static int H5Dwrite_int(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of long with data to be written to the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static native int H5Dwrite_long(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, long[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of long with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static int H5Dwrite_long(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of short with data to be written to the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static native int H5Dwrite_short(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, short[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of short with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static int H5Dwrite_short(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of string with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static native int H5Dwrite_string(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of variable-length with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static native int H5DwriteVL(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException; @@ -2628,7 +3982,7 @@ public class H5 implements java.io.Serializable { /** - * H5Epush2 pushes a new error record onto the error stack specified by estack_id. + * H5Epush pushes a new error record onto the error stack specified by estack_id. * * @param stack_id * IN: Error stack identifier. @@ -2657,6 +4011,31 @@ public class H5 implements java.io.Serializable { { H5Epush2(stack_id, file, func, line, cls_id, maj_id, min_id, msg); } + /** + * H5Epush2 pushes a new error record onto the error stack specified by estack_id. + * + * @param stack_id + * IN: Error stack identifier. + * @param file + * IN: Name of the file in which the error was detected. + * @param func + * IN: Name of the function in which the error was detected. + * @param line + * IN: Line number within the file at which the error was detected. + * @param cls_id + * IN: Error class identifier. + * @param maj_id + * IN: Major error identifier. + * @param min_id + * IN: Minor error identifier. + * @param msg + * IN: Error description string. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - file, func, or msg is null. + **/ public synchronized static native void H5Epush2(long stack_id, String file, String func, int line, long cls_id, long maj_id, long min_id, String msg) throws HDF5LibraryException, NullPointerException; @@ -2714,6 +4093,24 @@ public class H5 implements java.io.Serializable { { H5Ewalk2(stack_id, direction, func, client_data); } + /** + * H5Ewalk2 walks the error stack specified by estack_id for the current thread and calls the + * function specified in func for each error along the way. + * + * @param stack_id + * IN: Error stack identifier. + * @param direction + * IN: Direction in which the error stack is to be walked. + * @param func + * IN: Function to be called for each error encountered. + * @param client_data + * IN: Data to be passed with func. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - func is null. + **/ public synchronized static native void H5Ewalk2(long stack_id, long direction, H5E_walk_cb func, H5E_walk_t client_data) throws HDF5LibraryException, NullPointerException; @@ -2950,6 +4347,19 @@ public class H5 implements java.io.Serializable { private synchronized static native long _H5Fget_create_plist(long file_id) throws HDF5LibraryException; + /** + * H5Fget_filesize retrieves the file size of the HDF5 file. This function + * is called after an existing file is opened in order + * to learn the true size of the underlying file. + * + * @param file_id + * IN: File identifier for a currently-open HDF5 file + * + * @return the file size of the HDF5 file + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native long H5Fget_filesize(long file_id) throws HDF5LibraryException; /** @@ -3598,37 +5008,118 @@ public class H5 implements java.io.Serializable { return H5Gget_obj_info_all(loc_id, name, objNames, objTypes, null, null, tokens, HDF5Constants.H5_INDEX_NAME); } - public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] oname, int[] otype, + /** + * retrieves information of all objects under the group (name) located in the file or group specified by loc_id. + * + * @param loc_id + * IN: File or group identifier + * @param name + * IN: Name of group for which information is to be retrieved + * @param objNames + * OUT: Names of all objects under the group, name. + * @param objTypes + * OUT: Types of all objects under the group, name. + * @param ltype + * OUT: Link type + * @param tokens + * OUT: Object token of all objects under the group, name. + * @param indx_type + * IN: Index type for iterate + * + * @return the number of items found + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + */ + public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] objNames, int[] objTypes, int[] ltype, H5O_token_t[] tokens, int indx_type) throws HDF5LibraryException, NullPointerException { - return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, null, tokens, indx_type, -1); + return H5Gget_obj_info_full(loc_id, name, objNames, objTypes, ltype, null, tokens, indx_type, -1); } - public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] oname, int[] otype, + /** + * retrieves information of all objects under the group (name) located in the file or group specified by loc_id. + * + * @param loc_id + * IN: File or group identifier + * @param name + * IN: Name of group for which information is to be retrieved + * @param objNames + * OUT: Names of all objects under the group, name. + * @param objTypes + * OUT: Types of all objects under the group, name. + * @param ltype + * OUT: Link type + * @param fno + * OUT: File number + * @param tokens + * OUT: Object token of all objects under the group, name. + * @param indx_type + * IN: Index type for iterate + * + * @return the number of items found + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + */ + public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] objNames, int[] objTypes, int[] ltype, long[] fno, H5O_token_t[] tokens, int indx_type) throws HDF5LibraryException, NullPointerException { - return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, fno, tokens, indx_type, -1); + return H5Gget_obj_info_full(loc_id, name, objNames, objTypes, ltype, fno, tokens, indx_type, -1); } - public synchronized static int H5Gget_obj_info_full(long loc_id, String name, String[] oname, int[] otype, + /** + * retrieves information of all objects under the group (name) located in the file or group specified by loc_id. + * + * @param loc_id + * IN: File or group identifier + * @param name + * IN: Name of group for which information is to be retrieved + * @param objNames + * OUT: Names of all objects under the group, name. + * @param objTypes + * OUT: Types of all objects under the group, name. + * @param ltype + * OUT: Link type + * @param fno + * OUT: File number + * @param tokens + * OUT: Object token of all objects under the group, name. + * @param indx_type + * IN: Index type for iterate + * @param indx_order + * IN: Index order for iterate + * + * @return the number of items found + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + */ + public synchronized static int H5Gget_obj_info_full(long loc_id, String name, String[] objNames, int[] objTypes, int[] ltype, long[] fno, H5O_token_t[] tokens, int indx_type, int indx_order) throws HDF5LibraryException, NullPointerException { - if (oname == null) { + if (objNames == null) { throw new NullPointerException("H5Gget_obj_info_full(): name array is null"); } - if (otype == null) { + if (objTypes == null) { throw new NullPointerException("H5Gget_obj_info_full(): object type array is null"); } - if (oname.length == 0) { + if (objNames.length == 0) { throw new HDF5LibraryException("H5Gget_obj_info_full(): array size is zero"); } - if (oname.length != otype.length) { + if (objNames.length != objTypes.length) { throw new HDF5LibraryException("H5Gget_obj_info_full(): name and type array sizes are different"); } if (ltype == null) - ltype = new int[otype.length]; + ltype = new int[objTypes.length]; if (fno == null) fno = new long[tokens.length]; @@ -3639,15 +5130,15 @@ public class H5 implements java.io.Serializable { if (indx_order < 0) indx_order = HDF5Constants.H5_ITER_INC; - log.trace("H5Gget_obj_info_full: oname_len={}", oname.length); - int status = H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, fno, tokens, oname.length, indx_type, + log.trace("H5Gget_obj_info_full: objNames_len={}", objNames.length); + int status = H5Gget_obj_info_full(loc_id, name, objNames, objTypes, ltype, fno, tokens, objNames.length, indx_type, indx_order); - for (int indx = 0; indx < oname.length; indx++) - log.trace("H5Gget_obj_info_full: oname={}", oname[indx]); + for (int indx = 0; indx < objNames.length; indx++) + log.trace("H5Gget_obj_info_full: objNames={}", objNames[indx]); return status; } - private synchronized static native int H5Gget_obj_info_full(long loc_id, String name, String[] oname, int[] otype, + private synchronized static native int H5Gget_obj_info_full(long loc_id, String name, String[] objNames, int[] objTypes, int[] ltype, long[] fno, H5O_token_t[] tokens, int n, int indx_type, int indx_order) throws HDF5LibraryException, NullPointerException; @@ -3663,9 +5154,9 @@ public class H5 implements java.io.Serializable { * @param idx * IN: the index of the object to iterate. * @param oname - * the name of the object [OUT] + * OUT: the name of the object * @param type - * the type of the object [OUT] + * OUT: the type of the object * * @return non-negative if successful, -1 if not. * @@ -3866,13 +5357,40 @@ public class H5 implements java.io.Serializable { // // // //////////////////////////////////////////////////////////// + /** + * H5Iget_file_id obtains the file ID specified by the identifier, obj_id. + * + * @param obj_id + * IN: Identifier of the object. + * + * @return the file ID. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native long H5Iget_file_id(long obj_id) throws HDF5LibraryException; - @Deprecated + + /** + * H5Iget_name_long retrieves the name of an object specified by the identifier, obj_id. + * @deprecated + * + * @param obj_id + * IN: Identifier of the object. + * @param name + * OUT: Attribute name buffer. + * @param size + * IN: Maximum length of the name to retrieve. + * + * @return the length of the name retrieved. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native long H5Iget_name_long(long obj_id, String[] name, long size) throws HDF5LibraryException, NullPointerException; /** - * H5Iget_name_str retrieves the name of an object specified by the identifier, obj_id. + * H5Iget_name retrieves the name of an object specified by the identifier, obj_id. * * @param obj_id * IN: Identifier of the object. @@ -3885,10 +5403,44 @@ public class H5 implements java.io.Serializable { public synchronized static native String H5Iget_name(long obj_id) throws HDF5LibraryException; + /** + * H5Iget_ref obtains the number of references outstanding specified by the identifier, obj_id. + * + * @param obj_id + * IN: Identifier of the object. + * + * @return the reference count. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native int H5Iget_ref(long obj_id) throws HDF5LibraryException, NullPointerException; + /** + * H5Idec_ref decrements the reference count specified by the identifier, obj_id. + * If the reference count for an ID reaches zero, the object will be closed. + * + * @param obj_id + * IN: Identifier of the object. + * + * @return the reference count. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native int H5Idec_ref(long obj_id) throws HDF5LibraryException, NullPointerException; + /** + * H5Iinc_ref increments the reference count specified by the identifier, obj_id. + * + * @param obj_id + * IN: Identifier of the object. + * + * @return the reference count. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native int H5Iinc_ref(long obj_id) throws HDF5LibraryException, NullPointerException; /** @@ -5179,7 +6731,7 @@ public class H5 implements java.io.Serializable { return id; } - public synchronized static native long _H5Oopen_by_idx(long loc_id, String group_name, + private synchronized static native long _H5Oopen_by_idx(long loc_id, String group_name, int idx_type, int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException; /** @@ -5210,8 +6762,30 @@ public class H5 implements java.io.Serializable { **/ public synchronized static native void H5Orefresh(long object_id) throws HDF5LibraryException; + /** + * H5Odisable_mdc_flushes corks an object, keeping dirty entries associated with the object in the metadata cache. + * + * @param object_id + * IN: Identifier of the object to be corked. + **/ public synchronized static native void H5Odisable_mdc_flushes(long object_id); + /** + * H5Oenable_mdc_flushes uncorks an object, keeping dirty entries associated with the object in the metadata cache. + * + * @param object_id + * IN: Identifier of the object to be uncorked. + **/ public synchronized static native void H5Oenable_mdc_flushes(long object_id); + /** + * H5Oare_mdc_flushes_disabled retrieve the object's "cork" status. + * + * @param object_id + * IN: Identifier of the object to be flushed. + * + * @return the cork status + * TRUE if mdc flushes for the object is disabled + * FALSE if mdc flushes for the object is not disabled + **/ public synchronized static native boolean H5Oare_mdc_flushes_disabled(long object_id); // /////// unimplemented //////// @@ -5364,6 +6938,7 @@ public class H5 implements java.io.Serializable { * IN: First property object to be compared * @param plid2 * IN: Second property object to be compared + * * @return positive value if equal; zero if unequal, a negative value if failed * * @exception HDF5LibraryException @@ -5371,6 +6946,19 @@ public class H5 implements java.io.Serializable { */ public synchronized static native int H5Pequal(long plid1, long plid2) throws HDF5LibraryException; + /** + * H5Pequal determines if two property lists or classes are equal + * + * @param plid1 + * IN: First property object to be compared + * @param plid2 + * IN: Second property object to be compared + * + * @return TRUE if equal, FALSE if unequal + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + */ public static boolean H5P_equal(long plid1, long plid2) throws HDF5LibraryException { if (H5Pequal(plid1, plid2) == 1) return true; @@ -5456,7 +7044,7 @@ public class H5 implements java.io.Serializable { return _H5Pclose_class(plid); } - public synchronized static native int _H5Pclose_class(long plid) throws HDF5LibraryException; + private synchronized static native int _H5Pclose_class(long plid) throws HDF5LibraryException; /** * H5Pclose terminates access to a property list. @@ -5524,6 +7112,19 @@ public class H5 implements java.io.Serializable { // Define property list iteration function type // typedef herr_t (*H5P_iterate_t)(hid_t id, const char *name, void *iter_data); + /** + * H5Pcreate_class_nocb creates an new property class with no callback functions. + * + * @param parent_class + * IN: Identifier of the parent property class. + * @param name + * IN: Name of the property class. + * + * @return a property list identifier if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public static long H5Pcreate_class_nocb(long parent_class, String name) throws HDF5LibraryException { long id = _H5Pcreate_class_nocb(parent_class, name); if (id > 0) { @@ -5550,17 +7151,69 @@ public class H5 implements java.io.Serializable { // private synchronized static native long _H5Pcreate_class(long parent_class, String name, H5P_cls_create_func_cb create_op, H5P_cls_create_func_t create_data, // H5P_cls_copy_func_cb copy_op, H5P_cls_copy_func_t copy_data, H5P_cls_close_func_cb close_op, H5P_cls_close_func_t close_data) throws HDF5LibraryException; + /** + * H5Pregister2_nocb registers a property list with no callback functions. + * + * @param plist_class + * IN: Identifier of the property list. + * @param name + * IN: Name of the property. + * @param size + * IN: Size the property value. + * @param def_value + * IN: Defaul value of the property + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native void H5Pregister2_nocb(long plist_class, String name, long size, byte[] def_value) throws HDF5LibraryException; // public synchronized static native void H5Pregister2(long plist_class, String name, long size, byte[] def_value, H5P_prp_create_func_cb prp_create, H5P_prp_set_func_cb prp_set, // H5P_prp_get_func_cb prp_get, H5P_prp_delete_func_cb prp_delete, H5P_prp_copy_func_cb prp_copy, H5P_prp_compare_func_cb prp_cmp, H5P_prp_close_func_cb prp_close) throws HDF5LibraryException; + /** + * H5Pinsert2_nocb inserts a property list with no callback functions. + * + * @param plist + * IN: Identifier of the property list. + * @param name + * IN: Name of the property. + * @param size + * IN: Size the property value. + * @param value + * IN: Defaul value of the property + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native void H5Pinsert2_nocb(long plist, String name, long size, byte[] value) throws HDF5LibraryException; // public synchronized static native void H5Pinsert2(long plist, String name, long size, byte[] value, H5P_prp_set_func_cb prp_set, H5P_prp_get_func_cb prp_get, // H5P_prp_delete_func_cb prp_delete, H5P_prp_copy_func_cb prp_copy, H5P_prp_compare_func_cb prp_cmp, H5P_prp_close_func_cb prp_close) throws HDF5LibraryException; + /** + * H5Piterate iterates over the properties in a property list or class + * + * @param plist + * IN: ID of property object to iterate over + * @param idx + * IN/OUT: index of the property to begin with + * @param op + * IN: function to be called with each property iterated over. + * @param op_data + * IN: iteration data from user + * + * @return + * the return value of the last call to op if it was non-zero, + * zero if all properties have been processed + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - size is null. + * + **/ 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 /////// @@ -5573,7 +7226,7 @@ public class H5 implements java.io.Serializable { * @param attributes * The maximun and minimum no. of attributes to be stored. * - * 
+     * 
      *      attributes[0] =  The maximum number of attributes to be stored in compact storage
      *      attributes[1] =  The minimum number of attributes to be stored in dense storage
      * 

@@ -5673,6 +7326,51 @@ public class H5 implements java.io.Serializable {
     public synchronized static native void H5Pset_obj_track_times(long ocpl_id, boolean track_times)
             throws HDF5LibraryException;
 
+    /**
+     * H5Pmodify_filter modifies the specified FILTER in the transient or permanent output filter pipeline
+     *              depending on whether PLIST is a dataset creation or dataset
+     *              transfer property list.  The FLAGS argument specifies certain
+     *              general properties of the filter and is documented below.
+     *              The CD_VALUES is an array of CD_NELMTS integers which are
+     *              auxiliary data for the filter.  The integer vlues will be
+     *              stored in the dataset object header as part of the filter
+     *              information.
+     *

+     *              The FLAGS argument is a bit vector of the following fields:
+     *

+     *              H5Z_FLAG_OPTIONAL(0x0001)
+     *              If this bit is set then the filter is optional.  If the
+     *              filter fails during an H5Dwrite() operation then the filter
+     *              is just excluded from the pipeline for the chunk for which it
+     *              failed; the filter will not participate in the pipeline
+     *              during an H5Dread() of the chunk.  If this bit is clear and
+     *              the filter fails then the entire I/O operation fails.
+     *              If this bit is set but encoding is disabled for a filter,
+     *              attempting to write will generate an error.
+     *

+     * Note:        This function currently supports only the permanent filter
+     *              pipeline.  That is, PLIST_ID must be a dataset creation
+     *              property list.
+     *
+     * @param plist
+     *            IN: Property list identifier.
+     * @param filter
+     *            IN: Filter to be modified to the pipeline.
+     * @param flags
+     *            IN: Bit vector specifying certain general properties of the filter.
+     * @param cd_nelmts
+     *            IN: Number of elements in cd_values
+     * @param cd_values
+     *            IN: Auxiliary data for the filter.
+     *
+     * @return a non-negative value if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - name or an array is null.
+     *
+     **/
     public synchronized static native int H5Pmodify_filter(long plist, long filter, int flags, long cd_nelmts,
             int[] cd_values) throws HDF5LibraryException, NullPointerException;
 
@@ -5844,9 +7542,37 @@ public class H5 implements java.io.Serializable {
                     throws HDF5LibraryException, NullPointerException;
 
 
+    /**
+     * H5Pall_filters_avail query to verify that all the filters set
+     *                      in the dataset creation property list are available currently.
+     *
+     * @param dcpl_id
+     *            IN: Property list identifier.
+     *
+     * @return
+     *            TRUE if all filters available
+     *            FALSE if one or more filters not currently available.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native boolean H5Pall_filters_avail(long dcpl_id) throws HDF5LibraryException,
     NullPointerException;
 
+    /**
+     * H5Premove_filter deletes a filter from the dataset creation property list;
+     *                  deletes all filters if filter is H5Z_FILTER_NONE
+     *
+     * @param obj_id
+     *            IN: Property list identifier.
+     * @param filter
+     *            IN: Filter identifier.
+     *
+     * @return a non-negative value and the size of the user block; if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native int H5Premove_filter(long obj_id, long filter) throws HDF5LibraryException;
 
     /**
@@ -5864,6 +7590,18 @@ public class H5 implements java.io.Serializable {
      **/
     public synchronized static native int H5Pset_deflate(long plist, int level) throws HDF5LibraryException;
 
+    /**
+     * H5Pset_fletcher32 sets Fletcher32 checksum of EDC for a dataset creation
+     *                   property list or group creation property list.
+     *
+     * @param plist
+     *            IN: Property list identifier.
+     *
+     * @return a non-negative value and the size of the user block; if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native int H5Pset_fletcher32(long plist) throws HDF5LibraryException,
     NullPointerException;
 
@@ -6334,11 +8072,35 @@ public class H5 implements java.io.Serializable {
      */
     public synchronized static native long H5Pget_driver(long plid) throws HDF5LibraryException;
 
-    public synchronized static native long H5Pget_family_offset(long fapl_id) throws HDF5LibraryException,
-    NullPointerException;
+    /**
+     * H5Pget_family_offset gets offset for family driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     *
+     * @return the offset.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native long H5Pget_family_offset(long fapl_id) throws HDF5LibraryException;
 
-    public synchronized static native int H5Pset_family_offset(long fapl_id, long offset) throws HDF5LibraryException,
-    NullPointerException;
+    /**
+     * H5Pset_family_offset sets the offset for family driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param offset
+     *            IN: the offset value
+     *
+     * @return a non-negative value if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native int H5Pset_family_offset(long fapl_id, long offset) throws HDF5LibraryException;
 
     /**
      * Retrieves the maximum possible number of elements in the meta data cache and the maximum possible number of bytes
@@ -6389,9 +8151,8 @@ public class H5 implements java.io.Serializable {
             double rdcc_w0) throws HDF5LibraryException;
 
     /**
-     * H5Pget_mdc_config gets the initial metadata cache configuration contained in a file access property list and
-     * loads it into the instance of H5AC_cache_config_t pointed to by the config_ptr parameter. This configuration is
-     * used when the file is opened.
+     * H5Pget_mdc_config gets the initial metadata cache configuration contained in a file access property list.
+     *                   This configuration is used when the file is opened.
      *
      * @param plist_id
      *            IN: Identifier of the file access property list.
@@ -6403,6 +8164,19 @@ public class H5 implements java.io.Serializable {
      **/
     public synchronized static native H5AC_cache_config_t H5Pget_mdc_config(long plist_id) throws HDF5LibraryException;
 
+    /**
+     * H5Pset_mdc_config sets the initial metadata cache configuration contained in a file access property list and
+     * loads it into the instance of H5AC_cache_config_t pointed to by the config_ptr parameter. This configuration is
+     * used when the file is opened.
+     *
+     * @param plist_id
+     *            IN: Identifier of the file access property list.
+     * @param config_ptr
+     *            IN: H5AC_cache_config_t, the initial metadata cache configuration.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native void H5Pset_mdc_config(long plist_id, H5AC_cache_config_t config_ptr)
             throws HDF5LibraryException;
 
@@ -6437,10 +8211,35 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pset_gc_references(long fapl_id, boolean gc_ref)
             throws HDF5LibraryException;
 
-    public synchronized static native int H5Pget_fclose_degree(long plist_id) throws HDF5LibraryException,
+    /**
+     * H5Pget_fclose_degree returns the degree for the file close behavior for a file access
+     * property list.
+     *
+     * @param fapl_id
+     *            IN File access property list
+     *
+     * @return the degree for the file close behavior
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native int H5Pget_fclose_degree(long fapl_id) throws HDF5LibraryException,
     NullPointerException;
 
-    public synchronized static native int H5Pset_fclose_degree(long plist, int degree) throws HDF5LibraryException,
+    /**
+     * H5Pset_fclose_degree sets the degree for the file close behavior.
+     *
+     * @param fapl_id
+     *            IN File access property list
+     * @param degree
+     *            IN the degree for the file close behavior
+     *
+     * @return non-negative if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native int H5Pset_fclose_degree(long fapl_id, int degree) throws HDF5LibraryException,
     NullPointerException;
 
     /**
@@ -6467,12 +8266,44 @@ public class H5 implements java.io.Serializable {
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
-     *
+     *
+     **/
+    public synchronized static native void H5Pset_meta_block_size(long fapl_id, long size) throws HDF5LibraryException;
+
+    /**
+     * H5Pget_sieve_buf_size retrieves the current settings for the data sieve buffer size
+     *      property from a file access property list.
+     *
+     * @param fapl_id
+     *            IN: Identifier for property list to query.
+     *
+     * @return a non-negative value and the size of the user block; if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native long H5Pget_sieve_buf_size(long fapl_id) throws HDF5LibraryException;
+
+    /**
+     * H5Pset_sieve_buf_size Sets the maximum size of the data seive buffer used for file
+     *      drivers which are capable of using data sieving.  The data sieve
+     *      buffer is used when performing I/O on datasets in the file.  Using a
+     *      buffer which is large anough to hold several pieces of the dataset
+     *      being read in for hyperslab selections boosts performance by quite a
+     *      bit.
+     * 

+     *      The default value is set to 64KB, indicating that file I/O for raw data
+     *      reads and writes will occur in at least 64KB blocks. Setting the value to 0
+     *      with this function will turn off the data sieving
+     *
+     * @param fapl_id
+     *            IN: Identifier of property list to modify.
+     * @param size
+     *            IN: maximum size of the data seive buffer.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
      **/
-    public synchronized static native void H5Pset_meta_block_size(long fapl_id, long size) throws HDF5LibraryException;
-
-    public synchronized static native long H5Pget_sieve_buf_size(long fapl_id) throws HDF5LibraryException;
-
     public synchronized static native void H5Pset_sieve_buf_size(long fapl_id, long size) throws HDF5LibraryException;
 
     /**
@@ -6816,6 +8647,25 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pset_chunk(long plist, int ndims, byte[] dim) throws HDF5LibraryException,
     NullPointerException, IllegalArgumentException;
 
+    /**
+     * H5Pset_chunk sets the size of the chunks used to store a chunked layout dataset.
+     *
+     * @param plist
+     *            IN: Identifier for property list to query.
+     * @param ndims
+     *            IN: The number of dimensions of each chunk.
+     * @param dim
+     *            IN: An array containing the size of each chunk.
+     *
+     * @return a non-negative value if successful
+     *
+     * @exception HDF5Exception
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - dims array is null.
+     * @exception IllegalArgumentException
+     *                - dims <=0
+     **/
     public synchronized static int H5Pset_chunk(long plist, int ndims, long[] dim) throws HDF5Exception,
     NullPointerException, IllegalArgumentException {
         if (dim == null) {
@@ -7051,9 +8901,37 @@ public class H5 implements java.io.Serializable {
      **/
     public synchronized static native int H5Pget_external_count(long plist) throws HDF5LibraryException;
 
+    /**
+     * H5Pset_szip Sets up the use of the szip filter.
+     *
+     * @param plist
+     *            IN: Dataset creation property list identifier.
+     * @param options_mask
+     *            IN: Bit vector specifying certain general properties of the filter.
+     * @param pixels_per_block
+     *            IN: Number of pixels in blocks
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pset_szip(long plist, int options_mask, int pixels_per_block)
             throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_shuffle Sets up the use of the shuffle filter.
+     *
+     * @param plist_id
+     *            IN: Dataset creation property list identifier.
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pset_shuffle(long plist_id) throws HDF5LibraryException,
     NullPointerException;
 
@@ -7181,20 +9059,91 @@ public class H5 implements java.io.Serializable {
         return retVal;
     }
 
+    /**
+     * H5Pset_fill_value checks if the fill value is defined for a dataset creation property list.
+     *
+     * @param plist_id
+     *            IN: Property list identifier.
+     * @param status
+     *            IN: The fill value setting:
+     *                H5D_FILL_VALUE_UNDEFINED
+     *                H5D_FILL_VALUE_DEFAULT
+     *                H5D_FILL_VALUE_USER_DEFINED
+     *                H5D_FILL_VALUE_ERROR
+     *
+     * @return a non-negative value if successful
+     *
+     * @exception HDF5Exception
+     *                - Error converting data array
+     **/
     public synchronized static native int H5Pfill_value_defined(long plist_id, int[] status)
             throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_alloc_time Gets space allocation time for dataset during creation.
+     *
+     * @param plist_id
+     *            IN: Dataset creation property list identifier.
+     * @param alloc_time
+     *            OUT: allocation time.
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pget_alloc_time(long plist_id, int[] alloc_time)
             throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_alloc_time Sets space allocation time for dataset during creation.
+     *
+     * @param plist_id
+     *            IN: Dataset creation property list identifier.
+     * @param alloc_time
+     *            IN: allocation time.
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pset_alloc_time(long plist_id, int alloc_time) throws HDF5LibraryException,
     NullPointerException;
 
-    public synchronized static native int H5Pget_fill_time(long plist_id, int[] fill_time) throws HDF5LibraryException,
-    NullPointerException;
+    /**
+     * H5Pset_fill_time Gets fill value writing time.
+     *
+     * @param plist_id
+     *            IN: Dataset creation property list identifier.
+     * @param fill_time
+     *            OUT: fill time.
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native int H5Pget_fill_time(long plist_id, int[] fill_time) throws HDF5LibraryException;
 
-    public synchronized static native int H5Pset_fill_time(long plist_id, int fill_time) throws HDF5LibraryException,
-    NullPointerException;
+    /**
+     * H5Pset_fill_time Sets the fill value writing time.
+     *
+     * @param plist_id
+     *            IN: Dataset creation property list identifier.
+     * @param fill_time
+     *            IN: fill time.
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native int H5Pset_fill_time(long plist_id, int fill_time) throws HDF5LibraryException;
 
     /**
      * H5Pset_chunk_opts Sets the edge chunk option in a dataset creation property list.
@@ -7494,6 +9443,20 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pget_buffer(long plist, byte[] tconv, byte[] bkg)
             throws HDF5LibraryException, IllegalArgumentException;
 
+    /**
+     * H5Pget_buffer_size gets type conversion and background buffer size, in bytes, if successful;
+     * otherwise 0 on failure.
+     *
+     * @param plist
+     *            Identifier for the dataset transfer property list.
+     *
+     * @return buffer size, in bytes, if successful; otherwise 0 on failure
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception IllegalArgumentException
+     *                - plist is invalid.
+     **/
     public synchronized static native long H5Pget_buffer_size(long plist)
             throws HDF5LibraryException, IllegalArgumentException;
 
@@ -7524,11 +9487,33 @@ public class H5 implements java.io.Serializable {
     public synchronized static native void H5Pset_buffer_size(long plist, long size) throws HDF5LibraryException,
     IllegalArgumentException;
 
-    public synchronized static native int H5Pget_edc_check(long plist) throws HDF5LibraryException,
-    NullPointerException;
+    /**
+     * H5Pget_edc_check gets the error-detecting algorithm in use.
+     *
+     * @param plist
+     *            Identifier for the dataset transfer property list.
+     *
+     * @return the error-detecting algorithm
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native int H5Pget_edc_check(long plist) throws HDF5LibraryException;
 
-    public synchronized static native int H5Pset_edc_check(long plist, int check) throws HDF5LibraryException,
-    NullPointerException;
+    /**
+     * H5Pset_edc_check sets the error-detecting algorithm.
+     *
+     * @param plist
+     *            Identifier for the dataset transfer property list.
+     * @param check
+     *            the error-detecting algorithm to use.
+     *
+     * @return non-negative if succeed
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native int H5Pset_edc_check(long plist, int check) throws HDF5LibraryException;
 
     /**
      * H5Pget_btree_ratio Get the B-tree split ratios for a dataset transfer property list.
@@ -7573,9 +9558,46 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pset_btree_ratios(long plist_id, double left, double middle, double right)
             throws HDF5LibraryException;
 
+    /**
+     * H5Pget_hyper_vector_size reads values previously set with H5Pset_hyper_vector_size.
+     *
+     * @param dxpl_id
+     *            IN: Dataset transfer property list identifier.
+     * @param vector_size
+     *            OUT:  hyper vector size.
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pget_hyper_vector_size(long dxpl_id, long[] vector_size)
             throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_hyper_vector_size sets the number of
+     *              "I/O vectors" (offset and length pairs) which are to be
+     *              accumulated in memory before being issued to the lower levels
+     *              of the library for reading or writing the actual data.
+     *              Increasing the number should give better performance, but use
+     *              more memory during hyperslab I/O.  The vector size must be
+     *              greater than 1.
+     *,p.
+     *              The default is to use 1024 vectors for I/O during hyperslab
+     *              reading/writing.
+     *
+     * @param dxpl_id
+     *            IN: Dataset transfer property list identifier.
+     * @param vector_size
+     *            IN: hyper vestor size.
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pset_hyper_vector_size(long dxpl_id, long vector_size)
             throws HDF5LibraryException, NullPointerException;
 
@@ -7773,8 +9795,32 @@ public class H5 implements java.io.Serializable {
 
     // /////// String creation property list (STRCPL) routines ///////
 
+    /**
+     * H5Pget_char_encoding gets the character encoding of the string.
+     *
+     * @param plist_id
+     *            IN: the property list identifier
+     *
+     * @return Returns the character encoding of the string.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pget_char_encoding(long plist_id) throws HDF5LibraryException;
 
+    /**
+     * H5Pset_char_encoding sets the character encoding of the string.
+     *
+     * @param plist_id
+     *            IN: the property list identifier
+     * @param encoding
+     *            IN: the character encoding of the string
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native void H5Pset_char_encoding(long plist_id, int encoding)
             throws HDF5LibraryException;
 
@@ -7964,20 +10010,51 @@ public class H5 implements java.io.Serializable {
 
     // /////// file drivers property list routines ///////
 
+    /**
+     * H5Pget_fapl_core retrieve H5FD_CORE I/O settings.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param increment
+     *            OUT: how much to grow the memory each time
+     * @param backing_store
+     *            OUT: write to file name on flush setting
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native void H5Pget_fapl_core(long fapl_id, long[] increment, boolean[] backing_store)
             throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_fapl_core modifies the file access property list to use the H5FD_CORE driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param increment
+     *            IN: how much to grow the memory each time
+     * @param backing_store
+     *            IN: write to file name on flush setting
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pset_fapl_core(long fapl_id, long increment, boolean backing_store)
             throws HDF5LibraryException, NullPointerException;
 
     /**
-     * H5Pget_fapl_direct Retrieve direct I/O settings.
+     * H5Pget_fapl_direct queries properties set by the H5Pset_fapl_core.
      *
      * @param fapl_id
      *            IN: File access property list identifier
      * @param info
-     *            OUT: Returned property list information info[0] = alignment Required memory alignment boundary info[1]
-     *            = block_size File system block size info[2] = cbuf_size Copy buffer size
+     *            OUT: Returned property list information
+     *                 info[0] = increment -how much to grow the memory each time
+     *                 info[1] = backing_store - write to file name on flush setting
      *
      * @return a non-negative value if successful; otherwise returns a negative value.
      *
@@ -7988,34 +10065,92 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pget_fapl_direct(long fapl_id, long[] info) throws HDF5LibraryException;
 
     /**
-     * H5Pset_fapl_direct Sets up use of the direct I/O driver.
+     * H5Pset_fapl_direct Sets up use of the direct I/O driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param alignment
+     *            IN: Required memory alignment boundary
+     * @param block_size
+     *            IN: File system block size
+     * @param cbuf_size
+     *            IN: Copy buffer size
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native int H5Pset_fapl_direct(long fapl_id, long alignment, long block_size,
+            long cbuf_size) throws HDF5LibraryException;
+
+    /**
+     * H5Pget_fapl_family Returns information about the family file access property list.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param memb_size
+     *            OUT: the size in bytes of each file member (used only when creating a new file)
+     * @param memb_fapl_id
+     *            OUT: the file access property list to be used for each family member
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native int H5Pget_fapl_family(long fapl_id, long[] memb_size, long[] memb_fapl_id)
+            throws HDF5LibraryException, NullPointerException;
+
+    /**
+     * H5Pset_fapl_family Sets up use of the direct I/O driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param memb_size
+     *            IN: the size in bytes of each file member (used only when creating a new file)
+     * @param memb_fapl_id
+     *            IN: the file access property list to be used for each family member
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native int H5Pset_fapl_family(long fapl_id, long memb_size, long memb_fapl_id)
+            throws HDF5LibraryException, NullPointerException;
+
+    /**
+     * H5Pset_fapl_hdfs Modify the file access property list to use the H5FD_HDFS driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param fapl_conf
+     *            IN: the properties of the hdfs driver
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native int H5Pset_fapl_hdfs(long fapl_id, H5FD_hdfs_fapl_t fapl_conf) throws HDF5LibraryException, NullPointerException;
+
+    /**
+     * H5Pget_fapl_hdfs gets the properties hdfs I/O driver.
      *
      * @param fapl_id
      *            IN: File access property list identifier
-     * @param alignment
-     *            IN: Required memory alignment boundary
-     * @param block_size
-     *            IN: File system block size
-     * @param cbuf_size
-     *            IN: Copy buffer size
      *
-     * @return a non-negative value if successful; otherwise returns a negative value.
+     * @return the properties of the hdfs driver.
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      *
      **/
-    public synchronized static native int H5Pset_fapl_direct(long fapl_id, long alignment, long block_size,
-            long cbuf_size) throws HDF5LibraryException;
-
-    public synchronized static native int H5Pget_fapl_family(long fapl_id, long[] memb_size, long[] memb_fapl_id)
-            throws HDF5LibraryException, NullPointerException;
-
-    public synchronized static native int H5Pset_fapl_family(long fapl_id, long memb_size, long memb_fapl_id)
-            throws HDF5LibraryException, NullPointerException;
-
-    public synchronized static native int H5Pset_fapl_hdfs(long fapl_id, H5FD_hdfs_fapl_t fapl_conf) throws HDF5LibraryException, NullPointerException;
-
     public synchronized static native H5FD_hdfs_fapl_t H5Pget_fapl_hdfs(long fapl_id) throws HDF5LibraryException, NullPointerException;
 
     /**
@@ -8093,17 +10228,99 @@ public class H5 implements java.io.Serializable {
     public synchronized static native void H5Pset_fapl_log(long fapl_id, String logfile, long flags, long buf_size)
             throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_fapl_sec2 Sets up use of the sec2 I/O driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pset_fapl_sec2(long fapl_id) throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_fapl_split Sets up use of the split I/O driver. Makes the multi driver act like the
+     *        old split driver which stored meta data in one file and raw
+     *        data in another file
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param meta_ext
+     *            IN: meta filename extension
+     * @param meta_plist_id
+     *            IN: File access property list identifier for metadata
+     * @param raw_ext
+     *            IN: raw data filename extension
+     * @param raw_plist_id
+     *            IN: File access property list identifier raw data
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native void H5Pset_fapl_split(long fapl_id, String meta_ext, long meta_plist_id,
             String raw_ext, long raw_plist_id) throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_fapl_stdio Sets up use of the stdio I/O driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pset_fapl_stdio(long fapl_id) throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_fapl_windows Sets up use of the windows I/O driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pset_fapl_windows(long fapl_id) throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pset_fapl_ros3 Modify the file access property list to use the H5FD_ROS3 driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param fapl_conf
+     *            IN: the properties of the ros3 driver
+     *
+     * @return a non-negative value if successful; otherwise returns a negative value.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native int H5Pset_fapl_ros3(long fapl_id, H5FD_ros3_fapl_t fapl_conf) throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Pget_fapl_ros3 gets the properties of the ros3 I/O driver.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     *
+     * @return the properties of the ros3 driver.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
     public synchronized static native H5FD_ros3_fapl_t H5Pget_fapl_ros3(long fapl_id) throws HDF5LibraryException, NullPointerException;
 
     // /////// unimplemented ////////
@@ -9191,6 +11408,21 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Soffset_simple(long space_id, byte[] offset) throws HDF5LibraryException,
             NullPointerException;
 
+    /**
+     * H5Soffset_simple sets the offset of a simple dataspace space_id.
+     *
+     * @param space_id
+     *            IN: The identifier for the dataspace object to reset.
+     * @param offset
+     *            IN: The offset at which to position the selection.
+     *
+     * @return a non-negative value if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - offset array is null.
+     **/
     public synchronized static int H5Soffset_simple(long space_id, long[] offset) throws HDF5Exception,
             NullPointerException {
         if (offset == null) {
@@ -9317,6 +11549,32 @@ public class H5 implements java.io.Serializable {
         return H5Sselect_hyperslab(space_id, op, lastart, lastride, lacount, lablock);
     }
 
+    /**
+     * H5Sselect_hyperslab selects a hyperslab region to add to the current selected region for the dataspace specified
+     * by space_id. The start, stride, count, and block arrays must be the same size as the rank of the dataspace.
+     *
+     * @param space_id
+     *            IN: Identifier of dataspace selection to modify
+     * @param op
+     *            IN: Operation to perform on current selection.
+     * @param start
+     *            IN: Offset of start of hyperslab
+     * @param stride
+     *            IN: Hyperslab stride.
+     * @param count
+     *            IN: Number of blocks included in hyperslab.
+     * @param block
+     *            IN: Size of block in hyperslab.
+     *
+     * @return a non-negative value if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - an input array is null.
+     * @exception IllegalArgumentException
+     *                - an input array is invalid.
+     **/
     public synchronized static native int H5Sselect_hyperslab(long space_id, int op, long[] start, long[] stride,
             long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
 
@@ -9378,6 +11636,23 @@ public class H5 implements java.io.Serializable {
     public synchronized static native long H5Sset_extent_simple(long space_id, int rank, long[] current_size,
             long[] maximum_size) throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Sset_extent_simple sets or resets the size of an existing dataspace.
+     *
+     * @param space_id
+     *            Dataspace identifier.
+     * @param rank
+     *            Rank, or dimensionality, of the dataspace.
+     * @param current_size
+     *            Array containing current size of dataspace.
+     * @param maximum_size
+     *            Array containing maximum size of dataspace.
+     *
+     * @return a dataspace identifier if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static long H5Sset_extent_simple(long space_id, int rank, byte[] current_size,
             byte[] maximum_size) throws HDF5LibraryException, NullPointerException {
         ByteBuffer csbb = ByteBuffer.wrap(current_size);
@@ -9786,6 +12061,23 @@ public class H5 implements java.io.Serializable {
         return H5Tenum_insert_int(type, name, value);
     }
 
+    /**
+     * H5Tenum_insert inserts a new enumeration datatype member into an enumeration datatype.
+     *
+     * @param type
+     *            IN: Identifier of datatype.
+     * @param name
+     *            IN: The name of the member
+     * @param value
+     *            IN: The value of the member, data of the correct type
+     *
+     * @return a non-negative value if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - name is null.
+     **/
     public static int H5Tenum_insert(long type, String name, int value) throws HDF5LibraryException,
             NullPointerException {
         int[] val = { value };
@@ -10942,15 +13234,128 @@ public class H5 implements java.io.Serializable {
     // ////////////////////////////////////////////////////////////
 
     /// VOL Connector Functionality
+    /**
+     * H5VLregister_connector_by_name registers a new VOL connector as a member of the virtual object layer class.
+     *
+     * @param connector_name
+     *            IN: name of the connector.
+     * @param vipl_id
+     *            IN: VOL initialization property list which must be
+     *                created with H5Pcreate(H5P_VOL_INITIALIZE) (or H5P_DEFAULT).
+     *
+     * @return a VOL connector ID
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native long H5VLregister_connector_by_name(String connector_name, long vipl_id);
+    /**
+     * H5VLregister_connector_by_value registers a new VOL connector as a member of the virtual object layer class.
+     *
+     * @param connector_value
+     *            IN: value of the connector.
+     * @param vipl_id
+     *            IN: VOL initialization property list which must be
+     *                created with H5Pcreate(H5P_VOL_INITIALIZE) (or H5P_DEFAULT).
+     *
+     * @return a VOL connector ID
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native long H5VLregister_connector_by_value(int connector_value, long vipl_id);
+    /**
+     * H5VLis_connector_registered_by_name tests whether a VOL class has been registered.
+     *
+     * @param name
+     *            IN: name of the connector.
+     *
+     * @return true if a VOL connector with that name has been registered
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native boolean H5VLis_connector_registered_by_name(String name);
+    /**
+     * H5VLis_connector_registered_by_value tests whether a VOL class has been registered.
+     *
+     * @param connector_value
+     *            IN: value of the connector.
+     *
+     * @return  true if a VOL connector with that value has been registered
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native boolean H5VLis_connector_registered_by_value(int connector_value);
+    /**
+     * H5VLget_connector_id retrieves the ID for a registered VOL connector for a given object.
+     *
+     * @param object_id
+     *            IN: Identifier of the object.
+     *
+     * @return a VOL connector ID
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native long H5VLget_connector_id(long object_id);
+    /**
+     * H5VLget_connector_id_by_name retrieves the ID for a registered VOL connector.
+     *
+     * @param name
+     *            IN: name of the connector.
+     *
+     * @return a VOL connector ID
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native long H5VLget_connector_id_by_name(String name);
+    /**
+     * H5VLget_connector_id_by_value retrieves the ID for a registered VOL connector.
+     *
+     * @param connector_value
+     *            IN: value of the connector.
+     *
+     * @return a VOL connector ID
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native long H5VLget_connector_id_by_value(int connector_value);
+    /**
+     * H5VLget_connector_name returns the connector name for the VOL associated with the
+     *              object or file ID.
+     *
+     * @param object_id
+     *            IN: Identifier of the object.
+     *
+     * @return the connector name
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native String H5VLget_connector_name(long object_id);
+    /**
+     * H5VLclose closes a VOL connector ID.
+     *
+     * @param connector_id
+     *            IN: Identifier of the connector.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native void H5VLclose(long connector_id);
+    /**
+     * H5VLunregister_connector removes a VOL connector ID from the library.
+     *
+     * @param connector_id
+     *            IN: Identifier of the connector.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native void H5VLunregister_connector(long connector_id);
 
     // /////// unimplemented ////////
@@ -10963,11 +13368,44 @@ public class H5 implements java.io.Serializable {
     // //
     // ////////////////////////////////////////////////////////////
 
-    public synchronized static native int H5Zfilter_avail(int filter) throws HDF5LibraryException, NullPointerException;
+    /**
+     * H5Zfilter_avail checks if a filter is available.
+     *
+     * @param filter
+     *            IN: filter number.
+     *
+     * @return a non-negative(TRUE/FALSE) value if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native int H5Zfilter_avail(int filter) throws HDF5LibraryException;
 
+    /**
+     * H5Zget_filter_info gets information about a pipeline data filter.
+     *
+     * @param filter
+     *            IN: filter number.
+     *
+     * @return the filter information flags
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
     public synchronized static native int H5Zget_filter_info(int filter) throws HDF5LibraryException;
 
-    public synchronized static native int H5Zunregister(int filter) throws HDF5LibraryException, NullPointerException;
+    /**
+     * H5Zunregister unregisters a filter.
+     *
+     * @param filter
+     *            IN: filter number.
+     *
+     * @return a non-negative value if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native int H5Zunregister(int filter) throws HDF5LibraryException;
 
     // /////// unimplemented ////////
 
diff --git a/java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java b/java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java
index 988c8fb..69c9709 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java
@@ -15,7 +15,28 @@ package hdf.hdf5lib.callbacks;
 
 import hdf.hdf5lib.structs.H5A_info_t;
 
-//Information class for link callback(for H5Aiterate)
+/**
+ * Information class for link callback for H5Aiterate.
+ *
+ */
 public interface H5A_iterate_cb extends Callbacks {
-    int callback(long group, String name, H5A_info_t info, H5A_iterate_t op_data);
+    /**
+     *  application callback for each attribute
+     *
+     *  @param loc_id    the ID for the group or dataset being iterated over
+     *  @param name      the name of the current attribute about the object
+     *  @param info      the attribute's "info" struct
+     *  @param op_data   the operator data passed in to H5Aiterate
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
+    int callback(long loc_id, String name, H5A_info_t info, H5A_iterate_t op_data);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java b/java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java
index 51d67d5..bdc96fa 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java
@@ -13,6 +13,10 @@
 
 package hdf.hdf5lib.callbacks;
 
+/**
+ * Data class for link callback for H5Aiterate.
+ *
+ */
 public interface H5A_iterate_t {
 /**    public ArrayList iterdata = new ArrayList();
   * Any derived interfaces must define the single public variable as above.
diff --git a/java/src/hdf/hdf5lib/callbacks/H5D_append_cb.java b/java/src/hdf/hdf5lib/callbacks/H5D_append_cb.java
index ead8f73..8ad336f 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5D_append_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5D_append_cb.java
@@ -13,7 +13,27 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pset/get_append_flush)
+/**
+ * Information class for link callback for H5Pset/get_append_flush.
+ *
+ */
 public interface H5D_append_cb extends Callbacks {
+    /**
+     *  application callback for each dataset access property list
+     *
+     *  @param dataset_id    the ID for the dataset being iterated over
+     *  @param cur_dims      the dimension sizes for determining boundary
+     *  @param op_data       the operator data passed in to H5Pset/get_append_flush
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(long dataset_id, long[] cur_dims, H5D_append_t op_data);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5D_append_t.java b/java/src/hdf/hdf5lib/callbacks/H5D_append_t.java
index 8bf6410..795ed1e 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5D_append_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5D_append_t.java
@@ -13,6 +13,10 @@
 
 package hdf.hdf5lib.callbacks;
 
+/**
+ * Data class for link callback for H5Dappend.
+ *
+ */
 public interface H5D_append_t {
 /**    public ArrayList iterdata = new ArrayList();
   * Any derived interfaces must define the single public variable as above.
diff --git a/java/src/hdf/hdf5lib/callbacks/H5D_iterate_cb.java b/java/src/hdf/hdf5lib/callbacks/H5D_iterate_cb.java
index a911a1c..ca10342 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5D_iterate_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5D_iterate_cb.java
@@ -13,7 +13,29 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Diterate)
+/**
+ * Information class for link callback for H5Diterate.
+ *
+ */
 public interface H5D_iterate_cb extends Callbacks {
+    /**
+     *  application callback for each dataset element
+     *
+     *  @param elem      the pointer to the element in memory containing the current point
+     *  @param elem_type the datatype ID for the elements stored in elem
+     *  @param ndim      the number of dimensions for POINT array
+     *  @param point     the array containing the location of the element within the original dataspace
+     *  @param op_data   the operator data passed in to H5Diterate
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(byte[] elem, long elem_type, int ndim, long[] point, H5D_iterate_t op_data);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5D_iterate_t.java b/java/src/hdf/hdf5lib/callbacks/H5D_iterate_t.java
index d049711..43fc159 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5D_iterate_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5D_iterate_t.java
@@ -13,6 +13,10 @@
 
 package hdf.hdf5lib.callbacks;
 
+/**
+ * Data class for link callback for H5Diterate.
+ *
+ */
 public interface H5D_iterate_t {
 /**    public ArrayList iterdata = new ArrayList();
   * Any derived interfaces must define the single public variable as above.
diff --git a/java/src/hdf/hdf5lib/callbacks/H5E_walk_cb.java b/java/src/hdf/hdf5lib/callbacks/H5E_walk_cb.java
index afc04ae..e5914c1 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5E_walk_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5E_walk_cb.java
@@ -15,7 +15,27 @@ package hdf.hdf5lib.callbacks;
 
 import hdf.hdf5lib.structs.H5E_error2_t;
 
-//Information class for link callback(for H5Ewalk)
+/**
+ * Information class for link callback for H5Ewalk.
+ *
+ */
 public interface H5E_walk_cb extends Callbacks {
+    /**
+     *  application callback for each error stack element
+     *
+     *  @param nidx      the index of the current error stack element
+     *  @param info      the error stack "info" struct
+     *  @param op_data   the operator data passed in to H5Ewalk
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(int nidx, H5E_error2_t info, H5E_walk_t op_data);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5E_walk_t.java b/java/src/hdf/hdf5lib/callbacks/H5E_walk_t.java
index 0be8977..3ff09ec 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5E_walk_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5E_walk_t.java
@@ -13,6 +13,10 @@
 
 package hdf.hdf5lib.callbacks;
 
+/**
+ * Data class for link callback for H5Ewalk.
+ *
+ */
 public interface H5E_walk_t {
 /**    public ArrayList iterdata = new ArrayList();
   * Any derived interfaces must define the single public variable as above.
diff --git a/java/src/hdf/hdf5lib/callbacks/H5L_iterate_opdata_t.java b/java/src/hdf/hdf5lib/callbacks/H5L_iterate_opdata_t.java
index ad9ad8c..ad28b04 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5L_iterate_opdata_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5L_iterate_opdata_t.java
@@ -13,6 +13,10 @@
 
 package hdf.hdf5lib.callbacks;
 
+/**
+ * Data class for link callback for H5Lvisit/H5Lvisit_by_name.
+ *
+ */
 public interface H5L_iterate_opdata_t {
 
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5L_iterate_t.java b/java/src/hdf/hdf5lib/callbacks/H5L_iterate_t.java
index f92fbc4..d08001a 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5L_iterate_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5L_iterate_t.java
@@ -15,7 +15,28 @@ package hdf.hdf5lib.callbacks;
 
 import hdf.hdf5lib.structs.H5L_info_t;
 
-// Information class for link callback (for H5Lvisit/H5Lvisit_by_name).
+/**
+ * Information class for link callback for H5Lvisit/H5Lvisit_by_name.
+ *
+ */
 public interface H5L_iterate_t extends Callbacks {
-    int callback(long group, String name, H5L_info_t info, H5L_iterate_opdata_t op_data);
+    /**
+     *  application callback for each group
+     *
+     *  @param loc_id    the ID for the group being iterated over
+     *  @param name      the name of the current link
+     *  @param info      the link's "info" struct
+     *  @param op_data   the operator data passed in to H5Literate
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
+    int callback(long loc_id, String name, H5L_info_t info, H5L_iterate_opdata_t op_data);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5O_iterate_opdata_t.java b/java/src/hdf/hdf5lib/callbacks/H5O_iterate_opdata_t.java
index e1c47b5..15eb1a1 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5O_iterate_opdata_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5O_iterate_opdata_t.java
@@ -13,6 +13,10 @@
 
 package hdf.hdf5lib.callbacks;
 
+/**
+ * Data class for link callback for H5Ovisit/H5Ovisit_by_name.
+ *
+ */
 public interface H5O_iterate_opdata_t {
 
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5O_iterate_t.java b/java/src/hdf/hdf5lib/callbacks/H5O_iterate_t.java
index 9a55106..e627775 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5O_iterate_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5O_iterate_t.java
@@ -15,7 +15,28 @@ package hdf.hdf5lib.callbacks;
 
 import hdf.hdf5lib.structs.H5O_info_t;
 
-// Information class for link callback(for H5Ovisit/H5Ovisit_by_name)
+/**
+ * Information class for link callback for H5Ovisit/H5Ovisit_by_name.
+ *
+ */
 public interface H5O_iterate_t extends Callbacks {
-    int callback(long group, String name, H5O_info_t info, H5O_iterate_opdata_t op_data);
+    /**
+     *  application callback for each group
+     *
+     *  @param loc_id    the ID for the group or dataset being iterated over
+     *  @param name      the name of the current object
+     *  @param info      the object's "info" struct
+     *  @param op_data   the operator data passed in to H5Oiterate
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
+    int callback(long loc_id, String name, H5O_info_t info, H5O_iterate_opdata_t op_data);
 }
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
index e77d386..78a87ad 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_cb.java
@@ -13,7 +13,26 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pcreate_class)
+/**
+ * Information class for link callback for H5Pcreate_class.
+ *
+ */
 public interface H5P_cls_close_func_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param prop_id     the ID for the property list class being iterated over
+     *  @param close_data  the function to call when a property list is closed
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(long prop_id, H5P_cls_close_func_t close_data);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_t.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_t.java
index 0d5ad9e..709ee494 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_t.java
@@ -13,6 +13,10 @@
 
 package hdf.hdf5lib.callbacks;
 
+/**
+ * Data class for link callback for H5Pcreate_class.
+ *
+ */
 public interface H5P_cls_close_func_t {
 /**    public ArrayList iterdata = new ArrayList();
   * Any derived interfaces must define the single public variable as above.
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
index 139f877..878bbd3 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_cb.java
@@ -13,7 +13,27 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pcreate_class)
+/**
+ * Information class for link callback for H5Pcreate_class
+ *
+ */
 public interface H5P_cls_copy_func_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param new_prop_id   the ID for the property list copy
+     *  @param old_prop_id   the ID for the property list class being copied
+     *  @param copy_data     the function to call when each property list in this class is copied
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(long new_prop_id, long old_prop_id, H5P_cls_copy_func_t copy_data);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_t.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_t.java
index 12c2601..b3e7f09 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_t.java
@@ -13,6 +13,10 @@
 
 package hdf.hdf5lib.callbacks;
 
+/**
+ * Data class for link callback for H5Pcreate_class.
+ *
+ */
 public interface H5P_cls_copy_func_t {
 /**    public ArrayList iterdata = new ArrayList();
   * Any derived interfaces must define the single public variable as above.
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
index e64ec6f..88d0aa6 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_cb.java
@@ -13,7 +13,26 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pcreate_class)
+/**
+ * Information class for link callback for H5Pcreate_class.
+ *
+ */
 public interface H5P_cls_create_func_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param prop_id       the ID for the property list class being iterated over
+     *  @param create_data   the function to call when each property list in this class is created
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(long prop_id, H5P_cls_create_func_t create_data);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_t.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_t.java
index 73646f1..8e259cc 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_t.java
@@ -13,6 +13,10 @@
 
 package hdf.hdf5lib.callbacks;
 
+/**
+ * Data class for link callback for H5Pcreate_class.
+ *
+ */
 public interface H5P_cls_create_func_t {
 /**    public ArrayList iterdata = new ArrayList();
   * Any derived interfaces must define the single public variable as above.
diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_iterate_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_iterate_cb.java
index 5ecb88d..60e1884 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_iterate_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_iterate_cb.java
@@ -13,7 +13,27 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Piterate)
+/**
+ * Information class for link callback for H5Piterate.
+ *
+ */
 public interface H5P_iterate_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param plist     the ID for the property list being iterated over
+     *  @param name      the name of the current property list
+     *  @param op_data   the operator data passed in to H5Piterate
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(long plist, String name, H5P_iterate_t op_data);
 }
diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_iterate_t.java b/java/src/hdf/hdf5lib/callbacks/H5P_iterate_t.java
index 2e320b4..4c5d222 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_iterate_t.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_iterate_t.java
@@ -13,6 +13,10 @@
 
 package hdf.hdf5lib.callbacks;
 
+/**
+ * Data class for link callback for H5Piterate.
+ *
+ */
 public interface H5P_iterate_t {
 /**    public ArrayList iterdata = new ArrayList();
   * Any derived interfaces must define the single public variable as above.
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
index 103fe5f..40569bc 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_close_func_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_close_func_cb.java
@@ -13,7 +13,27 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pregister2)
+/**
+ * Information class for link callback for H5Pregister2.
+ *
+ */
 public interface H5P_prp_close_func_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param name    the name of the property being closed
+     *  @param size    the size of the property value
+     *  @param value   the value of the property being closed
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(String name, long size, byte[] value);
 }
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
index 46477b9..cc466a6 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_compare_func_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_compare_func_cb.java
@@ -13,7 +13,27 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pregister2)
+/**
+ * Information class for link callback for H5Pregister2.
+ *
+ */
 public interface H5P_prp_compare_func_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param value1  the value of the first property being compared
+     *  @param value2  the value of the second property being compared
+     *  @param size    the size of the property value
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(byte[] value1, byte[] value2, long size);
 }
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
index 57994bb5..59e4bb8 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_copy_func_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_copy_func_cb.java
@@ -13,7 +13,27 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pregister2)
+/**
+ * Information class for link callback for H5Pregister2.
+ *
+ */
 public interface H5P_prp_copy_func_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param name      the name of the property being copied
+     *  @param size      the size of the property value
+     *  @param value     the value of the property being copied
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(String name, long size, byte[] value);
 }
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
index 8791c22..5c6df7a 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_create_func_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_create_func_cb.java
@@ -13,7 +13,27 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pregister2)
+/**
+ * Information class for link callback for H5Pregister2.
+ *
+ */
 public interface H5P_prp_create_func_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param name      the name of the property list being created
+     *  @param size      the size of the property value
+     *  @param value     the initial value for the property being created
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(String name, long size, byte[] value);
 }
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
index 46cd097..5206d4f 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_delete_func_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_delete_func_cb.java
@@ -13,7 +13,28 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pregister2)
+/**
+ * Information class for link callback for H5Pregister2.
+ *
+ */
 public interface H5P_prp_delete_func_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param prop_id   the ID of the property list the property is deleted from
+     *  @param name      the name of the property being deleted
+     *  @param size      the size of the property value
+     *  @param value     the value of the property being deleted
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(long prop_id, String name, long size, byte[] value);
 }
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
index 04599a0..8f44497 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_get_func_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_get_func_cb.java
@@ -13,7 +13,28 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pregister2)
+/**
+ * Information class for link callback for H5Pregister2.
+ *
+ */
 public interface H5P_prp_get_func_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param prop_id   the ID for the property list being queried
+     *  @param name      the name of the property being queried
+     *  @param size      the size of the property value
+     *  @param value     the value being retrieved for the property
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(long prop_id, String name, long size, byte[] value);
 }
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
index 6ac750f..2a2d3a1 100644
--- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_set_func_cb.java
+++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_set_func_cb.java
@@ -13,7 +13,28 @@
 
 package hdf.hdf5lib.callbacks;
 
-//Information class for link callback(for H5Pregister2)
+/**
+ * Information class for link callback for H5Pregister2.
+ *
+ */
 public interface H5P_prp_set_func_cb extends Callbacks {
+    /**
+     *  application callback for each property list
+     *
+     *  @param prop_id   the ID for the property list being modified
+     *  @param name      the name of the property being modified
+     *  @param size      the size of the property value
+     *  @param value     the value being set for the property
+     *
+     *  @return operation status
+     *      A. Zero causes the iterator to continue, returning zero when all
+     *          attributes have been processed.
+     *      B. Positive causes the iterator to immediately return that positive
+     *          value, indicating short-circuit success.  The iterator can be
+     *          restarted at the next attribute.
+     *      C. Negative causes the iterator to immediately return that value,
+     *          indicating failure.  The iterator can be restarted at the next
+     *          attribute.
+     */
     int callback(long prop_id, String name, long size, byte[] value);
 }
diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java b/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java
index 1e4b5fd..70fdd11 100644
--- a/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java
+++ b/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java
@@ -31,6 +31,9 @@ package hdf.hdf5lib.exceptions;
  *
  */
 public class HDF5Exception extends RuntimeException {
+    /**
+     *  the specified detail message of this exception
+     */
     protected String detailMessage;
 
     /**
diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5ReferenceException.java b/java/src/hdf/hdf5lib/exceptions/HDF5ReferenceException.java
index ea4a89a..fea5b6d 100644
--- a/java/src/hdf/hdf5lib/exceptions/HDF5ReferenceException.java
+++ b/java/src/hdf/hdf5lib/exceptions/HDF5ReferenceException.java
@@ -13,6 +13,12 @@
 
 package hdf.hdf5lib.exceptions;
 
+/**
+ * The class HDF5LibraryException returns errors raised by the HDF5 library.
+ * 

+ * This sub-class represents HDF-5 major error code H5E_REFERENCE
+ */
+
 public class HDF5ReferenceException extends HDF5LibraryException {
     /**
      * Constructs an HDF5ReferenceException with no specified
diff --git a/java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java b/java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java
index 20863dc..a118d05 100644
--- a/java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java
@@ -15,7 +15,10 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-//Information struct for H5Pget_mdc_config/H5Pset_mdc_config
+/**
+ * Information struct for H5Pget_mdc_config/H5Pset_mdc_config
+ *
+ */
 public class H5AC_cache_config_t implements Serializable{
     private static final long serialVersionUID = -6748085696476149972L;
     // general configuration fields:
diff --git a/java/src/hdf/hdf5lib/structs/H5A_info_t.java b/java/src/hdf/hdf5lib/structs/H5A_info_t.java
index a46a495..cd7a397 100644
--- a/java/src/hdf/hdf5lib/structs/H5A_info_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5A_info_t.java
@@ -15,7 +15,10 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-//Information struct for Attribute (For H5Aget_info/H5Aget_info_by_idx/H5Aget_info_by_name)
+/**
+ * Information struct for Attribute (For H5Aget_info/H5Aget_info_by_idx/H5Aget_info_by_name)
+ *
+ */
 public class H5A_info_t implements Serializable{
     private static final long serialVersionUID = 2791443594041667613L;
     public boolean corder_valid; // Indicate if creation order is valid
diff --git a/java/src/hdf/hdf5lib/structs/H5E_error2_t.java b/java/src/hdf/hdf5lib/structs/H5E_error2_t.java
index 257ad05..083537f 100644
--- a/java/src/hdf/hdf5lib/structs/H5E_error2_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5E_error2_t.java
@@ -15,7 +15,10 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-//Information struct for Attribute (For H5Ewalk)
+/**
+ * Information struct for Attribute (For H5Ewalk)
+ *
+ */
 public class H5E_error2_t implements Serializable{
     private static final long serialVersionUID = 279144359041667613L;
 
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 9fcff2e..26690ec 100644
--- a/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java
@@ -16,7 +16,7 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-/*
+/**
  * Java representation of the HDFS VFD file access property list (fapl)
  * structure.
  *
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 a899e10..735cc7e 100644
--- a/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java
@@ -16,7 +16,7 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-/*
+/**
  * Java representation of the ROS3 VFD file access property list (fapl)
  * structure.
  *
diff --git a/java/src/hdf/hdf5lib/structs/H5F_info2_t.java b/java/src/hdf/hdf5lib/structs/H5F_info2_t.java
index 4664b5b..836b683 100644
--- a/java/src/hdf/hdf5lib/structs/H5F_info2_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5F_info2_t.java
@@ -15,7 +15,10 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-//Information struct for object (for H5Fget_info)
+/**
+ * Information struct for object (for H5Fget_info)
+ *
+ */
 public class H5F_info2_t implements Serializable{
     private static final long serialVersionUID = 4691681162544054518L;
     public int         super_version;    // Superblock version #
diff --git a/java/src/hdf/hdf5lib/structs/H5G_info_t.java b/java/src/hdf/hdf5lib/structs/H5G_info_t.java
index 56c876e..9a5c72e 100644
--- a/java/src/hdf/hdf5lib/structs/H5G_info_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5G_info_t.java
@@ -15,7 +15,10 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-//Information struct for group (for H5Gget_info/H5Gget_info_by_name/H5Gget_info_by_idx)
+/**
+ * Information struct for group (for H5Gget_info/H5Gget_info_by_name/H5Gget_info_by_idx)
+ *
+ */
 public class H5G_info_t implements Serializable{
     private static final long serialVersionUID = -3746463015312132912L;
     public int storage_type; // Type of storage for links in group
diff --git a/java/src/hdf/hdf5lib/structs/H5L_info_t.java b/java/src/hdf/hdf5lib/structs/H5L_info_t.java
index 377e617..16d9bbf 100644
--- a/java/src/hdf/hdf5lib/structs/H5L_info_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5L_info_t.java
@@ -17,7 +17,10 @@ import java.io.Serializable;
 
 import hdf.hdf5lib.HDF5Constants;
 
-// Information struct for link (for H5Lget_info/H5Lget_info_by_idx)
+/**
+ * Information struct for link (for H5Lget_info/H5Lget_info_by_idx)
+ *
+ */
 public class H5L_info_t implements Serializable {
     private static final long serialVersionUID = -4754320605310155033L;
     public int         type;
diff --git a/java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java b/java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java
index 73aaa47..df76638 100644
--- a/java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java
@@ -15,7 +15,10 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-// Information struct for object header metadata (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx)
+/**
+ * Information struct for object header metadata (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx)
+ *
+ */
 public class H5O_hdr_info_t implements Serializable {
     private static final long serialVersionUID = 7883826382952577189L;
     public int version;       /* Version number of header format in file */
@@ -56,25 +59,25 @@ public class H5O_hdr_info_t implements Serializable {
         H5O_hdr_info_t info = (H5O_hdr_info_t) o;
 
         if (this.version != info.version)
-        	return false;
+            return false;
         if (this.nmesgs != info.nmesgs)
-        	return false;
+            return false;
         if (this.nchunks != info.nchunks)
-        	return false;
+            return false;
         if (this.flags != info.flags)
-        	return false;
+            return false;
         if (this.space_total != info.space_total)
-        	return false;
+            return false;
         if (this.space_meta != info.space_meta)
-        	return false;
+            return false;
         if (this.space_mesg != info.space_mesg)
-        	return false;
+            return false;
         if (this.space_free != info.space_free)
-        	return false;
+            return false;
         if (this.mesg_present != info.mesg_present)
-        	return false;
+            return false;
         if (this.mesg_shared != info.mesg_shared)
-        	return false;
+            return false;
 
         return true;
     }
diff --git a/java/src/hdf/hdf5lib/structs/H5O_info_t.java b/java/src/hdf/hdf5lib/structs/H5O_info_t.java
index 6a26a10..2f76384 100644
--- a/java/src/hdf/hdf5lib/structs/H5O_info_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5O_info_t.java
@@ -15,7 +15,10 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-// Information struct for object (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx)
+/**
+ * Information struct for object (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx)
+ *
+ */
 public class H5O_info_t implements Serializable {
     private static final long serialVersionUID = 4691681163544054518L;
     public long        fileno;     /* File number that object is located in */
diff --git a/java/src/hdf/hdf5lib/structs/H5O_native_info_t.java b/java/src/hdf/hdf5lib/structs/H5O_native_info_t.java
index f410a7f..89a5c5f 100644
--- a/java/src/hdf/hdf5lib/structs/H5O_native_info_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5O_native_info_t.java
@@ -15,7 +15,10 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-// Information struct for native HDF5 object info, such as object header metadata (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx).
+/**
+ * Information struct for native HDF5 object info, such as object header metadata (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx).
+ *
+ */
 public class H5O_native_info_t implements Serializable {
     private static final long serialVersionUID = 7883826382952577189L;
 
@@ -45,7 +48,7 @@ public class H5O_native_info_t implements Serializable {
         if (!this.hdr_info.equals(info.hdr_info)
          || !this.obj_info.equals(info.obj_info)
          || !this.attr_info.equals(info.attr_info))
-        	return false;
+            return false;
 
         return true;
     }
diff --git a/java/src/hdf/hdf5lib/structs/H5O_token_t.java b/java/src/hdf/hdf5lib/structs/H5O_token_t.java
index e6d2474..be934e4 100644
--- a/java/src/hdf/hdf5lib/structs/H5O_token_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5O_token_t.java
@@ -17,7 +17,10 @@ import java.util.Arrays;
 
 import hdf.hdf5lib.HDF5Constants;
 
-// Object token, which is a unique and permanent identifier, for an HDF5 object within a container.
+/**
+ * Object token, which is a unique and permanent identifier, for an HDF5 object within a container.
+ *
+ */
 public class H5O_token_t implements Serializable {
     private static final long serialVersionUID = -4754320605310155032L;
     public byte[] data;
diff --git a/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java b/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java
index 7159f02..1c3ab80 100644
--- a/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java
@@ -15,7 +15,10 @@ package hdf.hdf5lib.structs;
 
 import java.io.Serializable;
 
-//Information struct for group (for H5Gget_info/H5Gget_info_by_name/H5Gget_info_by_idx)
+/**
+ * Information struct for group (for H5Gget_info/H5Gget_info_by_name/H5Gget_info_by_idx)
+ *
+ */
 public class H5_ih_info_t implements Serializable {
     private static final long serialVersionUID = -142238015615462707L;
     public long     index_size;     /* btree and/or list */
@@ -38,9 +41,9 @@ public class H5_ih_info_t implements Serializable {
         H5_ih_info_t info = (H5_ih_info_t) o;
 
         if (this.index_size != info.index_size)
-        	return false;
+            return false;
         if (this.heap_size != info.heap_size)
-        	return false;
+            return false;
 
         return true;
     }
diff --git a/src/H5FDhdfs.c b/src/H5FDhdfs.c
index 569b889..e1b06d3 100644
--- a/src/H5FDhdfs.c
+++ b/src/H5FDhdfs.c
@@ -593,7 +593,7 @@ done:
  * Function:    H5Pset_fapl_hdfs
  *
  * Purpose:     Modify the file access property list to use the H5FD_HDFS
- *              driver defined in this source file.  All driver specfic
+ *              driver defined in this source file.  All driver specific
  *              properties are passed in as a pointer to a suitably
  *              initialized instance of H5FD_hdfs_fapl_t
  *
-- 
cgit v0.12


From 176eef273765d4a197347ae16ed18a3c73f328ba Mon Sep 17 00:00:00 2001
From: Allen Byrne 
Date: Mon, 19 Oct 2020 09:42:09 -0500
Subject: Whitespace and url correction

---
 config/cmake/scripts/HDF5config.cmake |  2 +-
 release_docs/README_HPC               |  2 +-
 src/H5FDcore.c                        |  6 +++---
 src/H5FDhdfs.c                        | 23 ++++++++++++-----------
 src/H5FDhdfs.h                        |  2 +-
 5 files changed, 18 insertions(+), 17 deletions(-)

diff --git a/config/cmake/scripts/HDF5config.cmake b/config/cmake/scripts/HDF5config.cmake
index 3a8d5b7..61c535e 100644
--- a/config/cmake/scripts/HDF5config.cmake
+++ b/config/cmake/scripts/HDF5config.cmake
@@ -204,7 +204,7 @@ endif ()
 #set (LOCAL_NO_PACKAGE "TRUE")
 #####       Following controls source update                  #####
 #set (LOCAL_UPDATE "TRUE")
-set (REPOSITORY_URL "https://git@bitbucket.hdfgroup.org/scm/hdffv/hdf5.git")
+set (REPOSITORY_URL "https://github.com/HDFGroup/hdf5.git")
 set (REPOSITORY_BRANCH "develop")
 
 #uncomment to use a compressed source file: *.tar on linux or mac *.zip on windows
diff --git a/release_docs/README_HPC b/release_docs/README_HPC
index 513064c..6b31ce6 100644
--- a/release_docs/README_HPC
+++ b/release_docs/README_HPC
@@ -32,7 +32,7 @@ II. Obtain HDF5 source
 Obtain HDF5 source code from the HDF5 repository using a git command or
 from a release tar file in a working directory:
 
-    git clone https://git@bitbucket.hdfgroup.org/scm/hdffv/hdf5.git
+    git clone https://github.com/HDFGroup/hdf5.git
         [-b branch] [source directory]
 
 If no branch is specified, then the 'develop' version will be checked out.
diff --git a/src/H5FDcore.c b/src/H5FDcore.c
index 419a0d9..61f46c7 100644
--- a/src/H5FDcore.c
+++ b/src/H5FDcore.c
@@ -281,13 +281,13 @@ H5FD__core_add_dirty_region(H5FD_core_t *file, haddr_t start, haddr_t end)
         else {
             /* Store the new item endpoint if it's bigger */
             item->end = (item->end < end) ? end : item->end;
-        } /* end else */
-    }     /* end if */
+        }
+    }
     else {
         /* Update the size of the before region */
         if (b_item->end < end)
             b_item->end = end;
-    } /* end else */
+    }
 
 done:
     FUNC_LEAVE_NOAPI(ret_value)
diff --git a/src/H5FDhdfs.c b/src/H5FDhdfs.c
index e1b06d3..a7c6aae 100644
--- a/src/H5FDhdfs.c
+++ b/src/H5FDhdfs.c
@@ -231,8 +231,7 @@ typedef struct {
  *
  * Programmer: Jacob Smith
  *
- ***************************************************************************
- */
+ ***************************************************************************/
 typedef struct H5FD_hdfs_t {
     H5FD_t           pub;
     H5FD_hdfs_fapl_t fa;
@@ -362,7 +361,7 @@ H5FD_hdfs_init(void)
     unsigned int bin_i;
 #endif
 
-    FUNC_ENTER_NOAPI(FAIL)
+    FUNC_ENTER_NOAPI(H5I_INVALID_HID)
 
 #if HDFS_DEBUG
     HDfprintf(stdout, "called %s.\n", FUNC);
@@ -379,7 +378,7 @@ H5FD_hdfs_init(void)
 
         HDFS_STATS_POW(bin_i, &value)
         hdfs_stats_boundaries[bin_i] = value;
-    } /* end for */
+    }
 #endif
 
     ret_value = H5FD_HDFS_g;
@@ -662,9 +661,11 @@ H5Pget_fapl_hdfs(hid_t fapl_id, H5FD_hdfs_fapl_t *fa_out)
 
     if (fa_out == NULL)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "fa_out is NULL")
+
     plist = H5P_object_verify(fapl_id, H5P_FILE_ACCESS);
     if (plist == NULL)
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file access list")
+
     if (H5FD_HDFS != H5P_peek_driver(plist))
         HGOTO_ERROR(H5E_PLIST, H5E_BADVALUE, FAIL, "incorrect VFL driver")
 
@@ -813,7 +814,7 @@ hdfs__reset_stats(H5FD_hdfs_t *file)
     FUNC_ENTER_STATIC
 
 #if HDFS_DEBUG
-    HDprintf("hdfs__reset_stats() called\n");
+    HDfprintf(stdout, "called %s.\n", FUNC);
 #endif
 
     if (file == NULL)
@@ -1203,8 +1204,8 @@ done:
 static herr_t
 H5FD__hdfs_close(H5FD_t *_file)
 {
-    herr_t       ret_value = SUCCEED;
     H5FD_hdfs_t *file      = (H5FD_hdfs_t *)_file;
+    herr_t       ret_value = SUCCEED;
 
     FUNC_ENTER_STATIC
 
@@ -1245,8 +1246,8 @@ done:
  *     field-by-field.
  *
  * Return:
- *     + Equivalent:      0
- *     + Not Equivalent: -1
+ *      Equivalent:      0
+ *      Not Equivalent: -1
  *
  * Programmer: Gerd Herber
  *             May 2018
@@ -1470,8 +1471,8 @@ H5FD__hdfs_get_eof(const H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type)
 static herr_t
 H5FD__hdfs_get_handle(H5FD_t *_file, hid_t H5_ATTR_UNUSED fapl, void **file_handle)
 {
-    herr_t       ret_value = SUCCEED;
     H5FD_hdfs_t *file      = (H5FD_hdfs_t *)_file;
+    herr_t       ret_value = SUCCEED;
 
     FUNC_ENTER_STATIC
 
@@ -1514,9 +1515,9 @@ static herr_t
 H5FD__hdfs_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUSED dxpl_id, haddr_t addr,
                 size_t size, void *buf)
 {
-    herr_t       ret_value = SUCCEED;
     H5FD_hdfs_t *file      = (H5FD_hdfs_t *)_file;
     size_t       filesize  = 0;
+    herr_t       ret_value = SUCCEED;
 #if HDFS_STATS
     /* working variables for storing stats */
     hdfs_statsbin *bin   = NULL;
@@ -1655,7 +1656,7 @@ done:
  *     No effect on Read-Only S3 file.
  *
  *     Suggestion: remove lock/unlock from class
- *               > would result in error at H5FD_[un]lock() (H5FD.c)
+ *                 would result in error at H5FD_[un]lock() (H5FD.c)
  *
  * Return:
  *
diff --git a/src/H5FDhdfs.h b/src/H5FDhdfs.h
index 05506d4..9d14e9a 100644
--- a/src/H5FDhdfs.h
+++ b/src/H5FDhdfs.h
@@ -16,7 +16,7 @@
  * Programmer:  Jacob Smith
  *              2018-04-23
  *
- * Purpose:	The public header file for the hdfs driver.
+ * Purpose:    The public header file for the hdfs driver.
  */
 
 #ifndef H5FDhdfs_H
-- 
cgit v0.12


From 4a88f0c8d780c27aa611edbf3562b0264fd8b97f Mon Sep 17 00:00:00 2001
From: Allen Byrne 
Date: Mon, 19 Oct 2020 16:21:57 -0500
Subject: URL and options corrections

---
 config/cmake/scripts/HDF5options.cmake | 2 ++
 release_docs/INSTALL                   | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/config/cmake/scripts/HDF5options.cmake b/config/cmake/scripts/HDF5options.cmake
index f132234..33ec74b 100644
--- a/config/cmake/scripts/HDF5options.cmake
+++ b/config/cmake/scripts/HDF5options.cmake
@@ -57,7 +57,9 @@ set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRIN
 #set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=GIT")
 ### ext libs on system
 #set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=NO")
+#set(ENV{ZLIB_ROOT} "some_location")
 #set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DZLIB_LIBRARY:FILEPATH=some_location/lib/zlib.lib -DZLIB_INCLUDE_DIR:PATH=some_location/include")
+#set(ENV{SZIP_ROOT} "some_location")
 #set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DSZIP_LIBRARY:FILEPATH=some_location/lib/szlib.lib -DSZIP_INCLUDE_DIR:PATH=some_location/include")
 
 ### disable using ext zlib
diff --git a/release_docs/INSTALL b/release_docs/INSTALL
index d1addc9..9546615 100644
--- a/release_docs/INSTALL
+++ b/release_docs/INSTALL
@@ -354,7 +354,7 @@ CONTENTS
         `--enable-build-mode=debug'; to compile with optimizations
         (the default for supported public releases),
         say `--enable-build-mode=production'. For a 'clean slate' configuration
-        with optimization disabled and nothing turned on, 
+        with optimization disabled and nothing turned on,
         say `--enable-build-mode=clean'. On some systems the
         library can also be compiled for profiling with gprof by saying
         `--enable-profiling'.
-- 
cgit v0.12


From c849825c9d9e6c183d7d147445235d1605562ca2 Mon Sep 17 00:00:00 2001
From: Allen Byrne 
Date: Wed, 21 Oct 2020 15:40:42 -0500
Subject: Correct SZ options for building plugins

---
 config/cmake/HDF5PluginMacros.cmake |  8 ++++----
 config/cmake/cacheinit.cmake        | 10 +++++-----
 release_docs/INSTALL_CMake.txt      | 10 +++++-----
 3 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/config/cmake/HDF5PluginMacros.cmake b/config/cmake/HDF5PluginMacros.cmake
index 3cded02..2c9e5e6 100644
--- a/config/cmake/HDF5PluginMacros.cmake
+++ b/config/cmake/HDF5PluginMacros.cmake
@@ -49,8 +49,8 @@ macro (EXTERNAL_PLUGIN_LIBRARY compress_type)
             -DLZ4_PACKAGE_NAME:STRING=${LZ4_PACKAGE_NAME}
             -DLZF_TGZ_NAME:STRING=${LZF_TGZ_NAME}
             -DLZF_PACKAGE_NAME:STRING=${LZF_PACKAGE_NAME}
-            #-DSZ_TGZ_NAME:STRING=${SZ_TGZ_NAME}
-            #-DSZ_PACKAGE_NAME:STRING=${SZ_PACKAGE_NAME}
+            -DSZF_TGZ_NAME:STRING=${SZF_TGZ_NAME}
+            -DSZF_PACKAGE_NAME:STRING=${SZF_PACKAGE_NAME}
             -DZFP_TGZ_NAME:STRING=${ZFP_TGZ_NAME}
             -DZFP_PACKAGE_NAME:STRING=${ZFP_PACKAGE_NAME}
     )
@@ -101,8 +101,8 @@ macro (EXTERNAL_PLUGIN_LIBRARY compress_type)
             -DLZ4_PACKAGE_NAME:STRING=${LZ4_PACKAGE_NAME}
             -DLZF_TGZ_NAME:STRING=${LZF_TGZ_NAME}
             -DLZF_PACKAGE_NAME:STRING=${LZF_PACKAGE_NAME}
-            #-DSZ_TGZ_NAME:STRING=${SZ_TGZ_NAME}
-            #-DSZ_PACKAGE_NAME:STRING=${SZ_PACKAGE_NAME}
+            -DSZF_TGZ_NAME:STRING=${SZF_TGZ_NAME}
+            -DSZF_PACKAGE_NAME:STRING=${SZF_PACKAGE_NAME}
             -DZFP_TGZ_NAME:STRING=${ZFP_TGZ_NAME}
             -DZFP_PACKAGE_NAME:STRING=${ZFP_PACKAGE_NAME}
     )
diff --git a/config/cmake/cacheinit.cmake b/config/cmake/cacheinit.cmake
index 926e230..f8ab3a2 100644
--- a/config/cmake/cacheinit.cmake
+++ b/config/cmake/cacheinit.cmake
@@ -155,15 +155,15 @@ set (LZF_PACKAGE_NAME "lzf" CACHE STRING "Name of LZF package" FORCE)
 #set (MAFISC_PACKAGE_NAME "mafisc" CACHE STRING "Name of MAFISC package" FORCE)
 
 ######
-# sz
+# szf
 ######
 
-set (SZ_GIT_URL "https://github.com/disheng222/SZ" CACHE STRING "Use SZ from github repository" FORCE)
-set (SZ_GIT_BRANCH "master" CACHE STRING "" FORCE)
+set (SZF_GIT_URL "https://github.com/disheng222/SZ" CACHE STRING "Use SZ from github repository" FORCE)
+set (SZF_GIT_BRANCH "master" CACHE STRING "" FORCE)
 
-set (SZ_TGZ_NAME "sz.tar.gz" CACHE STRING "Use SZ from compressed file" FORCE)
+set (SZF_TGZ_NAME "szf.tar.gz" CACHE STRING "Use SZ from compressed file" FORCE)
 
-set (SZ_PACKAGE_NAME "sz" CACHE STRING "Name of SZ package" FORCE)
+set (SZF_PACKAGE_NAME "szf" CACHE STRING "Name of SZ package" FORCE)
 
 ######
 # zfp
diff --git a/release_docs/INSTALL_CMake.txt b/release_docs/INSTALL_CMake.txt
index 478e2eb..0d35b3f 100644
--- a/release_docs/INSTALL_CMake.txt
+++ b/release_docs/INSTALL_CMake.txt
@@ -570,12 +570,12 @@ These five steps are described in detail below.
                 #set (BUILD_MAFISC_LIBRARY_SOURCE OFF CACHE BOOL "build the mafisc library within the plugin" FORCE)
                 #set (MAFISC_PACKAGE_NAME "mafisc" CACHE STRING "Name of MAFISC package" FORCE)
                 ######
-                # sz
+                # szf
                 ######
-                set (SZ_GIT_URL "https://github.com/disheng222/SZ" CACHE STRING "Use SZ from github repository" FORCE)
-                set (SZ_GIT_BRANCH "master" CACHE STRING "" FORCE)
-                set (SZ_TGZ_NAME "sz.tar.gz" CACHE STRING "Use SZ from compressed file" FORCE)
-                set (SZ_PACKAGE_NAME "sz" CACHE STRING "Name of SZ package" FORCE)
+                set (SZF_GIT_URL "https://github.com/disheng222/SZ" CACHE STRING "Use SZ from github repository" FORCE)
+                set (SZF_GIT_BRANCH "master" CACHE STRING "" FORCE)
+                set (SZF_TGZ_NAME "szf.tar.gz" CACHE STRING "Use SZ from compressed file" FORCE)
+                set (SZF_PACKAGE_NAME "szf" CACHE STRING "Name of SZ package" FORCE)
                 ######
                 # zfp
                 ######
-- 
cgit v0.12


From 3606f20c0243c77998171906473668500cd007ac Mon Sep 17 00:00:00 2001
From: Dana Robinson 
Date: Thu, 22 Oct 2020 09:22:58 -0700
Subject: Removes -Wimplicit-fallthrough=5 from the gcc warnings

-Wimplicit-fallthrough=3 is added by -Wextra, which we already set.
Bumping the warning level only changes how fall-through comments are
parsed, with level 5 turning off fall-through comments entirely.
This is unnecessary and results in having to do extra work to squash
warnings when included external code uses fall-through.

This change also adds /* FALLTHROUGH */ comments where
H5_ATTR_FALLTHROUGH is used so compilers that don't use attributes
but do respect fall-through comments don't raise spurious warnings.
---
 config/gnu-warnings/7 |  1 -
 src/H5SM.c            |  2 +-
 src/H5Shyper.c        |  9 ++++++++-
 src/H5Tref.c          |  1 +
 src/H5Zshuffle.c      | 14 ++++++++++++++
 src/H5checksum.c      | 11 +++++++++++
 src/H5private.h       |  4 ++++
 7 files changed, 39 insertions(+), 3 deletions(-)

diff --git a/config/gnu-warnings/7 b/config/gnu-warnings/7
index 266f5c1..9d5b44d 100644
--- a/config/gnu-warnings/7
+++ b/config/gnu-warnings/7
@@ -3,5 +3,4 @@
 -Wduplicated-branches
 -Wformat-overflow=2
 -Wformat-truncation=1
--Wimplicit-fallthrough=5
 -Wrestrict
diff --git a/src/H5SM.c b/src/H5SM.c
index 2e3fe04..52a5e8c 100644
--- a/src/H5SM.c
+++ b/src/H5SM.c
@@ -266,7 +266,7 @@ H5SM__type_to_flag(unsigned type_id, unsigned *type_flag)
     switch (type_id) {
         case H5O_FILL_ID:
             type_id = H5O_FILL_NEW_ID;
-            /* Fall through... */
+            /* FALLTHROUGH */
             H5_ATTR_FALLTHROUGH
 
         case H5O_SDSPACE_ID:
diff --git a/src/H5Shyper.c b/src/H5Shyper.c
index 6b3d750..02ec885 100644
--- a/src/H5Shyper.c
+++ b/src/H5Shyper.c
@@ -2138,24 +2138,31 @@ H5S__hyper_iter_get_seq_list_opt(H5S_sel_iter_t *iter, size_t maxseq, size_t max
                 case 0:
                     do {
                         DUFF_GUTS
+                        /* FALLTHROUGH */
                         H5_ATTR_FALLTHROUGH
                         case 7:
                             DUFF_GUTS
+                            /* FALLTHROUGH */
                             H5_ATTR_FALLTHROUGH
                         case 6:
                             DUFF_GUTS
+                            /* FALLTHROUGH */
                             H5_ATTR_FALLTHROUGH
                         case 5:
                             DUFF_GUTS
+                            /* FALLTHROUGH */
                             H5_ATTR_FALLTHROUGH
                         case 4:
                             DUFF_GUTS
+                            /* FALLTHROUGH */
                             H5_ATTR_FALLTHROUGH
                         case 3:
                             DUFF_GUTS
+                            /* FALLTHROUGH */
                             H5_ATTR_FALLTHROUGH
                         case 2:
                             DUFF_GUTS
+                            /* FALLTHROUGH */
                             H5_ATTR_FALLTHROUGH
                         case 1:
                             DUFF_GUTS
@@ -10101,7 +10108,7 @@ H5S_select_hyperslab(H5S_t *space, H5S_seloper_t op, const hsize_t start[], cons
         case H5S_SEL_POINTS:          /* Can't combine hyperslab operations and point selections currently */
             if (op == H5S_SELECT_SET) /* Allow only "set" operation to proceed */
                 break;
-            /* Else fall through to error */
+            /* FALLTHROUGH (to error) */
             H5_ATTR_FALLTHROUGH
 
         case H5S_SEL_ERROR:
diff --git a/src/H5Tref.c b/src/H5Tref.c
index 7092a71..ccb5232 100644
--- a/src/H5Tref.c
+++ b/src/H5Tref.c
@@ -650,6 +650,7 @@ H5T__ref_mem_write(H5VL_object_t *src_file, const void *src_buf, size_t src_size
             /* Pass the correct encoding version for the selection depending on the
              * file libver bounds, this is later retrieved in H5S hyper decode */
             H5CX_set_libver_bounds(src_f);
+            /* FALLTHROUGH */
             H5_ATTR_FALLTHROUGH
         case H5R_OBJECT2:
         case H5R_ATTR:
diff --git a/src/H5Zshuffle.c b/src/H5Zshuffle.c
index bd28f84..2e3ff97 100644
--- a/src/H5Zshuffle.c
+++ b/src/H5Zshuffle.c
@@ -177,24 +177,31 @@ H5Z__filter_shuffle(unsigned flags, size_t cd_nelmts, const unsigned cd_values[]
                         case 0:
                             do {
                                 DUFF_GUTS
+                                /* FALLTHROUGH */
                                 H5_ATTR_FALLTHROUGH
                                 case 7:
                                     DUFF_GUTS
+                                    /* FALLTHROUGH */
                                     H5_ATTR_FALLTHROUGH
                                 case 6:
                                     DUFF_GUTS
+                                    /* FALLTHROUGH */
                                     H5_ATTR_FALLTHROUGH
                                 case 5:
                                     DUFF_GUTS
+                                    /* FALLTHROUGH */
                                     H5_ATTR_FALLTHROUGH
                                 case 4:
                                     DUFF_GUTS
+                                    /* FALLTHROUGH */
                                     H5_ATTR_FALLTHROUGH
                                 case 3:
                                     DUFF_GUTS
+                                    /* FALLTHROUGH */
                                     H5_ATTR_FALLTHROUGH
                                 case 2:
                                     DUFF_GUTS
+                                    /* FALLTHROUGH */
                                     H5_ATTR_FALLTHROUGH
                                 case 1:
                                     DUFF_GUTS
@@ -241,24 +248,31 @@ H5Z__filter_shuffle(unsigned flags, size_t cd_nelmts, const unsigned cd_values[]
                         case 0:
                             do {
                                 DUFF_GUTS
+                                /* FALLTHROUGH */
                                 H5_ATTR_FALLTHROUGH
                                 case 7:
                                     DUFF_GUTS
+                                    /* FALLTHROUGH */
                                     H5_ATTR_FALLTHROUGH
                                 case 6:
                                     DUFF_GUTS
+                                    /* FALLTHROUGH */
                                     H5_ATTR_FALLTHROUGH
                                 case 5:
                                     DUFF_GUTS
+                                    /* FALLTHROUGH */
                                     H5_ATTR_FALLTHROUGH
                                 case 4:
                                     DUFF_GUTS
+                                    /* FALLTHROUGH */
                                     H5_ATTR_FALLTHROUGH
                                 case 3:
                                     DUFF_GUTS
+                                    /* FALLTHROUGH */
                                     H5_ATTR_FALLTHROUGH
                                 case 2:
                                     DUFF_GUTS
+                                    /* FALLTHROUGH */
                                     H5_ATTR_FALLTHROUGH
                                 case 1:
                                     DUFF_GUTS
diff --git a/src/H5checksum.c b/src/H5checksum.c
index 7ae588e..bc36bb9 100644
--- a/src/H5checksum.c
+++ b/src/H5checksum.c
@@ -414,36 +414,47 @@ H5_checksum_lookup3(const void *key, size_t length, uint32_t initval)
     {
         case 12:
             c += ((uint32_t)k[11]) << 24;
+            /* FALLTHROUGH */
             H5_ATTR_FALLTHROUGH
         case 11:
             c += ((uint32_t)k[10]) << 16;
+            /* FALLTHROUGH */
             H5_ATTR_FALLTHROUGH
         case 10:
             c += ((uint32_t)k[9]) << 8;
+            /* FALLTHROUGH */
             H5_ATTR_FALLTHROUGH
         case 9:
             c += k[8];
+            /* FALLTHROUGH */
             H5_ATTR_FALLTHROUGH
         case 8:
             b += ((uint32_t)k[7]) << 24;
+            /* FALLTHROUGH */
             H5_ATTR_FALLTHROUGH
         case 7:
             b += ((uint32_t)k[6]) << 16;
+            /* FALLTHROUGH */
             H5_ATTR_FALLTHROUGH
         case 6:
             b += ((uint32_t)k[5]) << 8;
+            /* FALLTHROUGH */
             H5_ATTR_FALLTHROUGH
         case 5:
             b += k[4];
+            /* FALLTHROUGH */
             H5_ATTR_FALLTHROUGH
         case 4:
             a += ((uint32_t)k[3]) << 24;
+            /* FALLTHROUGH */
             H5_ATTR_FALLTHROUGH
         case 3:
             a += ((uint32_t)k[2]) << 16;
+            /* FALLTHROUGH */
             H5_ATTR_FALLTHROUGH
         case 2:
             a += ((uint32_t)k[1]) << 8;
+            /* FALLTHROUGH */
             H5_ATTR_FALLTHROUGH
         case 1:
             a += k[0];
diff --git a/src/H5private.h b/src/H5private.h
index ca005f6..1390b3f 100644
--- a/src/H5private.h
+++ b/src/H5private.h
@@ -298,6 +298,10 @@
  * Note that Solaris Studio supports attribute, but does not support the
  * attributes we use.
  *
+ * When using H5_ATTR_FALLTHROUGH, you should also include a comment that
+ * says FALLTHROUGH to reduce warnings on compilers that don't use
+ * attributes but do respect fall-through comments.
+ *
  * H5_ATTR_CONST is redefined in tools/h5repack/dynlib_rpk.c to quiet
  * gcc warnings (it has to use the public API and can't include this
  * file). Be sure to update that file if the #ifdefs change here.
-- 
cgit v0.12


From ca3659a01427cd58e5fddb57349b7030e5cb2dcd Mon Sep 17 00:00:00 2001
From: Dana Robinson 
Date: Fri, 23 Oct 2020 17:13:05 -0700
Subject: HD prefix updates in src/ and test/

Adds missing HD prefixes to API calls in src and test.

Adds some extra processing to bin/checkposix to keep the noise
levels down when running the script (not comprehensive).
---
 bin/checkposix            | 91 ++++++++++++++++++++++++++++++++++++++++++++---
 src/H5FDs3comms.c         | 10 +++---
 src/H5Tdbg.c              |  6 ++--
 src/H5VLnative_object.c   |  2 +-
 src/H5Z.c                 |  6 ++--
 test/accum.c              |  2 +-
 test/btree2.c             |  4 +--
 test/cache_api.c          | 10 +++---
 test/chunk_info.c         | 16 ++++-----
 test/cmpd_dset.c          | 46 ++++++++++++------------
 test/dangle.c             | 10 +++---
 test/direct_chunk.c       |  2 +-
 test/dsets.c              | 42 +++++++++++-----------
 test/dt_arith.c           | 22 ++++++------
 test/dtypes.c             | 10 +++---
 test/earray.c             | 16 ++++-----
 test/enum.c               |  4 +--
 test/external.c           |  4 +--
 test/farray.c             |  2 +-
 test/filenotclosed.c      |  2 +-
 test/fillval.c            | 58 +++++++++++++++---------------
 test/filter_fail.c        |  4 +--
 test/gen_cross.c          |  2 +-
 test/gen_filters.c        |  4 +--
 test/getname.c            |  4 +--
 test/gheap.c              |  6 ++--
 test/hdfs.c               | 38 ++++++++++----------
 test/hyperslab.c          | 14 ++++----
 test/istore.c             |  6 ++--
 test/lheap.c              |  4 +--
 test/links.c              |  8 ++---
 test/links_env.c          |  2 +-
 test/mf.c                 |  6 ++--
 test/mirror_vfd.c         |  6 ++--
 test/mtime.c              |  2 +-
 test/objcopy.c            |  6 ++--
 test/page_buffer.c        |  2 +-
 test/pool.c               |  4 +--
 test/ros3.c               | 58 +++++++++++++++---------------
 test/s3comms.c            | 74 +++++++++++++++++++-------------------
 test/set_extent.c         |  2 +-
 test/tarray.c             |  2 +-
 test/tcoords.c            | 20 +++++------
 test/testframe.c          | 10 +++---
 test/testhdf5.c           |  2 +-
 test/testmeta.c           |  4 +--
 test/tfile.c              |  2 +-
 test/tgenprop.c           |  2 +-
 test/th5o.c               |  2 +-
 test/th5s.c               | 12 +++----
 test/thread_id.c          | 14 ++++----
 test/timer.c              |  9 ++---
 test/titerate.c           |  2 +-
 test/tmisc.c              |  4 +--
 test/trefer_deprec.c      |  4 +--
 test/tselect.c            |  8 ++---
 test/ttsafe.c             |  2 +-
 test/ttsafe_cancel.c      | 24 ++++++-------
 test/ttsafe_dcreate.c     |  2 +-
 test/tunicode.c           |  8 ++---
 test/tvlstr.c             |  6 ++--
 test/tvltypes.c           | 14 ++++----
 test/twriteorder.c        | 10 +++---
 test/unlink.c             |  2 +-
 test/use_append_mchunks.c | 10 +++---
 test/use_common.c         |  2 +-
 test/vfd.c                | 12 +++----
 67 files changed, 445 insertions(+), 361 deletions(-)

diff --git a/bin/checkposix b/bin/checkposix
index 233d15c..c29c290 100755
--- a/bin/checkposix
+++ b/bin/checkposix
@@ -44,7 +44,27 @@ foreach $arg (@ARGV) {
     #
     # If a user specifies one file, process it no matter what so people
     # can inspect files we normally skip (like H5system.c).
+
+    $ignore = 0;
+
+    # Ignored files in src/
     if($#ARGV gt 0 and $filename =~ /H5FDmulti|H5FDstdio|H5VLpassthru|H5system|H5detect|H5make_libsettings/) {
+        $ignore = 1;
+    }
+    # Ignored atomic test files in test/
+    if($#ARGV gt 0 and $filename =~ /atomic_reader|atomic_writer/) {
+        $ignore = 1;
+    }
+    # Ignored filter plugins in test/
+    if($#ARGV gt 0 and $filename =~ /^filter_plugin\d_/) {
+        $ignore = 1;
+    }
+    # Ignored generators in test/
+    if($#ARGV gt 0 and $filename =~ /^gen_/) {
+        $ignore = 1;
+    }
+
+    if($ignore) {
         print "$filename is exempt from using Standard library macro wrappers\n";
         next;
     }
@@ -95,13 +115,13 @@ foreach $arg (@ARGV) {
 
             # These are really HDF5 functions/macros even though they don't
             # start with `h' or `H'.
-            next if $name =~ /^FUNC_(ENTER|LEAVE)(_(NO)?API|_PACKAGE|_STATIC)?(_NOFS|_NOCLEAR|_NOINIT)?(_NOFUNC|_TAG)?$/;
+            next if $name =~ /^FUNC_(ENTER|LEAVE)(_(NO)?API|_PACKAGE|_STATIC)?(_NOFS|_NOCLEAR|_NOINIT|_NOPUSH)?(_NOFUNC|_TAG)?$/;
             next if $name =~ /^(BEGIN|END)_FUNC$/;
             next if $name =~ /^U?INT(8|16|32|64)(ENCODE|DECODE)(_VAR)?$/;
             next if $name =~ /^CI_(PRINT_STATS|INC_SRC|INC_DST)$/;
             next if $name =~ /^(ABS|ADDR_OVERFLOW|ALL_MEMBERS|BOUND|CONSTR|DETECT_[I|F|M]|DOWN)$/;
             next if $name =~ /^(MIN3?|MAX3?|NELMTS|POWER_OF_TWO|REGION_OVERFLOW)$/;
-            next if $name =~ /^(UNIQUE_MEMBERS|S_ISDIR)$/;
+            next if $name =~ /^(SIZE_OVERFLOW|UNIQUE_MEMBERS|S_ISDIR)$/;
             next if $name =~ /^addr_defined$/;
 
             # These functions/macros are exempt.
@@ -140,15 +160,38 @@ foreach $arg (@ARGV) {
                 next if $name =~ /^(pow_fun|round_fun|abs_fun|lround_fun|llround_fun)$/;
             }
 
+            # This is a macro parameter in H5Rint.c. Ignore it in this file.
+            if($filename =~ /H5Rint/) {
+                next if $name =~ /^(func)$/;
+            }
+
+            # Internal calls in the HDFS VFD (H5FDhdfs.c). Ignore it in this file.
+            if($filename =~ /H5FDhdfs/) {
+                next if $name =~ /^(hdfs)/;
+            }
+
+            # Macros, etc. from the mirror VFD (H5FDmirror.c). Ignore in this file.
+            if($filename =~ /H5FDmirror/) {
+                next if $name =~ /^(LOG)/;
+                next if $name =~ /^(BSWAP_64|is_host_little_endian)$/;
+            }
+
+            # These are things in H5FDs3comms.c and H5FDros3.c. Ignore them in these files.
+            if($filename =~ /H5FDs3comms|H5FDros3/) {
+                next if $name =~ /^(curl_|curlwritecallback|gmnow)/;
+                next if $name =~ /^(ros3_|ROS3_|S3COMMS_)/;
+                next if $name =~ /^(EVP_sha256|SHA256|ISO8601NOW)$/;
+            }
+
             # TESTING (not comprehensive - just noise reduction)
             
             # Test macros and functions (testhdf5.h)
             next if $name =~ /^(AddTest|TestErrPrintf|TestSummary|TestCleanup|TestShutdown)$/;
             next if $name =~ /^(CHECK|CHECK_PTR|CHECK_PTR_NULL|CHECK_PTR_EQ|CHECK_I)$/;
-            next if $name =~ /^(VERIFY|VERIFY_STR|VERIFY|TYPE|MESSAGE|ERROR)$/;
+            next if $name =~ /^(VERIFY|VERIFY_STR|VERIFY_TYPE|MESSAGE|ERROR)$/;
 
             # Test macros and functions (h5test.h)
-            next if $name =~ /^(TESTING|PASSED|SKIPPED|FAIL_PUTS_ERROR|FAIL_STACK_ERROR|TEST_ERROR)$/;
+            next if $name =~ /^(TESTING|PASSED|SKIPPED|PUTS_ERROR|FAIL_PUTS_ERROR|FAIL_STACK_ERROR|TEST_ERROR|AT)$/;
             next if $name =~ /^(GetTestExpress)$/;
 
             # Ignore functions that start with test_ or check_
@@ -158,9 +201,49 @@ foreach $arg (@ARGV) {
             # Ignore functions that start with h5_
             next if $name =~ /^h5_/;
 
+            # Ignore process completed status
+            next if $name =~ /(WIFEXITED|WEXITSTATUS|WIFSIGNALED|WTERMSIG|WCOREDUMP|WIFSTOPPED|WSTOPSIG)/;
+
             # Ignore usage functions
             next if $name =~ /^usage$/;
 
+            # Ignore callbacks
+            next if $name =~ /(_cb\d?)$/;
+
+            # Specific tests (not even remotely comprehensive)
+
+            # accum test code
+            if($filename =~ /accum/) {
+                next if $name =~ /^(accum_)/;
+            }
+
+            # cache test code
+            if($filename =~ /cache/) {
+                next if $name =~ /(_entry|_entries|_cache|_check|_dependency|_status|_op)$/;
+                next if $name =~ /^(verify_|smoke_check_|row_major_|col_major_)/;
+                next if $name =~ /^(resize_configs_are_equal|CACHE_ERROR)$/
+            }
+
+            # Splitter VFD test code. Ignore in vfd.c.
+            if($filename =~ /vfd/) {
+                next if $name =~ /^(SPLITTER_|splitter_)/;
+                next if $name =~ /(_splitter_)/;
+                next if $name =~ /^(file_exists)$/;
+            }
+
+            # S3 VFD test code. Ignore in ros3.c and s3comms.c.
+            # HDFS VFD test code. Ignore in hdfs.c.
+            if($filename =~ /ros3|s3comms|hdfs/) {
+                next if $name =~ /^(JSVERIFY|JSFAILED_|JSERR_|jserr_|FAIL_)/;
+                next if $name =~ /^(curl_)/;
+                next if $name =~ /^(S3COMMS_FORMAT_CREDENTIAL|ISO8601NOW|gmnow)$/;
+            }
+
+            # VDS test code. Ignore in vds.c.
+            if($filename =~ /vds/) {
+                next if $name =~ /^(vds_)/;
+            }
+
             print "$filename:$.: $name\n";
         }
 
diff --git a/src/H5FDs3comms.c b/src/H5FDs3comms.c
index 2ac27d0..42586ff 100644
--- a/src/H5FDs3comms.c
+++ b/src/H5FDs3comms.c
@@ -1925,7 +1925,7 @@ H5FD__s3comms_load_aws_creds_from_file(FILE *file, const char *profile_name, cha
     };
     char *const setting_pointers[] = {
         aws_region,
-        key_id,
+
         access_key,
     };
     unsigned setting_count = 3;
@@ -1951,7 +1951,7 @@ H5FD__s3comms_load_aws_creds_from_file(FILE *file, const char *profile_name, cha
         for (buffer_i = 0; buffer_i < 128; buffer_i++)
             buffer[buffer_i] = 0;
 
-        line_buffer = fgets(line_buffer, 128, file);
+        line_buffer = HDfgets(line_buffer, 128, file);
         if (line_buffer == NULL) /* reached end of file */
             goto done;
     } while (HDstrncmp(line_buffer, profile_line, HDstrlen(profile_line)));
@@ -1963,7 +1963,7 @@ H5FD__s3comms_load_aws_creds_from_file(FILE *file, const char *profile_name, cha
             buffer[buffer_i] = 0;
 
         /* collect a line from file */
-        line_buffer = fgets(line_buffer, 128, file);
+        line_buffer = HDfgets(line_buffer, 128, file);
         if (line_buffer == NULL)
             goto done; /* end of file */
 
@@ -2062,9 +2062,9 @@ H5FD_s3comms_load_aws_profile(const char *profile_name, char *key_id_out, char *
 #endif
 
 #ifdef H5_HAVE_WIN32_API
-    ret = HDsnprintf(awspath, 117, "%s/.aws/", getenv("USERPROFILE"));
+    ret = HDsnprintf(awspath, 117, "%s/.aws/", HDgetenv("USERPROFILE"));
 #else
-    ret = HDsnprintf(awspath, 117, "%s/.aws/", getenv("HOME"));
+    ret = HDsnprintf(awspath, 117, "%s/.aws/", HDgetenv("HOME"));
 #endif
     if (ret < 0 || (size_t)ret >= 117)
         HGOTO_ERROR(H5E_ARGS, H5E_CANTCOPY, FAIL, "unable to format home-aws path")
diff --git a/src/H5Tdbg.c b/src/H5Tdbg.c
index 5d0c5cd..758430b 100644
--- a/src/H5Tdbg.c
+++ b/src/H5Tdbg.c
@@ -120,9 +120,9 @@ H5T__print_stats(H5T_path_t H5_ATTR_UNUSED *path, int H5_ATTR_UNUSED *nprint /*i
         HDfprintf(H5DEBUG(T), "   %-16s %10" PRIdHSIZE " %10u %8s %8s %8s %10s\n", path->name,
                   path->stats.nelmts, path->stats.ncalls, timestrs.user, timestrs.system, timestrs.elapsed,
                   bandwidth);
-        free(timestrs.user);
-        free(timestrs.system);
-        free(timestrs.elapsed);
+        HDfree(timestrs.user);
+        HDfree(timestrs.system);
+        HDfree(timestrs.elapsed);
     }
 #endif
 
diff --git a/src/H5VLnative_object.c b/src/H5VLnative_object.c
index ac717b0..81ff5ea 100644
--- a/src/H5VLnative_object.c
+++ b/src/H5VLnative_object.c
@@ -338,7 +338,7 @@ H5VL__native_object_specific(void *obj, const H5VL_loc_params_t *loc_params,
 
         /* Lookup object */
         case H5VL_OBJECT_LOOKUP: {
-            H5O_token_t *token = va_arg(arguments, H5O_token_t *);
+            H5O_token_t *token = HDva_arg(arguments, H5O_token_t *);
 
             HDassert(token);
 
diff --git a/src/H5Z.c b/src/H5Z.c
index ac7756e..65b9821 100644
--- a/src/H5Z.c
+++ b/src/H5Z.c
@@ -175,9 +175,9 @@ H5Z_term_package(void)
                               H5Z_stat_table_g[i].stats[dir].errors, timestrs.user, timestrs.system,
                               timestrs.elapsed, bandwidth);
 next:
-                    free(timestrs.user);
-                    free(timestrs.system);
-                    free(timestrs.elapsed);
+                    HDfree(timestrs.user);
+                    HDfree(timestrs.system);
+                    HDfree(timestrs.elapsed);
                 } /* end for */
             }     /* end for */
         }         /* end if */
diff --git a/test/accum.c b/test/accum.c
index 183f955..0b9fbad 100644
--- a/test/accum.c
+++ b/test/accum.c
@@ -2243,7 +2243,7 @@ test_swmr_write_big(hbool_t newest_format)
         char *const new_argv[]    = {swmr_reader, NULL};
         /* Run the reader */
         status = HDexecv(SWMR_READER, new_argv);
-        HDprintf("errno from execv = %s\n", strerror(errno));
+        HDprintf("errno from execv = %s\n", HDstrerror(errno));
         FAIL_STACK_ERROR;
     } /* end if */
 
diff --git a/test/btree2.c b/test/btree2.c
index 4391a3b..42f9a61 100644
--- a/test/btree2.c
+++ b/test/btree2.c
@@ -10023,14 +10023,14 @@ main(void)
     if (nerrors)
         goto error;
 
-    puts("All v2 B-tree tests passed.");
+    HDputs("All v2 B-tree tests passed.");
 
     h5_cleanup(FILENAME, fapl);
 
     return 0;
 
 error:
-    puts("*** TESTS FAILED ***");
+    HDputs("*** TESTS FAILED ***");
 
     H5E_BEGIN_TRY { H5Pclose(fapl); }
     H5E_END_TRY;
diff --git a/test/cache_api.c b/test/cache_api.c
index acdb4ba..143cc71 100644
--- a/test/cache_api.c
+++ b/test/cache_api.c
@@ -1216,9 +1216,9 @@ mdc_api_call_smoke_check(int express_test, unsigned paged, hid_t fcpl_id)
     /* do random reads on all datasets */
     n = 0;
     while ((pass) && (n < NUM_RANDOM_ACCESSES)) {
-        m = rand() % NUM_DSETS;
-        i = (rand() % (DSET_SIZE / CHUNK_SIZE)) * CHUNK_SIZE;
-        j = (rand() % (DSET_SIZE / CHUNK_SIZE)) * CHUNK_SIZE;
+        m = HDrand() % NUM_DSETS;
+        i = (HDrand() % (DSET_SIZE / CHUNK_SIZE)) * CHUNK_SIZE;
+        j = (HDrand() % (DSET_SIZE / CHUNK_SIZE)) * CHUNK_SIZE;
 
         /* select on disk hyperslab */
         offset[0] = (hsize_t)i; /*offset of hyperslab in file*/
@@ -1328,8 +1328,8 @@ mdc_api_call_smoke_check(int express_test, unsigned paged, hid_t fcpl_id)
     m = 0;
     n = 0;
     while ((pass) && (n < NUM_RANDOM_ACCESSES)) {
-        i = (rand() % (DSET_SIZE / CHUNK_SIZE)) * CHUNK_SIZE;
-        j = (rand() % (DSET_SIZE / CHUNK_SIZE)) * CHUNK_SIZE;
+        i = (HDrand() % (DSET_SIZE / CHUNK_SIZE)) * CHUNK_SIZE;
+        j = (HDrand() % (DSET_SIZE / CHUNK_SIZE)) * CHUNK_SIZE;
 
         /* select on disk hyperslab */
         offset[0] = (hsize_t)i; /*offset of hyperslab in file*/
diff --git a/test/chunk_info.c b/test/chunk_info.c
index 99b5b1e..f45a4dd 100644
--- a/test/chunk_info.c
+++ b/test/chunk_info.c
@@ -421,7 +421,7 @@ verify_idx_nchunks(hid_t dset, hid_t dspace, H5D_chunk_index_t exp_idx_type, hsi
     /* Ensure the correct chunk indexing scheme is used */
     if (idx_type != exp_idx_type) {
         char msg[256];
-        sprintf(msg, "Should be using %s.\n", index_type_str(idx_type));
+        HDsprintf(msg, "Should be using %s.\n", index_type_str(idx_type));
         FAIL_PUTS_ERROR(msg);
     }
 
@@ -542,7 +542,7 @@ test_get_chunk_info_highest_v18(hid_t fapl)
 
 #ifdef H5_HAVE_FILTER_DEFLATE
     /* Allocate input (compressed) buffer */
-    inbuf = malloc(z_dst_nbytes);
+    inbuf = HDmalloc(z_dst_nbytes);
 
     /* Set chunk size to the compressed chunk size and the chunk point
        to the compressed data chunk */
@@ -554,20 +554,20 @@ test_get_chunk_info_highest_v18(hid_t fapl)
 
     /* Check for various zlib errors */
     if (Z_BUF_ERROR == ret) {
-        fprintf(stderr, "overflow");
+        HDfprintf(stderr, "overflow");
         TEST_ERROR
     }
     else if (Z_MEM_ERROR == ret) {
-        fprintf(stderr, "deflate memory error");
+        HDfprintf(stderr, "deflate memory error");
         TEST_ERROR
     }
     else if (Z_OK != ret) {
-        fprintf(stderr, "other deflate error");
+        HDfprintf(stderr, "other deflate error");
         TEST_ERROR
     }
 #else
     /* Allocate input (non-compressed) buffer */
-    inbuf = malloc(CHK_SIZE);
+    inbuf = HDmalloc(CHK_SIZE);
     HDmemcpy(inbuf, direct_buf, CHK_SIZE);
 #endif /* end H5_HAVE_FILTER_DEFLATE */
 
@@ -1638,7 +1638,7 @@ test_basic_query(hid_t fapl)
         TEST_ERROR
 
     /* Remove the test file */
-    remove(filename);
+    HDremove(filename);
 
     PASSED();
     return SUCCEED;
@@ -2040,7 +2040,7 @@ test_flt_msk_with_skip_compress(hid_t fapl)
         TEST_ERROR
 
     /* Remove the test file */
-    remove(filename);
+    HDremove(filename);
 
     PASSED();
     return SUCCEED;
diff --git a/test/cmpd_dset.c b/test/cmpd_dset.c
index 6e5dd07..37217e7 100644
--- a/test/cmpd_dset.c
+++ b/test/cmpd_dset.c
@@ -302,7 +302,7 @@ test_compound(char *filename, hid_t fapl)
             s1[i].c[1] != s2[i].c[1] || s1[i].c[2] != s2[i].c[2] || s1[i].c[3] != s2[i].c[3] ||
             s1[i].d != s2[i].d || s1[i].e != s2[i].e) {
             H5_FAILED();
-            puts("    Incorrect values read from the file");
+            HDputs("    Incorrect values read from the file");
             goto error;
         }
     }
@@ -339,7 +339,7 @@ test_compound(char *filename, hid_t fapl)
             s1[i].c[1] != s3[i].c[1] || s1[i].c[2] != s3[i].c[2] || s1[i].c[3] != s3[i].c[3] ||
             s1[i].d != s3[i].d || s1[i].e != s3[i].e) {
             H5_FAILED();
-            puts("    Incorrect values read from the file");
+            HDputs("    Incorrect values read from the file");
             goto error;
         }
     }
@@ -369,7 +369,7 @@ test_compound(char *filename, hid_t fapl)
     for (i = 0; i < NX * NY; i++) {
         if (s1[i].b != s4[i].b || s1[i].d != s4[i].d) {
             H5_FAILED();
-            puts("    Incorrect values read from the file");
+            HDputs("    Incorrect values read from the file");
             goto error;
         }
     }
@@ -413,7 +413,7 @@ test_compound(char *filename, hid_t fapl)
             s1[i].c[1] != s5[i].c[1] || s1[i].c[2] != s5[i].c[2] || s1[i].c[3] != s5[i].c[3] ||
             s1[i].d != s5[i].d || s1[i].e != s5[i].e) {
             H5_FAILED();
-            puts("    Incorrect values read from the file");
+            HDputs("    Incorrect values read from the file");
             goto error;
         }
     }
@@ -423,7 +423,7 @@ test_compound(char *filename, hid_t fapl)
         if (s5[i].pre != 1000 + 4 * i || s5[i].mid1 != 1001 + 4 * i || s5[i].mid2 != 1002 + 4 * i ||
             s5[i].post != 1003 + 4 * i) {
             H5_FAILED();
-            puts("    Memory values were clobbered");
+            HDputs("    Memory values were clobbered");
             goto error;
         }
     }
@@ -482,7 +482,7 @@ test_compound(char *filename, hid_t fapl)
             s1[i].c[1] != s6[i].c[1] || s1[i].c[2] != s6[i].c[2] || s1[i].c[3] != s6[i].c[3] ||
             s1[i].d != s6[i].d || s1[i].e != s6[i].e) {
             H5_FAILED();
-            puts("    Incorrect values read from the file");
+            HDputs("    Incorrect values read from the file");
             goto error;
         }
     }
@@ -492,7 +492,7 @@ test_compound(char *filename, hid_t fapl)
         if (s6[i].pre != 1000 + 4 * i || s6[i].mid1 != 1001 + 4 * i || s6[i].mid2 != 1002 + 4 * i ||
             s6[i].post != 1003 + 4 * i) {
             H5_FAILED();
-            puts("    Memory values were clobbered");
+            HDputs("    Memory values were clobbered");
             goto error;
         }
     }
@@ -561,7 +561,7 @@ test_compound(char *filename, hid_t fapl)
             s2[i].c[1] != s1[i].c[1] || s2[i].c[2] != s1[i].c[2] || s2[i].c[3] != s1[i].c[3] ||
             s2[i].d != s1[i].d || s2[i].e != s1[i].e) {
             H5_FAILED();
-            puts("    Incorrect values read from file");
+            HDputs("    Incorrect values read from file");
             goto error;
         }
     }
@@ -590,7 +590,7 @@ test_compound(char *filename, hid_t fapl)
 
     /* Read the dataset */
     s8 = (s1_t *)HDcalloc((size_t)(h_size[0] * h_size[1]), sizeof(s1_t));
-    assert(s8);
+    HDassert(s8);
     if (H5Dread(dataset, s1_tid, s8_m_sid, s8_f_sid, H5P_DEFAULT, s8) < 0) {
         goto error;
     }
@@ -604,7 +604,7 @@ test_compound(char *filename, hid_t fapl)
             if (ps8->a != ps1->a || ps8->b != ps1->b || ps8->c[0] != ps1->c[0] || ps8->c[1] != ps1->c[1] ||
                 ps8->c[2] != ps1->c[2] || ps8->c[3] != ps1->c[3] || ps8->d != ps1->d || ps8->e != ps1->e) {
                 H5_FAILED();
-                puts("    Incorrect values read from file");
+                HDputs("    Incorrect values read from file");
                 goto error;
             }
         }
@@ -643,7 +643,7 @@ test_compound(char *filename, hid_t fapl)
                     ps2->c[1] != ps1->c[1] || ps2->c[2] != ps1->c[2] || ps2->c[3] != ps1->c[3] ||
                     ps2->d != ps1->d || ps2->e != ps1->e) {
                     H5_FAILED();
-                    puts("    Memory values clobbered");
+                    HDputs("    Memory values clobbered");
                     goto error;
                 }
             }
@@ -652,7 +652,7 @@ test_compound(char *filename, hid_t fapl)
                     ps2->c[1] != (unsigned)(-1) || ps2->c[2] != (unsigned)(-1) ||
                     ps2->c[3] != (unsigned)(-1) || ps2->d != (unsigned)(-1) || ps2->e != (unsigned)(-1)) {
                     H5_FAILED();
-                    puts("    Incorrect values read from file");
+                    HDputs("    Incorrect values read from file");
                     goto error;
                 }
             }
@@ -691,7 +691,7 @@ test_compound(char *filename, hid_t fapl)
                     ps5->c[2] != ps1->c[2] || ps5->c[3] != ps1->c[3] || ps5->mid2 != (unsigned)(-1) ||
                     ps5->d != ps1->d || ps5->e != ps1->e || ps5->post != (unsigned)(-1)) {
                     H5_FAILED();
-                    puts("    Memory values clobbered");
+                    HDputs("    Memory values clobbered");
                     goto error;
                 }
             }
@@ -702,7 +702,7 @@ test_compound(char *filename, hid_t fapl)
                     ps5->c[3] != (unsigned)(-1) || ps5->mid2 != (unsigned)(-1) || ps5->d != (unsigned)(-1) ||
                     ps5->e != (unsigned)(-1) || ps5->post != (unsigned)(-1)) {
                     H5_FAILED();
-                    puts("    Incorrect values read from file");
+                    HDputs("    Incorrect values read from file");
                     goto error;
                 }
             }
@@ -723,7 +723,7 @@ test_compound(char *filename, hid_t fapl)
     h_size[0]   = 2 * NX / 3 - f_offset[0];
     h_size[1]   = 2 * NY / 3 - f_offset[1];
     s11         = (s4_t *)HDmalloc((size_t)h_size[0] * (size_t)h_size[1] * sizeof(s4_t));
-    assert(s11);
+    HDassert(s11);
 
     /* Initialize */
     for (i = 0; i < h_size[0] * h_size[1]; i++) {
@@ -751,7 +751,7 @@ test_compound(char *filename, hid_t fapl)
                 ps1->c[1] != 8 * (i * NY + j) + 3 || ps1->c[2] != 8 * (i * NY + j) + 4 ||
                 ps1->c[3] != 8 * (i * NY + j) + 5 || ps1->e != 8 * (i * NY + j) + 7) {
                 H5_FAILED();
-                puts("    Write clobbered values");
+                HDputs("    Write clobbered values");
                 goto error;
             }
 
@@ -759,14 +759,14 @@ test_compound(char *filename, hid_t fapl)
                 j < f_offset[1] + h_size[1]) {
                 if (ps1->b != (unsigned)(-1) || ps1->d != (unsigned)(-1)) {
                     H5_FAILED();
-                    puts("    Wrong values written or read");
+                    HDputs("    Wrong values written or read");
                     goto error;
                 }
             }
             else {
                 if (ps1->b != 8 * (i * NY + j) + 1 || ps1->d != 8 * (i * NY + j) + 6) {
                     H5_FAILED();
-                    puts("    Write clobbered values");
+                    HDputs("    Write clobbered values");
                     goto error;
                 }
             }
@@ -792,7 +792,7 @@ test_compound(char *filename, hid_t fapl)
     return 0;
 
 error:
-    puts("*** DATASET TESTS FAILED ***");
+    HDputs("*** DATASET TESTS FAILED ***");
 
     /* Release resources */
     if (s1)
@@ -1669,7 +1669,7 @@ test_hdf5_dst_subset(char *filename, hid_t fapl)
     return 0;
 
 error:
-    puts("*** DATASET TESTS FAILED ***");
+    HDputs("*** DATASET TESTS FAILED ***");
     return 1;
 }
 
@@ -1684,7 +1684,7 @@ error:
         for (_i = 0; _i < PACK_NMEMBS; _i++)                                                                 \
             HDprintf(" %d", order[_i]);                                                                      \
         HDprintf("\n    Inner compound order = %d, location = %d\n", sub_cmpd_order, order[sub_cmpd_order]); \
-        fflush(stdout);                                                                                      \
+        HDfflush(stdout);                                                                                    \
         goto error;                                                                                          \
     }
 
@@ -1719,7 +1719,7 @@ test_pack_ooo(void)
                                        * the compound */
     unsigned i, j;                    /* Indices */
 
-    HDsrand((unsigned)time(NULL));
+    HDsrand((unsigned)HDtime(NULL));
 
     /* Initialize "free_order" array to indicate that all slots in order are
      * free */
@@ -2233,7 +2233,7 @@ main(int argc, char *argv[])
 
     /* Turn off optimized compound converter? */
     if (argc > 1) {
-        if (argc > 2 || strcmp("--noopt", argv[1])) {
+        if (argc > 2 || HDstrcmp("--noopt", argv[1])) {
             HDfprintf(stderr, "usage: %s [--noopt]\n", argv[0]);
             HDexit(EXIT_FAILURE);
         }
diff --git a/test/dangle.c b/test/dangle.c
index 4728923..d7c7dfc 100644
--- a/test/dangle.c
+++ b/test/dangle.c
@@ -660,7 +660,7 @@ main(void)
     int nerrors = 0;
 
     /* Run tests w/weak file close */
-    puts("Testing dangling objects with weak file close:");
+    HDputs("Testing dangling objects with weak file close:");
     nerrors += test_dangle_dataset(H5F_CLOSE_WEAK);
     nerrors += test_dangle_group(H5F_CLOSE_WEAK);
     nerrors += test_dangle_datatype1(H5F_CLOSE_WEAK);
@@ -668,7 +668,7 @@ main(void)
     nerrors += test_dangle_attribute(H5F_CLOSE_WEAK);
 
     /* Run tests w/semi file close */
-    puts("Testing dangling objects with semi file close:");
+    HDputs("Testing dangling objects with semi file close:");
     nerrors += test_dangle_dataset(H5F_CLOSE_SEMI);
     nerrors += test_dangle_group(H5F_CLOSE_SEMI);
     nerrors += test_dangle_datatype1(H5F_CLOSE_SEMI);
@@ -676,7 +676,7 @@ main(void)
     nerrors += test_dangle_attribute(H5F_CLOSE_SEMI);
 
     /* Run tests w/strong file close */
-    puts("Testing dangling objects with strong file close:");
+    HDputs("Testing dangling objects with strong file close:");
     nerrors += test_dangle_dataset(H5F_CLOSE_STRONG);
     nerrors += test_dangle_group(H5F_CLOSE_STRONG);
     nerrors += test_dangle_datatype1(H5F_CLOSE_STRONG);
@@ -689,11 +689,11 @@ main(void)
     /* Check for errors */
     if (nerrors)
         goto error;
-    puts("All dangling ID tests passed.");
+    HDputs("All dangling ID tests passed.");
 
     return 0;
 
 error:
-    puts("***** DANGLING ID TESTS FAILED *****");
+    HDputs("***** DANGLING ID TESTS FAILED *****");
     return 1;
 }
diff --git a/test/direct_chunk.c b/test/direct_chunk.c
index 388f2cc..00fc06f 100644
--- a/test/direct_chunk.c
+++ b/test/direct_chunk.c
@@ -2320,7 +2320,7 @@ main(void)
             need_comma = TRUE;
         } /* end if */
         HDprintf(":\n");
-        fflush(stdout);
+        HDfflush(stdout);
 
         nerrors += test_single_chunk(config);
     } /* end for */
diff --git a/test/dsets.c b/test/dsets.c
index 8a4332d..a7b67ef 100644
--- a/test/dsets.c
+++ b/test/dsets.c
@@ -375,13 +375,13 @@ test_create(hid_t file)
     dims[0] = 256;
     dims[1] = 512;
     space   = H5Screate_simple(2, dims, NULL);
-    assert(space >= 0);
+    HDassert(space >= 0);
 
     /* Create a small data space for compact dataset */
     small_dims[0] = 16;
     small_dims[1] = 8;
     small_space   = H5Screate_simple(2, small_dims, NULL);
-    assert(space >= 0);
+    HDassert(space >= 0);
 
     /*
      * Create a dataset using the default dataset creation properties.    We're
@@ -447,13 +447,13 @@ test_create(hid_t file)
      * layout.
      */
     create_parms = H5Pcreate(H5P_DATASET_CREATE);
-    assert(create_parms >= 0);
+    HDassert(create_parms >= 0);
 
     /* Attempt to create a dataset with invalid chunk sizes */
     csize[0] = dims[0] * 2;
     csize[1] = dims[1] * 2;
     status   = H5Pset_chunk(create_parms, 2, csize);
-    assert(status >= 0);
+    HDassert(status >= 0);
     H5E_BEGIN_TRY
     {
         dataset = H5Dcreate2(file, DSET_CHUNKED_NAME, H5T_NATIVE_DOUBLE, space, H5P_DEFAULT, create_parms,
@@ -469,7 +469,7 @@ test_create(hid_t file)
     csize[0] = 5;
     csize[1] = 100;
     status   = H5Pset_chunk(create_parms, 2, csize);
-    assert(status >= 0);
+    HDassert(status >= 0);
 
     dataset =
         H5Dcreate2(file, DSET_CHUNKED_NAME, H5T_NATIVE_DOUBLE, space, H5P_DEFAULT, create_parms, H5P_DEFAULT);
@@ -491,11 +491,11 @@ test_create(hid_t file)
      * Create a compact dataset, then close it.
      */
     create_parms = H5Pcreate(H5P_DATASET_CREATE);
-    assert(create_parms >= 0);
+    HDassert(create_parms >= 0);
     status = H5Pset_layout(create_parms, H5D_COMPACT);
-    assert(status >= 0);
+    HDassert(status >= 0);
     status = H5Pset_alloc_time(create_parms, H5D_ALLOC_TIME_EARLY);
-    assert(status >= 0);
+    HDassert(status >= 0);
 
     dataset = H5Dcreate2(file, DSET_COMPACT_NAME, H5T_NATIVE_DOUBLE, small_space, H5P_DEFAULT, create_parms,
                          H5P_DEFAULT);
@@ -567,7 +567,7 @@ test_simple_io(const char *env_h5_drvr, hid_t fapl)
         /* Create a small conversion buffer to test strip mining */
         tconv_buf = HDmalloc((size_t)1000);
         xfer      = H5Pcreate(H5P_DATASET_XFER);
-        assert(xfer >= 0);
+        HDassert(xfer >= 0);
         if (H5Pset_buffer(xfer, (size_t)1000, tconv_buf, NULL) < 0)
             goto error;
 
@@ -4336,9 +4336,9 @@ test_nbit_compound_3(hid_t file)
 
     /* Check that the values read are the same as the values written */
     for (i = 0; i < (size_t)size[0]; i++) {
-        if (new_data[i].i != orig_data[i].i || strcmp(new_data[i].str, orig_data[i].str) != 0 ||
-            strcmp(new_data[i].vl_str, orig_data[i].vl_str) != 0 || new_data[i].v.len != orig_data[i].v.len ||
-            new_data[i].r != orig_data[i].r) {
+        if (new_data[i].i != orig_data[i].i || HDstrcmp(new_data[i].str, orig_data[i].str) != 0 ||
+            HDstrcmp(new_data[i].vl_str, orig_data[i].vl_str) != 0 ||
+            new_data[i].v.len != orig_data[i].v.len || new_data[i].r != orig_data[i].r) {
             H5_FAILED();
             HDprintf("    Read different values than written.\n");
             HDprintf("    At index %lu\n", (unsigned long)i);
@@ -7832,7 +7832,7 @@ test_random_chunks_real(const char *testname, hbool_t early_alloc, hid_t fapl)
 
     TESTING(testname);
 
-    assert(NPOINTS < 100);
+    HDassert(NPOINTS < 100);
 
     h5_fixname(FILENAME[6], fapl, filename, sizeof filename);
 
@@ -8354,13 +8354,13 @@ test_deprec(hid_t file)
     dims[0] = 256;
     dims[1] = 512;
     space   = H5Screate_simple(2, dims, NULL);
-    assert(space >= 0);
+    HDassert(space >= 0);
 
     /* Create a small data space for compact dataset */
     small_dims[0] = 16;
     small_dims[1] = 8;
     small_space   = H5Screate_simple(2, small_dims, NULL);
-    assert(space >= 0);
+    HDassert(space >= 0);
 
     /*
      * Create a dataset using the default dataset creation properties.    We're
@@ -8413,7 +8413,7 @@ test_deprec(hid_t file)
      * layout.
      */
     create_parms = H5Pcreate(H5P_DATASET_CREATE);
-    assert(create_parms >= 0);
+    HDassert(create_parms >= 0);
 
     /* Add the deflate filter, if available */
 #if defined H5_HAVE_FILTER_DEFLATE
@@ -8449,7 +8449,7 @@ test_deprec(hid_t file)
     csize[0] = dims[0] * 2;
     csize[1] = dims[1] * 2;
     status   = H5Pset_chunk(create_parms, 2, csize);
-    assert(status >= 0);
+    HDassert(status >= 0);
     H5E_BEGIN_TRY
     {
         dataset = H5Dcreate1(file, DSET_DEPREC_NAME_CHUNKED, H5T_NATIVE_DOUBLE, space, create_parms);
@@ -8464,7 +8464,7 @@ test_deprec(hid_t file)
     csize[0] = 5;
     csize[1] = 100;
     status   = H5Pset_chunk(create_parms, 2, csize);
-    assert(status >= 0);
+    HDassert(status >= 0);
 
     if ((dataset = H5Dcreate1(file, DSET_DEPREC_NAME_CHUNKED, H5T_NATIVE_DOUBLE, space, create_parms)) < 0)
         goto error;
@@ -8489,11 +8489,11 @@ test_deprec(hid_t file)
      * Create a compact dataset, then close it.
      */
     create_parms = H5Pcreate(H5P_DATASET_CREATE);
-    assert(create_parms >= 0);
+    HDassert(create_parms >= 0);
     status = H5Pset_layout(create_parms, H5D_COMPACT);
-    assert(status >= 0);
+    HDassert(status >= 0);
     status = H5Pset_alloc_time(create_parms, H5D_ALLOC_TIME_EARLY);
-    assert(status >= 0);
+    HDassert(status >= 0);
 
     if ((dataset = H5Dcreate1(file, DSET_DEPREC_NAME_COMPACT, H5T_NATIVE_DOUBLE, small_space, create_parms)) <
         0)
diff --git a/test/dt_arith.c b/test/dt_arith.c
index 466554c..7b2274c 100644
--- a/test/dt_arith.c
+++ b/test/dt_arith.c
@@ -359,7 +359,7 @@ static int without_hardware_g = 0;
                                                                                                              \
         for (n = 0; n < 2; n++) {                                                                            \
             if (n == 1) {                                                                                    \
-                memset(value, 0, SRC_SIZE * sizeof(unsigned char));                                          \
+                HDmemset(value, 0, SRC_SIZE * sizeof(unsigned char));                                        \
                 /* -0 */                                                                                     \
                 H5T__bit_set(value, (size_t)(SRC_PREC - 1), (size_t)1, TRUE);                                \
                 CHANGE_ORDER(value, SRC_ORDR, SRC_SIZE); /*change order for big endian*/                     \
@@ -566,7 +566,7 @@ generates_sigfpe(void)
 
     HDfflush(stdout);
     HDfflush(stderr);
-    if ((pid = fork()) < 0) {
+    if ((pid = HDfork()) < 0) {
         HDperror("fork");
         HDexit(EXIT_FAILURE);
     }
@@ -580,7 +580,7 @@ generates_sigfpe(void)
         HDexit(EXIT_SUCCESS);
     }
 
-    while (pid != waitpid(pid, &status, 0))
+    while (pid != HDwaitpid(pid, &status, 0))
         /*void*/;
     if (WIFEXITED(status) && 0 == WEXITSTATUS(status)) {
         HDputs("Floating-point overflow cases will be tested.");
@@ -2388,7 +2388,7 @@ test_conv_int_1(const char *name, hid_t src, hid_t dst)
         }
 
         /* Make certain that there isn't some weird number of destination bits */
-        assert(dst_nbits % 8 == 0);
+        HDassert(dst_nbits % 8 == 0);
 
         /* Are the two results the same? */
         for (k = (dst_size - (dst_nbits / 8)); k < dst_size; k++)
@@ -2945,12 +2945,12 @@ test_conv_flt_1(const char *name, int run_test, hid_t src, hid_t dst)
      */
     HDfflush(stdout);
     HDfflush(stderr);
-    if ((child_pid = fork()) < 0) {
+    if ((child_pid = HDfork()) < 0) {
         HDperror("fork");
         return 1;
     }
     else if (child_pid > 0) {
-        while (child_pid != waitpid(child_pid, &status, 0)) /*void*/
+        while (child_pid != HDwaitpid(child_pid, &status, 0)) /*void*/
             ;
         if (WIFEXITED(status) && 255 == WEXITSTATUS(status)) {
             return 0; /*child exit after catching SIGFPE*/
@@ -3019,7 +3019,7 @@ test_conv_flt_1(const char *name, int run_test, hid_t src, hid_t dst)
     if (sizeof(float) == sizeof(double))
         HDputs("Sizeof(float)==sizeof(double) - some tests may not be sensible.");
     if (OTHER == src_type || OTHER == dst_type) {
-        if (!strcmp(name, "noop"))
+        if (!HDstrcmp(name, "noop"))
             HDsnprintf(str, sizeof(str), "Testing %s %s -> %s conversions", name, src_type_name,
                        dst_type_name);
         else if (run_test == TEST_SPECIAL)
@@ -3038,7 +3038,7 @@ test_conv_flt_1(const char *name, int run_test, hid_t src, hid_t dst)
         goto error;
     }
     else {
-        if (!strcmp(name, "noop"))
+        if (!HDstrcmp(name, "noop"))
             HDsnprintf(str, sizeof(str), "Testing %s %s -> %s conversions", name, src_type_name,
                        dst_type_name);
         else if (run_test == TEST_SPECIAL)
@@ -4347,7 +4347,7 @@ test_conv_int_fp(const char *name, int run_test, hid_t src, hid_t dst)
         }
 
         /* Make certain that there isn't some weird number of destination bits */
-        assert(dst_nbits % 8 == 0);
+        HDassert(dst_nbits % 8 == 0);
 
         /* For Intel machines, the size of "long double" is 12 bytes, precision
          * is 80 bits; for AMD processors, the size of "long double" is 16 bytes,
@@ -5006,7 +5006,7 @@ run_fp_tests(const char *name)
 {
     int nerrors = 0;
 
-    if (!strcmp(name, "noop")) {
+    if (!HDstrcmp(name, "noop")) {
         nerrors += test_conv_flt_1("noop", TEST_NOOP, H5T_NATIVE_FLOAT, H5T_NATIVE_FLOAT);
         nerrors += test_conv_flt_1("noop", TEST_NOOP, H5T_NATIVE_DOUBLE, H5T_NATIVE_DOUBLE);
 #if H5_SIZEOF_LONG_DOUBLE != 0
@@ -5243,7 +5243,7 @@ run_fp_int_conv(const char *name)
 #endif
 
 #if H5_SIZEOF_LONG_LONG != H5_SIZEOF_LONG
-        if (!strcmp(name, "hw")) { /* Hardware conversion */
+        if (!HDstrcmp(name, "hw")) { /* Hardware conversion */
             nerrors += test_conv_int_fp(name, test_values, H5T_NATIVE_FLOAT, H5T_NATIVE_LLONG);
             nerrors += test_conv_int_fp(name, test_values, H5T_NATIVE_DOUBLE, H5T_NATIVE_LLONG);
         }
diff --git a/test/dtypes.c b/test/dtypes.c
index bb9bb2e..184c099 100644
--- a/test/dtypes.c
+++ b/test/dtypes.c
@@ -1891,7 +1891,7 @@ test_compound_9(void)
         goto error;
     } /* end if */
 
-    if (rdata.i1 != wdata.i1 || rdata.i2 != wdata.i2 || strcmp(rdata.str, wdata.str)) {
+    if (rdata.i1 != wdata.i1 || rdata.i2 != wdata.i2 || HDstrcmp(rdata.str, wdata.str)) {
         H5_FAILED();
         AT();
         HDprintf("incorrect read data\n");
@@ -2097,7 +2097,7 @@ test_compound_10(void)
 
         t1 = rdata[i].text.p;
         t2 = wdata[i].text.p;
-        if (strcmp((char *)t1, (char *)t2)) {
+        if (HDstrcmp((char *)t1, (char *)t2)) {
             H5_FAILED();
             AT();
             HDprintf("incorrect VL read data\n");
@@ -2502,7 +2502,7 @@ test_compound_12(void)
     H5E_END_TRY;
     if (ret >= 0) {
         H5_FAILED();
-        puts("  Tries to cut off the last member. Should have failed.");
+        HDputs("  Tries to cut off the last member. Should have failed.");
         goto error;
     }
 
@@ -3054,7 +3054,7 @@ test_compound_14(void)
         goto error;
     } /* end if */
 
-    if (rdata1.c1 != wdata1.c1 || rdata1.c2 != wdata1.c2 || strcmp(rdata1.str, wdata1.str)) {
+    if (rdata1.c1 != wdata1.c1 || rdata1.c2 != wdata1.c2 || HDstrcmp(rdata1.str, wdata1.str)) {
         H5_FAILED();
         AT();
         HDprintf("incorrect read data\n");
@@ -3885,7 +3885,7 @@ test_query(void)
         HDprintf("Can't get name for enum member\n");
         goto error;
     } /* end if */
-    if (strcmp("YELLOW", enum_name)) {
+    if (HDstrcmp("YELLOW", enum_name)) {
         H5_FAILED();
         HDprintf("Incorrect name for enum member\n");
         goto error;
diff --git a/test/earray.c b/test/earray.c
index 79bf0f1..4ef79ee 100644
--- a/test/earray.c
+++ b/test/earray.c
@@ -759,7 +759,7 @@ test_create(hid_t fapl, H5EA_create_t *cparam, earray_test_param_t H5_ATTR_UNUSE
     }
 #else  /* NDEBUG */
     SKIPPED();
-    puts("    Not tested when assertions are disabled");
+    HDputs("    Not tested when assertions are disabled");
 #endif /* NDEBUG */
 
     /*
@@ -2427,12 +2427,12 @@ main(void)
         switch (curr_test) {
             /* "Normal" testing parameters */
             case EARRAY_TEST_NORMAL:
-                puts("Testing with normal parameters");
+                HDputs("Testing with normal parameters");
                 break;
 
             /* "Re-open array" testing parameters */
             case EARRAY_TEST_REOPEN:
-                puts("Testing with reopen array flag set");
+                HDputs("Testing with reopen array flag set");
                 tparam.reopen_array = EARRAY_TEST_REOPEN;
                 break;
 
@@ -2461,31 +2461,31 @@ main(void)
             switch (curr_iter) {
                 /* "Forward" testing parameters */
                 case EARRAY_ITER_FW:
-                    puts("Testing with forward iteration");
+                    HDputs("Testing with forward iteration");
                     tparam.eiter = &ea_iter_fw;
                     break;
 
                 /* "Reverse" testing parameters */
                 case EARRAY_ITER_RV:
-                    puts("Testing with reverse iteration");
+                    HDputs("Testing with reverse iteration");
                     tparam.eiter = &ea_iter_rv;
                     break;
 
                 /* "Random" testing parameters */
                 case EARRAY_ITER_RND:
-                    puts("Testing with random iteration");
+                    HDputs("Testing with random iteration");
                     tparam.eiter = &ea_iter_rnd;
                     break;
 
                 /* "Random #2" testing parameters */
                 case EARRAY_ITER_RND2:
-                    puts("Testing with random #2 iteration");
+                    HDputs("Testing with random #2 iteration");
                     tparam.eiter = &ea_iter_rnd2;
                     break;
 
                 /* "Cyclic" testing parameters */
                 case EARRAY_ITER_CYC:
-                    puts("Testing with cyclic iteration");
+                    HDputs("Testing with cyclic iteration");
                     tparam.eiter = &ea_iter_cyc;
                     break;
 
diff --git a/test/enum.c b/test/enum.c
index eafce72..4a13358 100644
--- a/test/enum.c
+++ b/test/enum.c
@@ -768,11 +768,11 @@ main(void)
 
     if (nerrors)
         goto error;
-    puts("All enum tests passed.");
+    HDputs("All enum tests passed.");
     h5_cleanup(FILENAME, fapl);
     return 0;
 
 error:
-    puts("*** ENUM TESTS FAILED ***");
+    HDputs("*** ENUM TESTS FAILED ***");
     return 1;
 }
diff --git a/test/external.c b/test/external.c
index 376204a..d106555 100644
--- a/test/external.c
+++ b/test/external.c
@@ -476,12 +476,12 @@ __add_external_files(hid_t dcpl_id, unsigned int n_external_files, off_t offset,
     for (i = 0; i < n_external_files; i++) {
         if (HDsnprintf(exname, AEF_EXNAME_MAX_LEN, "ext%d.data", i + 1) > AEF_EXNAME_MAX_LEN) {
             HDfprintf(stderr, "External file %d overflows name buffer\n", i + 1);
-            fflush(stderr);
+            HDfflush(stderr);
             return -1;
         }
         if (H5Pset_external(dcpl_id, exname, offset, max_ext_size) < 0) {
             HDfprintf(stderr, "Problem adding external file %s\n", exname);
-            fflush(stderr);
+            HDfflush(stderr);
             return -1;
         }
     }
diff --git a/test/farray.c b/test/farray.c
index b6a6c31..46889a3 100644
--- a/test/farray.c
+++ b/test/farray.c
@@ -483,7 +483,7 @@ test_create(hid_t fapl, H5FA_create_t *cparam, farray_test_param_t H5_ATTR_UNUSE
     }
 #else  /* NDEBUG */
     SKIPPED();
-    puts("    Not tested when assertions are disabled");
+    HDputs("    Not tested when assertions are disabled");
 #endif /* NDEBUG */
 
     /*
diff --git a/test/filenotclosed.c b/test/filenotclosed.c
index 13ce9fd..330224d 100644
--- a/test/filenotclosed.c
+++ b/test/filenotclosed.c
@@ -80,7 +80,7 @@ main(void)
     contig_addr_vfd = (hbool_t)(HDstrcmp(env_h5_drvr, "split") && HDstrcmp(env_h5_drvr, "multi"));
     if (!contig_addr_vfd) {
         SKIPPED();
-        puts("    Temporary skipped for a spilt/multi driver");
+        HDputs("    Temporary skipped for a spilt/multi driver");
         HDexit(EXIT_SUCCESS);
     }
 
diff --git a/test/fillval.c b/test/fillval.c
index 05570f0..2decbfa 100644
--- a/test/fillval.c
+++ b/test/fillval.c
@@ -201,7 +201,7 @@ test_getset(void)
     H5E_END_TRY;
     if (fill_i != 0) {
         H5_FAILED();
-        puts("    H5Pget_fill_value() should return default 0");
+        HDputs("    H5Pget_fill_value() should return default 0");
         goto error;
     }
 
@@ -220,8 +220,8 @@ test_getset(void)
         goto error;
     if (fill_ss.v1 != fill_ss_rd.v1 || fill_ss.v2 != fill_ss_rd.v2) {
         H5_FAILED();
-        puts("    Failed to get fill value using same data type that was ");
-        puts("    used to set the fill value.");
+        HDputs("    Failed to get fill value using same data type that was ");
+        HDputs("    used to set the fill value.");
         goto error;
     }
 
@@ -232,8 +232,8 @@ test_getset(void)
         goto error;
     if (fill_ss.v1 != fill_si.v1 || fill_ss.v2 != fill_si.v2) {
         H5_FAILED();
-        puts("    Failed to get fill value using a data type other than what");
-        puts("    was used to set the fill value.");
+        HDputs("    Failed to get fill value using a data type other than what");
+        HDputs("    was used to set the fill value.");
         goto error;
     }
 
@@ -246,7 +246,7 @@ test_getset(void)
         goto error;
     if (fill_si.v1 != fill_ss.v1 || fill_si.v2 != fill_ss.v2) {
         H5_FAILED();
-        puts("    Resetting the fill value was unsuccessful.");
+        HDputs("    Resetting the fill value was unsuccessful.");
         goto error;
     }
 
@@ -662,12 +662,12 @@ test_create(hid_t fapl, const char *base_name, H5D_layout_t layout)
             goto error;
         if (alloc_time != H5D_ALLOC_TIME_LATE) {
             H5_FAILED();
-            puts("    Got non-H5D_ALLOC_TIME_LATE space allocation time.");
+            HDputs("    Got non-H5D_ALLOC_TIME_LATE space allocation time.");
             HDprintf("    Got %d\n", alloc_time);
         }
         if (fill_time != H5D_FILL_TIME_ALLOC) {
             H5_FAILED();
-            puts("    Got non-H5D_FILL_TIME_ALLOC fill value write time.");
+            HDputs("    Got non-H5D_FILL_TIME_ALLOC fill value write time.");
             HDprintf("    Got %d\n", fill_time);
         }
         if (H5Dclose(dset3) < 0)
@@ -682,7 +682,7 @@ test_create(hid_t fapl, const char *base_name, H5D_layout_t layout)
             goto error;
         if (layout == H5D_CONTIGUOUS && allocation != H5D_SPACE_STATUS_NOT_ALLOCATED) {
             H5_FAILED();
-            puts("    Got allocated space instead of unallocated.");
+            HDputs("    Got allocated space instead of unallocated.");
             HDprintf("    Got %d\n", allocation);
             goto error;
         }
@@ -694,12 +694,12 @@ test_create(hid_t fapl, const char *base_name, H5D_layout_t layout)
             goto error;
         if (alloc_time != H5D_ALLOC_TIME_LATE) {
             H5_FAILED();
-            puts("    Got non-H5D_ALLOC_TIME_LATE space allocation time.");
+            HDputs("    Got non-H5D_ALLOC_TIME_LATE space allocation time.");
             HDprintf("    Got %d\n", alloc_time);
         }
         if (fill_time != H5D_FILL_TIME_NEVER) {
             H5_FAILED();
-            puts("    Got non-H5D_FILL_TIME_NEVER fill value write time.");
+            HDputs("    Got non-H5D_FILL_TIME_NEVER fill value write time.");
             HDprintf("    Got %d\n", fill_time);
         }
         if (H5Dclose(dset4) < 0)
@@ -717,7 +717,7 @@ test_create(hid_t fapl, const char *base_name, H5D_layout_t layout)
         if (!H5_FLT_ABS_EQUAL(rd_c.a, 0) || !H5_DBL_ABS_EQUAL(rd_c.y, fill_ctype.y) || rd_c.x != 0 ||
             rd_c.z != '\0') {
             H5_FAILED();
-            puts("    Got wrong fill value");
+            HDputs("    Got wrong fill value");
             HDprintf("    Got rd_c.a=%f, rd_c.y=%f and rd_c.x=%d, rd_c.z=%c\n", (double)rd_c.a, rd_c.y,
                      rd_c.x, rd_c.z);
         }
@@ -746,14 +746,14 @@ test_create(hid_t fapl, const char *base_name, H5D_layout_t layout)
         goto error;
     if (alloc_time != H5D_ALLOC_TIME_EARLY) {
         H5_FAILED();
-        puts("    Got non-H5D_ALLOC_TIME_EARLY space allocation time.");
+        HDputs("    Got non-H5D_ALLOC_TIME_EARLY space allocation time.");
         HDprintf("    Got %d\n", alloc_time);
     }
     if (H5Pget_fill_time(dcpl, &fill_time) < 0)
         goto error;
     if (fill_time != H5D_FILL_TIME_NEVER) {
         H5_FAILED();
-        puts("    Got non-H5D_FILL_TIME_NEVER fill value write time.");
+        HDputs("    Got non-H5D_FILL_TIME_NEVER fill value write time.");
         HDprintf("    Got %d\n", fill_time);
     }
     if (H5Dclose(dset5) < 0)
@@ -786,14 +786,14 @@ test_create(hid_t fapl, const char *base_name, H5D_layout_t layout)
         goto error;
     if (alloc_time != H5D_ALLOC_TIME_EARLY) {
         H5_FAILED();
-        puts("    Got non-H5D_ALLOC_TIME_EARLY space allocation time.");
+        HDputs("    Got non-H5D_ALLOC_TIME_EARLY space allocation time.");
         HDprintf("    Got %d\n", alloc_time);
     }
     if (H5Pget_fill_time(dcpl, &fill_time) < 0)
         goto error;
     if (fill_time != H5D_FILL_TIME_ALLOC) {
         H5_FAILED();
-        puts("    Got non-H5D_FILL_TIME_ALLOC fill value write time.");
+        HDputs("    Got non-H5D_FILL_TIME_ALLOC fill value write time.");
         HDprintf("    Got %d\n", fill_time);
     }
     if (H5Dclose(dset6) < 0)
@@ -811,7 +811,7 @@ test_create(hid_t fapl, const char *base_name, H5D_layout_t layout)
     if (!H5_FLT_ABS_EQUAL(rd_c.a, 0) || !H5_DBL_ABS_EQUAL(rd_c.y, fill_ctype.y) || rd_c.x != 0 ||
         rd_c.z != '\0') {
         H5_FAILED();
-        puts("    Got wrong fill value");
+        HDputs("    Got wrong fill value");
         HDprintf("    Got rd_c.a=%f, rd_c.y=%f and rd_c.x=%d, rd_c.z=%c\n", (double)rd_c.a, rd_c.y, rd_c.x,
                  rd_c.z);
     }
@@ -1649,7 +1649,7 @@ test_extend_cases(hid_t file, hid_t _dcpl, const char *dset_name, hsize_t *ch_si
     } /* end if */
     else {
         /* Sanity check */
-        assert(dtype_class == H5T_COMPOUND);
+        HDassert(dtype_class == H5T_COMPOUND);
 
         /* Initialize specific values for this datatype */
         val_size    = sizeof(comp_vl_datatype);
@@ -1701,7 +1701,7 @@ test_extend_cases(hid_t file, hid_t _dcpl, const char *dset_name, hsize_t *ch_si
     } /* end for */
 
     /* Check for overflow */
-    assert((nelmts * val_size) == (hsize_t)((size_t)(nelmts * val_size)));
+    HDassert((nelmts * val_size) == (hsize_t)((size_t)(nelmts * val_size)));
 
     /* Allocate & initialize buffer */
     buf = HDmalloc((size_t)(nelmts * val_size));
@@ -2141,7 +2141,7 @@ test_extend(hid_t fapl, const char *base_name, H5D_layout_t layout)
      */
     if (H5D_CONTIGUOUS == layout) {
         SKIPPED();
-        puts("    Not implemented yet -- needs H5S_SELECT_DIFF operator");
+        HDputs("    Not implemented yet -- needs H5S_SELECT_DIFF operator");
         goto skip;
     }
 #endif
@@ -2259,7 +2259,7 @@ test_compatible(void)
         goto error;
     if (dims[0] != 8 || dims[1] != 8) {
         H5_FAILED();
-        puts("    Got a different dimension size than what was set.");
+        HDputs("    Got a different dimension size than what was set.");
         HDprintf("    Got dims[0]=%ld, dims[1]=%ld, set 8x8\n", (long)dims[0], (long)dims[1]);
         goto error;
     }
@@ -2271,7 +2271,7 @@ test_compatible(void)
         goto error;
     if (val_rd != 0) {
         H5_FAILED();
-        puts("    Got a different value than what was set.");
+        HDputs("    Got a different value than what was set.");
         HDprintf("    Got %ld, set 0\n", (long)val_rd);
         goto error;
     }
@@ -2312,7 +2312,7 @@ test_compatible(void)
         goto error;
     if (dims[0] != 8 || dims[1] != 8) {
         H5_FAILED();
-        puts("    Got a different dimension size than what was set.");
+        HDputs("    Got a different dimension size than what was set.");
         HDprintf("    Got dims[0]=%ld, dims[1]=%ld, set 8x8\n", (long)dims[0], (long)dims[1]);
         goto error;
     }
@@ -2324,7 +2324,7 @@ test_compatible(void)
         goto error;
     if (val_rd != fill_val) {
         H5_FAILED();
-        puts("    Got a different value than what was set.");
+        HDputs("    Got a different value than what was set.");
         HDprintf("    Got %ld, set %ld\n", (long)val_rd, (long)fill_val);
         goto error;
     }
@@ -2659,11 +2659,11 @@ main(int argc, char *argv[])
     if (argc >= 2) {
         test_contig = test_chunk = test_compact = 0;
         for (argno = 1; argno < argc; argno++) {
-            if (!strcmp(argv[argno], "contiguous"))
+            if (!HDstrcmp(argv[argno], "contiguous"))
                 test_contig = 1;
-            else if (!strcmp(argv[argno], "chunked"))
+            else if (!HDstrcmp(argv[argno], "chunked"))
                 test_chunk = 1;
-            else if (!strcmp(argv[argno], "compact"))
+            else if (!HDstrcmp(argv[argno], "compact"))
                 test_compact = 1;
             else {
                 HDfprintf(stderr, "usage: %s [contiguous] [chunked] [compact]\n", argv[0]);
@@ -2693,11 +2693,11 @@ main(int argc, char *argv[])
 
         /* Set the FAPL for the type of format */
         if (new_format) {
-            puts("\nTesting with new file format:");
+            HDputs("\nTesting with new file format:");
             my_fapl = fapl2;
         } /* end if */
         else {
-            puts("Testing with old file format:");
+            HDputs("Testing with old file format:");
             my_fapl = fapl;
         } /* end else */
 
diff --git a/test/filter_fail.c b/test/filter_fail.c
index dca9a20..d7f784c 100644
--- a/test/filter_fail.c
+++ b/test/filter_fail.c
@@ -171,7 +171,7 @@ test_filter_write(char *file_name, hid_t my_fapl, hbool_t cache_enabled)
         H5E_END_TRY;
         if (ret >= 0) {
             H5_FAILED();
-            puts("    Data writing is supposed to fail because the chunk can't be written to file.");
+            HDputs("    Data writing is supposed to fail because the chunk can't be written to file.");
             TEST_ERROR
         }
     }
@@ -189,7 +189,7 @@ test_filter_write(char *file_name, hid_t my_fapl, hbool_t cache_enabled)
         H5E_END_TRY;
         if (ret >= 0) {
             H5_FAILED();
-            puts("    Dataset is supposed to fail because the chunk can't be flushed to file.");
+            HDputs("    Dataset is supposed to fail because the chunk can't be flushed to file.");
             TEST_ERROR
         }
     }
diff --git a/test/gen_cross.c b/test/gen_cross.c
index 37c6dcf..030cc65 100644
--- a/test/gen_cross.c
+++ b/test/gen_cross.c
@@ -928,7 +928,7 @@ create_deflate_dsets_float(hid_t fid, hid_t fsid, hid_t msid)
 #else  /* H5_HAVE_FILTER_DEFLATE */
     const char *not_supported = "Deflate filter is not enabled. Can't create the dataset.";
 
-    puts(not_supported);
+    HDputs(not_supported);
 #endif /* H5_HAVE_FILTER_DEFLATE */
 
     return 0;
diff --git a/test/gen_filters.c b/test/gen_filters.c
index 502e041..0d107a9 100644
--- a/test/gen_filters.c
+++ b/test/gen_filters.c
@@ -243,12 +243,12 @@ main(void)
 
     if (nerrors)
         goto error;
-    printf("All tests passed.\n");
+    HDprintf("All tests passed.\n");
 
     return 0;
 
 error:
     nerrors = MAX(1, nerrors);
-    printf("***** %d GEN_FILTERS FAILURES *****\n", nerrors);
+    HDprintf("***** %d GEN_FILTERS FAILURES *****\n", nerrors);
     return 1;
 }
diff --git a/test/getname.c b/test/getname.c
index 61feee6..0cf9768 100644
--- a/test/getname.c
+++ b/test/getname.c
@@ -3787,7 +3787,7 @@ main(void)
 
     if (nerrors)
         goto error;
-    puts("All getname tests passed.");
+    HDputs("All getname tests passed.");
 
     h5_cleanup(FILENAME, fapl);
 
@@ -3797,7 +3797,7 @@ error:
     H5E_BEGIN_TRY { H5Fclose(file_id); }
     H5E_END_TRY;
 
-    puts("***** GET NAME TESTS FAILED *****");
+    HDputs("***** GET NAME TESTS FAILED *****");
 
     return 1;
 }
diff --git a/test/gheap.c b/test/gheap.c
index 51e1dd2..1a8a4c0 100644
--- a/test/gheap.c
+++ b/test/gheap.c
@@ -42,9 +42,9 @@
         nerrors++;                                                                                           \
         if (nerrors <= GHEAP_REPEATED_ERR_LIM) {                                                             \
             H5_FAILED();                                                                                     \
-            puts(MSG);                                                                                       \
+            HDputs(MSG);                                                                                     \
             if (nerrors == GHEAP_REPEATED_ERR_LIM)                                                           \
-                puts("    Suppressing further errors...");                                                   \
+                HDputs("    Suppressing further errors...");                                                 \
         } /* end if */                                                                                       \
     }     /* end GHEAP_REPEATED_ERR */
 
@@ -226,7 +226,7 @@ test_2(hid_t fapl)
             HDputs("    Unable to read object");
             nerrors++;
         }
-        else if (memcmp(in, out, size)) {
+        else if (HDmemcmp(in, out, size)) {
             H5_FAILED();
             HDputs("    Value read doesn't match value written");
             nerrors++;
diff --git a/test/hdfs.c b/test/hdfs.c
index ee66314..701df47 100644
--- a/test/hdfs.c
+++ b/test/hdfs.c
@@ -303,7 +303,7 @@
  *----------------------------------------------------------------------------
  */
 #define JSVERIFY_STR(expected, actual, reason)                                                               \
-    if (strcmp((actual), (expected)) != 0) {                                                                 \
+    if (HDstrcmp((actual), (expected)) != 0) {                                                               \
         JSERR_STR((expected), (actual), (reason));                                                           \
         goto error;                                                                                          \
     } /* JSVERIFY_STR */
@@ -348,7 +348,7 @@
  *----------------------------------------------------------------------------
  */
 #define JSVERIFY_STR(actual, expected, reason)                                                               \
-    if (strcmp((actual), (expected)) != 0) {                                                                 \
+    if (HDstrcmp((actual), (expected)) != 0) {                                                               \
         JSERR_STR((expected), (actual), (reason));                                                           \
         goto error;                                                                                          \
     } /* JSVERIFY_STR */
@@ -414,8 +414,8 @@ test_fapl_config_validation(void)
 #ifndef H5_HAVE_LIBHDFS
     TESTING("HDFS fapl configuration validation");
     SKIPPED();
-    puts("    HDFS VFD is not enabled");
-    fflush(stdout);
+    HDputs("    HDFS VFD is not enabled");
+    HDfflush(stdout);
     return 0;
 
 #else
@@ -620,8 +620,8 @@ test_hdfs_fapl(void)
 #ifndef H5_HAVE_LIBHDFS
     TESTING("HDFS fapl ");
     SKIPPED();
-    puts("    HDFS VFD is not enabled");
-    fflush(stdout);
+    HDputs("    HDFS VFD is not enabled");
+    HDfflush(stdout);
     return 0;
 
 #else
@@ -703,8 +703,8 @@ test_vfd_open(void)
 #ifndef H5_HAVE_LIBHDFS
     TESTING("HDFS VFD-level open");
     SKIPPED();
-    puts("    HDFS VFD is not enabled");
-    fflush(stdout);
+    HDputs("    HDFS VFD is not enabled");
+    HDfflush(stdout);
     return 0;
 
 #else
@@ -956,8 +956,8 @@ test_eof_eoa(void)
 #ifndef H5_HAVE_LIBHDFS
     TESTING("HDFS eof/eoa gets and sets");
     SKIPPED();
-    puts("    HDFS VFD is not enabled");
-    fflush(stdout);
+    HDputs("    HDFS VFD is not enabled");
+    HDfflush(stdout);
     return 0;
 
 #else
@@ -1066,8 +1066,8 @@ test_H5FDread_without_eoa_set_fails(void)
 #ifndef H5_HAVE_LIBHDFS
     TESTING("HDFS VFD read-eoa temporal coupling library limitation");
     SKIPPED();
-    puts("    HDFS VFD is not enabled");
-    fflush(stdout);
+    HDputs("    HDFS VFD is not enabled");
+    HDfflush(stdout);
     return 0;
 
 #else
@@ -1165,8 +1165,8 @@ test_read(void)
 #ifndef H5_HAVE_LIBHDFS
     TESTING("HDFS VFD read/range-gets");
     SKIPPED();
-    puts("    HDFS VFD is not enabled");
-    fflush(stdout);
+    HDputs("    HDFS VFD is not enabled");
+    HDfflush(stdout);
     return 0;
 
 #else
@@ -1376,8 +1376,8 @@ test_noops_and_autofails(void)
 #ifndef H5_HAVE_LIBHDFS
     TESTING("HDFS VFD always-fail and no-op routines");
     SKIPPED();
-    puts("    HDFS VFD is not enabled");
-    fflush(stdout);
+    HDputs("    HDFS VFD is not enabled");
+    HDfflush(stdout);
     return 0;
 
 #else
@@ -1528,8 +1528,8 @@ test_H5F_integration(void)
 #ifndef H5_HAVE_LIBHDFS
     TESTING("HDFS file access through HD5F library (H5F API)");
     SKIPPED();
-    puts("    HDFS VFD is not enabled");
-    fflush(stdout);
+    HDputs("    HDFS VFD is not enabled");
+    HDfflush(stdout);
     return 0;
 
 #else
@@ -1597,7 +1597,7 @@ error:
 
 #if HDFS_TEST_DEBUG
     HDprintf("\nerror!");
-    fflush(stdout);
+    HDfflush(stdout);
 #endif /* HDFS_TEST_DEBUG */
 
     if (fapl_id >= 0) {
diff --git a/test/hyperslab.c b/test/hyperslab.c
index 43992de..5c7b78f 100644
--- a/test/hyperslab.c
+++ b/test/hyperslab.c
@@ -177,7 +177,7 @@ test_fill(size_t nx, size_t ny, size_t nz, size_t di, size_t dj, size_t dk, size
     } /* end else */
     HDsprintf(s, "Testing hyperslab fill %-11s variable hyperslab", dim);
     HDprintf("%-70s", s);
-    fflush(stdout);
+    HDfflush(stdout);
 
     /* Allocate array */
     if (NULL == (dst = (uint8_t *)HDcalloc((size_t)1, nx * ny * nz)))
@@ -366,7 +366,7 @@ test_copy(int mode, size_t nx, size_t ny, size_t nz, size_t di, size_t dj, size_
 
     HDsprintf(s, "Testing hyperslab copy %-11s %s", dim, sub);
     HDprintf("%-70s", s);
-    fflush(stdout);
+    HDfflush(stdout);
 
     /*
      * Allocate arrays
@@ -575,7 +575,7 @@ test_multifill(size_t nx)
     hsize_t i, j;
 
     HDprintf("%-70s", "Testing multi-byte fill value");
-    fflush(stdout);
+    HDfflush(stdout);
 
     /* Initialize the source and destination */
     if (NULL == (src = (struct a_struct *)HDmalloc(nx * sizeof(*src))))
@@ -687,7 +687,7 @@ test_endian(size_t nx)
     hsize_t  i, j;
 
     HDprintf("%-70s", "Testing endian conversion by stride");
-    fflush(stdout);
+    HDfflush(stdout);
 
     /* Initialize arrays */
     if (NULL == (src = (uint8_t *)HDmalloc(nx * 4)))
@@ -773,7 +773,7 @@ test_transpose(size_t nx, size_t ny)
 
     HDsprintf(s, "Testing 2d transpose by stride %4lux%-lud", (unsigned long)nx, (unsigned long)ny);
     HDprintf("%-70s", s);
-    fflush(stdout);
+    HDfflush(stdout);
 
     /* Initialize */
     if (NULL == (src = (int *)HDmalloc(nx * ny * sizeof(*src))))
@@ -872,7 +872,7 @@ test_sub_super(size_t nx, size_t ny)
     HDsprintf(s, "Testing image sampling %4lux%-4lu to %4lux%-4lu ", (unsigned long)(2 * nx),
               (unsigned long)(2 * ny), (unsigned long)nx, (unsigned long)ny);
     HDprintf("%-70s", s);
-    fflush(stdout);
+    HDfflush(stdout);
 
     /* Initialize */
     if (NULL == (full = (uint8_t *)HDmalloc(4 * nx * ny)))
@@ -922,7 +922,7 @@ test_sub_super(size_t nx, size_t ny)
     HDsprintf(s, "Testing image sampling %4lux%-4lu to %4lux%-4lu ", (unsigned long)nx, (unsigned long)ny,
               (unsigned long)(2 * nx), (unsigned long)(2 * ny));
     HDprintf("%-70s", s);
-    fflush(stdout);
+    HDfflush(stdout);
 
     /* Setup stride */
     size[0]       = nx;
diff --git a/test/istore.c b/test/istore.c
index a724359..c600c31 100644
--- a/test/istore.c
+++ b/test/istore.c
@@ -619,13 +619,13 @@ main(int argc, char *argv[])
     else {
         int i;
         for (i = 1, size_of_test = 0; i < argc; i++) {
-            if (!strcmp(argv[i], "small")) {
+            if (!HDstrcmp(argv[i], "small")) {
                 size_of_test |= TEST_SMALL;
             }
-            else if (!strcmp(argv[i], "medium")) {
+            else if (!HDstrcmp(argv[i], "medium")) {
                 size_of_test |= TEST_MEDIUM;
             }
-            else if (!strcmp(argv[i], "large")) {
+            else if (!HDstrcmp(argv[i], "large")) {
                 size_of_test |= TEST_LARGE;
             }
             else {
diff --git a/test/lheap.c b/test/lheap.c
index 17e3082..27e025e 100644
--- a/test/lheap.c
+++ b/test/lheap.c
@@ -103,7 +103,7 @@ main(void)
         if (j > 4)
             buf[j] = '\0';
 
-        if (UFAIL == (obj[i] = H5HL_insert(f, heap, strlen(buf) + 1, buf))) {
+        if (UFAIL == (obj[i] = H5HL_insert(f, heap, HDstrlen(buf) + 1, buf))) {
             H5_FAILED();
             H5Eprint2(H5E_DEFAULT, stdout);
             goto error;
@@ -155,7 +155,7 @@ main(void)
             goto error;
         }
 
-        if (strcmp(s, buf)) {
+        if (HDstrcmp(s, buf)) {
             H5_FAILED();
             HDprintf("    i=%d, heap offset=%lu\n", i, (unsigned long)(obj[i]));
             HDprintf("    got: \"%s\"\n", s);
diff --git a/test/links.c b/test/links.c
index 43cd83d..f0932dc 100644
--- a/test/links.c
+++ b/test/links.c
@@ -14138,7 +14138,7 @@ UD_cb_create(const char *link_name, hid_t loc_group, const void *udata, size_t u
     if (lcpl_id < 0)
         TEST_ERROR
 
-    if (HDstrcmp(link_name, UD_CB_LINK_NAME) && strcmp(link_name, NEW_UD_CB_LINK_NAME))
+    if (HDstrcmp(link_name, UD_CB_LINK_NAME) && HDstrcmp(link_name, NEW_UD_CB_LINK_NAME))
         TEST_ERROR
     if (HDstrcmp((const char *)udata, UD_CB_TARGET))
         TEST_ERROR
@@ -14165,7 +14165,7 @@ UD_cb_traverse(const char *link_name, hid_t cur_group, const void *udata, size_t
     if (udata_size > 0 && !udata)
         TEST_ERROR
 
-    if (HDstrcmp(link_name, UD_CB_LINK_NAME) && strcmp(link_name, NEW_UD_CB_LINK_NAME))
+    if (HDstrcmp(link_name, UD_CB_LINK_NAME) && HDstrcmp(link_name, NEW_UD_CB_LINK_NAME))
         TEST_ERROR
     if (HDstrcmp((const char *)udata, UD_CB_TARGET))
         TEST_ERROR
@@ -14537,7 +14537,7 @@ lapl_udata(hid_t fapl, hbool_t new_format)
         TEST_ERROR
 
     /* Now use the same ud link to access group_b */
-    strcpy(group_b_name, "group_b");
+    HDstrcpy(group_b_name, "group_b");
     if (H5Pset(plist_id, DEST_PROP_NAME, group_b_name) < 0)
         TEST_ERROR
 
@@ -14851,7 +14851,7 @@ ud_link_errors(hid_t fapl, hbool_t new_format)
     H5E_END_TRY;
 
     /* Create a user-defined link to the group. */
-    strcpy(group_name, "/group");
+    HDstrcpy(group_name, "/group");
     if (H5Lcreate_ud(fid, "/ud_link", (H5L_type_t)UD_CBFAIL_TYPE, &group_name, HDstrlen(group_name) + 1,
                      H5P_DEFAULT, H5P_DEFAULT) < 0)
         FAIL_STACK_ERROR
diff --git a/test/links_env.c b/test/links_env.c
index 0e5d1c0..2cfa3fa 100644
--- a/test/links_env.c
+++ b/test/links_env.c
@@ -112,7 +112,7 @@ external_link_env(hid_t fapl, hbool_t new_format)
     /* Should be able to find the target file from pathnames set via HDF5_EXT_PREFIX */
     if (gid < 0) {
         H5_FAILED();
-        puts("    Should have found the file in tmp_links_env directory.");
+        HDputs("    Should have found the file in tmp_links_env directory.");
         goto error;
     }
 
diff --git a/test/mf.c b/test/mf.c
index c4a2aa1..a9240f9 100644
--- a/test/mf.c
+++ b/test/mf.c
@@ -6112,7 +6112,7 @@ test_mf_bug1(const char *env_h5_drvr, hid_t fapl)
 
             /* Free memb_name */
             for (mt = H5FD_MEM_DEFAULT; mt < H5FD_MEM_NTYPES; mt++)
-                free(memb_name[mt]);
+                HDfree(memb_name[mt]);
         } /* end else */
 
         /* Close memb_fapl */
@@ -7685,7 +7685,7 @@ set_multi_split(hid_t fapl, hsize_t pagesize, hbool_t is_multi_or_split)
 
     /* Free memb_name */
     for (mt = H5FD_MEM_DEFAULT; mt < H5FD_MEM_NTYPES; mt++)
-        free(memb_name[mt]);
+        HDfree(memb_name[mt]);
 
     return 0;
 
@@ -8841,7 +8841,7 @@ test_page_alignment(const char *env_h5_drvr, hid_t fapl)
 
             /* Free memb_name */
             for (mt = H5FD_MEM_DEFAULT; mt < H5FD_MEM_NTYPES; mt++)
-                free(memb_name[mt]);
+                HDfree(memb_name[mt]);
 
             /* Close memb_fapl */
             if (H5Pclose(memb_fapl) < 0)
diff --git a/test/mirror_vfd.c b/test/mirror_vfd.c
index 325999b..43141e0 100644
--- a/test/mirror_vfd.c
+++ b/test/mirror_vfd.c
@@ -63,8 +63,8 @@ static unsigned int g_verbosity = DEFAULT_VERBOSITY;
 #define LOGPRINT(lvl, ...)                                                                                   \
     do {                                                                                                     \
         if ((lvl) <= g_verbosity) {                                                                          \
-            fprintf(g_log_stream, __VA_ARGS__);                                                              \
-            fflush(g_log_stream);                                                                            \
+            HDfprintf(g_log_stream, __VA_ARGS__);                                                            \
+            HDfflush(g_log_stream);                                                                          \
         }                                                                                                    \
     } while (0)
 
@@ -150,7 +150,7 @@ _populate_filepath(const char *dirname, const char *_basename, hid_t fapl_id, ch
     }
 
     if (HDsnprintf(_path, H5FD_SPLITTER_PATH_MAX, "%s%s%s", dirname,
-                   (dirname[strlen(dirname)] == '/') ? "" : "/", /* slash iff needed */
+                   (dirname[HDstrlen(dirname)] == '/') ? "" : "/", /* slash iff needed */
                    _basename) > H5FD_SPLITTER_PATH_MAX) {
         TEST_ERROR;
     }
diff --git a/test/mtime.c b/test/mtime.c
index c28b81a..a8ad6ae 100644
--- a/test/mtime.c
+++ b/test/mtime.c
@@ -147,7 +147,7 @@ main(void)
                 H5_FAILED();
                 /* If this fails, examine H5Omtime.c.  Modification time is very
                  * system dependent (e.g., on Windows DST must be hardcoded). */
-                puts("    Old modification time incorrect");
+                HDputs("    Old modification time incorrect");
                 goto error;
             }
             if (H5Fclose(file) < 0)
diff --git a/test/objcopy.c b/test/objcopy.c
index 383bd05..876e7de 100644
--- a/test/objcopy.c
+++ b/test/objcopy.c
@@ -4494,7 +4494,7 @@ test_copy_dataset_compressed(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, hid
 
 #ifndef H5_HAVE_FILTER_DEFLATE
     SKIPPED();
-    puts("    Deflation filter not available");
+    HDputs("    Deflation filter not available");
 #else  /* H5_HAVE_FILTER_DEFLATE */
     /* set initial data values */
     for (i = 0; i < DIM_SIZE_1; i++)
@@ -4919,7 +4919,7 @@ test_copy_dataset_no_edge_filt(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl, h
 
 #ifndef H5_HAVE_FILTER_DEFLATE
     SKIPPED();
-    puts("    Deflation filter not available");
+    HDputs("    Deflation filter not available");
 #else  /* H5_HAVE_FILTER_DEFLATE */
     /* set initial data values */
     for (i = 0; i < DIM_SIZE_1; i++)
@@ -7273,7 +7273,7 @@ test_copy_dataset_compressed_vl(hid_t fcpl_src, hid_t fcpl_dst, hid_t src_fapl,
 
 #ifndef H5_HAVE_FILTER_DEFLATE
     SKIPPED();
-    puts("    Deflation filter not available");
+    HDputs("    Deflation filter not available");
 #else  /* H5_HAVE_FILTER_DEFLATE */
     /* set initial data values */
     for (i = 0; i < DIM_SIZE_1; i++) {
diff --git a/test/page_buffer.c b/test/page_buffer.c
index ca33872..abbae32 100644
--- a/test/page_buffer.c
+++ b/test/page_buffer.c
@@ -349,7 +349,7 @@ set_multi_split(const char *env_h5_drvr, hid_t fapl, hsize_t pagesize)
 
         /* Free memb_name */
         for (mt = H5FD_MEM_DEFAULT; mt < H5FD_MEM_NTYPES; mt++)
-            free(memb_name[mt]);
+            HDfree(memb_name[mt]);
 
     } /* end if */
 
diff --git a/test/pool.c b/test/pool.c
index 05304e5..ef2a627 100644
--- a/test/pool.c
+++ b/test/pool.c
@@ -784,11 +784,11 @@ main(void)
 
     if (nerrors)
         goto error;
-    puts("All memory pool tests passed.");
+    HDputs("All memory pool tests passed.");
 
     return 0;
 
 error:
-    puts("*** TESTS FAILED ***");
+    HDputs("*** TESTS FAILED ***");
     return 1;
 }
diff --git a/test/ros3.c b/test/ros3.c
index 7ecba0e..654082b 100644
--- a/test/ros3.c
+++ b/test/ros3.c
@@ -318,7 +318,7 @@ jserr_str(const char *expected, const char *actual, const char *reason)
  *----------------------------------------------------------------------------
  */
 #define JSVERIFY_STR(expected, actual, reason)                                                               \
-    if (strcmp((actual), (expected)) != 0) {                                                                 \
+    if (HDstrcmp((actual), (expected)) != 0) {                                                               \
         JSERR_STR((expected), (actual), (reason));                                                           \
         goto error;                                                                                          \
     } /* JSVERIFY_STR */
@@ -363,7 +363,7 @@ jserr_str(const char *expected, const char *actual, const char *reason)
  *----------------------------------------------------------------------------
  */
 #define JSVERIFY_STR(actual, expected, reason)                                                               \
-    if (strcmp((actual), (expected)) != 0) {                                                                 \
+    if (HDstrcmp((actual), (expected)) != 0) {                                                               \
         JSERR_STR((expected), (actual), (reason));                                                           \
         goto error;                                                                                          \
     } /* JSVERIFY_STR */
@@ -560,8 +560,8 @@ test_fapl_config_validation(void)
 
     if (FALSE == s3_test_bucket_defined) {
         SKIPPED();
-        puts("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
-        fflush(stdout);
+        HDputs("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
+        HDfflush(stdout);
         return 0;
     }
 
@@ -835,8 +835,8 @@ test_vfd_open(void)
 
     if (FALSE == s3_test_bucket_defined) {
         SKIPPED();
-        puts("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
-        fflush(stdout);
+        HDputs("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
+        HDfflush(stdout);
         return 0;
     }
 
@@ -969,15 +969,15 @@ test_eof_eoa(void)
 
     if (s3_test_credentials_loaded == 0) {
         SKIPPED();
-        puts("    s3 credentials are not loaded");
-        fflush(stdout);
+        HDputs("    s3 credentials are not loaded");
+        HDfflush(stdout);
         return 0;
     }
 
     if (FALSE == s3_test_bucket_defined) {
         SKIPPED();
-        puts("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
-        fflush(stdout);
+        HDputs("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
+        HDfflush(stdout);
         return 0;
     }
 
@@ -1077,15 +1077,15 @@ test_H5FDread_without_eoa_set_fails(void)
 
     if (s3_test_credentials_loaded == 0) {
         SKIPPED();
-        puts("    s3 credentials are not loaded");
-        fflush(stdout);
+        HDputs("    s3 credentials are not loaded");
+        HDfflush(stdout);
         return 0;
     }
 
     if (FALSE == s3_test_bucket_defined) {
         SKIPPED();
-        puts("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
-        fflush(stdout);
+        HDputs("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
+        HDfflush(stdout);
         return 0;
     }
 
@@ -1248,15 +1248,15 @@ test_read(void)
 
     if (s3_test_credentials_loaded == 0) {
         SKIPPED();
-        puts("    s3 credentials are not loaded");
-        fflush(stdout);
+        HDputs("    s3 credentials are not loaded");
+        HDfflush(stdout);
         return 0;
     }
 
     if (FALSE == s3_test_bucket_defined) {
         SKIPPED();
-        puts("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
-        fflush(stdout);
+        HDputs("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
+        HDfflush(stdout);
         return 0;
     }
 
@@ -1389,8 +1389,8 @@ test_noops_and_autofails(void)
 
     if (FALSE == s3_test_bucket_defined) {
         SKIPPED();
-        puts("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
-        fflush(stdout);
+        HDputs("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
+        HDfflush(stdout);
         return 0;
     }
 
@@ -1515,15 +1515,15 @@ test_cmp(void)
 
     if (s3_test_credentials_loaded == 0) {
         SKIPPED();
-        puts("    s3 credentials are not loaded");
-        fflush(stdout);
+        HDputs("    s3 credentials are not loaded");
+        HDfflush(stdout);
         return 0;
     }
 
     if (FALSE == s3_test_bucket_defined) {
         SKIPPED();
-        puts("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
-        fflush(stdout);
+        HDputs("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
+        HDfflush(stdout);
         return 0;
     }
 
@@ -1636,15 +1636,15 @@ test_H5F_integration(void)
 
     if (s3_test_credentials_loaded == 0) {
         SKIPPED();
-        puts("    s3 credentials are not loaded");
-        fflush(stdout);
+        HDputs("    s3 credentials are not loaded");
+        HDfflush(stdout);
         return 0;
     }
 
     if (FALSE == s3_test_bucket_defined) {
         SKIPPED();
-        puts("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
-        fflush(stdout);
+        HDputs("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
+        HDfflush(stdout);
         return 0;
     }
 
@@ -1691,7 +1691,7 @@ error:
      * CLEANUP *
      ***********/
     HDprintf("\nerror!");
-    fflush(stdout);
+    HDfflush(stdout);
 
     if (fapl_id >= 0) {
         H5E_BEGIN_TRY { (void)H5Pclose(fapl_id); }
diff --git a/test/s3comms.c b/test/s3comms.c
index 862914e..c6173fd 100644
--- a/test/s3comms.c
+++ b/test/s3comms.c
@@ -311,7 +311,7 @@ jserr_str(const char *expected, const char *actual, const char *reason)
  *----------------------------------------------------------------------------
  */
 #define JSVERIFY_STR(expected, actual, reason)                                                               \
-    if (strcmp((actual), (expected)) != 0) {                                                                 \
+    if (HDstrcmp((actual), (expected)) != 0) {                                                               \
         JSERR_STR((expected), (actual), (reason));                                                           \
         goto error;                                                                                          \
     } /* JSVERIFY_STR */
@@ -359,7 +359,7 @@ jserr_str(const char *expected, const char *actual, const char *reason)
  *----------------------------------------------------------------------------
  */
 #define JSVERIFY_STR(actual, expected, reason)                                                               \
-    if (strcmp((actual), (expected)) != 0) {                                                                 \
+    if (HDstrcmp((actual), (expected)) != 0) {                                                               \
         JSERR_STR((expected), (actual), (reason));                                                           \
         goto error;                                                                                          \
     } /* JSVERIFY_STR */
@@ -1281,10 +1281,10 @@ test_HMAC_SHA256(void)
             cases[i].msg);
         if (cases[i].ret == SUCCEED) {
 #ifdef VERBOSE
-            if (0 != strncmp(cases[i].exp, dest, HDstrlen(cases[i].exp))) {
+            if (0 != HDstrncmp(cases[i].exp, dest, HDstrlen(cases[i].exp))) {
                 /* print out how wrong things are, and then fail
                  */
-                dest = (char *)realloc(dest, cases[i].dest_size + 1);
+                dest = (char *)HDrealloc(dest, cases[i].dest_size + 1);
                 HDassert(dest != NULL);
                 dest[cases[i].dest_size] = 0;
                 HDfprintf(stdout, "ERROR:\n!!! \"%s\"\n != \"%s\"\n", cases[i].exp, dest);
@@ -1293,17 +1293,17 @@ test_HMAC_SHA256(void)
 #else  /* VERBOSE not defined */
             /* simple pass/fail test
              */
-            JSVERIFY(0, strncmp(cases[i].exp, dest, HDstrlen(cases[i].exp)), NULL);
+            JSVERIFY(0, HDstrncmp(cases[i].exp, dest, HDstrlen(cases[i].exp)), NULL);
 #endif /* VERBOSE */
         }
-        free(dest);
+        HDfree(dest);
     }
 
     PASSED();
     return 0;
 
 error:
-    free(dest);
+    HDfree(dest);
     return -1;
 
 } /* end test_HMAC_SHA256() */
@@ -1369,9 +1369,9 @@ test_nlowercase(void)
 
         JSVERIFY(SUCCEED, H5FD_s3comms_nlowercase(dest, cases[i].in, cases[i].len), cases[i].in)
         if (cases[i].len > 0) {
-            JSVERIFY(0, strncmp(dest, cases[i].exp, cases[i].len), NULL)
+            JSVERIFY(0, HDstrncmp(dest, cases[i].exp, cases[i].len), NULL)
         }
-        free(dest);
+        HDfree(dest);
     } /* end for each testcase */
 
     JSVERIFY(FAIL, H5FD_s3comms_nlowercase(NULL, cases[0].in, cases[0].len), "null distination should fail")
@@ -1380,7 +1380,7 @@ test_nlowercase(void)
     return 0;
 
 error:
-    free(dest);
+    HDfree(dest);
     return -1;
 
 } /* end test_nlowercase() */
@@ -1741,7 +1741,7 @@ test_percent_encode_char(void)
         JSVERIFY(SUCCEED, H5FD_s3comms_percent_encode_char(dest, (const unsigned char)cases[i].c, &dest_len),
                  NULL)
         JSVERIFY(cases[i].exp_len, dest_len, NULL)
-        JSVERIFY(0, strncmp(dest, cases[i].exp, dest_len), NULL)
+        JSVERIFY(0, HDstrncmp(dest, cases[i].exp, dest_len), NULL)
         JSVERIFY_STR(cases[i].exp, dest, NULL)
     }
 
@@ -1780,8 +1780,8 @@ test_s3r_get_filesize(void)
      */
     if (FALSE == s3_test_bucket_defined) {
         SKIPPED();
-        puts("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
-        fflush(stdout);
+        HDputs("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
+        HDfflush(stdout);
         return 0;
     }
 
@@ -1840,14 +1840,14 @@ test_s3r_open(void)
 
     if (s3_test_credentials_loaded == 0) {
         SKIPPED();
-        puts("    s3 credentials are not loaded");
-        fflush(stdout);
+        HDputs("    s3 credentials are not loaded");
+        HDfflush(stdout);
         return 0;
     }
     if (FALSE == s3_test_bucket_defined) {
         SKIPPED();
-        puts("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
-        fflush(stdout);
+        HDputs("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
+        HDfflush(stdout);
         return 0;
     }
 
@@ -1873,7 +1873,7 @@ test_s3r_open(void)
         FAIL_IF(purl->port == NULL);
         FAIL_IF(5 < HDsnprintf(purl->port, 5, "9000"))
     }
-    else if (strcmp(purl->port, "9000") != 0) {
+    else if (HDstrcmp(purl->port, "9000") != 0) {
         FAIL_IF(5 < HDsnprintf(purl->port, 5, "9000"))
     }
     else {
@@ -2044,8 +2044,8 @@ test_s3r_read(void)
      */
     if (FALSE == s3_test_bucket_defined) {
         SKIPPED();
-        puts("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
-        fflush(stdout);
+        HDputs("    environment variable HDF5_ROS3_TEST_BUCKET_URL not defined");
+        HDfflush(stdout);
         return 0;
     }
 
@@ -2105,7 +2105,7 @@ test_s3r_read(void)
     JSVERIFY(SUCCEED, H5FD_s3comms_s3r_read(handle, (haddr_t)6370, (size_t)0, buffer), NULL)
     JSVERIFY(
         0,
-        strncmp(
+        HDstrncmp(
             buffer,
             "And my soul from out that shadow that lies floating on the floor\nShall be lifted—nevermore!\n",
             94),
@@ -2122,7 +2122,7 @@ test_s3r_read(void)
              H5FD_s3comms_s3r_read(handle, (haddr_t)6400, (size_t)100, /* 6400+100 > 6464 */
                                    buffer),
              NULL)
-    JSVERIFY(0, strcmp("", buffer), NULL)
+    JSVERIFY(0, HDstrcmp("", buffer), NULL)
 
     /************************
      * read starts past eof *
@@ -2132,14 +2132,14 @@ test_s3r_read(void)
              H5FD_s3comms_s3r_read(handle, (haddr_t)1200699, /* 1200699 > 6464 */
                                    (size_t)100, buffer),
              NULL)
-    JSVERIFY(0, strcmp("", buffer), NULL)
+    JSVERIFY(0, HDstrcmp("", buffer), NULL)
 
     /**********************
      * read starts on eof *
      **********************/
 
     JSVERIFY(FAIL, H5FD_s3comms_s3r_read(handle, (haddr_t)6464, (size_t)0, buffer), NULL)
-    JSVERIFY(0, strcmp("", buffer), NULL)
+    JSVERIFY(0, HDstrcmp("", buffer), NULL)
 
     /*************
      * TEAR DOWN *
@@ -2229,10 +2229,10 @@ test_signing_key(void)
         JSVERIFY(SUCCEED, H5FD_s3comms_signing_key(key, cases[i].secret_key, cases[i].region, cases[i].when),
                  NULL)
 
-        JSVERIFY(0, strncmp((const char *)cases[i].exp, (const char *)key, SHA256_DIGEST_LENGTH),
+        JSVERIFY(0, HDstrncmp((const char *)cases[i].exp, (const char *)key, SHA256_DIGEST_LENGTH),
                  (const char *)cases[i].exp)
 
-        free(key);
+        HDfree(key);
         key = NULL;
     }
 
@@ -2255,7 +2255,7 @@ test_signing_key(void)
     JSVERIFY(FAIL, H5FD_s3comms_signing_key(key, cases[0].secret_key, cases[0].region, NULL),
              "time string cannot be NULL")
 
-    free(key);
+    HDfree(key);
     key = NULL;
 
     PASSED();
@@ -2263,7 +2263,7 @@ test_signing_key(void)
 
 error:
     if (key != NULL) {
-        free(key);
+        HDfree(key);
     }
 
     return -1;
@@ -2411,9 +2411,9 @@ test_trim(void)
         JSVERIFY(SUCCEED, H5FD_s3comms_trim(dest, str, cases[i].in_len, &dest_len), NULL)
         JSVERIFY(cases[i].exp_len, dest_len, cases[i].in)
         if (dest_len > 0) {
-            JSVERIFY(0, strncmp(cases[i].exp, dest, dest_len), cases[i].exp)
+            JSVERIFY(0, HDstrncmp(cases[i].exp, dest, dest_len), cases[i].exp)
         }
-        free(str);
+        HDfree(str);
         str = NULL;
     } /* end for each testcase */
 
@@ -2424,9 +2424,9 @@ test_trim(void)
     HDassert(str == NULL);
     str = (char *)HDmalloc(sizeof(char *) * 11);
     HDassert(str != NULL);
-    memcpy(str, "some text ", 11); /* string with null terminator */
+    HDmemcpy(str, "some text ", 11); /* string with null terminator */
     JSVERIFY(FAIL, H5FD_s3comms_trim(NULL, str, 10, &dest_len), "destination for trim cannot be NULL");
-    free(str);
+    HDfree(str);
     str = NULL;
 
     PASSED();
@@ -2434,7 +2434,7 @@ test_trim(void)
 
 error:
     if (str != NULL) {
-        free(str);
+        HDfree(str);
     }
     return -1;
 
@@ -2525,9 +2525,9 @@ test_uriencode(void)
                  H5FD_s3comms_uriencode(dest, cases[i].str, str_len, cases[i].encode_slash, &dest_written),
                  NULL);
         JSVERIFY(HDstrlen(cases[i].expected), dest_written, NULL)
-        JSVERIFY(0, strncmp(dest, cases[i].expected, dest_written), cases[i].expected);
+        JSVERIFY(0, HDstrncmp(dest, cases[i].expected, dest_written), cases[i].expected);
 
-        free(dest);
+        HDfree(dest);
         dest = NULL;
     } /* end for each testcase */
 
@@ -2543,7 +2543,7 @@ test_uriencode(void)
     JSVERIFY(FAIL, H5FD_s3comms_uriencode(dest, NULL, 5, false, &dest_written),
              "source string cannot be NULL");
 
-    free(dest);
+    HDfree(dest);
     dest = NULL;
 
     PASSED();
@@ -2551,7 +2551,7 @@ test_uriencode(void)
 
 error:
     if (dest != NULL) {
-        free(dest);
+        HDfree(dest);
     }
     return -1;
 
diff --git a/test/set_extent.c b/test/set_extent.c
index 133ba48..2ad4fd5 100644
--- a/test/set_extent.c
+++ b/test/set_extent.c
@@ -2621,7 +2621,7 @@ test_random_rank4_vl(hid_t fapl, hid_t dcpl, hbool_t do_fillvalue, hbool_t disab
         TEST_ERROR
     if (H5Treclaim(type, mspace, H5P_DEFAULT, wbuf) < 0)
         TEST_ERROR
-    free(fill_value.p);
+    HDfree(fill_value.p);
     if (H5Sclose(mspace) < 0)
         TEST_ERROR
     if (H5Pclose(my_dcpl) < 0)
diff --git a/test/tarray.c b/test/tarray.c
index ba0982f..d278f51 100644
--- a/test/tarray.c
+++ b/test/tarray.c
@@ -2222,5 +2222,5 @@ test_array(void)
 void
 cleanup_array(void)
 {
-    remove(FILENAME);
+    HDremove(FILENAME);
 } /* end cleanup_array() */
diff --git a/test/tcoords.c b/test/tcoords.c
index e92bdde..a52851d 100644
--- a/test/tcoords.c
+++ b/test/tcoords.c
@@ -87,10 +87,10 @@ test_singleEnd_selElements(hid_t file, hbool_t is_chunked)
     }
 
     /* Construct dataset's name */
-    memset(dset_name, 0, (size_t)NAME_LEN);
-    strcat(dset_name, SINGLE_END_DSET);
+    HDmemset(dset_name, 0, (size_t)NAME_LEN);
+    HDstrcat(dset_name, SINGLE_END_DSET);
     if (is_chunked)
-        strcat(dset_name, "_chunked");
+        HDstrcat(dset_name, "_chunked");
 
     did = H5Dcreate2(file, dset_name, H5T_NATIVE_INT, sid, H5P_DEFAULT, plid, H5P_DEFAULT);
     CHECK(did, FAIL, "H5Dcreate2");
@@ -259,10 +259,10 @@ test_singleEnd_selHyperslab(hid_t file, hbool_t is_chunked)
     hsize_t mem3_block[4]  = {1, 3, 6, 1};
 
     /* Construct dataset's name */
-    memset(dset_name, 0, NAME_LEN);
-    strcat(dset_name, SINGLE_END_DSET);
+    HDmemset(dset_name, 0, NAME_LEN);
+    HDstrcat(dset_name, SINGLE_END_DSET);
     if (is_chunked)
-        strcat(dset_name, "_chunked");
+        HDstrcat(dset_name, "_chunked");
 
     /* Dataspace for the dataset in file */
     sid = H5Screate_simple(4, da_dims, da_dims);
@@ -436,10 +436,10 @@ test_multiple_ends(hid_t file, hbool_t is_chunked)
     }
 
     /* Construct dataset's name */
-    memset(dset_name, 0, NAME_LEN);
-    strcat(dset_name, MULTI_ENDS_SEL_HYPER_DSET);
+    HDmemset(dset_name, 0, NAME_LEN);
+    HDstrcat(dset_name, MULTI_ENDS_SEL_HYPER_DSET);
     if (is_chunked)
-        strcat(dset_name, "_chunked");
+        HDstrcat(dset_name, "_chunked");
 
     did = H5Dcreate2(file, dset_name, H5T_NATIVE_INT, sid, H5P_DEFAULT, plid, H5P_DEFAULT);
     CHECK(did, FAIL, "H5Dcreate2");
@@ -687,5 +687,5 @@ test_coords(void)
 void
 cleanup_coords(void)
 {
-    remove(FILENAME);
+    HDremove(FILENAME);
 }
diff --git a/test/testframe.c b/test/testframe.c
index 22f694e..bf6a0e8 100644
--- a/test/testframe.c
+++ b/test/testframe.c
@@ -442,15 +442,15 @@ GetTestExpress(void)
 
     /* set it here for now.  Should be done in something like h5test_init(). */
     if (TestExpress == -1) {
-        env_val = getenv("HDF5TestExpress");
+        env_val = HDgetenv("HDF5TestExpress");
 
         if (env_val == NULL)
             SetTestExpress(1);
-        else if (strcmp(env_val, "0") == 0)
+        else if (HDstrcmp(env_val, "0") == 0)
             SetTestExpress(0);
-        else if (strcmp(env_val, "1") == 0)
+        else if (HDstrcmp(env_val, "1") == 0)
             SetTestExpress(1);
-        else if (strcmp(env_val, "2") == 0)
+        else if (HDstrcmp(env_val, "2") == 0)
             SetTestExpress(2);
         else
             SetTestExpress(3);
@@ -521,7 +521,7 @@ ParseTestVerbosity(char *argv)
     else if (*argv == 'h')
         SetTestVerbosity(VERBO_HI);
     else
-        SetTestVerbosity(atoi(argv));
+        SetTestVerbosity(HDatoi(argv));
 }
 
 /*
diff --git a/test/testhdf5.c b/test/testhdf5.c
index 152719a..ab79f28 100644
--- a/test/testhdf5.c
+++ b/test/testhdf5.c
@@ -82,7 +82,7 @@ main(int argc, char *argv[])
         TestSummary();
 
     /* Clean up test files, if allowed */
-    if (GetTestCleanup() && !getenv("HDF5_NOCLEANUP"))
+    if (GetTestCleanup() && !HDgetenv("HDF5_NOCLEANUP"))
         TestCleanup();
 
     /* Release test infrastructure */
diff --git a/test/testmeta.c b/test/testmeta.c
index fee1954..c3044a6 100644
--- a/test/testmeta.c
+++ b/test/testmeta.c
@@ -83,7 +83,7 @@ main(void)
 
     for (i = 0; i < NEXTARRAYS; i++) {
         /* Create dataset */
-        sprintf(name, "/ExtArray%06d", i);
+        HDsprintf(name, "/ExtArray%06d", i);
         dataset_id =
             H5Dcreate2(file_id, name, H5T_NATIVE_FLOAT, dataspace_id, H5P_DEFAULT, prop_id, H5P_DEFAULT);
 
@@ -103,7 +103,7 @@ main(void)
         /* Removed print statement as it would lock system resources on Windows */
         /*
          * HDprintf("\rWriting Object #%d of %d", j+1, NDATAOBJECTS);
-         * fflush(stdout);
+         * HDfflush(stdout);
          */
         floatval = (float)j;
 
diff --git a/test/tfile.c b/test/tfile.c
index 2d42cc5..a0bceac 100644
--- a/test/tfile.c
+++ b/test/tfile.c
@@ -4195,7 +4195,7 @@ set_multi_split(hid_t fapl, hsize_t pagesize, hbool_t split)
 
     /* Free memb_name */
     for (mt = H5FD_MEM_DEFAULT; mt < H5FD_MEM_NTYPES; mt++)
-        free(memb_name[mt]);
+        HDfree(memb_name[mt]);
 
     return 0;
 
diff --git a/test/tgenprop.c b/test/tgenprop.c
index 910153c..c1d9cac 100644
--- a/test/tgenprop.c
+++ b/test/tgenprop.c
@@ -2172,5 +2172,5 @@ test_genprop(void)
 void
 cleanup_genprop(void)
 {
-    remove(FILENAME);
+    HDremove(FILENAME);
 }
diff --git a/test/th5o.c b/test/th5o.c
index 8885eb4..8b67159 100644
--- a/test/th5o.c
+++ b/test/th5o.c
@@ -1767,5 +1767,5 @@ test_h5o(void)
 void
 cleanup_h5o(void)
 {
-    remove(TEST_FILENAME);
+    HDremove(TEST_FILENAME);
 }
diff --git a/test/th5s.c b/test/th5s.c
index 07cb0ab..04ac2e6 100644
--- a/test/th5s.c
+++ b/test/th5s.c
@@ -1936,7 +1936,7 @@ test_h5s_encode_irregular_hyper(H5F_libver_t low, H5F_libver_t high)
                 break;
 
             default:
-                assert(0);
+                HDassert(0);
                 break;
         }
 
@@ -3400,9 +3400,9 @@ test_h5s(void)
 void
 cleanup_h5s(void)
 {
-    remove(DATAFILE);
-    remove(NULLFILE);
-    remove(BASICFILE);
-    remove(ZEROFILE);
-    remove(VERBFNAME);
+    HDremove(DATAFILE);
+    HDremove(NULLFILE);
+    HDremove(BASICFILE);
+    HDremove(ZEROFILE);
+    HDremove(VERBFNAME);
 }
diff --git a/test/thread_id.c b/test/thread_id.c
index ce60893..d8ddaf8 100644
--- a/test/thread_id.c
+++ b/test/thread_id.c
@@ -73,7 +73,7 @@ pthread_barrier_init(pthread_barrier_t *barrier, const pthread_barrierattr_t *at
     if (attr != NULL)
         return EINVAL;
 
-    memset(barrier, 0, sizeof(*barrier));
+    HDmemset(barrier, 0, sizeof(*barrier));
 
     barrier->count = count;
 
@@ -96,7 +96,7 @@ barrier_lock(pthread_barrier_t *barrier)
     int rc;
 
     if ((rc = pthread_mutex_lock(&barrier->mtx)) != 0) {
-        my_errx(EXIT_FAILURE, "%s: pthread_mutex_lock: %s", __func__, strerror(rc));
+        my_errx(EXIT_FAILURE, "%s: pthread_mutex_lock: %s", __func__, HDstrerror(rc));
     }
 }
 
@@ -106,7 +106,7 @@ barrier_unlock(pthread_barrier_t *barrier)
     int rc;
 
     if ((rc = pthread_mutex_unlock(&barrier->mtx)) != 0) {
-        my_errx(EXIT_FAILURE, "%s: pthread_mutex_unlock: %s", __func__, strerror(rc));
+        my_errx(EXIT_FAILURE, "%s: pthread_mutex_unlock: %s", __func__, HDstrerror(rc));
     }
 }
 
@@ -203,16 +203,16 @@ atomic_printf(const char *fmt, ...)
     va_list ap;
     ssize_t nprinted, nwritten;
 
-    va_start(ap, fmt);
-    nprinted = vsnprintf(buf, sizeof(buf), fmt, ap);
-    va_end(ap);
+    HDva_start(ap, fmt);
+    nprinted = HDvsnprintf(buf, sizeof(buf), fmt, ap);
+    HDva_end(ap);
 
     if (nprinted == -1)
         my_err(EXIT_FAILURE, "%s.%d: vsnprintf", __func__, __LINE__);
     else if (nprinted >= (ssize_t)sizeof(buf))
         my_errx(EXIT_FAILURE, "%s.%d: vsnprintf overflowed", __func__, __LINE__);
 
-    nwritten = write(STDOUT_FILENO, buf, (size_t)nprinted);
+    nwritten = HDwrite(STDOUT_FILENO, buf, (size_t)nprinted);
     if (nwritten < nprinted) {
         my_errx(EXIT_FAILURE, "%s.%d: write error or short write", __func__, __LINE__);
     }
diff --git a/test/timer.c b/test/timer.c
index e907655..24f3245 100644
--- a/test/timer.c
+++ b/test/timer.c
@@ -146,7 +146,7 @@ test_timer_system_user(void)
      */
     if (timer.initial.system < (double)0.0f || timer.initial.user < (double)0.0f) {
         SKIPPED();
-        printf("NOTE: No suitable way to get system/user times on this platform.\n");
+        HDprintf("NOTE: No suitable way to get system/user times on this platform.\n");
         return 0;
     }
 
@@ -383,7 +383,7 @@ main(void)
 
     h5_reset();
 
-    printf("Testing platform-independent timer functionality.\n");
+    HDprintf("Testing platform-independent timer functionality.\n");
 
     nerrors += test_time_formatting() < 0 ? 1 : 0;
     nerrors += test_timer_system_user() < 0 ? 1 : 0;
@@ -391,11 +391,12 @@ main(void)
     nerrors += test_timer_functionality() < 0 ? 1 : 0;
 
     if (nerrors) {
-        printf("***** %d platform-independent timer TEST%s FAILED! *****\n", nerrors, nerrors > 1 ? "S" : "");
+        HDprintf("***** %d platform-independent timer TEST%s FAILED! *****\n", nerrors,
+                 nerrors > 1 ? "S" : "");
         return 1;
     }
     else {
-        printf("All platform-independent timer tests passed.\n");
+        HDprintf("All platform-independent timer tests passed.\n");
         return 0;
     }
 }
diff --git a/test/titerate.c b/test/titerate.c
index bcf19b9..050dcec 100644
--- a/test/titerate.c
+++ b/test/titerate.c
@@ -966,7 +966,7 @@ find_err_msg_cb(unsigned H5_ATTR_UNUSED n, const H5E_error2_t *err_desc, void *_
         return H5_ITER_ERROR;
 
     /* If the searched error message is found, stop the iteration */
-    if (err_desc->desc != NULL && strcmp(err_desc->desc, searched_err->message) == 0) {
+    if (err_desc->desc != NULL && HDstrcmp(err_desc->desc, searched_err->message) == 0) {
         searched_err->found = true;
         status              = H5_ITER_STOP;
     }
diff --git a/test/tmisc.c b/test/tmisc.c
index a6db198..2d842be 100644
--- a/test/tmisc.c
+++ b/test/tmisc.c
@@ -2837,7 +2837,7 @@ test_misc16(void)
         if (HDstrlen(wdata[i]) != HDstrlen(rdata[i])) {
             TestErrPrintf(
                 "Line %u: VL data length don't match!, strlen(wdata[%d])=%d, strlen(rdata[%d])=%d\n",
-                (unsigned)__LINE__, (int)i, (int)strlen(wdata[i]), (int)i, (int)strlen(rdata[i]));
+                (unsigned)__LINE__, (int)i, (int)HDstrlen(wdata[i]), (int)i, (int)HDstrlen(rdata[i]));
             continue;
         } /* end if */
         if (HDstrcmp(wdata[i], rdata[i]) != 0) {
@@ -2922,7 +2922,7 @@ test_misc17(void)
         if (HDstrlen(wdata[i]) != HDstrlen(rdata[i])) {
             TestErrPrintf(
                 "Line %u: VL data length don't match!, strlen(wdata[%d])=%d, strlen(rdata[%d])=%d\n",
-                (unsigned)__LINE__, (int)i, (int)strlen(wdata[i]), (int)i, (int)strlen(rdata[i]));
+                (unsigned)__LINE__, (int)i, (int)HDstrlen(wdata[i]), (int)i, (int)HDstrlen(rdata[i]));
             continue;
         } /* end if */
         if (HDstrcmp(wdata[i], rdata[i]) != 0) {
diff --git a/test/trefer_deprec.c b/test/trefer_deprec.c
index 6191526..d2a403f 100644
--- a/test/trefer_deprec.c
+++ b/test/trefer_deprec.c
@@ -1406,9 +1406,9 @@ test_reference_group(void)
 
     /* Create bottom dataset */
     did = H5Dcreate2(gid, DSETNAME2, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
-    assert(did > 0);
+    HDassert(did > 0);
     ret = H5Dclose(did);
-    assert(ret >= 0);
+    HDassert(ret >= 0);
 
     ret = H5Gclose(gid);
     CHECK(ret, FAIL, "H5Gclose");
diff --git a/test/tselect.c b/test/tselect.c
index f40b2b9..2aeba77 100644
--- a/test/tselect.c
+++ b/test/tselect.c
@@ -5239,7 +5239,7 @@ test_select_hyper_union_stagger(void)
     CHECK(error, FAIL, "H5Fclose");
 
     /* Initialize intput buffer */
-    memset(data_out, 0, 7 * 7 * sizeof(int));
+    HDmemset(data_out, 0, 7 * 7 * sizeof(int));
 
     /* Open file */
     file_id = H5Fopen(FILENAME, H5F_ACC_RDONLY, H5P_DEFAULT);
@@ -5537,7 +5537,7 @@ test_select_hyper_valid_combination(void)
 
     /* Output message about test being performed */
     MESSAGE(6, ("Testing Selection Combination Validity\n"));
-    assert(SPACE9_DIM2 >= POINT1_NPOINTS);
+    HDassert(SPACE9_DIM2 >= POINT1_NPOINTS);
 
     /* Create dataspace for single point selection */
     single_pt_sid = H5Screate_simple(SPACE9_RANK, dims2D, NULL);
@@ -8377,7 +8377,7 @@ test_shape_same(void)
 
     /* Output message about test being performed */
     MESSAGE(6, ("Testing Same Shape Comparisons\n"));
-    assert(SPACE9_DIM2 >= POINT1_NPOINTS);
+    HDassert(SPACE9_DIM2 >= POINT1_NPOINTS);
 
     /* Create dataspace for "all" selection */
     all_sid = H5Screate_simple(SPACE9_RANK, dims, NULL);
@@ -14648,7 +14648,7 @@ test_internal_consistency(void)
 
     /* Output message about test being performed */
     MESSAGE(6, ("Testing Consistency of Internal States\n"));
-    assert(SPACE9_DIM2 >= POINT1_NPOINTS);
+    HDassert(SPACE9_DIM2 >= POINT1_NPOINTS);
 
     /* Create dataspace for "all" selection */
     all_sid = H5Screate_simple(SPACE9_RANK, dims, NULL);
diff --git a/test/ttsafe.c b/test/ttsafe.c
index d2085b9..2b98ded 100644
--- a/test/ttsafe.c
+++ b/test/ttsafe.c
@@ -134,7 +134,7 @@ main(int argc, char *argv[])
         TestSummary();
 
     /* Clean up test files, if allowed */
-    if (GetTestCleanup() && !getenv("HDF5_NOCLEANUP"))
+    if (GetTestCleanup() && !HDgetenv("HDF5_NOCLEANUP"))
         TestCleanup();
 
     /* Release test infrastructure */
diff --git a/test/ttsafe_cancel.c b/test/ttsafe_cancel.c
index 1e40c58..2ec9a20 100644
--- a/test/ttsafe_cancel.c
+++ b/test/ttsafe_cancel.c
@@ -65,46 +65,46 @@ tts_cancel(void)
 
     /* make thread scheduling global */
     ret = pthread_attr_init(&attribute);
-    assert(ret == 0);
+    HDassert(ret == 0);
 #ifdef H5_HAVE_SYSTEM_SCOPE_THREADS
     ret = pthread_attr_setscope(&attribute, PTHREAD_SCOPE_SYSTEM);
-    assert(ret == 0);
+    HDassert(ret == 0);
 #endif /* H5_HAVE_SYSTEM_SCOPE_THREADS */
 
     /* Initialize mutex & condition variables */
     ret = pthread_mutex_init(&mutex, NULL);
-    assert(ret == 0);
+    HDassert(ret == 0);
     ret = pthread_cond_init(&cond, NULL);
-    assert(ret == 0);
+    HDassert(ret == 0);
 
     /*
      * Create a hdf5 file using H5F_ACC_TRUNC access, default file
      * creation plist and default file access plist
      */
     cancel_file = H5Fcreate(FILENAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
-    assert(cancel_file >= 0);
+    HDassert(cancel_file >= 0);
     ret = pthread_create(&childthread, &attribute, tts_cancel_thread, NULL);
-    assert(ret == 0);
+    HDassert(ret == 0);
     tts_cancel_barrier();
     ret = pthread_cancel(childthread);
-    assert(ret == 0);
+    HDassert(ret == 0);
 
     dataset = H5Dopen2(cancel_file, DATASETNAME, H5P_DEFAULT);
-    assert(dataset >= 0);
+    HDassert(dataset >= 0);
     ret = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &buffer);
-    assert(ret >= 0);
+    HDassert(ret >= 0);
 
     if (buffer != 11)
         TestErrPrintf("operation unsuccessful with value at %d instead of 11\n", buffer);
 
     ret = H5Dclose(dataset);
-    assert(ret >= 0);
+    HDassert(ret >= 0);
     ret = H5Fclose(cancel_file);
-    assert(ret >= 0);
+    HDassert(ret >= 0);
 
     /* Destroy the thread attribute */
     ret = pthread_attr_destroy(&attribute);
-    assert(ret == 0);
+    HDassert(ret == 0);
 } /* end tts_cancel() */
 
 void *
diff --git a/test/ttsafe_dcreate.c b/test/ttsafe_dcreate.c
index cedafd0..a5a22be 100644
--- a/test/ttsafe_dcreate.c
+++ b/test/ttsafe_dcreate.c
@@ -140,7 +140,7 @@ tts_dcreate_creator(void *_thread_data)
     hsize_t            dimsf[1]; /* dataset dimensions */
     struct thread_info thread_data;
 
-    memcpy(&thread_data, _thread_data, sizeof(struct thread_info));
+    HDmemcpy(&thread_data, _thread_data, sizeof(struct thread_info));
 
     /* define dataspace for dataset */
     dimsf[0]  = 1;
diff --git a/test/tunicode.c b/test/tunicode.c
index 28f819b..2fed891 100644
--- a/test/tunicode.c
+++ b/test/tunicode.c
@@ -532,7 +532,7 @@ test_attrname(hid_t fid, const char *string)
     CHECK(attr_id, FAIL, "H5Acreate2");
     size = H5Aget_name(attr_id, (size_t)MAX_STRING_LENGTH, read_buf);
     CHECK(size, FAIL, "H5Aget_name");
-    ret = strcmp(read_buf, string);
+    ret = HDstrcmp(read_buf, string);
     VERIFY(ret, 0, "strcmp");
     read_buf[0] = '\0';
 
@@ -541,7 +541,7 @@ test_attrname(hid_t fid, const char *string)
     CHECK(ret, FAIL, "H5Awrite");
     ret = H5Aread(attr_id, dtype_id, read_buf);
     CHECK(ret, FAIL, "H5Aread");
-    ret = strcmp(read_buf, string);
+    ret = HDstrcmp(read_buf, string);
     VERIFY(ret, 0, "strcmp");
 
     /* Clean up */
@@ -682,7 +682,7 @@ test_enum(hid_t H5_ATTR_UNUSED fid, const char *string)
     VERIFY(val, E1_WHITE, "H5Tenum_valueof");
     ret = H5Tenum_nameof(type_id, &val, readbuf, (size_t)MAX_STRING_LENGTH);
     CHECK(ret, FAIL, "H5Tenum_nameof");
-    ret = strcmp(readbuf, string);
+    ret = HDstrcmp(readbuf, string);
     VERIFY(ret, 0, "strcmp");
 
     /* Close the datatype */
@@ -709,7 +709,7 @@ test_opaque(hid_t H5_ATTR_UNUSED fid, const char *string)
 
     /* Read the tag back. */
     read_buf = H5Tget_tag(type_id);
-    ret      = strcmp(read_buf, string);
+    ret      = HDstrcmp(read_buf, string);
     VERIFY(ret, 0, "H5Tget_tag");
     H5free_memory(read_buf);
 
diff --git a/test/tvlstr.c b/test/tvlstr.c
index c8e65b5..c2d2f2d 100644
--- a/test/tvlstr.c
+++ b/test/tvlstr.c
@@ -203,7 +203,7 @@ test_vlstrings_basic(void)
     for (i = 0; i < SPACE1_DIM1; i++) {
         if (HDstrlen(wdata[i]) != HDstrlen(rdata[i])) {
             TestErrPrintf("VL data length don't match!, strlen(wdata[%d])=%d, strlen(rdata[%d])=%d\n", (int)i,
-                          (int)strlen(wdata[i]), (int)i, (int)HDstrlen(rdata[i]));
+                          (int)HDstrlen(wdata[i]), (int)i, (int)HDstrlen(rdata[i]));
             continue;
         } /* end if */
         if (HDstrcmp(wdata[i], rdata[i]) != 0) {
@@ -307,7 +307,7 @@ test_vlstrings_special(void)
     for (i = 0; i < SPACE1_DIM1; i++) {
         if (HDstrlen(wdata[i]) != HDstrlen(rdata[i])) {
             TestErrPrintf("VL data length don't match!, strlen(wdata[%d])=%d, strlen(rdata[%d])=%d\n", (int)i,
-                          (int)strlen(wdata[i]), (int)i, (int)HDstrlen(rdata[i]));
+                          (int)HDstrlen(wdata[i]), (int)i, (int)HDstrlen(rdata[i]));
             continue;
         } /* end if */
         if ((wdata[i] == NULL && rdata[i] != NULL) || (rdata[i] == NULL && wdata[i] != NULL)) {
@@ -536,7 +536,7 @@ test_compact_vlstring(void)
     for (i = 0; i < SPACE1_DIM1; i++) {
         if (HDstrlen(wdata[i]) != HDstrlen(rdata[i])) {
             TestErrPrintf("VL data length don't match!, strlen(wdata[%d])=%d, strlen(rdata[%d])=%d\n", (int)i,
-                          (int)strlen(wdata[i]), (int)i, (int)HDstrlen(rdata[i]));
+                          (int)HDstrlen(wdata[i]), (int)i, (int)HDstrlen(rdata[i]));
             continue;
         } /* end if */
         if (HDstrcmp(wdata[i], rdata[i]) != 0) {
diff --git a/test/tvltypes.c b/test/tvltypes.c
index 50cfbd7..47b28d3 100644
--- a/test/tvltypes.c
+++ b/test/tvltypes.c
@@ -2676,13 +2676,13 @@ test_vltypes_fill_value(void)
                 } break;
 
                 case H5D_VIRTUAL:
-                    assert(0 && "Invalid layout type!");
+                    HDassert(0 && "Invalid layout type!");
                     break;
 
                 case H5D_LAYOUT_ERROR:
                 case H5D_NLAYOUTS:
                 default:
-                    assert(0 && "Unknown layout type!");
+                    HDassert(0 && "Unknown layout type!");
                     break;
             } /* end switch */
 
@@ -2784,13 +2784,13 @@ test_vltypes_fill_value(void)
                     break;
 
                 case H5D_VIRTUAL:
-                    assert(0 && "Invalid layout type!");
+                    HDassert(0 && "Invalid layout type!");
                     break;
 
                 case H5D_LAYOUT_ERROR:
                 case H5D_NLAYOUTS:
                 default:
-                    assert(0 && "Unknown layout type!");
+                    HDassert(0 && "Unknown layout type!");
                     break;
             } /* end switch */
 
@@ -2969,13 +2969,13 @@ test_vltypes_fill_value(void)
                     break;
 
                 case H5D_VIRTUAL:
-                    assert(0 && "Invalid layout type!");
+                    HDassert(0 && "Invalid layout type!");
                     break;
 
                 case H5D_LAYOUT_ERROR:
                 case H5D_NLAYOUTS:
                 default:
-                    assert(0 && "Unknown layout type!");
+                    HDassert(0 && "Unknown layout type!");
                     break;
             } /* end switch */
 
@@ -3241,5 +3241,5 @@ test_vltypes(void)
 void
 cleanup_vltypes(void)
 {
-    remove(FILENAME);
+    HDremove(FILENAME);
 }
diff --git a/test/twriteorder.c b/test/twriteorder.c
index 83a615c..9c8a145 100644
--- a/test/twriteorder.c
+++ b/test/twriteorder.c
@@ -141,21 +141,21 @@ parse_option(int argc, char *const argv[])
                 HDexit(EXIT_SUCCESS);
                 break;
             case 'b': /* number of planes to write/read */
-                if ((blocksize_g = atoi(optarg)) <= 0) {
+                if ((blocksize_g = HDatoi(optarg)) <= 0) {
                     HDfprintf(stderr, "bad blocksize %s, must be a positive integer\n", optarg);
                     usage(progname_g);
                     Hgoto_error(-1);
                 };
                 break;
             case 'n': /* number of planes to write/read */
-                if ((nlinkedblock_g = atoi(optarg)) < 2) {
+                if ((nlinkedblock_g = HDatoi(optarg)) < 2) {
                     HDfprintf(stderr, "bad number of linked blocks %s, must be greater than 1.\n", optarg);
                     usage(progname_g);
                     Hgoto_error(-1);
                 };
                 break;
             case 'p': /* number of planes to write/read */
-                if ((part_size_g = atoi(optarg)) <= 0) {
+                if ((part_size_g = HDatoi(optarg)) <= 0) {
                     HDfprintf(stderr, "bad partition size %s, must be a positive integer\n", optarg);
                     usage(progname_g);
                     Hgoto_error(-1);
@@ -404,7 +404,7 @@ main(int argc, char *argv[])
             Hgoto_error(1);
         };
     };
-    mypid = getpid();
+    mypid = HDgetpid();
 
     /* ============= */
     /* launch reader */
@@ -440,7 +440,7 @@ main(int argc, char *argv[])
     /* If readwrite, collect exit code of child process */
     /* ================================================ */
     if (launch_g == UC_READWRITE) {
-        if ((tmppid = waitpid(childpid, &child_status, child_wait_option)) < 0) {
+        if ((tmppid = HDwaitpid(childpid, &child_status, child_wait_option)) < 0) {
             HDperror("waitpid");
             Hgoto_error(1);
         }
diff --git a/test/unlink.c b/test/unlink.c
index 8129cc9..2f68a69 100644
--- a/test/unlink.c
+++ b/test/unlink.c
@@ -575,7 +575,7 @@ test_filespace(hid_t fapl)
     size_t rdcc_nbytes;
     double rdcc_w0;
 
-    puts("Testing file space gets reused:");
+    HDputs("Testing file space gets reused:");
 
     /* Open file */
     h5_fixname(FILENAME[4], fapl, filename, sizeof filename);
diff --git a/test/use_append_mchunks.c b/test/use_append_mchunks.c
index 0b2c409..94adfb0 100644
--- a/test/use_append_mchunks.c
+++ b/test/use_append_mchunks.c
@@ -165,12 +165,12 @@ main(int argc, char *argv[])
     /* Fork process */
     /* ============ */
     if (UC_opts.launch == UC_READWRITE) {
-        if ((childpid = fork()) < 0) {
-            perror("fork");
+        if ((childpid = HDfork()) < 0) {
+            HDperror("fork");
             Hgoto_error(1);
         }
     }
-    mypid = getpid();
+    mypid = HDgetpid();
 
     /* ============= */
     /* launch reader */
@@ -239,8 +239,8 @@ main(int argc, char *argv[])
     /* If readwrite, collect exit code of child process */
     /* ================================================ */
     if (UC_opts.launch == UC_READWRITE) {
-        if ((tmppid = waitpid(childpid, &child_status, child_wait_option)) < 0) {
-            perror("waitpid");
+        if ((tmppid = HDwaitpid(childpid, &child_status, child_wait_option)) < 0) {
+            HDperror("waitpid");
             Hgoto_error(1);
         }
 
diff --git a/test/use_common.c b/test/use_common.c
index ccebd0b..7a3c95a 100644
--- a/test/use_common.c
+++ b/test/use_common.c
@@ -68,7 +68,7 @@ parse_option(int argc, char *const argv[], options_t *opts)
         switch (c) {
             case 'h':
                 usage(opts->progname);
-                exit(EXIT_SUCCESS);
+                HDexit(EXIT_SUCCESS);
                 break;
             case 'f': /* usecase data file name */
                 opts->filename = HDstrdup(optarg);
diff --git a/test/vfd.c b/test/vfd.c
index 373a57e..ae4921c 100644
--- a/test/vfd.c
+++ b/test/vfd.c
@@ -2201,9 +2201,9 @@ test_ros3(void)
     /* need a macro to compare instances of H5FD_ros3_fapl_t */
     if ((test_ros3_fa.version != ros3_fa_0.version) ||
         (test_ros3_fa.authenticate != ros3_fa_0.authenticate) ||
-        (strcmp(test_ros3_fa.aws_region, ros3_fa_0.aws_region) != 0) ||
-        (strcmp(test_ros3_fa.secret_id, ros3_fa_0.secret_id) != 0) ||
-        (strcmp(test_ros3_fa.secret_key, ros3_fa_0.secret_key) != 0))
+        (HDstrcmp(test_ros3_fa.aws_region, ros3_fa_0.aws_region) != 0) ||
+        (HDstrcmp(test_ros3_fa.secret_id, ros3_fa_0.secret_id) != 0) ||
+        (HDstrcmp(test_ros3_fa.secret_key, ros3_fa_0.secret_key) != 0))
         TEST_ERROR;
 
     h5_fixname(FILENAME[10], fapl_id, filename, sizeof(filename));
@@ -2252,7 +2252,7 @@ error:
         AT();                                                                                                \
         HDfprintf(stderr, mesg);                                                                             \
         H5Eprint2(H5E_DEFAULT, stderr);                                                                      \
-        fflush(stderr);                                                                                      \
+        HDfflush(stderr);                                                                                    \
         ret_value = -1;                                                                                      \
         goto done;                                                                                           \
     }
@@ -2464,7 +2464,7 @@ run_splitter_test(const struct splitter_dataset_def *data, hbool_t ignore_wo_err
     }
 
     /* Verify existence of logfile if appropriate */
-    logfile = fopen(vfd_config->log_file_path, "r");
+    logfile = HDfopen(vfd_config->log_file_path, "r");
     if ((TRUE == provide_logfile_path && NULL == logfile) ||
         (FALSE == provide_logfile_path && NULL != logfile)) {
         SPLITTER_TEST_FAULT("no logfile when one was expected\n");
@@ -2485,7 +2485,7 @@ done:
     }
 
     if (logfile != NULL)
-        fclose(logfile);
+        HDfclose(logfile);
 
     HDfree(vfd_config);
     HDfree(filename_rw);
-- 
cgit v0.12


From 2ae59f1c6199c62d6efeb43f91924e06f1fd6248 Mon Sep 17 00:00:00 2001
From: Dana Robinson 
Date: Fri, 23 Oct 2020 17:49:53 -0700
Subject: Restores erroneously deleted key_id field from S3 VFD

Accidentally deleted while preparing the PR. Only existed in a
branch.
---
 src/H5FDs3comms.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/H5FDs3comms.c b/src/H5FDs3comms.c
index 42586ff..92921ad 100644
--- a/src/H5FDs3comms.c
+++ b/src/H5FDs3comms.c
@@ -1925,7 +1925,7 @@ H5FD__s3comms_load_aws_creds_from_file(FILE *file, const char *profile_name, cha
     };
     char *const setting_pointers[] = {
         aws_region,
-
+        key_id,
         access_key,
     };
     unsigned setting_count = 3;
-- 
cgit v0.12


From 7bfa10018ecf5efe54b4a699bb684d31468c8b42 Mon Sep 17 00:00:00 2001
From: Binh-Minh Ribler 
Date: Mon, 26 Oct 2020 08:36:27 -0500
Subject: Fix HDFFV-10590

Description
    This is to fix the CVE issue CVE-2018-17432.
    h5repack produced a segfault on a corrupted file.  This fix modified the
    dataspace encode and decode functions per Quincey's suggestion to prevent
    the segfault.  h5repack only failed for the corrupted file now.
Platforms tested:
    Linux/64 (jelly)
---
 src/H5.c           |  10 ++---
 src/H5A.c          |  18 +++++---
 src/H5D.c          |   6 ++-
 src/H5Dio.c        |   6 ++-
 src/H5Dscatgath.c  |   3 +-
 src/H5E.c          |   7 ++--
 src/H5Edeprec.c    |   2 +-
 src/H5F.c          |   6 ++-
 src/H5G.c          |   3 +-
 src/H5L.c          |  27 ++++++++----
 src/H5Ldeprec.c    |   9 ++--
 src/H5Lexternal.c  |   6 ++-
 src/H5M.c          |  12 ++++--
 src/H5O.c          |   9 ++--
 src/H5Ocopy.c      |   3 +-
 src/H5Odeprec.c    |  12 ++++--
 src/H5Osdspace.c   |  23 +++++++----
 src/H5P.c          |  12 +++---
 src/H5Pdcpl.c      |   3 +-
 src/H5Pdeprec.c    |   8 ++--
 src/H5Pdxpl.c      |   6 ++-
 src/H5Pfapl.c      |   9 ++--
 src/H5Pfcpl.c      |   3 +-
 src/H5Pocpl.c      |  12 ++++--
 src/H5Sselect.c    |   3 +-
 src/H5VL.c         |   2 +-
 src/H5VLcallback.c | 119 ++++++++++++++++++++++++++++++++---------------------
 27 files changed, 212 insertions(+), 127 deletions(-)

diff --git a/src/H5.c b/src/H5.c
index e7514b4..72d87eb 100644
--- a/src/H5.c
+++ b/src/H5.c
@@ -448,7 +448,7 @@ H5dont_atexit(void)
     herr_t ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT_NOERR_NOFS
-    H5TRACE0("e", "");
+    H5TRACE0("e","");
 
     if (H5_dont_atexit_g)
         ret_value = FAIL;
@@ -481,7 +481,7 @@ H5garbage_collect(void)
     herr_t ret_value = SUCCEED;
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE0("e", "");
+    H5TRACE0("e","");
 
     /* Call the garbage collection routines in the library */
     if (H5FL_garbage_coll() < 0)
@@ -525,8 +525,8 @@ H5set_free_list_limits(int reg_global_lim, int reg_list_lim, int arr_global_lim,
     herr_t ret_value = SUCCEED;
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "IsIsIsIsIsIs", reg_global_lim, reg_list_lim, arr_global_lim, arr_list_lim, blk_global_lim,
-             blk_list_lim);
+    H5TRACE6("e", "IsIsIsIsIsIs", reg_global_lim, reg_list_lim, arr_global_lim,
+             arr_list_lim, blk_global_lim, blk_list_lim);
 
     /* Call the free list function to actually set the limits */
     if (H5FL_set_free_list_limits(reg_global_lim, reg_list_lim, arr_global_lim, arr_list_lim, blk_global_lim,
@@ -950,7 +950,7 @@ H5close(void)
      * this function for an uninitialized library.
      */
     FUNC_ENTER_API_NOINIT_NOERR_NOFS
-    H5TRACE0("e", "");
+    H5TRACE0("e","");
 
     H5_term_library();
 
diff --git a/src/H5A.c b/src/H5A.c
index 7071f05..b5bd0e8 100644
--- a/src/H5A.c
+++ b/src/H5A.c
@@ -350,7 +350,8 @@ H5Acreate_by_name(hid_t loc_id, const char *obj_name, const char *attr_name, hid
     hid_t             ret_value = H5I_INVALID_HID; /* Return value */
 
     FUNC_ENTER_API(H5I_INVALID_HID)
-    H5TRACE8("i", "i*s*siiiii", loc_id, obj_name, attr_name, type_id, space_id, acpl_id, aapl_id, lapl_id);
+    H5TRACE8("i", "i*s*siiiii", loc_id, obj_name, attr_name, type_id, space_id,
+             acpl_id, aapl_id, lapl_id);
 
     /* Check arguments */
     if (H5I_ATTR == H5I_get_type(loc_id))
@@ -574,7 +575,8 @@ H5Aopen_by_idx(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_iter_
     hid_t             ret_value = H5I_INVALID_HID; /* Return value */
 
     FUNC_ENTER_API(H5I_INVALID_HID)
-    H5TRACE7("i", "i*sIiIohii", loc_id, obj_name, idx_type, order, n, aapl_id, lapl_id);
+    H5TRACE7("i", "i*sIiIohii", loc_id, obj_name, idx_type, order, n, aapl_id,
+             lapl_id);
 
     /* Check arguments */
     if (H5I_ATTR == H5I_get_type(loc_id))
@@ -903,7 +905,8 @@ H5Aget_name_by_idx(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_i
     ssize_t           ret_value; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("Zs", "i*sIiIohxzi", loc_id, obj_name, idx_type, order, n, name, size, lapl_id);
+    H5TRACE8("Zs", "i*sIiIohxzi", loc_id, obj_name, idx_type, order, n, name, size,
+             lapl_id);
 
     /* Check args */
     if (H5I_ATTR == H5I_get_type(loc_id))
@@ -1101,7 +1104,8 @@ H5Aget_info_by_idx(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_i
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "i*sIiIoh*xi", loc_id, obj_name, idx_type, order, n, ainfo, lapl_id);
+    H5TRACE7("e", "i*sIiIoh*xi", loc_id, obj_name, idx_type, order, n, ainfo,
+             lapl_id);
 
     /* Check args */
     if (H5I_ATTR == H5I_get_type(loc_id))
@@ -1218,7 +1222,8 @@ H5Arename_by_name(hid_t loc_id, const char *obj_name, const char *old_attr_name,
     herr_t ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE5("e", "i*s*s*si", loc_id, obj_name, old_attr_name, new_attr_name, lapl_id);
+    H5TRACE5("e", "i*s*s*si", loc_id, obj_name, old_attr_name, new_attr_name,
+             lapl_id);
 
     /* check arguments */
     if (H5I_ATTR == H5I_get_type(loc_id))
@@ -1386,7 +1391,8 @@ H5Aiterate_by_name(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_i
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "i*sIiIo*hx*xi", loc_id, obj_name, idx_type, order, idx, op, op_data, lapl_id);
+    H5TRACE8("e", "i*sIiIo*hx*xi", loc_id, obj_name, idx_type, order, idx, op,
+             op_data, lapl_id);
 
     /* Check arguments */
     if (H5I_ATTR == H5I_get_type(loc_id))
diff --git a/src/H5D.c b/src/H5D.c
index b8b6f65..f342499 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -96,7 +96,8 @@ H5Dcreate2(hid_t loc_id, const char *name, hid_t type_id, hid_t space_id, hid_t
     hid_t             ret_value = H5I_INVALID_HID; /* Return value */
 
     FUNC_ENTER_API(H5I_INVALID_HID)
-    H5TRACE7("i", "i*siiiii", loc_id, name, type_id, space_id, lcpl_id, dcpl_id, dapl_id);
+    H5TRACE7("i", "i*siiiii", loc_id, name, type_id, space_id, lcpl_id, dcpl_id,
+             dapl_id);
 
     /* Check arguments */
     if (!name)
@@ -1051,7 +1052,8 @@ H5Dget_chunk_info(hid_t dset_id, hid_t fspace_id, hsize_t chk_index, hsize_t *of
     herr_t         ret_value = SUCCEED;
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "iih*h*Iu*a*h", dset_id, fspace_id, chk_index, offset, filter_mask, addr, size);
+    H5TRACE7("e", "iih*h*Iu*a*h", dset_id, fspace_id, chk_index, offset,
+             filter_mask, addr, size);
 
     /* Check arguments */
     if (NULL == offset && NULL == filter_mask && NULL == addr && NULL == size)
diff --git a/src/H5Dio.c b/src/H5Dio.c
index 50c474b..1629988 100644
--- a/src/H5Dio.c
+++ b/src/H5Dio.c
@@ -155,7 +155,8 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_i
     herr_t         ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "iiiiix", dset_id, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf);
+    H5TRACE6("e", "iiiiix", dset_id, mem_type_id, mem_space_id, file_space_id,
+             dxpl_id, buf);
 
     /* Check arguments */
     if (mem_space_id < 0)
@@ -267,7 +268,8 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_
     herr_t         ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "iiiii*x", dset_id, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf);
+    H5TRACE6("e", "iiiii*x", dset_id, mem_type_id, mem_space_id, file_space_id,
+             dxpl_id, buf);
 
     /* Check arguments */
     if (mem_space_id < 0)
diff --git a/src/H5Dscatgath.c b/src/H5Dscatgath.c
index 1a272d8..75047f6 100644
--- a/src/H5Dscatgath.c
+++ b/src/H5Dscatgath.c
@@ -1026,7 +1026,8 @@ H5Dgather(hid_t src_space_id, const void *src_buf, hid_t type_id, size_t dst_buf
     herr_t          ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "i*xiz*xx*x", src_space_id, src_buf, type_id, dst_buf_size, dst_buf, op, op_data);
+    H5TRACE7("e", "i*xiz*xx*x", src_space_id, src_buf, type_id, dst_buf_size,
+             dst_buf, op, op_data);
 
     /* Check args */
     if (NULL == (src_space = (H5S_t *)H5I_object_verify(src_space_id, H5I_DATASPACE)))
diff --git a/src/H5E.c b/src/H5E.c
index 731d263..498baec 100644
--- a/src/H5E.c
+++ b/src/H5E.c
@@ -876,7 +876,7 @@ H5Ecreate_stack(void)
     hid_t  ret_value = H5I_INVALID_HID; /* Return value */
 
     FUNC_ENTER_API(H5I_INVALID_HID)
-    H5TRACE0("i", "");
+    H5TRACE0("i","");
 
     /* Allocate a new error stack */
     if (NULL == (stk = H5FL_CALLOC(H5E_t)))
@@ -915,7 +915,7 @@ H5Eget_current_stack(void)
 
     /* Don't clear the error stack! :-) */
     FUNC_ENTER_API_NOCLEAR(H5I_INVALID_HID)
-    H5TRACE0("i", "");
+    H5TRACE0("i","");
 
     /* Get the current stack */
     if (NULL == (stk = H5E__get_current_stack()))
@@ -1330,7 +1330,8 @@ H5Epush2(hid_t err_stack, const char *file, const char *func, unsigned line, hid
 
     /* Don't clear the error stack! :-) */
     FUNC_ENTER_API_NOCLEAR(FAIL)
-    H5TRACE8("e", "i*s*sIuiii*s", err_stack, file, func, line, cls_id, maj_id, min_id, fmt);
+    H5TRACE8("e", "i*s*sIuiii*s", err_stack, file, func, line, cls_id, maj_id,
+             min_id, fmt);
 
     if (err_stack == H5E_DEFAULT)
         estack = NULL;
diff --git a/src/H5Edeprec.c b/src/H5Edeprec.c
index d3eef5d..4d248b7 100644
--- a/src/H5Edeprec.c
+++ b/src/H5Edeprec.c
@@ -230,7 +230,7 @@ H5Eclear1(void)
 
     /* Don't clear the error stack! :-) */
     FUNC_ENTER_API_NOCLEAR(FAIL)
-    H5TRACE0("e", "");
+    H5TRACE0("e","");
 
     /* Clear the default error stack */
     if (H5E_clear_stack(NULL) < 0)
diff --git a/src/H5F.c b/src/H5F.c
index 3c6df2b..5a8fd87 100644
--- a/src/H5F.c
+++ b/src/H5F.c
@@ -1164,7 +1164,8 @@ H5Fget_mdc_size(hid_t file_id, size_t *max_size_ptr, size_t *min_clean_size_ptr,
     herr_t         ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE5("e", "i*z*z*z*Is", file_id, max_size_ptr, min_clean_size_ptr, cur_size_ptr, cur_num_entries_ptr);
+    H5TRACE5("e", "i*z*z*z*Is", file_id, max_size_ptr, min_clean_size_ptr,
+             cur_size_ptr, cur_num_entries_ptr);
 
     /* Check args */
     if (NULL == (vol_obj = (H5VL_object_t *)H5I_object_verify(file_id, H5I_FILE)))
@@ -1697,7 +1698,8 @@ H5Fget_page_buffering_stats(hid_t file_id, unsigned accesses[2], unsigned hits[2
     herr_t         ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "i*Iu*Iu*Iu*Iu*Iu", file_id, accesses, hits, misses, evictions, bypasses);
+    H5TRACE6("e", "i*Iu*Iu*Iu*Iu*Iu", file_id, accesses, hits, misses, evictions,
+             bypasses);
 
     /* Check args */
     if (NULL == (vol_obj = (H5VL_object_t *)H5I_object_verify(file_id, H5I_FILE)))
diff --git a/src/H5G.c b/src/H5G.c
index a15e500..fae401c 100644
--- a/src/H5G.c
+++ b/src/H5G.c
@@ -668,7 +668,8 @@ H5Gget_info_by_idx(hid_t loc_id, const char *group_name, H5_index_t idx_type, H5
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "i*sIiIoh*xi", loc_id, group_name, idx_type, order, n, group_info, lapl_id);
+    H5TRACE7("e", "i*sIiIoh*xi", loc_id, group_name, idx_type, order, n, group_info,
+             lapl_id);
 
     /* Check args */
     if (!group_name)
diff --git a/src/H5L.c b/src/H5L.c
index 0fe632e..55d5785 100644
--- a/src/H5L.c
+++ b/src/H5L.c
@@ -267,7 +267,8 @@ H5Lmove(hid_t src_loc_id, const char *src_name, hid_t dst_loc_id, const char *ds
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "i*si*sii", src_loc_id, src_name, dst_loc_id, dst_name, lcpl_id, lapl_id);
+    H5TRACE6("e", "i*si*sii", src_loc_id, src_name, dst_loc_id, dst_name, lcpl_id,
+             lapl_id);
 
     /* Check arguments */
     if (src_loc_id == H5L_SAME_LOC && dst_loc_id == H5L_SAME_LOC)
@@ -357,7 +358,8 @@ H5Lcopy(hid_t src_loc_id, const char *src_name, hid_t dst_loc_id, const char *ds
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "i*si*sii", src_loc_id, src_name, dst_loc_id, dst_name, lcpl_id, lapl_id);
+    H5TRACE6("e", "i*si*sii", src_loc_id, src_name, dst_loc_id, dst_name, lcpl_id,
+             lapl_id);
 
     /* Check arguments */
     if (src_loc_id == H5L_SAME_LOC && dst_loc_id == H5L_SAME_LOC)
@@ -522,7 +524,8 @@ H5Lcreate_hard(hid_t cur_loc_id, const char *cur_name, hid_t new_loc_id, const c
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "i*si*sii", cur_loc_id, cur_name, new_loc_id, new_name, lcpl_id, lapl_id);
+    H5TRACE6("e", "i*si*sii", cur_loc_id, cur_name, new_loc_id, new_name, lcpl_id,
+             lapl_id);
 
     /* Check arguments */
     if (cur_loc_id == H5L_SAME_LOC && new_loc_id == H5L_SAME_LOC)
@@ -622,7 +625,8 @@ H5Lcreate_ud(hid_t link_loc_id, const char *link_name, H5L_type_t link_type, con
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "i*sLl*xzii", link_loc_id, link_name, link_type, udata, udata_size, lcpl_id, lapl_id);
+    H5TRACE7("e", "i*sLl*xzii", link_loc_id, link_name, link_type, udata,
+             udata_size, lcpl_id, lapl_id);
 
     /* Check arguments */
     if (!link_name || !*link_name)
@@ -860,7 +864,8 @@ H5Lget_val_by_idx(hid_t loc_id, const char *group_name, H5_index_t idx_type, H5_
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "i*sIiIohxzi", loc_id, group_name, idx_type, order, n, buf, size, lapl_id);
+    H5TRACE8("e", "i*sIiIohxzi", loc_id, group_name, idx_type, order, n, buf, size,
+             lapl_id);
 
     /* Check arguments */
     if (!group_name || !*group_name)
@@ -1018,7 +1023,8 @@ H5Lget_info_by_idx2(hid_t loc_id, const char *group_name, H5_index_t idx_type, H
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "i*sIiIohxi", loc_id, group_name, idx_type, order, n, linfo, lapl_id);
+    H5TRACE7("e", "i*sIiIohxi", loc_id, group_name, idx_type, order, n, linfo,
+             lapl_id);
 
     /* Check arguments */
     if (!group_name || !*group_name)
@@ -1215,7 +1221,8 @@ H5Lget_name_by_idx(hid_t loc_id, const char *group_name, H5_index_t idx_type, H5
     ssize_t           ret_value = -1; /* Return value */
 
     FUNC_ENTER_API((-1))
-    H5TRACE8("Zs", "i*sIiIohxzi", loc_id, group_name, idx_type, order, n, name, size, lapl_id);
+    H5TRACE8("Zs", "i*sIiIohxzi", loc_id, group_name, idx_type, order, n, name, size,
+             lapl_id);
 
     /* Check arguments */
     if (!group_name || !*group_name)
@@ -1341,7 +1348,8 @@ H5Literate_by_name2(hid_t loc_id, const char *group_name, H5_index_t idx_type, H
     herr_t            ret_value; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "i*sIiIo*hx*xi", loc_id, group_name, idx_type, order, idx_p, op, op_data, lapl_id);
+    H5TRACE8("e", "i*sIiIo*hx*xi", loc_id, group_name, idx_type, order, idx_p, op,
+             op_data, lapl_id);
 
     /* Check arguments */
     if (!group_name)
@@ -1482,7 +1490,8 @@ H5Lvisit_by_name2(hid_t loc_id, const char *group_name, H5_index_t idx_type, H5_
     herr_t            ret_value; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "i*sIiIox*xi", loc_id, group_name, idx_type, order, op, op_data, lapl_id);
+    H5TRACE7("e", "i*sIiIox*xi", loc_id, group_name, idx_type, order, op, op_data,
+             lapl_id);
 
     /* Check args */
     if (!group_name)
diff --git a/src/H5Ldeprec.c b/src/H5Ldeprec.c
index 843469f..da1940c 100644
--- a/src/H5Ldeprec.c
+++ b/src/H5Ldeprec.c
@@ -226,7 +226,8 @@ H5Literate_by_name1(hid_t loc_id, const char *group_name, H5_index_t idx_type, H
     herr_t            ret_value; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "i*sIiIo*hx*xi", loc_id, group_name, idx_type, order, idx_p, op, op_data, lapl_id);
+    H5TRACE8("e", "i*sIiIo*hx*xi", loc_id, group_name, idx_type, order, idx_p, op,
+             op_data, lapl_id);
 
     /* Check arguments */
     if (!group_name)
@@ -383,7 +384,8 @@ H5Lget_info_by_idx1(hid_t loc_id, const char *group_name, H5_index_t idx_type, H
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "i*sIiIohxi", loc_id, group_name, idx_type, order, n, linfo, lapl_id);
+    H5TRACE7("e", "i*sIiIohxi", loc_id, group_name, idx_type, order, n, linfo,
+             lapl_id);
 
     /* Check arguments */
     if (!group_name || !*group_name)
@@ -570,7 +572,8 @@ H5Lvisit_by_name1(hid_t loc_id, const char *group_name, H5_index_t idx_type, H5_
     herr_t            ret_value; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "i*sIiIox*xi", loc_id, group_name, idx_type, order, op, op_data, lapl_id);
+    H5TRACE7("e", "i*sIiIox*xi", loc_id, group_name, idx_type, order, op, op_data,
+             lapl_id);
 
     /* Check args */
     if (!group_name)
diff --git a/src/H5Lexternal.c b/src/H5Lexternal.c
index b978a73..2fce7cd 100644
--- a/src/H5Lexternal.c
+++ b/src/H5Lexternal.c
@@ -349,7 +349,8 @@ H5Lcreate_external(const char *file_name, const char *obj_name, hid_t link_loc_i
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "*s*si*sii", file_name, obj_name, link_loc_id, link_name, lcpl_id, lapl_id);
+    H5TRACE6("e", "*s*si*sii", file_name, obj_name, link_loc_id, link_name,
+             lcpl_id, lapl_id);
 
     /* Check arguments */
     if (!file_name || !*file_name)
@@ -472,7 +473,8 @@ H5Lunpack_elink_val(const void *_ext_linkval, size_t link_size, unsigned *flags,
     herr_t         ret_value = SUCCEED;                         /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE5("e", "*xz*Iu**s**s", _ext_linkval, link_size, flags, filename, obj_path);
+    H5TRACE5("e", "*xz*Iu**s**s", _ext_linkval, link_size, flags, filename,
+             obj_path);
 
     /* Sanity check external link buffer */
     if (ext_linkval == NULL)
diff --git a/src/H5M.c b/src/H5M.c
index 34d0105..e3091ca 100644
--- a/src/H5M.c
+++ b/src/H5M.c
@@ -246,7 +246,8 @@ H5Mcreate(hid_t loc_id, const char *name, hid_t key_type_id, hid_t val_type_id,
     hid_t             ret_value = H5I_INVALID_HID; /* Return value */
 
     FUNC_ENTER_API(H5I_INVALID_HID)
-    H5TRACE7("i", "i*siiiii", loc_id, name, key_type_id, val_type_id, lcpl_id, mcpl_id, mapl_id);
+    H5TRACE7("i", "i*siiiii", loc_id, name, key_type_id, val_type_id, lcpl_id,
+             mcpl_id, mapl_id);
 
     /* Check arguments */
     if (!name)
@@ -671,7 +672,8 @@ H5Mput(hid_t map_id, hid_t key_mem_type_id, const void *key, hid_t val_mem_type_
     herr_t         ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "ii*xi*xi", map_id, key_mem_type_id, key, val_mem_type_id, value, dxpl_id);
+    H5TRACE6("e", "ii*xi*xi", map_id, key_mem_type_id, key, val_mem_type_id, value,
+             dxpl_id);
 
     /* Check arguments */
     if (key_mem_type_id < 0)
@@ -728,7 +730,8 @@ H5Mget(hid_t map_id, hid_t key_mem_type_id, const void *key, hid_t val_mem_type_
     herr_t         ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "ii*xi*xi", map_id, key_mem_type_id, key, val_mem_type_id, value, dxpl_id);
+    H5TRACE6("e", "ii*xi*xi", map_id, key_mem_type_id, key, val_mem_type_id, value,
+             dxpl_id);
 
     /* Check arguments */
     if (key_mem_type_id < 0)
@@ -919,7 +922,8 @@ H5Miterate_by_name(hid_t loc_id, const char *map_name, hsize_t *idx, hid_t key_m
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "i*s*hix*xii", loc_id, map_name, idx, key_mem_type_id, op, op_data, dxpl_id, lapl_id);
+    H5TRACE8("e", "i*s*hix*xii", loc_id, map_name, idx, key_mem_type_id, op,
+             op_data, dxpl_id, lapl_id);
 
     /* Check arguments */
     if (!map_name)
diff --git a/src/H5O.c b/src/H5O.c
index e5d794c..39037a9 100644
--- a/src/H5O.c
+++ b/src/H5O.c
@@ -632,7 +632,8 @@ H5Oget_info_by_idx3(hid_t loc_id, const char *group_name, H5_index_t idx_type, H
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "i*sIiIoh*xIui", loc_id, group_name, idx_type, order, n, oinfo, fields, lapl_id);
+    H5TRACE8("e", "i*sIiIoh*xIui", loc_id, group_name, idx_type, order, n, oinfo,
+             fields, lapl_id);
 
     /* Check args */
     if (!group_name || !*group_name)
@@ -795,7 +796,8 @@ H5Oget_native_info_by_idx(hid_t loc_id, const char *group_name, H5_index_t idx_t
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "i*sIiIoh*xIui", loc_id, group_name, idx_type, order, n, oinfo, fields, lapl_id);
+    H5TRACE8("e", "i*sIiIoh*xIui", loc_id, group_name, idx_type, order, n, oinfo,
+             fields, lapl_id);
 
     /* Check args */
     if (!group_name || !*group_name)
@@ -1150,7 +1152,8 @@ H5Ovisit_by_name3(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_it
     herr_t            ret_value; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "i*sIiIox*xIui", loc_id, obj_name, idx_type, order, op, op_data, fields, lapl_id);
+    H5TRACE8("e", "i*sIiIox*xIui", loc_id, obj_name, idx_type, order, op, op_data,
+             fields, lapl_id);
 
     /* Check args */
     if (!obj_name)
diff --git a/src/H5Ocopy.c b/src/H5Ocopy.c
index 54a41c0..9f92925 100644
--- a/src/H5Ocopy.c
+++ b/src/H5Ocopy.c
@@ -195,7 +195,8 @@ H5Ocopy(hid_t src_loc_id, const char *src_name, hid_t dst_loc_id, const char *ds
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "i*si*sii", src_loc_id, src_name, dst_loc_id, dst_name, ocpypl_id, lcpl_id);
+    H5TRACE6("e", "i*si*sii", src_loc_id, src_name, dst_loc_id, dst_name,
+             ocpypl_id, lcpl_id);
 
     /* Check arguments */
     if (!src_name || !*src_name)
diff --git a/src/H5Odeprec.c b/src/H5Odeprec.c
index 1838234..b737783 100644
--- a/src/H5Odeprec.c
+++ b/src/H5Odeprec.c
@@ -487,7 +487,8 @@ H5Oget_info_by_idx1(hid_t loc_id, const char *group_name, H5_index_t idx_type, H
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "i*sIiIoh*xi", loc_id, group_name, idx_type, order, n, oinfo, lapl_id);
+    H5TRACE7("e", "i*sIiIoh*xi", loc_id, group_name, idx_type, order, n, oinfo,
+             lapl_id);
 
     /* Check args */
     if (!group_name || !*group_name)
@@ -669,7 +670,8 @@ H5Oget_info_by_idx2(hid_t loc_id, const char *group_name, H5_index_t idx_type, H
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "i*sIiIoh*xIui", loc_id, group_name, idx_type, order, n, oinfo, fields, lapl_id);
+    H5TRACE8("e", "i*sIiIoh*xIui", loc_id, group_name, idx_type, order, n, oinfo,
+             fields, lapl_id);
 
     /* Check args */
     if (!group_name || !*group_name)
@@ -831,7 +833,8 @@ H5Ovisit_by_name1(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_it
     herr_t               ret_value; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "i*sIiIox*xi", loc_id, obj_name, idx_type, order, op, op_data, lapl_id);
+    H5TRACE7("e", "i*sIiIox*xi", loc_id, obj_name, idx_type, order, op, op_data,
+             lapl_id);
 
     /* Check args */
     if (!obj_name)
@@ -1009,7 +1012,8 @@ H5Ovisit_by_name2(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_it
     herr_t               ret_value; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "i*sIiIox*xIui", loc_id, obj_name, idx_type, order, op, op_data, fields, lapl_id);
+    H5TRACE8("e", "i*sIiIox*xIui", loc_id, obj_name, idx_type, order, op, op_data,
+             fields, lapl_id);
 
     /* Check args */
     if (!obj_name)
diff --git a/src/H5Osdspace.c b/src/H5Osdspace.c
index b34eb76..e3ec4b0 100644
--- a/src/H5Osdspace.c
+++ b/src/H5Osdspace.c
@@ -138,8 +138,11 @@ H5O__sdspace_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, unsigned H5_ATTR_UN
     flags = *p++;
 
     /* Get or determine the type of the extent */
-    if (version >= H5O_SDSPACE_VERSION_2)
+    if (version >= H5O_SDSPACE_VERSION_2) {
         sdim->type = (H5S_class_t)*p++;
+        if(sdim->type != H5S_SIMPLE && sdim->rank > 0)
+            HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, NULL, "invalid rank for scalar or NULL dataspace")
+    } /* end if */
     else {
         /* Set the dataspace type to be simple or scalar as appropriate */
         if (sdim->rank > 0)
@@ -248,15 +251,17 @@ H5O__sdspace_encode(H5F_t *f, uint8_t *p, const void *_mesg)
         *p++ = 0; /*reserved*/
     }             /* end else */
 
-    /* Current & maximum dimensions */
-    if (sdim->rank > 0) {
-        for (u = 0; u < sdim->rank; u++)
-            H5F_ENCODE_LENGTH(f, p, sdim->size[u]);
-        if (flags & H5S_VALID_MAX) {
-            for (u = 0; u < sdim->rank; u++)
-                H5F_ENCODE_LENGTH(f, p, sdim->max[u]);
+    /* Encode dataspace dimensions for simple dataspaces */
+    if(H5S_SIMPLE == sdim->type) {
+        /* Encode current & maximum dimensions */
+        if(sdim->rank > 0) {
+            for(u = 0; u < sdim->rank; u++)
+                H5F_ENCODE_LENGTH(f, p, sdim->size[u]);
+            if(flags & H5S_VALID_MAX)
+                for(u = 0; u < sdim->rank; u++)
+                    H5F_ENCODE_LENGTH(f, p, sdim->max[u]);
         } /* end if */
-    }     /* end if */
+    } /* end if */
 
     FUNC_LEAVE_NOAPI(SUCCEED)
 } /* end H5O__sdspace_encode() */
diff --git a/src/H5P.c b/src/H5P.c
index 3ccdfd4..befdd77 100644
--- a/src/H5P.c
+++ b/src/H5P.c
@@ -173,8 +173,8 @@ H5Pcreate_class(hid_t parent, const char *name, H5P_cls_create_func_t cls_create
     hid_t           ret_value = H5I_INVALID_HID; /* Return value		   */
 
     FUNC_ENTER_API(H5I_INVALID_HID)
-    H5TRACE8("i", "i*sx*xx*xx*x", parent, name, cls_create, create_data, cls_copy, copy_data, cls_close,
-             close_data);
+    H5TRACE8("i", "i*sx*xx*xx*x", parent, name, cls_create, create_data, cls_copy,
+             copy_data, cls_close, close_data);
 
     /* Check arguments. */
     if (H5P_DEFAULT != parent && (H5I_GENPROP_CLS != H5I_get_type(parent)))
@@ -414,8 +414,8 @@ H5Pregister2(hid_t cls_id, const char *name, size_t size, void *def_value, H5P_p
     herr_t          ret_value;   /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE11("e", "i*sz*xxxxxxxx", cls_id, name, size, def_value, prp_create, prp_set, prp_get, prp_delete,
-              prp_copy, prp_cmp, prp_close);
+    H5TRACE11("e", "i*sz*xxxxxxxx", cls_id, name, size, def_value, prp_create,
+             prp_set, prp_get, prp_delete, prp_copy, prp_cmp, prp_close);
 
     /* Check arguments. */
     if (NULL == (pclass = (H5P_genclass_t *)H5I_object_verify(cls_id, H5I_GENPROP_CLS)))
@@ -598,8 +598,8 @@ H5Pinsert2(hid_t plist_id, const char *name, size_t size, void *value, H5P_prp_s
     herr_t          ret_value; /* return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE10("e", "i*sz*xxxxxxx", plist_id, name, size, value, prp_set, prp_get, prp_delete, prp_copy,
-              prp_cmp, prp_close);
+    H5TRACE10("e", "i*sz*xxxxxxx", plist_id, name, size, value, prp_set, prp_get,
+             prp_delete, prp_copy, prp_cmp, prp_close);
 
     /* Check arguments. */
     if (NULL == (plist = (H5P_genplist_t *)H5I_object_verify(plist_id, H5I_GENPROP_LST)))
diff --git a/src/H5Pdcpl.c b/src/H5Pdcpl.c
index 8c525e5..734a10a 100644
--- a/src/H5Pdcpl.c
+++ b/src/H5Pdcpl.c
@@ -2226,7 +2226,8 @@ H5Pset_virtual(hid_t dcpl_id, hid_t vspace_id, const char *src_file_name, const
     herr_t                     ret_value        = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE5("e", "ii*s*si", dcpl_id, vspace_id, src_file_name, src_dset_name, src_space_id);
+    H5TRACE5("e", "ii*s*si", dcpl_id, vspace_id, src_file_name, src_dset_name,
+             src_space_id);
 
     /* Check arguments */
     if (!src_file_name)
diff --git a/src/H5Pdeprec.c b/src/H5Pdeprec.c
index d80c153..5b70080 100644
--- a/src/H5Pdeprec.c
+++ b/src/H5Pdeprec.c
@@ -220,8 +220,8 @@ H5Pregister1(hid_t cls_id, const char *name, size_t size, void *def_value, H5P_p
     herr_t          ret_value;   /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE10("e", "i*sz*xxxxxxx", cls_id, name, size, def_value, prp_create, prp_set, prp_get, prp_delete,
-              prp_copy, prp_close);
+    H5TRACE10("e", "i*sz*xxxxxxx", cls_id, name, size, def_value, prp_create,
+             prp_set, prp_get, prp_delete, prp_copy, prp_close);
 
     /* Check arguments. */
     if (NULL == (pclass = (H5P_genclass_t *)H5I_object_verify(cls_id, H5I_GENPROP_CLS)))
@@ -404,8 +404,8 @@ H5Pinsert1(hid_t plist_id, const char *name, size_t size, void *value, H5P_prp_s
     herr_t          ret_value; /* return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE9("e", "i*sz*xxxxxx", plist_id, name, size, value, prp_set, prp_get, prp_delete, prp_copy,
-             prp_close);
+    H5TRACE9("e", "i*sz*xxxxxx", plist_id, name, size, value, prp_set, prp_get,
+             prp_delete, prp_copy, prp_close);
 
     /* Check arguments. */
     if (NULL == (plist = (H5P_genplist_t *)H5I_object_verify(plist_id, H5I_GENPROP_LST)))
diff --git a/src/H5Pdxpl.c b/src/H5Pdxpl.c
index 09eadfa..70f3056 100644
--- a/src/H5Pdxpl.c
+++ b/src/H5Pdxpl.c
@@ -1577,7 +1577,8 @@ H5Pset_vlen_mem_manager(hid_t plist_id, H5MM_allocate_t alloc_func, void *alloc_
     herr_t          ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE5("e", "ix*xx*x", plist_id, alloc_func, alloc_info, free_func, free_info);
+    H5TRACE5("e", "ix*xx*x", plist_id, alloc_func, alloc_info, free_func,
+             free_info);
 
     /* Check arguments */
     if (NULL == (plist = H5P_object_verify(plist_id, H5P_DATASET_XFER)))
@@ -2020,7 +2021,8 @@ H5Pget_mpio_no_collective_cause(hid_t plist_id, uint32_t *local_no_collective_ca
     herr_t          ret_value = SUCCEED; /* return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE3("e", "i*Iu*Iu", plist_id, local_no_collective_cause, global_no_collective_cause);
+    H5TRACE3("e", "i*Iu*Iu", plist_id, local_no_collective_cause,
+             global_no_collective_cause);
 
     /* Get the plist structure */
     if (NULL == (plist = H5P_object_verify(plist_id, H5P_DATASET_XFER)))
diff --git a/src/H5Pfapl.c b/src/H5Pfapl.c
index f9a730d..42d49d1 100644
--- a/src/H5Pfapl.c
+++ b/src/H5Pfapl.c
@@ -1683,7 +1683,8 @@ H5Pset_cache(hid_t plist_id, int H5_ATTR_UNUSED mdc_nelmts, size_t rdcc_nslots,
     herr_t          ret_value = SUCCEED; /* return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE5("e", "iIszzd", plist_id, mdc_nelmts, rdcc_nslots, rdcc_nbytes, rdcc_w0);
+    H5TRACE5("e", "iIszzd", plist_id, mdc_nelmts, rdcc_nslots, rdcc_nbytes,
+             rdcc_w0);
 
     /* Check arguments */
     if (rdcc_w0 < (double)0.0f || rdcc_w0 > (double)1.0f)
@@ -1729,7 +1730,8 @@ H5Pget_cache(hid_t plist_id, int *mdc_nelmts, size_t *rdcc_nslots, size_t *rdcc_
     herr_t          ret_value = SUCCEED; /* return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE5("e", "i*Is*z*z*d", plist_id, mdc_nelmts, rdcc_nslots, rdcc_nbytes, rdcc_w0);
+    H5TRACE5("e", "i*Is*z*z*d", plist_id, mdc_nelmts, rdcc_nslots, rdcc_nbytes,
+             rdcc_w0);
 
     /* Get the plist structure */
     if (NULL == (plist = H5P_object_verify(plist_id, H5P_FILE_ACCESS)))
@@ -4280,7 +4282,8 @@ H5Pget_mdc_log_options(hid_t plist_id, hbool_t *is_enabled, char *location, size
     herr_t          ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE5("e", "i*b*s*z*b", plist_id, is_enabled, location, location_size, start_on_access);
+    H5TRACE5("e", "i*b*s*z*b", plist_id, is_enabled, location, location_size,
+             start_on_access);
 
     /* Get the property list structure */
     if (NULL == (plist = H5P_object_verify(plist_id, H5P_FILE_ACCESS)))
diff --git a/src/H5Pfcpl.c b/src/H5Pfcpl.c
index fbf9aac..c703e1d 100644
--- a/src/H5Pfcpl.c
+++ b/src/H5Pfcpl.c
@@ -934,7 +934,8 @@ H5Pget_shared_mesg_index(hid_t plist_id, unsigned index_num, unsigned *mesg_type
     herr_t          ret_value = SUCCEED;                 /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE4("e", "iIu*Iu*Iu", plist_id, index_num, mesg_type_flags, min_mesg_size);
+    H5TRACE4("e", "iIu*Iu*Iu", plist_id, index_num, mesg_type_flags,
+             min_mesg_size);
 
     /* Get the plist structure */
     if (NULL == (plist = H5P_object_verify(plist_id, H5P_FILE_CREATE)))
diff --git a/src/H5Pocpl.c b/src/H5Pocpl.c
index bd6be75..b7312f2 100644
--- a/src/H5Pocpl.c
+++ b/src/H5Pocpl.c
@@ -807,7 +807,8 @@ H5Pget_filter2(hid_t plist_id, unsigned idx, unsigned int *flags /*out*/, size_t
     H5Z_filter_t             ret_value; /* return value */
 
     FUNC_ENTER_API(H5Z_FILTER_ERROR)
-    H5TRACE8("Zf", "iIux*zxzxx", plist_id, idx, flags, cd_nelmts, cd_values, namelen, name, filter_config);
+    H5TRACE8("Zf", "iIux*zxzxx", plist_id, idx, flags, cd_nelmts, cd_values,
+             namelen, name, filter_config);
 
     /* Check args */
     if (cd_nelmts || cd_values) {
@@ -937,7 +938,8 @@ H5Pget_filter_by_id2(hid_t plist_id, H5Z_filter_t id, unsigned int *flags /*out*
     herr_t          ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "iZfx*zxzx*Iu", plist_id, id, flags, cd_nelmts, cd_values, namelen, name, filter_config);
+    H5TRACE8("e", "iZfx*zxzx*Iu", plist_id, id, flags, cd_nelmts, cd_values,
+             namelen, name, filter_config);
 
     /* Check args */
     if (cd_nelmts || cd_values) {
@@ -1755,7 +1757,8 @@ H5Pget_filter1(hid_t plist_id, unsigned idx, unsigned int *flags /*out*/, size_t
     H5Z_filter_t             ret_value; /* return value */
 
     FUNC_ENTER_API(H5Z_FILTER_ERROR)
-    H5TRACE7("Zf", "iIux*zxzx", plist_id, idx, flags, cd_nelmts, cd_values, namelen, name);
+    H5TRACE7("Zf", "iIux*zxzx", plist_id, idx, flags, cd_nelmts, cd_values, namelen,
+             name);
 
     /* Check args */
     if (cd_nelmts || cd_values) {
@@ -1835,7 +1838,8 @@ H5Pget_filter_by_id1(hid_t plist_id, H5Z_filter_t id, unsigned int *flags /*out*
     herr_t          ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "iZfx*zxzx", plist_id, id, flags, cd_nelmts, cd_values, namelen, name);
+    H5TRACE7("e", "iZfx*zxzx", plist_id, id, flags, cd_nelmts, cd_values, namelen,
+             name);
 
     /* Check args */
     if (cd_nelmts || cd_values) {
diff --git a/src/H5Sselect.c b/src/H5Sselect.c
index 023ab80..f351982 100644
--- a/src/H5Sselect.c
+++ b/src/H5Sselect.c
@@ -3063,7 +3063,8 @@ H5Ssel_iter_get_seq_list(hid_t sel_iter_id, size_t maxseq, size_t maxbytes, size
     herr_t          ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "izz*z*z*h*z", sel_iter_id, maxseq, maxbytes, nseq, nbytes, off, len);
+    H5TRACE7("e", "izz*z*z*h*z", sel_iter_id, maxseq, maxbytes, nseq, nbytes, off,
+             len);
 
     /* Check args */
     if (NULL == (sel_iter = (H5S_sel_iter_t *)H5I_object_verify(sel_iter_id, H5I_SPACE_SEL_ITER)))
diff --git a/src/H5VL.c b/src/H5VL.c
index d60bd5f..d8c2435 100644
--- a/src/H5VL.c
+++ b/src/H5VL.c
@@ -842,7 +842,7 @@ H5VLreset_lib_state(void)
 
     /* Must use this, to avoid modifying the API context stack in FUNC_ENTER */
     FUNC_ENTER_API_NOINIT
-    H5TRACE0("e", "");
+    H5TRACE0("e","");
 
     /* Reset the library state */
     if (H5VL_reset_lib_state() < 0)
diff --git a/src/H5VLcallback.c b/src/H5VLcallback.c
index 6abbf8d..5b7eb8d 100644
--- a/src/H5VLcallback.c
+++ b/src/H5VLcallback.c
@@ -1000,8 +1000,8 @@ H5VLattr_create(void *obj, const H5VL_loc_params_t *loc_params, hid_t connector_
     void *        ret_value = NULL; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE10("*x", "*x*xi*siiiii**x", obj, loc_params, connector_id, name, type_id, space_id, acpl_id,
-              aapl_id, dxpl_id, req);
+    H5TRACE10("*x", "*x*xi*siiiii**x", obj, loc_params, connector_id, name,
+             type_id, space_id, acpl_id, aapl_id, dxpl_id, req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -1103,7 +1103,8 @@ H5VLattr_open(void *obj, const H5VL_loc_params_t *loc_params, hid_t connector_id
     void *        ret_value = NULL; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE7("*x", "*x*xi*sii**x", obj, loc_params, connector_id, name, aapl_id, dxpl_id, req);
+    H5TRACE7("*x", "*x*xi*sii**x", obj, loc_params, connector_id, name, aapl_id,
+             dxpl_id, req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -1405,7 +1406,8 @@ H5VLattr_get(void *obj, hid_t connector_id, H5VL_attr_get_t get_type, hid_t dxpl
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVai**xx", obj, connector_id, get_type, dxpl_id, req, arguments);
+    H5TRACE6("e", "*xiVai**xx", obj, connector_id, get_type, dxpl_id, req,
+             arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -1514,7 +1516,8 @@ H5VLattr_specific(void *obj, const H5VL_loc_params_t *loc_params, hid_t connecto
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE7("e", "*x*xiVbi**xx", obj, loc_params, connector_id, specific_type, dxpl_id, req, arguments);
+    H5TRACE7("e", "*x*xiVbi**xx", obj, loc_params, connector_id, specific_type,
+             dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -1623,7 +1626,8 @@ H5VLattr_optional(void *obj, hid_t connector_id, H5VL_attr_optional_t opt_type,
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVsi**xx", obj, connector_id, opt_type, dxpl_id, req, arguments);
+    H5TRACE6("e", "*xiVsi**xx", obj, connector_id, opt_type, dxpl_id, req,
+             arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -1819,8 +1823,8 @@ H5VLdataset_create(void *obj, const H5VL_loc_params_t *loc_params, hid_t connect
     void *        ret_value = NULL; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE11("*x", "*x*xi*siiiiii**x", obj, loc_params, connector_id, name, lcpl_id, type_id, space_id,
-              dcpl_id, dapl_id, dxpl_id, req);
+    H5TRACE11("*x", "*x*xi*siiiiii**x", obj, loc_params, connector_id, name,
+             lcpl_id, type_id, space_id, dcpl_id, dapl_id, dxpl_id, req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -1922,7 +1926,8 @@ H5VLdataset_open(void *obj, const H5VL_loc_params_t *loc_params, hid_t connector
     void *        ret_value = NULL; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE7("*x", "*x*xi*sii**x", obj, loc_params, connector_id, name, dapl_id, dxpl_id, req);
+    H5TRACE7("*x", "*x*xi*sii**x", obj, loc_params, connector_id, name, dapl_id,
+             dxpl_id, req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -2023,8 +2028,8 @@ H5VLdataset_read(void *obj, hid_t connector_id, hid_t mem_type_id, hid_t mem_spa
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE8("e", "*xiiiii*x**x", obj, connector_id, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf,
-             req);
+    H5TRACE8("e", "*xiiiii*x**x", obj, connector_id, mem_type_id, mem_space_id,
+             file_space_id, dxpl_id, buf, req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -2125,8 +2130,8 @@ H5VLdataset_write(void *obj, hid_t connector_id, hid_t mem_type_id, hid_t mem_sp
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE8("e", "*xiiiii*x**x", obj, connector_id, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf,
-             req);
+    H5TRACE8("e", "*xiiiii*x**x", obj, connector_id, mem_type_id, mem_space_id,
+             file_space_id, dxpl_id, buf, req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -2233,7 +2238,8 @@ H5VLdataset_get(void *obj, hid_t connector_id, H5VL_dataset_get_t get_type, hid_
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVci**xx", obj, connector_id, get_type, dxpl_id, req, arguments);
+    H5TRACE6("e", "*xiVci**xx", obj, connector_id, get_type, dxpl_id, req,
+             arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -2342,7 +2348,8 @@ H5VLdataset_specific(void *obj, hid_t connector_id, H5VL_dataset_specific_t spec
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVdi**xx", obj, connector_id, specific_type, dxpl_id, req, arguments);
+    H5TRACE6("e", "*xiVdi**xx", obj, connector_id, specific_type, dxpl_id, req,
+             arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -2450,7 +2457,8 @@ H5VLdataset_optional(void *obj, hid_t connector_id, H5VL_dataset_optional_t opt_
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVti**xx", obj, connector_id, opt_type, dxpl_id, req, arguments);
+    H5TRACE6("e", "*xiVti**xx", obj, connector_id, opt_type, dxpl_id, req,
+             arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -2660,8 +2668,8 @@ H5VLdatatype_commit(void *obj, const H5VL_loc_params_t *loc_params, hid_t connec
     void *        ret_value = NULL; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE10("*x", "*x*xi*siiiii**x", obj, loc_params, connector_id, name, type_id, lcpl_id, tcpl_id,
-              tapl_id, dxpl_id, req);
+    H5TRACE10("*x", "*x*xi*siiiii**x", obj, loc_params, connector_id, name,
+             type_id, lcpl_id, tcpl_id, tapl_id, dxpl_id, req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -2763,7 +2771,8 @@ H5VLdatatype_open(void *obj, const H5VL_loc_params_t *loc_params, hid_t connecto
     void *        ret_value = NULL; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE7("*x", "*x*xi*sii**x", obj, loc_params, connector_id, name, tapl_id, dxpl_id, req);
+    H5TRACE7("*x", "*x*xi*sii**x", obj, loc_params, connector_id, name, tapl_id,
+             dxpl_id, req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -2870,7 +2879,8 @@ H5VLdatatype_get(void *obj, hid_t connector_id, H5VL_datatype_get_t get_type, hi
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVei**xx", obj, connector_id, get_type, dxpl_id, req, arguments);
+    H5TRACE6("e", "*xiVei**xx", obj, connector_id, get_type, dxpl_id, req,
+             arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -2983,7 +2993,8 @@ H5VLdatatype_specific(void *obj, hid_t connector_id, H5VL_datatype_specific_t sp
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVfi**xx", obj, connector_id, specific_type, dxpl_id, req, arguments);
+    H5TRACE6("e", "*xiVfi**xx", obj, connector_id, specific_type, dxpl_id, req,
+             arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -3092,7 +3103,8 @@ H5VLdatatype_optional(void *obj, hid_t connector_id, H5VL_datatype_optional_t op
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVui**xx", obj, connector_id, opt_type, dxpl_id, req, arguments);
+    H5TRACE6("e", "*xiVui**xx", obj, connector_id, opt_type, dxpl_id, req,
+             arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -3505,7 +3517,8 @@ H5VLfile_get(void *obj, hid_t connector_id, H5VL_file_get_t get_type, hid_t dxpl
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVgi**xx", obj, connector_id, get_type, dxpl_id, req, arguments);
+    H5TRACE6("e", "*xiVgi**xx", obj, connector_id, get_type, dxpl_id, req,
+             arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -3649,7 +3662,8 @@ H5VLfile_specific(void *obj, hid_t connector_id, H5VL_file_specific_t specific_t
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVhi**xx", obj, connector_id, specific_type, dxpl_id, req, arguments);
+    H5TRACE6("e", "*xiVhi**xx", obj, connector_id, specific_type, dxpl_id, req,
+             arguments);
 
     /* Check args and get class pointer */
     if (NULL == (cls = (H5VL_class_t *)H5I_object_verify(connector_id, H5I_VOL)))
@@ -3755,7 +3769,8 @@ H5VLfile_optional(void *obj, hid_t connector_id, H5VL_file_optional_t opt_type,
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVvi**xx", obj, connector_id, opt_type, dxpl_id, req, arguments);
+    H5TRACE6("e", "*xiVvi**xx", obj, connector_id, opt_type, dxpl_id, req,
+             arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -3958,8 +3973,8 @@ H5VLgroup_create(void *obj, const H5VL_loc_params_t *loc_params, hid_t connector
     void *        ret_value = NULL; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE9("*x", "*x*xi*siiii**x", obj, loc_params, connector_id, name, lcpl_id, gcpl_id, gapl_id, dxpl_id,
-             req);
+    H5TRACE9("*x", "*x*xi*siiii**x", obj, loc_params, connector_id, name, lcpl_id,
+             gcpl_id, gapl_id, dxpl_id, req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -4061,7 +4076,8 @@ H5VLgroup_open(void *obj, const H5VL_loc_params_t *loc_params, hid_t connector_i
     void *        ret_value = NULL; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE7("*x", "*x*xi*sii**x", obj, loc_params, connector_id, name, gapl_id, dxpl_id, req);
+    H5TRACE7("*x", "*x*xi*sii**x", obj, loc_params, connector_id, name, gapl_id,
+             dxpl_id, req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -4168,7 +4184,8 @@ H5VLgroup_get(void *obj, hid_t connector_id, H5VL_group_get_t get_type, hid_t dx
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVii**xx", obj, connector_id, get_type, dxpl_id, req, arguments);
+    H5TRACE6("e", "*xiVii**xx", obj, connector_id, get_type, dxpl_id, req,
+             arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -4277,7 +4294,8 @@ H5VLgroup_specific(void *obj, hid_t connector_id, H5VL_group_specific_t specific
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVji**xx", obj, connector_id, specific_type, dxpl_id, req, arguments);
+    H5TRACE6("e", "*xiVji**xx", obj, connector_id, specific_type, dxpl_id, req,
+             arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -4386,7 +4404,8 @@ H5VLgroup_optional(void *obj, hid_t connector_id, H5VL_group_optional_t opt_type
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVwi**xx", obj, connector_id, opt_type, dxpl_id, req, arguments);
+    H5TRACE6("e", "*xiVwi**xx", obj, connector_id, opt_type, dxpl_id, req,
+             arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -4620,8 +4639,8 @@ H5VLlink_create(H5VL_link_create_type_t create_type, void *obj, const H5VL_loc_p
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE9("e", "Vk*x*xiiii**xx", create_type, obj, loc_params, connector_id, lcpl_id, lapl_id, dxpl_id,
-             req, arguments);
+    H5TRACE9("e", "Vk*x*xiiii**xx", create_type, obj, loc_params, connector_id,
+             lcpl_id, lapl_id, dxpl_id, req, arguments);
 
     /* Get class pointer */
     if (NULL == (cls = (H5VL_class_t *)H5I_object_verify(connector_id, H5I_VOL)))
@@ -4727,8 +4746,8 @@ H5VLlink_copy(void *src_obj, const H5VL_loc_params_t *loc_params1, void *dst_obj
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE9("e", "*x*x*x*xiiii**x", src_obj, loc_params1, dst_obj, loc_params2, connector_id, lcpl_id,
-             lapl_id, dxpl_id, req);
+    H5TRACE9("e", "*x*x*x*xiiii**x", src_obj, loc_params1, dst_obj, loc_params2,
+             connector_id, lcpl_id, lapl_id, dxpl_id, req);
 
     /* Get class pointer */
     if (NULL == (cls = (H5VL_class_t *)H5I_object_verify(connector_id, H5I_VOL)))
@@ -4834,8 +4853,8 @@ H5VLlink_move(void *src_obj, const H5VL_loc_params_t *loc_params1, void *dst_obj
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE9("e", "*x*x*x*xiiii**x", src_obj, loc_params1, dst_obj, loc_params2, connector_id, lcpl_id,
-             lapl_id, dxpl_id, req);
+    H5TRACE9("e", "*x*x*x*xiiii**x", src_obj, loc_params1, dst_obj, loc_params2,
+             connector_id, lcpl_id, lapl_id, dxpl_id, req);
 
     /* Get class pointer */
     if (NULL == (cls = (H5VL_class_t *)H5I_object_verify(connector_id, H5I_VOL)))
@@ -4942,7 +4961,8 @@ H5VLlink_get(void *obj, const H5VL_loc_params_t *loc_params, hid_t connector_id,
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE7("e", "*x*xiVli**xx", obj, loc_params, connector_id, get_type, dxpl_id, req, arguments);
+    H5TRACE7("e", "*x*xiVli**xx", obj, loc_params, connector_id, get_type, dxpl_id,
+             req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -5051,7 +5071,8 @@ H5VLlink_specific(void *obj, const H5VL_loc_params_t *loc_params, hid_t connecto
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE7("e", "*x*xiVmi**xx", obj, loc_params, connector_id, specific_type, dxpl_id, req, arguments);
+    H5TRACE7("e", "*x*xiVmi**xx", obj, loc_params, connector_id, specific_type,
+             dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -5159,7 +5180,8 @@ H5VLlink_optional(void *obj, hid_t connector_id, H5VL_link_optional_t opt_type,
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVxi**xx", obj, connector_id, opt_type, dxpl_id, req, arguments);
+    H5TRACE6("e", "*xiVxi**xx", obj, connector_id, opt_type, dxpl_id, req,
+             arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -5260,7 +5282,8 @@ H5VLobject_open(void *obj, const H5VL_loc_params_t *params, hid_t connector_id,
     void *        ret_value = NULL; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("*x", "*x*xi*Iti**x", obj, params, connector_id, opened_type, dxpl_id, req);
+    H5TRACE6("*x", "*x*xi*Iti**x", obj, params, connector_id, opened_type, dxpl_id,
+             req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -5370,8 +5393,9 @@ H5VLobject_copy(void *src_obj, const H5VL_loc_params_t *src_loc_params, const ch
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE11("e", "*x*x*s*x*x*siiii**x", src_obj, src_loc_params, src_name, dst_obj, dst_loc_params,
-              dst_name, connector_id, ocpypl_id, lcpl_id, dxpl_id, req);
+    H5TRACE11("e", "*x*x*s*x*x*siiii**x", src_obj, src_loc_params, src_name,
+             dst_obj, dst_loc_params, dst_name, connector_id, ocpypl_id, lcpl_id,
+             dxpl_id, req);
 
     /* Check args and get class pointers */
     if (NULL == src_obj || NULL == dst_obj)
@@ -5481,7 +5505,8 @@ H5VLobject_get(void *obj, const H5VL_loc_params_t *loc_params, hid_t connector_i
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE7("e", "*x*xiVni**xx", obj, loc_params, connector_id, get_type, dxpl_id, req, arguments);
+    H5TRACE7("e", "*x*xiVni**xx", obj, loc_params, connector_id, get_type, dxpl_id,
+             req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -5590,7 +5615,8 @@ H5VLobject_specific(void *obj, const H5VL_loc_params_t *loc_params, hid_t connec
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE7("e", "*x*xiVoi**xx", obj, loc_params, connector_id, specific_type, dxpl_id, req, arguments);
+    H5TRACE7("e", "*x*xiVoi**xx", obj, loc_params, connector_id, specific_type,
+             dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -5702,7 +5728,8 @@ H5VLobject_optional(void *obj, hid_t connector_id, H5VL_object_optional_t opt_ty
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVyi**xx", obj, connector_id, opt_type, dxpl_id, req, arguments);
+    H5TRACE6("e", "*xiVyi**xx", obj, connector_id, opt_type, dxpl_id, req,
+             arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
-- 
cgit v0.12


From 273c0c18368e5e54d61467e9e5b70e6fd87981c5 Mon Sep 17 00:00:00 2001
From: Binh-Minh Ribler 
Date: Mon, 26 Oct 2020 13:04:35 -0500
Subject: Fix HDFFV-10590

Description
    This is to fix the CVE issue CVE-2018-17432.
    h5repack produced a segfault on a corrupted file.  This fix modified the
    dataspace encode and decode functions per Quincey's suggestion to prevent
    the segfault and h5repack only failed for the corrupted file now.
Platforms tested:
    Linux/64 (jelly)
---
 src/H5.c           |  10 ++---
 src/H5A.c          |  18 +++-----
 src/H5D.c          |   6 +--
 src/H5Dio.c        |   6 +--
 src/H5Dscatgath.c  |   3 +-
 src/H5E.c          |   7 ++--
 src/H5Edeprec.c    |   2 +-
 src/H5F.c          |   6 +--
 src/H5G.c          |   3 +-
 src/H5L.c          |  27 ++++--------
 src/H5Ldeprec.c    |   9 ++--
 src/H5Lexternal.c  |   6 +--
 src/H5M.c          |  12 ++----
 src/H5O.c          |   9 ++--
 src/H5Ocopy.c      |   3 +-
 src/H5Odeprec.c    |  12 ++----
 src/H5Osdspace.c   |  14 +++----
 src/H5P.c          |  12 +++---
 src/H5Pdcpl.c      |   3 +-
 src/H5Pdeprec.c    |   8 ++--
 src/H5Pdxpl.c      |   6 +--
 src/H5Pfapl.c      |   9 ++--
 src/H5Pfcpl.c      |   3 +-
 src/H5Pocpl.c      |  12 ++----
 src/H5Sselect.c    |   3 +-
 src/H5VL.c         |   2 +-
 src/H5VLcallback.c | 119 +++++++++++++++++++++--------------------------------
 27 files changed, 125 insertions(+), 205 deletions(-)

diff --git a/src/H5.c b/src/H5.c
index 72d87eb..e7514b4 100644
--- a/src/H5.c
+++ b/src/H5.c
@@ -448,7 +448,7 @@ H5dont_atexit(void)
     herr_t ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT_NOERR_NOFS
-    H5TRACE0("e","");
+    H5TRACE0("e", "");
 
     if (H5_dont_atexit_g)
         ret_value = FAIL;
@@ -481,7 +481,7 @@ H5garbage_collect(void)
     herr_t ret_value = SUCCEED;
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE0("e","");
+    H5TRACE0("e", "");
 
     /* Call the garbage collection routines in the library */
     if (H5FL_garbage_coll() < 0)
@@ -525,8 +525,8 @@ H5set_free_list_limits(int reg_global_lim, int reg_list_lim, int arr_global_lim,
     herr_t ret_value = SUCCEED;
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "IsIsIsIsIsIs", reg_global_lim, reg_list_lim, arr_global_lim,
-             arr_list_lim, blk_global_lim, blk_list_lim);
+    H5TRACE6("e", "IsIsIsIsIsIs", reg_global_lim, reg_list_lim, arr_global_lim, arr_list_lim, blk_global_lim,
+             blk_list_lim);
 
     /* Call the free list function to actually set the limits */
     if (H5FL_set_free_list_limits(reg_global_lim, reg_list_lim, arr_global_lim, arr_list_lim, blk_global_lim,
@@ -950,7 +950,7 @@ H5close(void)
      * this function for an uninitialized library.
      */
     FUNC_ENTER_API_NOINIT_NOERR_NOFS
-    H5TRACE0("e","");
+    H5TRACE0("e", "");
 
     H5_term_library();
 
diff --git a/src/H5A.c b/src/H5A.c
index b5bd0e8..7071f05 100644
--- a/src/H5A.c
+++ b/src/H5A.c
@@ -350,8 +350,7 @@ H5Acreate_by_name(hid_t loc_id, const char *obj_name, const char *attr_name, hid
     hid_t             ret_value = H5I_INVALID_HID; /* Return value */
 
     FUNC_ENTER_API(H5I_INVALID_HID)
-    H5TRACE8("i", "i*s*siiiii", loc_id, obj_name, attr_name, type_id, space_id,
-             acpl_id, aapl_id, lapl_id);
+    H5TRACE8("i", "i*s*siiiii", loc_id, obj_name, attr_name, type_id, space_id, acpl_id, aapl_id, lapl_id);
 
     /* Check arguments */
     if (H5I_ATTR == H5I_get_type(loc_id))
@@ -575,8 +574,7 @@ H5Aopen_by_idx(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_iter_
     hid_t             ret_value = H5I_INVALID_HID; /* Return value */
 
     FUNC_ENTER_API(H5I_INVALID_HID)
-    H5TRACE7("i", "i*sIiIohii", loc_id, obj_name, idx_type, order, n, aapl_id,
-             lapl_id);
+    H5TRACE7("i", "i*sIiIohii", loc_id, obj_name, idx_type, order, n, aapl_id, lapl_id);
 
     /* Check arguments */
     if (H5I_ATTR == H5I_get_type(loc_id))
@@ -905,8 +903,7 @@ H5Aget_name_by_idx(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_i
     ssize_t           ret_value; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("Zs", "i*sIiIohxzi", loc_id, obj_name, idx_type, order, n, name, size,
-             lapl_id);
+    H5TRACE8("Zs", "i*sIiIohxzi", loc_id, obj_name, idx_type, order, n, name, size, lapl_id);
 
     /* Check args */
     if (H5I_ATTR == H5I_get_type(loc_id))
@@ -1104,8 +1101,7 @@ H5Aget_info_by_idx(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_i
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "i*sIiIoh*xi", loc_id, obj_name, idx_type, order, n, ainfo,
-             lapl_id);
+    H5TRACE7("e", "i*sIiIoh*xi", loc_id, obj_name, idx_type, order, n, ainfo, lapl_id);
 
     /* Check args */
     if (H5I_ATTR == H5I_get_type(loc_id))
@@ -1222,8 +1218,7 @@ H5Arename_by_name(hid_t loc_id, const char *obj_name, const char *old_attr_name,
     herr_t ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE5("e", "i*s*s*si", loc_id, obj_name, old_attr_name, new_attr_name,
-             lapl_id);
+    H5TRACE5("e", "i*s*s*si", loc_id, obj_name, old_attr_name, new_attr_name, lapl_id);
 
     /* check arguments */
     if (H5I_ATTR == H5I_get_type(loc_id))
@@ -1391,8 +1386,7 @@ H5Aiterate_by_name(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_i
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "i*sIiIo*hx*xi", loc_id, obj_name, idx_type, order, idx, op,
-             op_data, lapl_id);
+    H5TRACE8("e", "i*sIiIo*hx*xi", loc_id, obj_name, idx_type, order, idx, op, op_data, lapl_id);
 
     /* Check arguments */
     if (H5I_ATTR == H5I_get_type(loc_id))
diff --git a/src/H5D.c b/src/H5D.c
index f342499..b8b6f65 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -96,8 +96,7 @@ H5Dcreate2(hid_t loc_id, const char *name, hid_t type_id, hid_t space_id, hid_t
     hid_t             ret_value = H5I_INVALID_HID; /* Return value */
 
     FUNC_ENTER_API(H5I_INVALID_HID)
-    H5TRACE7("i", "i*siiiii", loc_id, name, type_id, space_id, lcpl_id, dcpl_id,
-             dapl_id);
+    H5TRACE7("i", "i*siiiii", loc_id, name, type_id, space_id, lcpl_id, dcpl_id, dapl_id);
 
     /* Check arguments */
     if (!name)
@@ -1052,8 +1051,7 @@ H5Dget_chunk_info(hid_t dset_id, hid_t fspace_id, hsize_t chk_index, hsize_t *of
     herr_t         ret_value = SUCCEED;
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "iih*h*Iu*a*h", dset_id, fspace_id, chk_index, offset,
-             filter_mask, addr, size);
+    H5TRACE7("e", "iih*h*Iu*a*h", dset_id, fspace_id, chk_index, offset, filter_mask, addr, size);
 
     /* Check arguments */
     if (NULL == offset && NULL == filter_mask && NULL == addr && NULL == size)
diff --git a/src/H5Dio.c b/src/H5Dio.c
index 1629988..50c474b 100644
--- a/src/H5Dio.c
+++ b/src/H5Dio.c
@@ -155,8 +155,7 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_i
     herr_t         ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "iiiiix", dset_id, mem_type_id, mem_space_id, file_space_id,
-             dxpl_id, buf);
+    H5TRACE6("e", "iiiiix", dset_id, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf);
 
     /* Check arguments */
     if (mem_space_id < 0)
@@ -268,8 +267,7 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_
     herr_t         ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "iiiii*x", dset_id, mem_type_id, mem_space_id, file_space_id,
-             dxpl_id, buf);
+    H5TRACE6("e", "iiiii*x", dset_id, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf);
 
     /* Check arguments */
     if (mem_space_id < 0)
diff --git a/src/H5Dscatgath.c b/src/H5Dscatgath.c
index 75047f6..1a272d8 100644
--- a/src/H5Dscatgath.c
+++ b/src/H5Dscatgath.c
@@ -1026,8 +1026,7 @@ H5Dgather(hid_t src_space_id, const void *src_buf, hid_t type_id, size_t dst_buf
     herr_t          ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "i*xiz*xx*x", src_space_id, src_buf, type_id, dst_buf_size,
-             dst_buf, op, op_data);
+    H5TRACE7("e", "i*xiz*xx*x", src_space_id, src_buf, type_id, dst_buf_size, dst_buf, op, op_data);
 
     /* Check args */
     if (NULL == (src_space = (H5S_t *)H5I_object_verify(src_space_id, H5I_DATASPACE)))
diff --git a/src/H5E.c b/src/H5E.c
index 498baec..731d263 100644
--- a/src/H5E.c
+++ b/src/H5E.c
@@ -876,7 +876,7 @@ H5Ecreate_stack(void)
     hid_t  ret_value = H5I_INVALID_HID; /* Return value */
 
     FUNC_ENTER_API(H5I_INVALID_HID)
-    H5TRACE0("i","");
+    H5TRACE0("i", "");
 
     /* Allocate a new error stack */
     if (NULL == (stk = H5FL_CALLOC(H5E_t)))
@@ -915,7 +915,7 @@ H5Eget_current_stack(void)
 
     /* Don't clear the error stack! :-) */
     FUNC_ENTER_API_NOCLEAR(H5I_INVALID_HID)
-    H5TRACE0("i","");
+    H5TRACE0("i", "");
 
     /* Get the current stack */
     if (NULL == (stk = H5E__get_current_stack()))
@@ -1330,8 +1330,7 @@ H5Epush2(hid_t err_stack, const char *file, const char *func, unsigned line, hid
 
     /* Don't clear the error stack! :-) */
     FUNC_ENTER_API_NOCLEAR(FAIL)
-    H5TRACE8("e", "i*s*sIuiii*s", err_stack, file, func, line, cls_id, maj_id,
-             min_id, fmt);
+    H5TRACE8("e", "i*s*sIuiii*s", err_stack, file, func, line, cls_id, maj_id, min_id, fmt);
 
     if (err_stack == H5E_DEFAULT)
         estack = NULL;
diff --git a/src/H5Edeprec.c b/src/H5Edeprec.c
index 4d248b7..d3eef5d 100644
--- a/src/H5Edeprec.c
+++ b/src/H5Edeprec.c
@@ -230,7 +230,7 @@ H5Eclear1(void)
 
     /* Don't clear the error stack! :-) */
     FUNC_ENTER_API_NOCLEAR(FAIL)
-    H5TRACE0("e","");
+    H5TRACE0("e", "");
 
     /* Clear the default error stack */
     if (H5E_clear_stack(NULL) < 0)
diff --git a/src/H5F.c b/src/H5F.c
index 5a8fd87..3c6df2b 100644
--- a/src/H5F.c
+++ b/src/H5F.c
@@ -1164,8 +1164,7 @@ H5Fget_mdc_size(hid_t file_id, size_t *max_size_ptr, size_t *min_clean_size_ptr,
     herr_t         ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE5("e", "i*z*z*z*Is", file_id, max_size_ptr, min_clean_size_ptr,
-             cur_size_ptr, cur_num_entries_ptr);
+    H5TRACE5("e", "i*z*z*z*Is", file_id, max_size_ptr, min_clean_size_ptr, cur_size_ptr, cur_num_entries_ptr);
 
     /* Check args */
     if (NULL == (vol_obj = (H5VL_object_t *)H5I_object_verify(file_id, H5I_FILE)))
@@ -1698,8 +1697,7 @@ H5Fget_page_buffering_stats(hid_t file_id, unsigned accesses[2], unsigned hits[2
     herr_t         ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "i*Iu*Iu*Iu*Iu*Iu", file_id, accesses, hits, misses, evictions,
-             bypasses);
+    H5TRACE6("e", "i*Iu*Iu*Iu*Iu*Iu", file_id, accesses, hits, misses, evictions, bypasses);
 
     /* Check args */
     if (NULL == (vol_obj = (H5VL_object_t *)H5I_object_verify(file_id, H5I_FILE)))
diff --git a/src/H5G.c b/src/H5G.c
index fae401c..a15e500 100644
--- a/src/H5G.c
+++ b/src/H5G.c
@@ -668,8 +668,7 @@ H5Gget_info_by_idx(hid_t loc_id, const char *group_name, H5_index_t idx_type, H5
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "i*sIiIoh*xi", loc_id, group_name, idx_type, order, n, group_info,
-             lapl_id);
+    H5TRACE7("e", "i*sIiIoh*xi", loc_id, group_name, idx_type, order, n, group_info, lapl_id);
 
     /* Check args */
     if (!group_name)
diff --git a/src/H5L.c b/src/H5L.c
index 55d5785..0fe632e 100644
--- a/src/H5L.c
+++ b/src/H5L.c
@@ -267,8 +267,7 @@ H5Lmove(hid_t src_loc_id, const char *src_name, hid_t dst_loc_id, const char *ds
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "i*si*sii", src_loc_id, src_name, dst_loc_id, dst_name, lcpl_id,
-             lapl_id);
+    H5TRACE6("e", "i*si*sii", src_loc_id, src_name, dst_loc_id, dst_name, lcpl_id, lapl_id);
 
     /* Check arguments */
     if (src_loc_id == H5L_SAME_LOC && dst_loc_id == H5L_SAME_LOC)
@@ -358,8 +357,7 @@ H5Lcopy(hid_t src_loc_id, const char *src_name, hid_t dst_loc_id, const char *ds
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "i*si*sii", src_loc_id, src_name, dst_loc_id, dst_name, lcpl_id,
-             lapl_id);
+    H5TRACE6("e", "i*si*sii", src_loc_id, src_name, dst_loc_id, dst_name, lcpl_id, lapl_id);
 
     /* Check arguments */
     if (src_loc_id == H5L_SAME_LOC && dst_loc_id == H5L_SAME_LOC)
@@ -524,8 +522,7 @@ H5Lcreate_hard(hid_t cur_loc_id, const char *cur_name, hid_t new_loc_id, const c
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "i*si*sii", cur_loc_id, cur_name, new_loc_id, new_name, lcpl_id,
-             lapl_id);
+    H5TRACE6("e", "i*si*sii", cur_loc_id, cur_name, new_loc_id, new_name, lcpl_id, lapl_id);
 
     /* Check arguments */
     if (cur_loc_id == H5L_SAME_LOC && new_loc_id == H5L_SAME_LOC)
@@ -625,8 +622,7 @@ H5Lcreate_ud(hid_t link_loc_id, const char *link_name, H5L_type_t link_type, con
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "i*sLl*xzii", link_loc_id, link_name, link_type, udata,
-             udata_size, lcpl_id, lapl_id);
+    H5TRACE7("e", "i*sLl*xzii", link_loc_id, link_name, link_type, udata, udata_size, lcpl_id, lapl_id);
 
     /* Check arguments */
     if (!link_name || !*link_name)
@@ -864,8 +860,7 @@ H5Lget_val_by_idx(hid_t loc_id, const char *group_name, H5_index_t idx_type, H5_
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "i*sIiIohxzi", loc_id, group_name, idx_type, order, n, buf, size,
-             lapl_id);
+    H5TRACE8("e", "i*sIiIohxzi", loc_id, group_name, idx_type, order, n, buf, size, lapl_id);
 
     /* Check arguments */
     if (!group_name || !*group_name)
@@ -1023,8 +1018,7 @@ H5Lget_info_by_idx2(hid_t loc_id, const char *group_name, H5_index_t idx_type, H
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "i*sIiIohxi", loc_id, group_name, idx_type, order, n, linfo,
-             lapl_id);
+    H5TRACE7("e", "i*sIiIohxi", loc_id, group_name, idx_type, order, n, linfo, lapl_id);
 
     /* Check arguments */
     if (!group_name || !*group_name)
@@ -1221,8 +1215,7 @@ H5Lget_name_by_idx(hid_t loc_id, const char *group_name, H5_index_t idx_type, H5
     ssize_t           ret_value = -1; /* Return value */
 
     FUNC_ENTER_API((-1))
-    H5TRACE8("Zs", "i*sIiIohxzi", loc_id, group_name, idx_type, order, n, name, size,
-             lapl_id);
+    H5TRACE8("Zs", "i*sIiIohxzi", loc_id, group_name, idx_type, order, n, name, size, lapl_id);
 
     /* Check arguments */
     if (!group_name || !*group_name)
@@ -1348,8 +1341,7 @@ H5Literate_by_name2(hid_t loc_id, const char *group_name, H5_index_t idx_type, H
     herr_t            ret_value; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "i*sIiIo*hx*xi", loc_id, group_name, idx_type, order, idx_p, op,
-             op_data, lapl_id);
+    H5TRACE8("e", "i*sIiIo*hx*xi", loc_id, group_name, idx_type, order, idx_p, op, op_data, lapl_id);
 
     /* Check arguments */
     if (!group_name)
@@ -1490,8 +1482,7 @@ H5Lvisit_by_name2(hid_t loc_id, const char *group_name, H5_index_t idx_type, H5_
     herr_t            ret_value; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "i*sIiIox*xi", loc_id, group_name, idx_type, order, op, op_data,
-             lapl_id);
+    H5TRACE7("e", "i*sIiIox*xi", loc_id, group_name, idx_type, order, op, op_data, lapl_id);
 
     /* Check args */
     if (!group_name)
diff --git a/src/H5Ldeprec.c b/src/H5Ldeprec.c
index da1940c..843469f 100644
--- a/src/H5Ldeprec.c
+++ b/src/H5Ldeprec.c
@@ -226,8 +226,7 @@ H5Literate_by_name1(hid_t loc_id, const char *group_name, H5_index_t idx_type, H
     herr_t            ret_value; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "i*sIiIo*hx*xi", loc_id, group_name, idx_type, order, idx_p, op,
-             op_data, lapl_id);
+    H5TRACE8("e", "i*sIiIo*hx*xi", loc_id, group_name, idx_type, order, idx_p, op, op_data, lapl_id);
 
     /* Check arguments */
     if (!group_name)
@@ -384,8 +383,7 @@ H5Lget_info_by_idx1(hid_t loc_id, const char *group_name, H5_index_t idx_type, H
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "i*sIiIohxi", loc_id, group_name, idx_type, order, n, linfo,
-             lapl_id);
+    H5TRACE7("e", "i*sIiIohxi", loc_id, group_name, idx_type, order, n, linfo, lapl_id);
 
     /* Check arguments */
     if (!group_name || !*group_name)
@@ -572,8 +570,7 @@ H5Lvisit_by_name1(hid_t loc_id, const char *group_name, H5_index_t idx_type, H5_
     herr_t            ret_value; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "i*sIiIox*xi", loc_id, group_name, idx_type, order, op, op_data,
-             lapl_id);
+    H5TRACE7("e", "i*sIiIox*xi", loc_id, group_name, idx_type, order, op, op_data, lapl_id);
 
     /* Check args */
     if (!group_name)
diff --git a/src/H5Lexternal.c b/src/H5Lexternal.c
index 2fce7cd..b978a73 100644
--- a/src/H5Lexternal.c
+++ b/src/H5Lexternal.c
@@ -349,8 +349,7 @@ H5Lcreate_external(const char *file_name, const char *obj_name, hid_t link_loc_i
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "*s*si*sii", file_name, obj_name, link_loc_id, link_name,
-             lcpl_id, lapl_id);
+    H5TRACE6("e", "*s*si*sii", file_name, obj_name, link_loc_id, link_name, lcpl_id, lapl_id);
 
     /* Check arguments */
     if (!file_name || !*file_name)
@@ -473,8 +472,7 @@ H5Lunpack_elink_val(const void *_ext_linkval, size_t link_size, unsigned *flags,
     herr_t         ret_value = SUCCEED;                         /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE5("e", "*xz*Iu**s**s", _ext_linkval, link_size, flags, filename,
-             obj_path);
+    H5TRACE5("e", "*xz*Iu**s**s", _ext_linkval, link_size, flags, filename, obj_path);
 
     /* Sanity check external link buffer */
     if (ext_linkval == NULL)
diff --git a/src/H5M.c b/src/H5M.c
index e3091ca..34d0105 100644
--- a/src/H5M.c
+++ b/src/H5M.c
@@ -246,8 +246,7 @@ H5Mcreate(hid_t loc_id, const char *name, hid_t key_type_id, hid_t val_type_id,
     hid_t             ret_value = H5I_INVALID_HID; /* Return value */
 
     FUNC_ENTER_API(H5I_INVALID_HID)
-    H5TRACE7("i", "i*siiiii", loc_id, name, key_type_id, val_type_id, lcpl_id,
-             mcpl_id, mapl_id);
+    H5TRACE7("i", "i*siiiii", loc_id, name, key_type_id, val_type_id, lcpl_id, mcpl_id, mapl_id);
 
     /* Check arguments */
     if (!name)
@@ -672,8 +671,7 @@ H5Mput(hid_t map_id, hid_t key_mem_type_id, const void *key, hid_t val_mem_type_
     herr_t         ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "ii*xi*xi", map_id, key_mem_type_id, key, val_mem_type_id, value,
-             dxpl_id);
+    H5TRACE6("e", "ii*xi*xi", map_id, key_mem_type_id, key, val_mem_type_id, value, dxpl_id);
 
     /* Check arguments */
     if (key_mem_type_id < 0)
@@ -730,8 +728,7 @@ H5Mget(hid_t map_id, hid_t key_mem_type_id, const void *key, hid_t val_mem_type_
     herr_t         ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "ii*xi*xi", map_id, key_mem_type_id, key, val_mem_type_id, value,
-             dxpl_id);
+    H5TRACE6("e", "ii*xi*xi", map_id, key_mem_type_id, key, val_mem_type_id, value, dxpl_id);
 
     /* Check arguments */
     if (key_mem_type_id < 0)
@@ -922,8 +919,7 @@ H5Miterate_by_name(hid_t loc_id, const char *map_name, hsize_t *idx, hid_t key_m
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "i*s*hix*xii", loc_id, map_name, idx, key_mem_type_id, op,
-             op_data, dxpl_id, lapl_id);
+    H5TRACE8("e", "i*s*hix*xii", loc_id, map_name, idx, key_mem_type_id, op, op_data, dxpl_id, lapl_id);
 
     /* Check arguments */
     if (!map_name)
diff --git a/src/H5O.c b/src/H5O.c
index 39037a9..e5d794c 100644
--- a/src/H5O.c
+++ b/src/H5O.c
@@ -632,8 +632,7 @@ H5Oget_info_by_idx3(hid_t loc_id, const char *group_name, H5_index_t idx_type, H
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "i*sIiIoh*xIui", loc_id, group_name, idx_type, order, n, oinfo,
-             fields, lapl_id);
+    H5TRACE8("e", "i*sIiIoh*xIui", loc_id, group_name, idx_type, order, n, oinfo, fields, lapl_id);
 
     /* Check args */
     if (!group_name || !*group_name)
@@ -796,8 +795,7 @@ H5Oget_native_info_by_idx(hid_t loc_id, const char *group_name, H5_index_t idx_t
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "i*sIiIoh*xIui", loc_id, group_name, idx_type, order, n, oinfo,
-             fields, lapl_id);
+    H5TRACE8("e", "i*sIiIoh*xIui", loc_id, group_name, idx_type, order, n, oinfo, fields, lapl_id);
 
     /* Check args */
     if (!group_name || !*group_name)
@@ -1152,8 +1150,7 @@ H5Ovisit_by_name3(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_it
     herr_t            ret_value; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "i*sIiIox*xIui", loc_id, obj_name, idx_type, order, op, op_data,
-             fields, lapl_id);
+    H5TRACE8("e", "i*sIiIox*xIui", loc_id, obj_name, idx_type, order, op, op_data, fields, lapl_id);
 
     /* Check args */
     if (!obj_name)
diff --git a/src/H5Ocopy.c b/src/H5Ocopy.c
index 9f92925..54a41c0 100644
--- a/src/H5Ocopy.c
+++ b/src/H5Ocopy.c
@@ -195,8 +195,7 @@ H5Ocopy(hid_t src_loc_id, const char *src_name, hid_t dst_loc_id, const char *ds
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE6("e", "i*si*sii", src_loc_id, src_name, dst_loc_id, dst_name,
-             ocpypl_id, lcpl_id);
+    H5TRACE6("e", "i*si*sii", src_loc_id, src_name, dst_loc_id, dst_name, ocpypl_id, lcpl_id);
 
     /* Check arguments */
     if (!src_name || !*src_name)
diff --git a/src/H5Odeprec.c b/src/H5Odeprec.c
index b737783..1838234 100644
--- a/src/H5Odeprec.c
+++ b/src/H5Odeprec.c
@@ -487,8 +487,7 @@ H5Oget_info_by_idx1(hid_t loc_id, const char *group_name, H5_index_t idx_type, H
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "i*sIiIoh*xi", loc_id, group_name, idx_type, order, n, oinfo,
-             lapl_id);
+    H5TRACE7("e", "i*sIiIoh*xi", loc_id, group_name, idx_type, order, n, oinfo, lapl_id);
 
     /* Check args */
     if (!group_name || !*group_name)
@@ -670,8 +669,7 @@ H5Oget_info_by_idx2(hid_t loc_id, const char *group_name, H5_index_t idx_type, H
     herr_t            ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "i*sIiIoh*xIui", loc_id, group_name, idx_type, order, n, oinfo,
-             fields, lapl_id);
+    H5TRACE8("e", "i*sIiIoh*xIui", loc_id, group_name, idx_type, order, n, oinfo, fields, lapl_id);
 
     /* Check args */
     if (!group_name || !*group_name)
@@ -833,8 +831,7 @@ H5Ovisit_by_name1(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_it
     herr_t               ret_value; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "i*sIiIox*xi", loc_id, obj_name, idx_type, order, op, op_data,
-             lapl_id);
+    H5TRACE7("e", "i*sIiIox*xi", loc_id, obj_name, idx_type, order, op, op_data, lapl_id);
 
     /* Check args */
     if (!obj_name)
@@ -1012,8 +1009,7 @@ H5Ovisit_by_name2(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_it
     herr_t               ret_value; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "i*sIiIox*xIui", loc_id, obj_name, idx_type, order, op, op_data,
-             fields, lapl_id);
+    H5TRACE8("e", "i*sIiIox*xIui", loc_id, obj_name, idx_type, order, op, op_data, fields, lapl_id);
 
     /* Check args */
     if (!obj_name)
diff --git a/src/H5Osdspace.c b/src/H5Osdspace.c
index e3ec4b0..83702eb 100644
--- a/src/H5Osdspace.c
+++ b/src/H5Osdspace.c
@@ -140,7 +140,7 @@ H5O__sdspace_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, unsigned H5_ATTR_UN
     /* Get or determine the type of the extent */
     if (version >= H5O_SDSPACE_VERSION_2) {
         sdim->type = (H5S_class_t)*p++;
-        if(sdim->type != H5S_SIMPLE && sdim->rank > 0)
+        if (sdim->type != H5S_SIMPLE && sdim->rank > 0)
             HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, NULL, "invalid rank for scalar or NULL dataspace")
     } /* end if */
     else {
@@ -252,16 +252,16 @@ H5O__sdspace_encode(H5F_t *f, uint8_t *p, const void *_mesg)
     }             /* end else */
 
     /* Encode dataspace dimensions for simple dataspaces */
-    if(H5S_SIMPLE == sdim->type) {
+    if (H5S_SIMPLE == sdim->type) {
         /* Encode current & maximum dimensions */
-        if(sdim->rank > 0) {
-            for(u = 0; u < sdim->rank; u++)
+        if (sdim->rank > 0) {
+            for (u = 0; u < sdim->rank; u++)
                 H5F_ENCODE_LENGTH(f, p, sdim->size[u]);
-            if(flags & H5S_VALID_MAX)
-                for(u = 0; u < sdim->rank; u++)
+            if (flags & H5S_VALID_MAX)
+                for (u = 0; u < sdim->rank; u++)
                     H5F_ENCODE_LENGTH(f, p, sdim->max[u]);
         } /* end if */
-    } /* end if */
+    }     /* end if */
 
     FUNC_LEAVE_NOAPI(SUCCEED)
 } /* end H5O__sdspace_encode() */
diff --git a/src/H5P.c b/src/H5P.c
index befdd77..3ccdfd4 100644
--- a/src/H5P.c
+++ b/src/H5P.c
@@ -173,8 +173,8 @@ H5Pcreate_class(hid_t parent, const char *name, H5P_cls_create_func_t cls_create
     hid_t           ret_value = H5I_INVALID_HID; /* Return value		   */
 
     FUNC_ENTER_API(H5I_INVALID_HID)
-    H5TRACE8("i", "i*sx*xx*xx*x", parent, name, cls_create, create_data, cls_copy,
-             copy_data, cls_close, close_data);
+    H5TRACE8("i", "i*sx*xx*xx*x", parent, name, cls_create, create_data, cls_copy, copy_data, cls_close,
+             close_data);
 
     /* Check arguments. */
     if (H5P_DEFAULT != parent && (H5I_GENPROP_CLS != H5I_get_type(parent)))
@@ -414,8 +414,8 @@ H5Pregister2(hid_t cls_id, const char *name, size_t size, void *def_value, H5P_p
     herr_t          ret_value;   /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE11("e", "i*sz*xxxxxxxx", cls_id, name, size, def_value, prp_create,
-             prp_set, prp_get, prp_delete, prp_copy, prp_cmp, prp_close);
+    H5TRACE11("e", "i*sz*xxxxxxxx", cls_id, name, size, def_value, prp_create, prp_set, prp_get, prp_delete,
+              prp_copy, prp_cmp, prp_close);
 
     /* Check arguments. */
     if (NULL == (pclass = (H5P_genclass_t *)H5I_object_verify(cls_id, H5I_GENPROP_CLS)))
@@ -598,8 +598,8 @@ H5Pinsert2(hid_t plist_id, const char *name, size_t size, void *value, H5P_prp_s
     herr_t          ret_value; /* return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE10("e", "i*sz*xxxxxxx", plist_id, name, size, value, prp_set, prp_get,
-             prp_delete, prp_copy, prp_cmp, prp_close);
+    H5TRACE10("e", "i*sz*xxxxxxx", plist_id, name, size, value, prp_set, prp_get, prp_delete, prp_copy,
+              prp_cmp, prp_close);
 
     /* Check arguments. */
     if (NULL == (plist = (H5P_genplist_t *)H5I_object_verify(plist_id, H5I_GENPROP_LST)))
diff --git a/src/H5Pdcpl.c b/src/H5Pdcpl.c
index 734a10a..8c525e5 100644
--- a/src/H5Pdcpl.c
+++ b/src/H5Pdcpl.c
@@ -2226,8 +2226,7 @@ H5Pset_virtual(hid_t dcpl_id, hid_t vspace_id, const char *src_file_name, const
     herr_t                     ret_value        = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE5("e", "ii*s*si", dcpl_id, vspace_id, src_file_name, src_dset_name,
-             src_space_id);
+    H5TRACE5("e", "ii*s*si", dcpl_id, vspace_id, src_file_name, src_dset_name, src_space_id);
 
     /* Check arguments */
     if (!src_file_name)
diff --git a/src/H5Pdeprec.c b/src/H5Pdeprec.c
index 5b70080..d80c153 100644
--- a/src/H5Pdeprec.c
+++ b/src/H5Pdeprec.c
@@ -220,8 +220,8 @@ H5Pregister1(hid_t cls_id, const char *name, size_t size, void *def_value, H5P_p
     herr_t          ret_value;   /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE10("e", "i*sz*xxxxxxx", cls_id, name, size, def_value, prp_create,
-             prp_set, prp_get, prp_delete, prp_copy, prp_close);
+    H5TRACE10("e", "i*sz*xxxxxxx", cls_id, name, size, def_value, prp_create, prp_set, prp_get, prp_delete,
+              prp_copy, prp_close);
 
     /* Check arguments. */
     if (NULL == (pclass = (H5P_genclass_t *)H5I_object_verify(cls_id, H5I_GENPROP_CLS)))
@@ -404,8 +404,8 @@ H5Pinsert1(hid_t plist_id, const char *name, size_t size, void *value, H5P_prp_s
     herr_t          ret_value; /* return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE9("e", "i*sz*xxxxxx", plist_id, name, size, value, prp_set, prp_get,
-             prp_delete, prp_copy, prp_close);
+    H5TRACE9("e", "i*sz*xxxxxx", plist_id, name, size, value, prp_set, prp_get, prp_delete, prp_copy,
+             prp_close);
 
     /* Check arguments. */
     if (NULL == (plist = (H5P_genplist_t *)H5I_object_verify(plist_id, H5I_GENPROP_LST)))
diff --git a/src/H5Pdxpl.c b/src/H5Pdxpl.c
index 70f3056..09eadfa 100644
--- a/src/H5Pdxpl.c
+++ b/src/H5Pdxpl.c
@@ -1577,8 +1577,7 @@ H5Pset_vlen_mem_manager(hid_t plist_id, H5MM_allocate_t alloc_func, void *alloc_
     herr_t          ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE5("e", "ix*xx*x", plist_id, alloc_func, alloc_info, free_func,
-             free_info);
+    H5TRACE5("e", "ix*xx*x", plist_id, alloc_func, alloc_info, free_func, free_info);
 
     /* Check arguments */
     if (NULL == (plist = H5P_object_verify(plist_id, H5P_DATASET_XFER)))
@@ -2021,8 +2020,7 @@ H5Pget_mpio_no_collective_cause(hid_t plist_id, uint32_t *local_no_collective_ca
     herr_t          ret_value = SUCCEED; /* return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE3("e", "i*Iu*Iu", plist_id, local_no_collective_cause,
-             global_no_collective_cause);
+    H5TRACE3("e", "i*Iu*Iu", plist_id, local_no_collective_cause, global_no_collective_cause);
 
     /* Get the plist structure */
     if (NULL == (plist = H5P_object_verify(plist_id, H5P_DATASET_XFER)))
diff --git a/src/H5Pfapl.c b/src/H5Pfapl.c
index 42d49d1..f9a730d 100644
--- a/src/H5Pfapl.c
+++ b/src/H5Pfapl.c
@@ -1683,8 +1683,7 @@ H5Pset_cache(hid_t plist_id, int H5_ATTR_UNUSED mdc_nelmts, size_t rdcc_nslots,
     herr_t          ret_value = SUCCEED; /* return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE5("e", "iIszzd", plist_id, mdc_nelmts, rdcc_nslots, rdcc_nbytes,
-             rdcc_w0);
+    H5TRACE5("e", "iIszzd", plist_id, mdc_nelmts, rdcc_nslots, rdcc_nbytes, rdcc_w0);
 
     /* Check arguments */
     if (rdcc_w0 < (double)0.0f || rdcc_w0 > (double)1.0f)
@@ -1730,8 +1729,7 @@ H5Pget_cache(hid_t plist_id, int *mdc_nelmts, size_t *rdcc_nslots, size_t *rdcc_
     herr_t          ret_value = SUCCEED; /* return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE5("e", "i*Is*z*z*d", plist_id, mdc_nelmts, rdcc_nslots, rdcc_nbytes,
-             rdcc_w0);
+    H5TRACE5("e", "i*Is*z*z*d", plist_id, mdc_nelmts, rdcc_nslots, rdcc_nbytes, rdcc_w0);
 
     /* Get the plist structure */
     if (NULL == (plist = H5P_object_verify(plist_id, H5P_FILE_ACCESS)))
@@ -4282,8 +4280,7 @@ H5Pget_mdc_log_options(hid_t plist_id, hbool_t *is_enabled, char *location, size
     herr_t          ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE5("e", "i*b*s*z*b", plist_id, is_enabled, location, location_size,
-             start_on_access);
+    H5TRACE5("e", "i*b*s*z*b", plist_id, is_enabled, location, location_size, start_on_access);
 
     /* Get the property list structure */
     if (NULL == (plist = H5P_object_verify(plist_id, H5P_FILE_ACCESS)))
diff --git a/src/H5Pfcpl.c b/src/H5Pfcpl.c
index c703e1d..fbf9aac 100644
--- a/src/H5Pfcpl.c
+++ b/src/H5Pfcpl.c
@@ -934,8 +934,7 @@ H5Pget_shared_mesg_index(hid_t plist_id, unsigned index_num, unsigned *mesg_type
     herr_t          ret_value = SUCCEED;                 /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE4("e", "iIu*Iu*Iu", plist_id, index_num, mesg_type_flags,
-             min_mesg_size);
+    H5TRACE4("e", "iIu*Iu*Iu", plist_id, index_num, mesg_type_flags, min_mesg_size);
 
     /* Get the plist structure */
     if (NULL == (plist = H5P_object_verify(plist_id, H5P_FILE_CREATE)))
diff --git a/src/H5Pocpl.c b/src/H5Pocpl.c
index b7312f2..bd6be75 100644
--- a/src/H5Pocpl.c
+++ b/src/H5Pocpl.c
@@ -807,8 +807,7 @@ H5Pget_filter2(hid_t plist_id, unsigned idx, unsigned int *flags /*out*/, size_t
     H5Z_filter_t             ret_value; /* return value */
 
     FUNC_ENTER_API(H5Z_FILTER_ERROR)
-    H5TRACE8("Zf", "iIux*zxzxx", plist_id, idx, flags, cd_nelmts, cd_values,
-             namelen, name, filter_config);
+    H5TRACE8("Zf", "iIux*zxzxx", plist_id, idx, flags, cd_nelmts, cd_values, namelen, name, filter_config);
 
     /* Check args */
     if (cd_nelmts || cd_values) {
@@ -938,8 +937,7 @@ H5Pget_filter_by_id2(hid_t plist_id, H5Z_filter_t id, unsigned int *flags /*out*
     herr_t          ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE8("e", "iZfx*zxzx*Iu", plist_id, id, flags, cd_nelmts, cd_values,
-             namelen, name, filter_config);
+    H5TRACE8("e", "iZfx*zxzx*Iu", plist_id, id, flags, cd_nelmts, cd_values, namelen, name, filter_config);
 
     /* Check args */
     if (cd_nelmts || cd_values) {
@@ -1757,8 +1755,7 @@ H5Pget_filter1(hid_t plist_id, unsigned idx, unsigned int *flags /*out*/, size_t
     H5Z_filter_t             ret_value; /* return value */
 
     FUNC_ENTER_API(H5Z_FILTER_ERROR)
-    H5TRACE7("Zf", "iIux*zxzx", plist_id, idx, flags, cd_nelmts, cd_values, namelen,
-             name);
+    H5TRACE7("Zf", "iIux*zxzx", plist_id, idx, flags, cd_nelmts, cd_values, namelen, name);
 
     /* Check args */
     if (cd_nelmts || cd_values) {
@@ -1838,8 +1835,7 @@ H5Pget_filter_by_id1(hid_t plist_id, H5Z_filter_t id, unsigned int *flags /*out*
     herr_t          ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "iZfx*zxzx", plist_id, id, flags, cd_nelmts, cd_values, namelen,
-             name);
+    H5TRACE7("e", "iZfx*zxzx", plist_id, id, flags, cd_nelmts, cd_values, namelen, name);
 
     /* Check args */
     if (cd_nelmts || cd_values) {
diff --git a/src/H5Sselect.c b/src/H5Sselect.c
index f351982..023ab80 100644
--- a/src/H5Sselect.c
+++ b/src/H5Sselect.c
@@ -3063,8 +3063,7 @@ H5Ssel_iter_get_seq_list(hid_t sel_iter_id, size_t maxseq, size_t maxbytes, size
     herr_t          ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE7("e", "izz*z*z*h*z", sel_iter_id, maxseq, maxbytes, nseq, nbytes, off,
-             len);
+    H5TRACE7("e", "izz*z*z*h*z", sel_iter_id, maxseq, maxbytes, nseq, nbytes, off, len);
 
     /* Check args */
     if (NULL == (sel_iter = (H5S_sel_iter_t *)H5I_object_verify(sel_iter_id, H5I_SPACE_SEL_ITER)))
diff --git a/src/H5VL.c b/src/H5VL.c
index d8c2435..d60bd5f 100644
--- a/src/H5VL.c
+++ b/src/H5VL.c
@@ -842,7 +842,7 @@ H5VLreset_lib_state(void)
 
     /* Must use this, to avoid modifying the API context stack in FUNC_ENTER */
     FUNC_ENTER_API_NOINIT
-    H5TRACE0("e","");
+    H5TRACE0("e", "");
 
     /* Reset the library state */
     if (H5VL_reset_lib_state() < 0)
diff --git a/src/H5VLcallback.c b/src/H5VLcallback.c
index 5b7eb8d..6abbf8d 100644
--- a/src/H5VLcallback.c
+++ b/src/H5VLcallback.c
@@ -1000,8 +1000,8 @@ H5VLattr_create(void *obj, const H5VL_loc_params_t *loc_params, hid_t connector_
     void *        ret_value = NULL; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE10("*x", "*x*xi*siiiii**x", obj, loc_params, connector_id, name,
-             type_id, space_id, acpl_id, aapl_id, dxpl_id, req);
+    H5TRACE10("*x", "*x*xi*siiiii**x", obj, loc_params, connector_id, name, type_id, space_id, acpl_id,
+              aapl_id, dxpl_id, req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -1103,8 +1103,7 @@ H5VLattr_open(void *obj, const H5VL_loc_params_t *loc_params, hid_t connector_id
     void *        ret_value = NULL; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE7("*x", "*x*xi*sii**x", obj, loc_params, connector_id, name, aapl_id,
-             dxpl_id, req);
+    H5TRACE7("*x", "*x*xi*sii**x", obj, loc_params, connector_id, name, aapl_id, dxpl_id, req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -1406,8 +1405,7 @@ H5VLattr_get(void *obj, hid_t connector_id, H5VL_attr_get_t get_type, hid_t dxpl
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVai**xx", obj, connector_id, get_type, dxpl_id, req,
-             arguments);
+    H5TRACE6("e", "*xiVai**xx", obj, connector_id, get_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -1516,8 +1514,7 @@ H5VLattr_specific(void *obj, const H5VL_loc_params_t *loc_params, hid_t connecto
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE7("e", "*x*xiVbi**xx", obj, loc_params, connector_id, specific_type,
-             dxpl_id, req, arguments);
+    H5TRACE7("e", "*x*xiVbi**xx", obj, loc_params, connector_id, specific_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -1626,8 +1623,7 @@ H5VLattr_optional(void *obj, hid_t connector_id, H5VL_attr_optional_t opt_type,
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVsi**xx", obj, connector_id, opt_type, dxpl_id, req,
-             arguments);
+    H5TRACE6("e", "*xiVsi**xx", obj, connector_id, opt_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -1823,8 +1819,8 @@ H5VLdataset_create(void *obj, const H5VL_loc_params_t *loc_params, hid_t connect
     void *        ret_value = NULL; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE11("*x", "*x*xi*siiiiii**x", obj, loc_params, connector_id, name,
-             lcpl_id, type_id, space_id, dcpl_id, dapl_id, dxpl_id, req);
+    H5TRACE11("*x", "*x*xi*siiiiii**x", obj, loc_params, connector_id, name, lcpl_id, type_id, space_id,
+              dcpl_id, dapl_id, dxpl_id, req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -1926,8 +1922,7 @@ H5VLdataset_open(void *obj, const H5VL_loc_params_t *loc_params, hid_t connector
     void *        ret_value = NULL; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE7("*x", "*x*xi*sii**x", obj, loc_params, connector_id, name, dapl_id,
-             dxpl_id, req);
+    H5TRACE7("*x", "*x*xi*sii**x", obj, loc_params, connector_id, name, dapl_id, dxpl_id, req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -2028,8 +2023,8 @@ H5VLdataset_read(void *obj, hid_t connector_id, hid_t mem_type_id, hid_t mem_spa
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE8("e", "*xiiiii*x**x", obj, connector_id, mem_type_id, mem_space_id,
-             file_space_id, dxpl_id, buf, req);
+    H5TRACE8("e", "*xiiiii*x**x", obj, connector_id, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf,
+             req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -2130,8 +2125,8 @@ H5VLdataset_write(void *obj, hid_t connector_id, hid_t mem_type_id, hid_t mem_sp
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE8("e", "*xiiiii*x**x", obj, connector_id, mem_type_id, mem_space_id,
-             file_space_id, dxpl_id, buf, req);
+    H5TRACE8("e", "*xiiiii*x**x", obj, connector_id, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf,
+             req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -2238,8 +2233,7 @@ H5VLdataset_get(void *obj, hid_t connector_id, H5VL_dataset_get_t get_type, hid_
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVci**xx", obj, connector_id, get_type, dxpl_id, req,
-             arguments);
+    H5TRACE6("e", "*xiVci**xx", obj, connector_id, get_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -2348,8 +2342,7 @@ H5VLdataset_specific(void *obj, hid_t connector_id, H5VL_dataset_specific_t spec
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVdi**xx", obj, connector_id, specific_type, dxpl_id, req,
-             arguments);
+    H5TRACE6("e", "*xiVdi**xx", obj, connector_id, specific_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -2457,8 +2450,7 @@ H5VLdataset_optional(void *obj, hid_t connector_id, H5VL_dataset_optional_t opt_
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVti**xx", obj, connector_id, opt_type, dxpl_id, req,
-             arguments);
+    H5TRACE6("e", "*xiVti**xx", obj, connector_id, opt_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -2668,8 +2660,8 @@ H5VLdatatype_commit(void *obj, const H5VL_loc_params_t *loc_params, hid_t connec
     void *        ret_value = NULL; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE10("*x", "*x*xi*siiiii**x", obj, loc_params, connector_id, name,
-             type_id, lcpl_id, tcpl_id, tapl_id, dxpl_id, req);
+    H5TRACE10("*x", "*x*xi*siiiii**x", obj, loc_params, connector_id, name, type_id, lcpl_id, tcpl_id,
+              tapl_id, dxpl_id, req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -2771,8 +2763,7 @@ H5VLdatatype_open(void *obj, const H5VL_loc_params_t *loc_params, hid_t connecto
     void *        ret_value = NULL; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE7("*x", "*x*xi*sii**x", obj, loc_params, connector_id, name, tapl_id,
-             dxpl_id, req);
+    H5TRACE7("*x", "*x*xi*sii**x", obj, loc_params, connector_id, name, tapl_id, dxpl_id, req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -2879,8 +2870,7 @@ H5VLdatatype_get(void *obj, hid_t connector_id, H5VL_datatype_get_t get_type, hi
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVei**xx", obj, connector_id, get_type, dxpl_id, req,
-             arguments);
+    H5TRACE6("e", "*xiVei**xx", obj, connector_id, get_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -2993,8 +2983,7 @@ H5VLdatatype_specific(void *obj, hid_t connector_id, H5VL_datatype_specific_t sp
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVfi**xx", obj, connector_id, specific_type, dxpl_id, req,
-             arguments);
+    H5TRACE6("e", "*xiVfi**xx", obj, connector_id, specific_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -3103,8 +3092,7 @@ H5VLdatatype_optional(void *obj, hid_t connector_id, H5VL_datatype_optional_t op
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVui**xx", obj, connector_id, opt_type, dxpl_id, req,
-             arguments);
+    H5TRACE6("e", "*xiVui**xx", obj, connector_id, opt_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -3517,8 +3505,7 @@ H5VLfile_get(void *obj, hid_t connector_id, H5VL_file_get_t get_type, hid_t dxpl
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVgi**xx", obj, connector_id, get_type, dxpl_id, req,
-             arguments);
+    H5TRACE6("e", "*xiVgi**xx", obj, connector_id, get_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -3662,8 +3649,7 @@ H5VLfile_specific(void *obj, hid_t connector_id, H5VL_file_specific_t specific_t
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVhi**xx", obj, connector_id, specific_type, dxpl_id, req,
-             arguments);
+    H5TRACE6("e", "*xiVhi**xx", obj, connector_id, specific_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == (cls = (H5VL_class_t *)H5I_object_verify(connector_id, H5I_VOL)))
@@ -3769,8 +3755,7 @@ H5VLfile_optional(void *obj, hid_t connector_id, H5VL_file_optional_t opt_type,
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVvi**xx", obj, connector_id, opt_type, dxpl_id, req,
-             arguments);
+    H5TRACE6("e", "*xiVvi**xx", obj, connector_id, opt_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -3973,8 +3958,8 @@ H5VLgroup_create(void *obj, const H5VL_loc_params_t *loc_params, hid_t connector
     void *        ret_value = NULL; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE9("*x", "*x*xi*siiii**x", obj, loc_params, connector_id, name, lcpl_id,
-             gcpl_id, gapl_id, dxpl_id, req);
+    H5TRACE9("*x", "*x*xi*siiii**x", obj, loc_params, connector_id, name, lcpl_id, gcpl_id, gapl_id, dxpl_id,
+             req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -4076,8 +4061,7 @@ H5VLgroup_open(void *obj, const H5VL_loc_params_t *loc_params, hid_t connector_i
     void *        ret_value = NULL; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE7("*x", "*x*xi*sii**x", obj, loc_params, connector_id, name, gapl_id,
-             dxpl_id, req);
+    H5TRACE7("*x", "*x*xi*sii**x", obj, loc_params, connector_id, name, gapl_id, dxpl_id, req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -4184,8 +4168,7 @@ H5VLgroup_get(void *obj, hid_t connector_id, H5VL_group_get_t get_type, hid_t dx
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVii**xx", obj, connector_id, get_type, dxpl_id, req,
-             arguments);
+    H5TRACE6("e", "*xiVii**xx", obj, connector_id, get_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -4294,8 +4277,7 @@ H5VLgroup_specific(void *obj, hid_t connector_id, H5VL_group_specific_t specific
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVji**xx", obj, connector_id, specific_type, dxpl_id, req,
-             arguments);
+    H5TRACE6("e", "*xiVji**xx", obj, connector_id, specific_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -4404,8 +4386,7 @@ H5VLgroup_optional(void *obj, hid_t connector_id, H5VL_group_optional_t opt_type
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVwi**xx", obj, connector_id, opt_type, dxpl_id, req,
-             arguments);
+    H5TRACE6("e", "*xiVwi**xx", obj, connector_id, opt_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -4639,8 +4620,8 @@ H5VLlink_create(H5VL_link_create_type_t create_type, void *obj, const H5VL_loc_p
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE9("e", "Vk*x*xiiii**xx", create_type, obj, loc_params, connector_id,
-             lcpl_id, lapl_id, dxpl_id, req, arguments);
+    H5TRACE9("e", "Vk*x*xiiii**xx", create_type, obj, loc_params, connector_id, lcpl_id, lapl_id, dxpl_id,
+             req, arguments);
 
     /* Get class pointer */
     if (NULL == (cls = (H5VL_class_t *)H5I_object_verify(connector_id, H5I_VOL)))
@@ -4746,8 +4727,8 @@ H5VLlink_copy(void *src_obj, const H5VL_loc_params_t *loc_params1, void *dst_obj
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE9("e", "*x*x*x*xiiii**x", src_obj, loc_params1, dst_obj, loc_params2,
-             connector_id, lcpl_id, lapl_id, dxpl_id, req);
+    H5TRACE9("e", "*x*x*x*xiiii**x", src_obj, loc_params1, dst_obj, loc_params2, connector_id, lcpl_id,
+             lapl_id, dxpl_id, req);
 
     /* Get class pointer */
     if (NULL == (cls = (H5VL_class_t *)H5I_object_verify(connector_id, H5I_VOL)))
@@ -4853,8 +4834,8 @@ H5VLlink_move(void *src_obj, const H5VL_loc_params_t *loc_params1, void *dst_obj
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE9("e", "*x*x*x*xiiii**x", src_obj, loc_params1, dst_obj, loc_params2,
-             connector_id, lcpl_id, lapl_id, dxpl_id, req);
+    H5TRACE9("e", "*x*x*x*xiiii**x", src_obj, loc_params1, dst_obj, loc_params2, connector_id, lcpl_id,
+             lapl_id, dxpl_id, req);
 
     /* Get class pointer */
     if (NULL == (cls = (H5VL_class_t *)H5I_object_verify(connector_id, H5I_VOL)))
@@ -4961,8 +4942,7 @@ H5VLlink_get(void *obj, const H5VL_loc_params_t *loc_params, hid_t connector_id,
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE7("e", "*x*xiVli**xx", obj, loc_params, connector_id, get_type, dxpl_id,
-             req, arguments);
+    H5TRACE7("e", "*x*xiVli**xx", obj, loc_params, connector_id, get_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -5071,8 +5051,7 @@ H5VLlink_specific(void *obj, const H5VL_loc_params_t *loc_params, hid_t connecto
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE7("e", "*x*xiVmi**xx", obj, loc_params, connector_id, specific_type,
-             dxpl_id, req, arguments);
+    H5TRACE7("e", "*x*xiVmi**xx", obj, loc_params, connector_id, specific_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -5180,8 +5159,7 @@ H5VLlink_optional(void *obj, hid_t connector_id, H5VL_link_optional_t opt_type,
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVxi**xx", obj, connector_id, opt_type, dxpl_id, req,
-             arguments);
+    H5TRACE6("e", "*xiVxi**xx", obj, connector_id, opt_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -5282,8 +5260,7 @@ H5VLobject_open(void *obj, const H5VL_loc_params_t *params, hid_t connector_id,
     void *        ret_value = NULL; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("*x", "*x*xi*Iti**x", obj, params, connector_id, opened_type, dxpl_id,
-             req);
+    H5TRACE6("*x", "*x*xi*Iti**x", obj, params, connector_id, opened_type, dxpl_id, req);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -5393,9 +5370,8 @@ H5VLobject_copy(void *src_obj, const H5VL_loc_params_t *src_loc_params, const ch
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE11("e", "*x*x*s*x*x*siiii**x", src_obj, src_loc_params, src_name,
-             dst_obj, dst_loc_params, dst_name, connector_id, ocpypl_id, lcpl_id,
-             dxpl_id, req);
+    H5TRACE11("e", "*x*x*s*x*x*siiii**x", src_obj, src_loc_params, src_name, dst_obj, dst_loc_params,
+              dst_name, connector_id, ocpypl_id, lcpl_id, dxpl_id, req);
 
     /* Check args and get class pointers */
     if (NULL == src_obj || NULL == dst_obj)
@@ -5505,8 +5481,7 @@ H5VLobject_get(void *obj, const H5VL_loc_params_t *loc_params, hid_t connector_i
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE7("e", "*x*xiVni**xx", obj, loc_params, connector_id, get_type, dxpl_id,
-             req, arguments);
+    H5TRACE7("e", "*x*xiVni**xx", obj, loc_params, connector_id, get_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -5615,8 +5590,7 @@ H5VLobject_specific(void *obj, const H5VL_loc_params_t *loc_params, hid_t connec
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE7("e", "*x*xiVoi**xx", obj, loc_params, connector_id, specific_type,
-             dxpl_id, req, arguments);
+    H5TRACE7("e", "*x*xiVoi**xx", obj, loc_params, connector_id, specific_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
@@ -5728,8 +5702,7 @@ H5VLobject_optional(void *obj, hid_t connector_id, H5VL_object_optional_t opt_ty
     herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
-    H5TRACE6("e", "*xiVyi**xx", obj, connector_id, opt_type, dxpl_id, req,
-             arguments);
+    H5TRACE6("e", "*xiVyi**xx", obj, connector_id, opt_type, dxpl_id, req, arguments);
 
     /* Check args and get class pointer */
     if (NULL == obj)
-- 
cgit v0.12


From f8b3f576cebf168fea70c2a39fbe404ac1c7e4e7 Mon Sep 17 00:00:00 2001
From: Allen Byrne 
Date: Tue, 27 Oct 2020 16:48:02 -0500
Subject: HDFFV-10868 - add H5Sselect API java wrappers.

Also added javadoc comments to H5E and H5s constants.
---
 README.txt                                 |   4 +-
 java/src/hdf/hdf5lib/H5.java               | 620 ++++++++++++++++++-----------
 java/src/hdf/hdf5lib/HDF5Constants.java    | 484 +++++++++++++++++++++-
 java/src/jni/h5Constants.c                 | 374 ++++++++++++++++-
 java/src/jni/h5sImp.c                      | 383 ++++++++++++++++++
 java/src/jni/h5sImp.h                      |  59 +++
 java/test/TestH5Sbasic.java                | 138 +++++++
 java/test/testfiles/JUnit-TestH5Sbasic.txt |  16 +-
 8 files changed, 1834 insertions(+), 244 deletions(-)

diff --git a/README.txt b/README.txt
index 021f217..fb027aa 100644
--- a/README.txt
+++ b/README.txt
@@ -75,6 +75,6 @@ Periodically development code snapshots are provided at the following URL:
 Source packages for current and previous releases are located at:
     https://portal.hdfgroup.org/display/support/Downloads
 
-Development code is available at our BitBucket Server:
-    https://bitbucket.hdfgroup.org/projects/HDFFV/repos/hdf5/browse
+Development code is available at our Github location:
+    https://github.com/HDFGroup/hdf5.git
 
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index f7d8dc4..6ad7cf2 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -10047,7 +10047,7 @@ public class H5 implements java.io.Serializable {
             throws HDF5LibraryException, NullPointerException;
 
     /**
-     * H5Pget_fapl_direct queries properties set by the H5Pset_fapl_core.
+     * H5Pget_fapl_direct queries properties set by the H5Pset_fapl_direct.
      *
      * @param fapl_id
      *            IN: File access property list identifier
@@ -11028,50 +11028,7 @@ public class H5 implements java.io.Serializable {
     // //
     // ////////////////////////////////////////////////////////////
 
-    /**
-     * H5Sclose releases a dataspace.
-     *
-     * @param space_id
-     *            Identifier of dataspace to release.
-     *
-     * @return a non-negative value if successful
-     *
-     * @exception HDF5LibraryException
-     *                - Error from the HDF-5 Library.
-     **/
-    public static int H5Sclose(long space_id) throws HDF5LibraryException {
-        if (space_id < 0)
-            return 0; // throw new HDF5LibraryException("Negative ID");;
-
-        log.trace("OPEN_IDS: H5Sclose remove {}", space_id);
-        OPEN_IDS.remove(space_id);
-        log.trace("OPEN_IDS: {}", OPEN_IDS.size());
-        return _H5Sclose(space_id);
-    }
-
-    private synchronized static native int _H5Sclose(long space_id) throws HDF5LibraryException;
-
-    /**
-     * H5Scopy creates a new dataspace which is an exact copy of the dataspace identified by space_id.
-     *
-     * @param space_id
-     *            Identifier of dataspace to copy.
-     * @return a dataspace identifier if successful
-     *
-     * @exception HDF5LibraryException
-     *                - Error from the HDF-5 Library.
-     **/
-    public static long H5Scopy(long space_id) throws HDF5LibraryException {
-        long id = _H5Scopy(space_id);
-        if (id > 0) {
-            log.trace("OPEN_IDS: H5Scopy add {}", id);
-            OPEN_IDS.add(id);
-            log.trace("OPEN_IDS: {}", OPEN_IDS.size());
-        }
-        return id;
-    }
-
-    private synchronized static native long _H5Scopy(long space_id) throws HDF5LibraryException;
+    /**************** Operations on dataspaces ********************/
 
     /**
      * H5Screate creates a new dataspace of a particular type.
@@ -11128,19 +11085,96 @@ public class H5 implements java.io.Serializable {
             throws HDF5Exception, NullPointerException;
 
     /**
-     * H5Sdecode reconstructs the HDF5 data space object and returns a new object handle for it.
+     * H5Sset_extent_simple sets or resets the size of an existing dataspace.
      *
-     * @param buf
-     *            IN: Buffer for the data space object to be decoded.
+     * @param space_id
+     *            Dataspace identifier.
+     * @param rank
+     *            Rank, or dimensionality, of the dataspace.
+     * @param current_size
+     *            Array containing current size of dataspace.
+     * @param maximum_size
+     *            Array containing maximum size of dataspace.
      *
-     * @return a new object handle
+     * @return a dataspace identifier if successful
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
-     * @exception NullPointerException
-     *                - buf is null.
      **/
-    public synchronized static native long H5Sdecode(byte[] buf) throws HDF5LibraryException, NullPointerException;
+    public synchronized static native long H5Sset_extent_simple(long space_id, int rank, long[] current_size,
+            long[] maximum_size) throws HDF5LibraryException, NullPointerException;
+
+    /**
+     * H5Sset_extent_simple sets or resets the size of an existing dataspace.
+     *
+     * @param space_id
+     *            Dataspace identifier.
+     * @param rank
+     *            Rank, or dimensionality, of the dataspace.
+     * @param current_size
+     *            Array containing current size of dataspace.
+     * @param maximum_size
+     *            Array containing maximum size of dataspace.
+     *
+     * @return a dataspace identifier if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static long H5Sset_extent_simple(long space_id, int rank, byte[] current_size,
+            byte[] maximum_size) throws HDF5LibraryException, NullPointerException {
+        ByteBuffer csbb = ByteBuffer.wrap(current_size);
+        long[] lacs = (csbb.asLongBuffer()).array();
+        ByteBuffer maxsbb = ByteBuffer.wrap(maximum_size);
+        long[] lamaxs = (maxsbb.asLongBuffer()).array();
+
+        return H5Sset_extent_simple(space_id, rank, lacs, lamaxs);
+    }
+
+    /**
+     * H5Scopy creates a new dataspace which is an exact copy of the dataspace identified by space_id.
+     *
+     * @param space_id
+     *            Identifier of dataspace to copy.
+     * @return a dataspace identifier if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public static long H5Scopy(long space_id) throws HDF5LibraryException {
+        long id = _H5Scopy(space_id);
+        if (id > 0) {
+            log.trace("OPEN_IDS: H5Scopy add {}", id);
+            OPEN_IDS.add(id);
+            log.trace("OPEN_IDS: {}", OPEN_IDS.size());
+        }
+        return id;
+    }
+
+    private synchronized static native long _H5Scopy(long space_id) throws HDF5LibraryException;
+
+    /**
+     * H5Sclose releases a dataspace.
+     *
+     * @param space_id
+     *            Identifier of dataspace to release.
+     *
+     * @return a non-negative value if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public static int H5Sclose(long space_id) throws HDF5LibraryException {
+        if (space_id < 0)
+            return 0; // throw new HDF5LibraryException("Negative ID");;
+
+        log.trace("OPEN_IDS: H5Sclose remove {}", space_id);
+        OPEN_IDS.remove(space_id);
+        log.trace("OPEN_IDS: {}", OPEN_IDS.size());
+        return _H5Sclose(space_id);
+    }
+
+    private synchronized static native int _H5Sclose(long space_id) throws HDF5LibraryException;
 
     /**
      * H5Sencode converts a data space description into binary form in a buffer.
@@ -11156,154 +11190,139 @@ public class H5 implements java.io.Serializable {
     public synchronized static native byte[] H5Sencode(long obj_id) throws HDF5LibraryException, NullPointerException;
 
     /**
-     * H5Sextent_copy copies the extent from source_space_id to dest_space_id. This action may change the type of the
-     * dataspace.
+     * H5Sdecode reconstructs the HDF5 data space object and returns a new object handle for it.
      *
-     * @param dest_space_id
-     *            IN: The identifier for the dataspace from which the extent is copied.
-     * @param source_space_id
-     *            IN: The identifier for the dataspace to which the extent is copied.
+     * @param buf
+     *            IN: Buffer for the data space object to be decoded.
      *
-     * @return a non-negative value if successful
+     * @return a new object handle
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - buf is null.
      **/
-    public synchronized static native int H5Sextent_copy(long dest_space_id, long source_space_id)
-            throws HDF5LibraryException;
+    public synchronized static native long H5Sdecode(byte[] buf) throws HDF5LibraryException, NullPointerException;
 
     /**
-     * H5Sextent_equal determines whether the dataspace extents of two dataspaces, space1_id and space2_id, are equal.
+     * H5Sget_simple_extent_npoints determines the number of elements in a dataspace.
      *
-     * @param first_space_id
-     *            IN: The identifier for the first dataspace.
-     * @param second_space_id
-     *            IN: The identifier for the seconddataspace.
+     * @param space_id
+     *            ID of the dataspace object to query
+     * @return the number of elements in the dataspace if successful
      *
-     * @return true if successful, else false
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native long H5Sget_simple_extent_npoints(long space_id) throws HDF5LibraryException;
+
+    /**
+     * H5Sget_simple_extent_ndims determines the dimensionality (or rank) of a dataspace.
+     *
+     * @param space_id
+     *            IN: Identifier of the dataspace
+     *
+     * @return the number of dimensions in the dataspace if successful
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
-    public synchronized static native boolean H5Sextent_equal(long first_space_id, long second_space_id)
-            throws HDF5LibraryException;
+    public synchronized static native int H5Sget_simple_extent_ndims(long space_id) throws HDF5LibraryException;
 
     /**
-     * H5Sget_select_bounds retrieves the coordinates of the bounding box containing the current selection and places
-     * them into user-supplied buffers.
-     * 

-     * The start and end buffers must be large enough to hold the dataspace rank number of coordinates.
+     * H5Sget_simple_extent_dims returns the size and maximum sizes of each dimension of a dataspace through the dims
+     * and maxdims parameters.
      *
-     * @param spaceid
-     *            Identifier of dataspace to release.
-     * @param start
-     *            coordinates of lowest corner of bounding box.
-     * @param end
-     *            coordinates of highest corner of bounding box.
+     * @param space_id
+     *            IN: Identifier of the dataspace object to query
+     * @param dims
+     *            OUT: Pointer to array to store the size of each dimension.
+     * @param maxdims
+     *            OUT: Pointer to array to store the maximum size of each dimension.
      *
-     * @return a non-negative value if successful,with start and end initialized.
+     * @return the number of dimensions in the dataspace if successful
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      * @exception NullPointerException
-     *                - start or end is null.
+     *                - dims or maxdims is null.
      **/
-    public synchronized static native int H5Sget_select_bounds(long spaceid, long[] start, long[] end)
+    public synchronized static native int H5Sget_simple_extent_dims(long space_id, long[] dims, long[] maxdims)
             throws HDF5LibraryException, NullPointerException;
 
     /**
-     * H5Sget_select_elem_npoints returns the number of element points in the current dataspace selection.
+     * H5Sis_simple determines whether a dataspace is a simple dataspace.
      *
-     * @param spaceid
-     *            Identifier of dataspace to release.
+     * @param space_id
+     *            Identifier of the dataspace to query
      *
-     * @return a non-negative value if successful
+     * @return true if is a simple dataspace
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
-    public synchronized static native long H5Sget_select_elem_npoints(long spaceid) throws HDF5LibraryException;
+    public synchronized static native boolean H5Sis_simple(long space_id) throws HDF5LibraryException;
 
     /**
-     * H5Sget_select_elem_pointlist returns an array of of element points in the current dataspace selection. The point
-     * coordinates have the same dimensionality (rank) as the dataspace they are located within, one coordinate per
-     * point.
+     * H5Sget_simple_extent_type queries a dataspace to determine the current class of a dataspace.
      *
-     * @param spaceid
-     *            Identifier of dataspace to release.
-     * @param startpoint
-     *            first point to retrieve
-     * @param numpoints
-     *            number of points to retrieve
-     * @param buf
-     *            returns points startblock to startblock+num-1, each points is rank longs.
+     * @param space_id
+     *            Dataspace identifier.
      *
-     * @return a non-negative value if successful
+     * @return a dataspace class name if successful
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
-     * @exception NullPointerException
-     *                - buf is null.
      **/
-    public synchronized static native int H5Sget_select_elem_pointlist(long spaceid, long startpoint, long numpoints,
-            long[] buf) throws HDF5LibraryException, NullPointerException;
+    public synchronized static native int H5Sget_simple_extent_type(long space_id) throws HDF5LibraryException;
 
     /**
-     * H5Sget_select_hyper_blocklist returns an array of hyperslab blocks. The block coordinates have the same
-     * dimensionality (rank) as the dataspace they are located within. The list of blocks is formatted as follows:
-     *
-     * 
-     *    <"start" coordinate>, immediately followed by
-     *    <"opposite" corner coordinate>, followed by
-     *   the next "start" and "opposite" coordinates,
-     *   etc.
-     *   until all of the selected blocks have been listed.
-     * 

+     * H5Sset_extent_none removes the extent from a dataspace and sets the type to H5S_NONE.
      *
-     * @param spaceid
-     *            Identifier of dataspace to release.
-     * @param startblock
-     *            first block to retrieve
-     * @param numblocks
-     *            number of blocks to retrieve
-     * @param buf
-     *            returns blocks startblock to startblock+num-1, each block is rank * 2 (corners) longs.
+     * @param space_id
+     *            The identifier for the dataspace from which the extent is to be removed.
      *
      * @return a non-negative value if successful
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
-     * @exception NullPointerException
-     *                - buf is null.
      **/
-    public synchronized static native int H5Sget_select_hyper_blocklist(long spaceid, long startblock, long numblocks,
-            long[] buf) throws HDF5LibraryException, NullPointerException;
+    public synchronized static native int H5Sset_extent_none(long space_id) throws HDF5LibraryException;
 
     /**
-     * H5Sget_select_hyper_nblocks returns the number of hyperslab blocks in the current dataspace selection.
+     * H5Sextent_copy copies the extent from source_space_id to dest_space_id. This action may change the type of the
+     * dataspace.
      *
-     * @param spaceid
-     *            Identifier of dataspace to release.
+     * @param dest_space_id
+     *            IN: The identifier for the dataspace from which the extent is copied.
+     * @param source_space_id
+     *            IN: The identifier for the dataspace to which the extent is copied.
      *
      * @return a non-negative value if successful
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
-    public synchronized static native long H5Sget_select_hyper_nblocks(long spaceid) throws HDF5LibraryException;
+    public synchronized static native int H5Sextent_copy(long dest_space_id, long source_space_id)
+            throws HDF5LibraryException;
 
     /**
-     * H5Sget_select_npoints determines the number of elements in the current selection of a dataspace.
+     * H5Sextent_equal determines whether the dataspace extents of two dataspaces, space1_id and space2_id, are equal.
      *
-     * @param space_id
-     *            IN: Identifier of the dataspace object to query
+     * @param first_space_id
+     *            IN: The identifier for the first dataspace.
+     * @param second_space_id
+     *            IN: The identifier for the seconddataspace.
      *
-     * @return the number of elements in the selection if successful
+     * @return true if successful, else false
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
-    public synchronized static native long H5Sget_select_npoints(long space_id) throws HDF5LibraryException;
+    public synchronized static native boolean H5Sextent_equal(long first_space_id, long second_space_id)
+            throws HDF5LibraryException;
+
+    /***************** Operations on dataspace selections *****************/
 
     /**
      * H5Sget_select_type retrieves the type of selection currently defined for the dataspace space_id.
@@ -11319,76 +11338,118 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Sget_select_type(long space_id) throws HDF5LibraryException;
 
     /**
-     * H5Sget_simple_extent_dims returns the size and maximum sizes of each dimension of a dataspace through the dims
-     * and maxdims parameters.
+     * H5Sget_select_npoints determines the number of elements in the current selection of a dataspace.
      *
      * @param space_id
      *            IN: Identifier of the dataspace object to query
-     * @param dims
-     *            OUT: Pointer to array to store the size of each dimension.
-     * @param maxdims
-     *            OUT: Pointer to array to store the maximum size of each dimension.
      *
-     * @return the number of dimensions in the dataspace if successful
+     * @return the number of elements in the selection if successful
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
-     * @exception NullPointerException
-     *                - dims or maxdims is null.
      **/
-    public synchronized static native int H5Sget_simple_extent_dims(long space_id, long[] dims, long[] maxdims)
-            throws HDF5LibraryException, NullPointerException;
+    public synchronized static native long H5Sget_select_npoints(long space_id) throws HDF5LibraryException;
 
     /**
-     * H5Sget_simple_extent_ndims determines the dimensionality (or rank) of a dataspace.
+     * H5Sselect_copy copies all the selection information (including offset) from the source
+     * dataspace to the destination dataspace.
+     * @param dst_id              ID of the destination dataspace
+     * @param src_id              ID of the source dataspace
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native void H5Sselect_copy(long dst_id, long src_id) throws HDF5LibraryException;
+
+    /**
+     * H5Sselect_valid verifies that the selection for the dataspace.
      *
      * @param space_id
-     *            IN: Identifier of the dataspace
+     *            The identifier for the dataspace in which the selection is being reset.
      *
-     * @return the number of dimensions in the dataspace if successful
+     * @return true if the selection is contained within the extent and FALSE if it is not or is an error.
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
-    public synchronized static native int H5Sget_simple_extent_ndims(long space_id) throws HDF5LibraryException;
+    public synchronized static native boolean H5Sselect_valid(long space_id) throws HDF5LibraryException;
 
     /**
-     * H5Sget_simple_extent_npoints determines the number of elements in a dataspace.
+     * H5Sselect_adjust moves a selection by subtracting an offset from it.
      *
      * @param space_id
-     *            ID of the dataspace object to query
-     * @return the number of elements in the dataspace if successful
+     *            ID of dataspace to adjust
+     * @param offset
+     *            Offset to subtract
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - offset is null.
      **/
-    public synchronized static native long H5Sget_simple_extent_npoints(long space_id) throws HDF5LibraryException;
+     public synchronized static native void H5Sselect_adjust(long space_id, long[][] offset)
+             throws HDF5LibraryException, NullPointerException;
 
     /**
-     * H5Sget_simple_extent_type queries a dataspace to determine the current class of a dataspace.
+     * H5Sget_select_bounds retrieves the coordinates of the bounding box containing the current selection and places
+     * them into user-supplied buffers.
+     * 

+     * The start and end buffers must be large enough to hold the dataspace rank number of coordinates.
      *
      * @param space_id
-     *            Dataspace identifier.
+     *            Identifier of dataspace to release.
+     * @param start
+     *            coordinates of lowest corner of bounding box.
+     * @param end
+     *            coordinates of highest corner of bounding box.
      *
-     * @return a dataspace class name if successful
+     * @return a non-negative value if successful,with start and end initialized.
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - start or end is null.
      **/
-    public synchronized static native int H5Sget_simple_extent_type(long space_id) throws HDF5LibraryException;
+    public synchronized static native int H5Sget_select_bounds(long space_id, long[] start, long[] end)
+            throws HDF5LibraryException, NullPointerException;
 
     /**
-     * H5Sis_simple determines whether a dataspace is a simple dataspace.
+     * H5Sselect_shape_same checks to see if the current selection in the dataspaces are the same
+     * dimensionality and shape.
+     * This is primarily used for reading the entire selection in one swoop.
+     *
+     * @param   space1_id         ID of 1st Dataspace pointer to compare
+     * @param   space2_id         ID of 2nd Dataspace pointer to compare
+     *
+     * @return true if the selection is the same dimensionality and shape;
+     *         false otherwise
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native boolean H5Sselect_shape_same(long space1_id, long space2_id) throws HDF5LibraryException;
+
+    /**
+     * H5Sselect_intersect_block checks to see if the current selection in the
+     * dataspace intersects with the block given.
      *
      * @param space_id
-     *            Identifier of the dataspace to query
+     *             ID of dataspace pointer to compare
+     * @param start
+     *             Starting coordinate of block
+     * @param end
+     *             Opposite ("ending") coordinate of block
      *
-     * @return true if is a simple dataspace
+     * @return a TRUE  if the current selection in the dataspace intersects with the block given
+     *           FALSE otherwise
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - offset is null.
      **/
-    public synchronized static native boolean H5Sis_simple(long space_id) throws HDF5LibraryException;
+     public synchronized static native boolean H5Sselect_intersect_block(long space_id, long[] start, long[] end)
+             throws HDF5LibraryException, NullPointerException;
 
     /**
      * H5Soffset_simple sets the offset of a simple dataspace space_id.
@@ -11453,6 +11514,18 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Sselect_all(long space_id) throws HDF5LibraryException;
 
     /**
+     * H5Sselect_none resets the selection region for the dataspace space_id to include no elements.
+     *
+     * @param space_id
+     *            IN: The identifier of the dataspace to be reset.
+     * @return a non-negative value if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native int H5Sselect_none(long space_id) throws HDF5LibraryException;
+
+    /**
      * H5Sselect_elements selects array elements to be included in the selection for the space_id dataspace.
      *
      * @param space_id
@@ -11510,6 +11583,43 @@ public class H5 implements java.io.Serializable {
     }
 
     /**
+     * H5Sget_select_elem_npoints returns the number of element points in the current dataspace selection.
+     *
+     * @param spaceid
+     *            Identifier of dataspace to release.
+     *
+     * @return a non-negative value if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native long H5Sget_select_elem_npoints(long spaceid) throws HDF5LibraryException;
+
+    /**
+     * H5Sget_select_elem_pointlist returns an array of of element points in the current dataspace selection. The point
+     * coordinates have the same dimensionality (rank) as the dataspace they are located within, one coordinate per
+     * point.
+     *
+     * @param spaceid
+     *            Identifier of dataspace to release.
+     * @param startpoint
+     *            first point to retrieve
+     * @param numpoints
+     *            number of points to retrieve
+     * @param buf
+     *            returns points startblock to startblock+num-1, each points is rank longs.
+     *
+     * @return a non-negative value if successful
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - buf is null.
+     **/
+    public synchronized static native int H5Sget_select_elem_pointlist(long spaceid, long startpoint, long numpoints,
+            long[] buf) throws HDF5LibraryException, NullPointerException;
+
+    /**
      * H5Sselect_hyperslab selects a hyperslab region to add to the current selected region for the dataspace specified
      * by space_id. The start, stride, count, and block arrays must be the same size as the rank of the dataspace.
      *
@@ -11578,90 +11688,89 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Sselect_hyperslab(long space_id, int op, long[] start, long[] stride,
             long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
 
-    /**
-     * H5Sselect_none resets the selection region for the dataspace space_id to include no elements.
-     *
-     * @param space_id
-     *            IN: The identifier of the dataspace to be reset.
-     * @return a non-negative value if successful
-     *
-     * @exception HDF5LibraryException
-     *                - Error from the HDF-5 Library.
-     **/
-    public synchronized static native int H5Sselect_none(long space_id) throws HDF5LibraryException;
 
     /**
-     * H5Sselect_valid verifies that the selection for the dataspace.
+     * H5Scombine_hyperslab combines a hyperslab selection with the current selection for a dataspace,
+     * creating a new dataspace to return the generated selection.
+     * If the current selection is not a hyperslab, it is freed and the hyperslab
+     * parameters passed in are combined with the H5S_SEL_ALL hyperslab (ie. a
+     * selection composing the entire current extent).  If STRIDE or BLOCK is
+     * NULL, they are assumed to be set to all '1'.
      *
      * @param space_id
-     *            The identifier for the dataspace in which the selection is being reset.
+     *            IN: Dataspace ID of selection to use
+     * @param op
+     *            IN: Operation to perform on current selection.
+     * @param start
+     *            IN: Offset of start of hyperslab
+     * @param stride
+     *            IN: Hyperslab stride.
+     * @param count
+     *            IN: Number of blocks included in hyperslab.
+     * @param block
+     *            IN: Size of block in hyperslab.
      *
-     * @return true if the selection is contained within the extent and FALSE if it is not or is an error.
+     * @return a dataspace ID on success / H5I_INVALID_HID on failure
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - an input array is null.
+     * @exception IllegalArgumentException
+     *                - an input array is invalid.
      **/
-    public synchronized static native boolean H5Sselect_valid(long space_id) throws HDF5LibraryException;
+    public synchronized static native long H5Scombine_hyperslab(long space_id, int op, long[] start, long[] stride,
+            long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
 
     /**
-     * H5Sset_extent_none removes the extent from a dataspace and sets the type to H5S_NONE.
-     *
-     * @param space_id
-     *            The identifier for the dataspace from which the extent is to be removed.
+     * H5Smodify_select refine an existing hyperslab selection with an operation, using a second
+     * hyperslab.  The first selection is modified to contain the result of
+     * space1 operated on by space2.
      *
-     * @return a non-negative value if successful
+     * @param space1_id
+     *               ID of the destination dataspace
+     * @param op
+     *               Operation to perform on current selection.
+     * @param space2_id
+     *               ID of the source dataspace
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
-    public synchronized static native int H5Sset_extent_none(long space_id) throws HDF5LibraryException;
+    public synchronized static native void H5Smodify_select(long space1_id, int op, long space2_id) throws HDF5LibraryException;
 
     /**
-     * H5Sset_extent_simple sets or resets the size of an existing dataspace.
+     * H5Scombine_select combines two existing hyperslab selections with an operation, returning
+     * a new dataspace with the resulting selection.  The dataspace extent from
+     * space1 is copied for the dataspace extent of the newly created dataspace.
      *
-     * @param space_id
-     *            Dataspace identifier.
-     * @param rank
-     *            Rank, or dimensionality, of the dataspace.
-     * @param current_size
-     *            Array containing current size of dataspace.
-     * @param maximum_size
-     *            Array containing maximum size of dataspace.
+     * @param space1_id
+     *               ID of the first dataspace
+     * @param op
+     *               Operation to perform on current selection.
+     * @param space2_id
+     *               ID of the second dataspace
      *
-     * @return a dataspace identifier if successful
+     * @return a dataspace ID on success / H5I_INVALID_HID on failure
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
-    public synchronized static native long H5Sset_extent_simple(long space_id, int rank, long[] current_size,
-            long[] maximum_size) throws HDF5LibraryException, NullPointerException;
+    public synchronized static native long H5Scombine_select(long space1_id, int op, long space2_id) throws HDF5LibraryException;
 
     /**
-     * H5Sset_extent_simple sets or resets the size of an existing dataspace.
+     * H5Sis_regular_hyperslab retrieves a regular hyperslab selection for the dataspace specified
+     * by space_id.
      *
      * @param space_id
-     *            Dataspace identifier.
-     * @param rank
-     *            Rank, or dimensionality, of the dataspace.
-     * @param current_size
-     *            Array containing current size of dataspace.
-     * @param maximum_size
-     *            Array containing maximum size of dataspace.
+     *            IN: Identifier of dataspace selection to query
      *
-     * @return a dataspace identifier if successful
+     * @return a TRUE/FALSE for hyperslab selection if successful
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
-    public synchronized static long H5Sset_extent_simple(long space_id, int rank, byte[] current_size,
-            byte[] maximum_size) throws HDF5LibraryException, NullPointerException {
-        ByteBuffer csbb = ByteBuffer.wrap(current_size);
-        long[] lacs = (csbb.asLongBuffer()).array();
-        ByteBuffer maxsbb = ByteBuffer.wrap(maximum_size);
-        long[] lamaxs = (maxsbb.asLongBuffer()).array();
-
-        return H5Sset_extent_simple(space_id, rank, lacs, lamaxs);
-    }
+     public synchronized static native boolean H5Sis_regular_hyperslab(long space_id) throws HDF5LibraryException;
 
     /**
      * H5Sget_regular_hyperslab determines if a hyperslab selection is regular for the dataspace specified
@@ -11687,33 +11796,82 @@ public class H5 implements java.io.Serializable {
      **/
      public synchronized static native void H5Sget_regular_hyperslab(long space_id, long[] start, long[] stride, long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
 
+     /**
+      * H5Sget_select_hyper_nblocks returns the number of hyperslab blocks in the current dataspace selection.
+      *
+      * @param spaceid
+      *            Identifier of dataspace to release.
+      *
+      * @return a non-negative value if successful
+      *
+      * @exception HDF5LibraryException
+      *                - Error from the HDF-5 Library.
+      **/
+     public synchronized static native long H5Sget_select_hyper_nblocks(long spaceid) throws HDF5LibraryException;
+
     /**
-     * H5Sis_regular_hyperslab retrieves a regular hyperslab selection for the dataspace specified
-     * by space_id.
+     * H5Sget_select_hyper_blocklist returns an array of hyperslab blocks. The block coordinates have the same
+     * dimensionality (rank) as the dataspace they are located within. The list of blocks is formatted as follows:
      *
-     * @param space_id
-     *            IN: Identifier of dataspace selection to query
+     * 
+     *    <"start" coordinate>, immediately followed by
+     *    <"opposite" corner coordinate>, followed by
+     *   the next "start" and "opposite" coordinates,
+     *   etc.
+     *   until all of the selected blocks have been listed.
+     * 

      *
-     * @return a TRUE/FALSE for hyperslab selection if successful
+     * @param spaceid
+     *            Identifier of dataspace to release.
+     * @param startblock
+     *            first block to retrieve
+     * @param numblocks
+     *            number of blocks to retrieve
+     * @param buf
+     *            returns blocks startblock to startblock+num-1, each block is rank * 2 (corners) longs.
+     *
+     * @return a non-negative value if successful
      *
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - buf is null.
      **/
-     public synchronized static native boolean H5Sis_regular_hyperslab(long space_id) throws HDF5LibraryException;
+    public synchronized static native int H5Sget_select_hyper_blocklist(long spaceid, long startblock, long numblocks,
+            long[] buf) throws HDF5LibraryException, NullPointerException;
 
-    // /////// unimplemented ////////
-    // #ifdef NEW_HYPERSLAB_API
-    //  hid_t H5Scombine_hyperslab(hid_t space_id, H5S_seloper_t op,
-    //                                  const hsize_t start[],
-    //                                  const hsize_t _stride[],
-    //                                  const hsize_t count[],
-    //                                  const hsize_t _block[]);
-    // herr_t H5Sselect_select(hid_t space1_id, H5S_seloper_t op,
-    //                                  hid_t space2_id);
-    // hid_t H5Scombine_select(hid_t space1_id, H5S_seloper_t op,
-    //                                  hid_t space2_id);
-    // #endif /* NEW_HYPERSLAB_API */
-    // herr_t H5Sselect_copy(hid_t dst_id, hid_t src_id);
+    /**
+     * H5Sselect_project_intersection projects the intersection of the selections of src_space_id and
+     * src_intersect_space_id within the selection of src_space_id as a
+     * selection within the selection of dst_space_id.
+     *
+     * @param src_space_id
+     *          Selection that is mapped to dst_space_id, and intersected with src_intersect_space_id
+     * @param dst_space_id
+     *          Selection that is mapped to src_space_id
+     * @param src_intersect_space_id
+     *          Selection whose intersection with src_space_id is projected to dst_space_id to obtain the result
+     *
+     * @return a dataspace with a selection equal to the intersection of
+     *         src_intersect_space_id and src_space_id projected from src_space to dst_space on success
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native long H5Sselect_project_intersection(long src_space_id, long dst_space_id,
+            long src_intersect_space_id) throws HDF5LibraryException;
+
+
+     // /////// unimplemented ////////
+     ///// Operations on dataspace selections /////
+
+     //
+     ///// Operations on dataspace selection iterators /////
+     //public synchronized static native     H5Ssel_iter_create(hid_t spaceid, size_t elmt_size, unsigned flags);
+     //public synchronized static native    H5Ssel_iter_get_seq_list(hid_t sel_iter_id, size_t maxseq, size_t maxbytes, size_t *nseq,
+     //                                       size_t *nbytes, hsize_t *off, size_t *len);
+     //public synchronized static native    H5Ssel_iter_reset(hid_t sel_iter_id, hid_t space_id);
+     //public synchronized static native    H5Ssel_iter_close(hid_t sel_iter_id);
 
 
 
diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java
index beba1d1..7ecfe95 100644
--- a/java/src/hdf/hdf5lib/HDF5Constants.java
+++ b/java/src/hdf/hdf5lib/HDF5Constants.java
@@ -35,12 +35,17 @@ public class HDF5Constants {
     // Get the HDF5 constants from the library //
     // /////////////////////////////////////////////////////////////////////////
 
-    public static final long H5_QUARTER_HADDR_MAX = H5_QUARTER_HADDR_MAX();
+    //public static final long H5_QUARTER_HADDR_MAX = H5_QUARTER_HADDR_MAX();
 
+    /** Special parameters for szip compression */
     public static final int H5_SZIP_MAX_PIXELS_PER_BLOCK = H5_SZIP_MAX_PIXELS_PER_BLOCK();
+    /** Special parameters for szip compression */
     public static final int H5_SZIP_NN_OPTION_MASK = H5_SZIP_NN_OPTION_MASK();
+    /** Special parameters for szip compression */
     public static final int H5_SZIP_EC_OPTION_MASK = H5_SZIP_EC_OPTION_MASK();
+    /** Special parameters for szip compression */
     public static final int H5_SZIP_ALLOW_K13_OPTION_MASK = H5_SZIP_ALLOW_K13_OPTION_MASK();
+    /** Special parameters for szip compression */
     public static final int H5_SZIP_CHIP_OPTION_MASK = H5_SZIP_CHIP_OPTION_MASK();
     public static final int H5_INDEX_UNKNOWN = H5_INDEX_UNKNOWN();
     public static final int H5_INDEX_NAME = H5_INDEX_NAME();
@@ -92,110 +97,359 @@ public class HDF5Constants {
     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();
 
+    /** Different kinds of error information - H5E_type_t */
     public static final int H5E_MAJOR = H5E_MAJOR();
+    /** Different kinds of error information - H5E_type_t */
     public static final int H5E_MINOR = H5E_MINOR();
+    /** Minor error codes - Object header related errors - Alignment error */
     public static final long H5E_ALIGNMENT = H5E_ALIGNMENT();
+    /** Minor error codes - Resource errors - Object already exists */
     public static final long H5E_ALREADYEXISTS = H5E_ALREADYEXISTS();
+    /** Minor error codes - Function entry/exit interface - Object already initialized */
     public static final long H5E_ALREADYINIT = H5E_ALREADYINIT();
+    /** Major error codes - Invalid arguments to routine */
     public static final long H5E_ARGS = H5E_ARGS();
+    /** Major error codes - Object atom */
     public static final long H5E_ATOM = H5E_ATOM();
+    /** Major error codes - Attribute */
     public static final long H5E_ATTR = H5E_ATTR();
+    /** Minor error codes - Object atom related errors - Unable to find atom information (already closed?) */
     public static final long H5E_BADATOM = H5E_BADATOM();
+    /** Minor error codes - File accessibility errors - Bad file ID accessed */
     public static final long H5E_BADFILE = H5E_BADFILE();
+    /** Minor error codes - Object atom related errors - Unable to find ID group information */
     public static final long H5E_BADGROUP = H5E_BADGROUP();
+    /** Minor error codes - Object header related errors - Iteration failed */
+    public static final long H5E_BADITER = H5E_BADITER();
+    /** Minor error codes - Object header related errors - Unrecognized message */
     public static final long H5E_BADMESG = H5E_BADMESG();
+    /** Minor error codes - Argument errors - Out of range */
     public static final long H5E_BADRANGE = H5E_BADRANGE();
+    /** Minor error codes - Dataspace errors - Invalid selection */
     public static final long H5E_BADSELECT = H5E_BADSELECT();
+    /** Datatype conversion errors - Bad size for object */
     public static final long H5E_BADSIZE = H5E_BADSIZE();
+    /** Minor error codes - Argument errors - Inappropriate type */
     public static final long H5E_BADTYPE = H5E_BADTYPE();
+    /** Minor error codes - Argument errors - Bad value */
     public static final long H5E_BADVALUE = H5E_BADVALUE();
+    /** Major error codes - B-Tree node */
     public static final long H5E_BTREE = H5E_BTREE();
+    /** Major error codes - Object cache */
     public static final long H5E_CACHE = H5E_CACHE();
+    /** I/O pipeline errors - Callback failed */
     public static final long H5E_CALLBACK = H5E_CALLBACK();
+    /** I/O pipeline errors - Error from filter 'can apply' callback */
     public static final long H5E_CANAPPLY = H5E_CANAPPLY();
-    // public static final long H5E_CANTALLOC = H5E_CANTALLOC();
+    /** Minor error codes - Resource errors - Can't allocate space */
+    public static final long H5E_CANTALLOC = H5E_CANTALLOC();
+    /** Minor error codes - Dataspace errors - Can't append object */
+    public static final long H5E_CANTAPPEND = H5E_CANTAPPEND();
+    /** Minor error codes - Heap errors - Can't attach object */
+    public static final long H5E_CANTATTACH = H5E_CANTATTACH();
+    /** Minor error codes - Cache related errors - Unable to mark metadata as clean */
+    public static final long H5E_CANTCLEAN = H5E_CANTCLEAN();
+    /** Minor error codes - Dataspace errors - Can't clip hyperslab region */
     public static final long H5E_CANTCLIP = H5E_CANTCLIP();
+    /** Minor error codes - File accessibility errors - Unable to close file */
     public static final long H5E_CANTCLOSEFILE = H5E_CANTCLOSEFILE();
+    /** Minor error codes - Group related errors - Can't close object */
+    public static final long H5E_CANTCLOSEOBJ = H5E_CANTCLOSEOBJ();
+    /** Minor error codes - Dataspace errors - Can't compare objects */
+    public static final long H5E_CANTCOMPARE = H5E_CANTCOMPARE();
+    /** Minor error codes - Heap errors - Can't compute value */
+    public static final long H5E_CANTCOMPUTE = H5E_CANTCOMPUTE();
+    /** Datatype conversion errors - Can't convert datatypes */
     public static final long H5E_CANTCONVERT = H5E_CANTCONVERT();
+    /** Minor error codes - Resource errors - Unable to copy object */
     public static final long H5E_CANTCOPY = H5E_CANTCOPY();
+    /** Minor error codes - Cache related errors - Unable to cork an object */
+    public static final long H5E_CANTCORK = H5E_CANTCORK();
+    /** Minor error codes - Dataspace errors - Can't count elements */
     public static final long H5E_CANTCOUNT = H5E_CANTCOUNT();
+    /** Minor error codes - File accessibility errors - Unable to create file */
     public static final long H5E_CANTCREATE = H5E_CANTCREATE();
+    /** Minor error codes - Object atom related errors - Unable to decrement reference count */
     public static final long H5E_CANTDEC = H5E_CANTDEC();
+    /** Minor error codes - B-tree related errors - Unable to decode value */
     public static final long H5E_CANTDECODE = H5E_CANTDECODE();
+    /** Minor error codes - Object header related errors - Can't delete message */
     public static final long H5E_CANTDELETE = H5E_CANTDELETE();
+    /** Minor error codes - File accessibility errors - Unable to delete file */
     public static final long H5E_CANTDELETEFILE = H5E_CANTDELETEFILE();
+    /** Minor error codes - Cache related errors - Unable to create a flush dependency */
+    public static final long H5E_CANTDEPEND = H5E_CANTDEPEND();
+    /** Minor error codes - Cache related errors - Unable to mark metadata as dirty */
+    public static final long H5E_CANTDIRTY = H5E_CANTDIRTY();
+    /** Minor error codes - B-tree related errors - Unable to encode value */
     public static final long H5E_CANTENCODE = H5E_CANTENCODE();
+    /** Minor error codes - Cache related errors - Unable to expunge a metadata cache entry */
+    public static final long H5E_CANTEXPUNGE = H5E_CANTEXPUNGE();
+    /** Minor error codes - Heap errors - Can't extend heap's space */
+    public static final long H5E_CANTEXTEND = H5E_CANTEXTEND();
+    /** I/O pipeline errors - Filter operation failed */
+    public static final long H5E_CANTFILTER = H5E_CANTFILTER();
+    /** Minor error codes - Cache related errors - Unable to flush data from cache */
     public static final long H5E_CANTFLUSH = H5E_CANTFLUSH();
+    /** Minor error codes - Resource errors - Unable to free object */
     public static final long H5E_CANTFREE = H5E_CANTFREE();
+    /** Minor error codes - Parallel MPI - Can't gather data */
+    public static final long H5E_CANTGATHER = H5E_CANTGATHER();
+    /** Minor error codes - Resource errors - Unable to garbage collect */
+    public static final long H5E_CANTGC = H5E_CANTGC();
+    /** Minor error codes - Property list errors - Can't get value */
     public static final long H5E_CANTGET = H5E_CANTGET();
+    /** Minor error codes - Resource errors - Unable to compute size */
+    public static final long H5E_CANTGETSIZE = H5E_CANTGETSIZE();
+    /** Minor error codes - Object atom related errors - Unable to increment reference count */
     public static final long H5E_CANTINC = H5E_CANTINC();
+    /** Minor error codes - Function entry/exit interface - Unable to initialize object */
     public static final long H5E_CANTINIT = H5E_CANTINIT();
+    /** Minor error codes - Cache related errors - Unable to insert metadata into cache */
+    public static final long H5E_CANTINS = H5E_CANTINS();
+    /** Minor error codes - B-tree related errors - Unable to insert object */
     public static final long H5E_CANTINSERT = H5E_CANTINSERT();
+    /** Minor error codes - B-tree related errors - Unable to list node */
     public static final long H5E_CANTLIST = H5E_CANTLIST();
+    /** Minor error codes - Cache related errors - Unable to load metadata into cache */
     public static final long H5E_CANTLOAD = H5E_CANTLOAD();
+    /** Minor error codes - Resource errors - Unable to lock object */
     public static final long H5E_CANTLOCK = H5E_CANTLOCK();
+    /** Minor error codes - File accessibility errors  Unable to lock file */
+    public static final long H5E_CANTLOCKFILE = H5E_CANTLOCKFILE();
+    /** Minor error codes - Cache related errors - Unable to mark a pinned entry as clean */
+    public static final long H5E_CANTMARKCLEAN = H5E_CANTMARKCLEAN();
+    /** Minor error codes - Cache related errors - Unable to mark a pinned entry as dirty */
+    public static final long H5E_CANTMARKDIRTY = H5E_CANTMARKDIRTY();
+    /** Minor error codes - Cache related errors - Unable to mark an entry as unserialized */
+    public static final long H5E_CANTMARKSERIALIZED = H5E_CANTMARKSERIALIZED();
+    /** Minor error codes - Cache related errors - Unable to mark an entry as serialized */
+    public static final long H5E_CANTMARKUNSERIALIZED = H5E_CANTMARKUNSERIALIZED();
+    /** Minor error codes - Free space errors - Can't merge objects */
+    public static final long H5E_CANTMERGE = H5E_CANTMERGE();
+    /** Minor error codes - B-tree related errors - Unable to modify record */
+    public static final long H5E_CANTMODIFY = H5E_CANTMODIFY();
+    /** Minor error codes - Link related errors - Can't move object */
+    public static final long H5E_CANTMOVE = H5E_CANTMOVE();
+    /** Minor error codes - Dataspace errors - Can't move to next iterator location */
     public static final long H5E_CANTNEXT = H5E_CANTNEXT();
+    /** Minor error codes - Cache related errors - Unable to notify object about action */
+    public static final long H5E_CANTNOTIFY = H5E_CANTNOTIFY();
+    /** Minor error codes - File accessibility errors - Unable to open file */
     public static final long H5E_CANTOPENFILE = H5E_CANTOPENFILE();
+    /** Minor error codes - Group related errors - Can't open object */
     public static final long H5E_CANTOPENOBJ = H5E_CANTOPENOBJ();
-    // public static final long H5E_CANTRECV = H5E_CANTRECV();
+    /** Minor error codes - Heap errors - Can't operate on object */
+    public static final long H5E_CANTOPERATE = H5E_CANTOPERATE();
+    /** Minor error codes - Object header related errors - Can't pack messages */
+    public static final long H5E_CANTPACK = H5E_CANTPACK();
+    /** Minor error codes - Cache related errors - Unable to pin cache entry */
+    public static final long H5E_CANTPIN = H5E_CANTPIN();
+    /** Minor error codes - Cache related errors - Unable to protect metadata */
+    public static final long H5E_CANTPROTECT = H5E_CANTPROTECT();
+    /** Minor error codes - Parallel MPI - Can't receive data */
+    public static final long H5E_CANTRECV = H5E_CANTRECV();
+    /** Minor error codes - B-tree related errors - Unable to redistribute records */
+    public static final long H5E_CANTREDISTRIBUTE = H5E_CANTREDISTRIBUTE();
+    /** Minor error codes - Object atom related errors - Unable to register new atom */
     public static final long H5E_CANTREGISTER = H5E_CANTREGISTER();
+    /** Minor error codes - Function entry/exit interface - Unable to release object */
     public static final long H5E_CANTRELEASE = H5E_CANTRELEASE();
+    /** Minor error codes - B-tree related errors - Unable to remove object */
+    public static final long H5E_CANTREMOVE = H5E_CANTREMOVE();
+    /** Minor error codes - Object header related errors - Unable to rename object */
+    public static final long H5E_CANTRENAME = H5E_CANTRENAME();
+    /** Minor error codes - Object header related errors - Can't reset object */
+    public static final long H5E_CANTRESET = H5E_CANTRESET();
+    /** Minor error codes - Cache related errors - Unable to resize a metadata cache entry */
+    public static final long H5E_CANTRESIZE = H5E_CANTRESIZE();
+    /** Minor error codes - Heap errors - Can't restore condition */
+    public static final long H5E_CANTRESTORE = H5E_CANTRESTORE();
+    /** Minor error codes - Free space errors - Can't revive object */
+    public static final long H5E_CANTREVIVE = H5E_CANTREVIVE();
+    /** Minor error codes - Free space errors - Can't shrink container */
+    public static final long H5E_CANTSHRINK = H5E_CANTSHRINK();
+    /** Minor error codes - Dataspace errors - Can't select hyperslab */
     public static final long H5E_CANTSELECT = H5E_CANTSELECT();
+    /** Minor error codes - Cache related errors - Unable to serialize data from cache */
+    public static final long H5E_CANTSERIALIZE = H5E_CANTSERIALIZE();
+    /** Minor error codes - Property list errors - Can't set value */
     public static final long H5E_CANTSET = H5E_CANTSET();
+    /** Minor error codes - Link related errors - Can't sort objects */
+    public static final long H5E_CANTSORT = H5E_CANTSORT();
+    /** Minor error codes - B-tree related errors - Unable to split node */
     public static final long H5E_CANTSPLIT = H5E_CANTSPLIT();
+    /** Minor error codes - B-tree related errors - Unable to swap records */
+    public static final long H5E_CANTSWAP = H5E_CANTSWAP();
+    /** Minor error codes - Cache related errors - Unable to tag metadata in the cache */
+    public static final long H5E_CANTTAG = H5E_CANTTAG();
+    /** Minor error codes - Cache related errors - Unable to uncork an object */
+    public static final long H5E_CANTUNCORK = H5E_CANTUNCORK();
+    /** Minor error codes - Cache related errors - Unable to destroy a flush dependency */
+    public static final long H5E_CANTUNDEPEND = H5E_CANTUNDEPEND();
+    /** Minor error codes - Resource errors - Unable to unlock object */
     public static final long H5E_CANTUNLOCK = H5E_CANTUNLOCK();
+    /** Minor error codes - File accessibility errors  Unable to unlock file */
+    public static final long H5E_CANTUNLOCKFILE = H5E_CANTUNLOCKFILE();
+    /** Minor error codes - Cache related errors - Unable to un-pin cache entry */
+    public static final long H5E_CANTUNPIN = H5E_CANTUNPIN();
+    /** Minor error codes - Cache related errors - Unable to unprotect metadata */
+    public static final long H5E_CANTUNPROTECT = H5E_CANTUNPROTECT();
+    /** Minor error codes - Cache related errors - Unable to mark metadata as unserialized */
+    public static final long H5E_CANTUNSERIALIZE = H5E_CANTUNSERIALIZE();
+    /** Minor error codes - Heap errors - Can't update object */
+    public static final long H5E_CANTUPDATE = H5E_CANTUPDATE();
+    /** Generic low-level file I/O errors - Close failed */
     public static final long H5E_CLOSEERROR = H5E_CLOSEERROR();
+    /** Minor error codes - Group related errors - Name component is too long */
     public static final long H5E_COMPLEN = H5E_COMPLEN();
+    /** Major error codes - API Context */
+    public static final long H5E_CONTEXT = H5E_CONTEXT();
+    /** Major error codes - Dataset */
     public static final long H5E_DATASET = H5E_DATASET();
+    /** Major error codes - Dataspace */
     public static final long H5E_DATASPACE = H5E_DATASPACE();
+    /** Major error codes - Datatype */
     public static final long H5E_DATATYPE = H5E_DATATYPE();
+    /** Value for the default error stack */
     public static final long H5E_DEFAULT = H5E_DEFAULT();
+    /** Minor error codes - Property list errors - Duplicate class name in parent class */
     public static final long H5E_DUPCLASS = H5E_DUPCLASS();
+    /** Major error codes - Extensible Array */
+    public static final long H5E_EARRAY = H5E_EARRAY();
+    /** Major error codes - External file list */
     public static final long H5E_EFL = H5E_EFL();
+    /** Major error codes - Error API */
+    public static final long H5E_ERROR = H5E_ERROR();
+    /** Minor error codes - B-tree related errors - Object already exists */
     public static final long H5E_EXISTS = H5E_EXISTS();
+    /** Major error codes - Fixed Array */
+    public static final long H5E_FARRAY = H5E_FARRAY();
+    /** Generic low-level file I/O errors - File control (fcntl) failed */
     public static final long H5E_FCNTL = H5E_FCNTL();
+    /** Major error codes - File accessibility */
     public static final long H5E_FILE = H5E_FILE();
+    /** Minor error codes - File accessibility errors - File already exists */
     public static final long H5E_FILEEXISTS = H5E_FILEEXISTS();
+    /** Minor error codes - File accessibility errors - File already open */
     public static final long H5E_FILEOPEN = H5E_FILEOPEN();
+    /** Major error codes - Free Space Manager */
+    public static final long H5E_FSPACE = H5E_FSPACE();
+    /** Major error codes - Function entry/exit */
     public static final long H5E_FUNC = H5E_FUNC();
+    /** Major error codes - Heap */
     public static final long H5E_HEAP = H5E_HEAP();
+    /** Minor error codes - Dataspace errors - Internal states are inconsistent */
+    public static final long H5E_INCONSISTENTSTATE = H5E_INCONSISTENTSTATE();
+    /** Major error codes - Internal error (too specific to document in detail) */
     public static final long H5E_INTERNAL = H5E_INTERNAL();
+    /** Major error codes - Low-level I/O */
     public static final long H5E_IO = H5E_IO();
+    /** Major error codes - Links */
     public static final long H5E_LINK = H5E_LINK();
+    /** Minor error codes - Object header related errors - Bad object header link count */
     public static final long H5E_LINKCOUNT = H5E_LINKCOUNT();
+    /** Minor error codes - Cache related errors - Failure in the cache logging framework */
+    public static final long H5E_LOGGING = H5E_LOGGING();
+    /** Major error codes - Map */
+    public static final long H5E_MAP = H5E_MAP();
+    /** Minor error codes - File accessibility errors - File mount error */
     public static final long H5E_MOUNT = H5E_MOUNT();
+    /** Minor error codes - Parallel MPI - Some MPI function failed */
     public static final long H5E_MPI = H5E_MPI();
+    /** Minor error codes - Parallel MPI - MPI Error String */
     public static final long H5E_MPIERRSTR = H5E_MPIERRSTR();
+    /** Minor error codes - Link related errors - Too many soft links in path */
+    public static final long H5E_NLINKS = H5E_NLINKS();
+    /** Minor error codes - Parallel MPI - Can't perform independent IO */
+    public static final long H5E_NO_INDEPENDENT = H5E_NO_INDEPENDENT();
+    /** I/O pipeline errors - Filter present but encoding disabled */
+    public static final long H5E_NOENCODER = H5E_NOENCODER();
+    /** I/O pipeline errors - Requested filter is not available */
     public static final long H5E_NOFILTER = H5E_NOFILTER();
+    /** Minor error codes - Object atom related errors - Out of IDs for group */
     public static final long H5E_NOIDS = H5E_NOIDS();
+    /** Major error codes - No error */
     public static final long H5E_NONE_MAJOR = H5E_NONE_MAJOR();
+    /** No error */
     public static final long H5E_NONE_MINOR = H5E_NONE_MINOR();
+    /** Minor error codes - Resource errors - No space available for allocation */
     public static final long H5E_NOSPACE = H5E_NOSPACE();
+    /** Minor error codes - Cache related errors - Metadata not currently cached */
     public static final long H5E_NOTCACHED = H5E_NOTCACHED();
+    /** Minor error codes - B-tree related errors - Object not found */
     public static final long H5E_NOTFOUND = H5E_NOTFOUND();
+    /** Minor error codes - File accessibility errors - Not an HDF5 file */
     public static final long H5E_NOTHDF5 = H5E_NOTHDF5();
+    /** Minor error codes - Link related errors - Link class not registered */
+    public static final long H5E_NOTREGISTERED = H5E_NOTREGISTERED();
+    /** Minor error codes - Resource errors - Object is already open */
+    public static final long H5E_OBJOPEN = H5E_OBJOPEN();
+    /** Major error codes - Object header */
     public static final long H5E_OHDR = H5E_OHDR();
+    /** Minor error codes - Plugin errors - Can't open directory or file */
+    public static final long H5E_OPENERROR = H5E_OPENERROR();
+    /** Generic low-level file I/O errors - Address overflowed */
     public static final long H5E_OVERFLOW = H5E_OVERFLOW();
+    /** Major error codes - Page Buffering */
+    public static final long H5E_PAGEBUF = H5E_PAGEBUF();
+    /** Minor error codes - Group related errors - Problem with path to object */
+    public static final long H5E_PATH = H5E_PATH();
+    /** Major error codes - Data filters */
     public static final long H5E_PLINE = H5E_PLINE();
+    /** Major error codes - Property lists */
     public static final long H5E_PLIST = H5E_PLIST();
+    /** Major error codes - Plugin for dynamically loaded library */
+    public static final long H5E_PLUGIN = H5E_PLUGIN();
+    /** Minor error codes - Cache related errors - Protected metadata error */
     public static final long H5E_PROTECT = H5E_PROTECT();
+    /** Generic low-level file I/O errors - Read failed */
     public static final long H5E_READERROR = H5E_READERROR();
+    /** Major error codes - References */
     public static final long H5E_REFERENCE = H5E_REFERENCE();
+    /** Major error codes - Resource unavailable */
     public static final long H5E_RESOURCE = H5E_RESOURCE();
+    /** Major error codes - Reference Counted Strings */
     public static final long H5E_RS = H5E_RS();
+    /** Generic low-level file I/O errors - Seek failed */
     public static final long H5E_SEEKERROR = H5E_SEEKERROR();
+    /** Minor error codes - Property list errors - Disallowed operation */
+    public static final long H5E_SETDISALLOWED = H5E_SETDISALLOWED();
+    /** I/O pipeline errors - Error from filter 'set local' callback */
     public static final long H5E_SETLOCAL = H5E_SETLOCAL();
+    /** Major error codes - Skip Lists */
+    public static final long H5E_SLIST = H5E_SLIST();
+    /** Major error codes - Shared Object Header Messages */
+    public static final long H5E_SOHM = H5E_SOHM();
+    /** Major error codes - Data storage */
     public static final long H5E_STORAGE = H5E_STORAGE();
+    /** Major error codes - Symbol table */
     public static final long H5E_SYM = H5E_SYM();
+    /** Minor error codes - System level errors - System error message */
+    public static final long H5E_SYSERRSTR = H5E_SYSERRSTR();
+    /** Minor error codes - Cache related errors - Internal error detected */
+    public static final long H5E_SYSTEM = H5E_SYSTEM();
+    /** Minor error codes - Link related errors - Link traversal failure */
+    public static final long H5E_TRAVERSE = H5E_TRAVERSE();
+    /** Minor error codes - File accessibility errors - File has been truncated */
     public static final long H5E_TRUNCATED = H5E_TRUNCATED();
+    /** Major error codes - Ternary Search Trees */
     public static final long H5E_TST = H5E_TST();
+    /** Minor error codes - Argument errors - Information is uinitialized */
     public static final long H5E_UNINITIALIZED = H5E_UNINITIALIZED();
+    /** Minor error codes - Argument errors - Feature is unsupported */
     public static final long H5E_UNSUPPORTED = H5E_UNSUPPORTED();
+    /** Minor error codes - Object header related errors - Wrong version number */
     public static final long H5E_VERSION = H5E_VERSION();
+    /** Major error codes - Virtual File Layer */
     public static final long H5E_VFL = H5E_VFL();
+    /** Major error codes - Virtual Object Layer */
     public static final long H5E_VOL = H5E_VOL();
+    /** Error stack traversal direction - begin at API function, end deep */
     public static final long H5E_WALK_DOWNWARD = H5E_WALK_DOWNWARD();
+    /** Error stack traversal direction - begin deep, end at API function */
     public static final long H5E_WALK_UPWARD = H5E_WALK_UPWARD();
+    /** Generic low-level file I/O errors - Write failed */
     public static final long H5E_WRITEERROR = H5E_WRITEERROR();
 
     private static final int H5ES_STATUS_IN_PROGRESS = H5ES_STATUS_IN_PROGRESS();
@@ -424,29 +678,53 @@ public class HDF5Constants {
     public static final int H5R_OBJECT1 = H5R_OBJECT1();
     public static final int H5R_OBJECT2 = H5R_OBJECT2();
 
+    /** Define atomic datatypes */
     public static final int H5S_ALL = H5S_ALL();
+    /** Define user-level maximum number of dimensions */
     public static final int H5S_MAX_RANK = H5S_MAX_RANK();
+    /** Different types of dataspaces - error */
     public static final int H5S_NO_CLASS = H5S_NO_CLASS();
+    /** Different types of dataspaces - null dataspace */
     public static final int H5S_NULL = H5S_NULL();
+    /** Different types of dataspaces - scalar variable */
     public static final int H5S_SCALAR = H5S_SCALAR();
+    /** Enumerated type for the type of selection - Entire extent selected */
     public static final int H5S_SEL_ALL = H5S_SEL_ALL();
+    /** Enumerated type for the type of selection - Error */
     public static final int H5S_SEL_ERROR = H5S_SEL_ERROR();
+    /** Enumerated type for the type of selection - Hyperslab selected */
     public static final int H5S_SEL_HYPERSLABS = H5S_SEL_HYPERSLABS();
+    /** Enumerated type for the type of selection - LAST */
     public static final int H5S_SEL_N = H5S_SEL_N();
+    /** Enumerated type for the type of selection - Nothing selected */
     public static final int H5S_SEL_NONE = H5S_SEL_NONE();
+    /** Enumerated type for the type of selection - Points / elements selected */
     public static final int H5S_SEL_POINTS = H5S_SEL_POINTS();
+    /** Different ways of combining selections - Binary "and" operation for hyperslabs */
     public static final int H5S_SELECT_AND = H5S_SELECT_AND();
+    /** Different ways of combining selections - Append elements to end of point selection */
     public static final int H5S_SELECT_APPEND = H5S_SELECT_APPEND();
+    /** Different ways of combining selections - Invalid upper bound on selection operations */
     public static final int H5S_SELECT_INVALID = H5S_SELECT_INVALID();
+    /** Different ways of combining selections - error */
     public static final int H5S_SELECT_NOOP = H5S_SELECT_NOOP();
+    /** Different ways of combining selections - Binary "not" operation for hyperslabs */
     public static final int H5S_SELECT_NOTA = H5S_SELECT_NOTA();
+    /** Different ways of combining selections - Binary "not" operation for hyperslabs */
     public static final int H5S_SELECT_NOTB = H5S_SELECT_NOTB();
+    /** Different ways of combining selections - Binary "or" operation for hyperslabs */
     public static final int H5S_SELECT_OR = H5S_SELECT_OR();
+    /** Different ways of combining selections - Prepend elements to beginning of point selection */
     public static final int H5S_SELECT_PREPEND = H5S_SELECT_PREPEND();
+    /** Different ways of combining selections - Select "set" operation */
     public static final int H5S_SELECT_SET = H5S_SELECT_SET();
+    /** Different ways of combining selections - Binary "xor" operation for hyperslabs */
     public static final int H5S_SELECT_XOR = H5S_SELECT_XOR();
+    /** Different types of dataspaces - simple dataspace */
     public static final int H5S_SIMPLE = H5S_SIMPLE();
+    /** Define atomic datatypes */
     public static final int H5S_UNLIMITED = H5S_UNLIMITED();
+
     public static final long H5T_ALPHA_B16 = H5T_ALPHA_B16();
     public static final long H5T_ALPHA_B32 = H5T_ALPHA_B32();
     public static final long H5T_ALPHA_B64 = H5T_ALPHA_B64();
@@ -665,48 +943,96 @@ public class HDF5Constants {
     public static final int H5_VOL_RESERVED = H5_VOL_RESERVED();
     public static final int H5_VOL_MAX = H5_VOL_MAX();
 
+    /** Return values for filter callback function */
     public static final int H5Z_CB_CONT = H5Z_CB_CONT();
+    /** Return values for filter callback function */
     public static final int H5Z_CB_ERROR = H5Z_CB_ERROR();
+    /** Return values for filter callback function */
     public static final int H5Z_CB_FAIL = H5Z_CB_FAIL();
+    /** Return values for filter callback function */
     public static final int H5Z_CB_NO = H5Z_CB_NO();
+    /** Values to decide if EDC is enabled for reading data */
     public static final int H5Z_DISABLE_EDC = H5Z_DISABLE_EDC();
+    /** Values to decide if EDC is enabled for reading data */
     public static final int H5Z_ENABLE_EDC = H5Z_ENABLE_EDC();
+    /** Values to decide if EDC is enabled for reading data */
     public static final int H5Z_ERROR_EDC = H5Z_ERROR_EDC();
+    /** Filter IDs - deflation like gzip */
     public static final int H5Z_FILTER_DEFLATE = H5Z_FILTER_DEFLATE();
+    /** Filter IDs - no filter */
     public static final int H5Z_FILTER_ERROR = H5Z_FILTER_ERROR();
+    /** Filter IDs - fletcher32 checksum of EDC */
     public static final int H5Z_FILTER_FLETCHER32 = H5Z_FILTER_FLETCHER32();
+    /** Filter IDs - maximum filter id */
     public static final int H5Z_FILTER_MAX = H5Z_FILTER_MAX();
+    /** Filter IDs - nbit compression */
     public static final int H5Z_FILTER_NBIT = H5Z_FILTER_NBIT();
+    /** Filter IDs - reserved indefinitely */
     public static final int H5Z_FILTER_NONE = H5Z_FILTER_NONE();
+    /** Filter IDs - filter ids below this value are reserved for library use */
     public static final int H5Z_FILTER_RESERVED = H5Z_FILTER_RESERVED();
+    /** Filter IDs - scale+offset compression */
     public static final int H5Z_FILTER_SCALEOFFSET = H5Z_FILTER_SCALEOFFSET();
+    /** Filter IDs - shuffle the data */
     public static final int H5Z_FILTER_SHUFFLE = H5Z_FILTER_SHUFFLE();
+    /** Filter IDs - szip compression */
     public static final int H5Z_FILTER_SZIP = H5Z_FILTER_SZIP();
+    /** Flags for filter definition (stored)
+     * definition flag mask */
     public static final int H5Z_FLAG_DEFMASK = H5Z_FLAG_DEFMASK();
+    /** Additional flags for filter invocation (not stored)
+     * invocation flag mask */
     public static final int H5Z_FLAG_INVMASK = H5Z_FLAG_INVMASK();
+    /** Flags for filter definition (stored)
+     * filter is mandatory */
     public static final int H5Z_FLAG_MANDATORY = H5Z_FLAG_MANDATORY();
+    /** Flags for filter definition (stored)
+     * filter is optional */
     public static final int H5Z_FLAG_OPTIONAL = H5Z_FLAG_OPTIONAL();
+    /** Additional flags for filter invocation (not stored)
+     * reverse direction; read */
     public static final int H5Z_FLAG_REVERSE = H5Z_FLAG_REVERSE();
+    /** Additional flags for filter invocation (not stored)
+     * skip EDC filters for read */
     public static final int H5Z_FLAG_SKIP_EDC = H5Z_FLAG_SKIP_EDC();
+    /** Symbol to remove all filters in H5Premove_filter */
+    public static final int H5Z_FILTER_ALL = H5Z_FILTER_ALL();
+    /** Maximum number of filters allowed in a pipeline */
     public static final int H5Z_MAX_NFILTERS = H5Z_MAX_NFILTERS();
+    /** Values to decide if EDC is enabled for reading data */
     public static final int H5Z_NO_EDC = H5Z_NO_EDC();
+    /** Bit flags for H5Zget_filter_info */
     public static final int H5Z_FILTER_CONFIG_ENCODE_ENABLED = H5Z_FILTER_CONFIG_ENCODE_ENABLED();
+    /** Bit flags for H5Zget_filter_info */
     public static final int H5Z_FILTER_CONFIG_DECODE_ENABLED = H5Z_FILTER_CONFIG_DECODE_ENABLED();
+    /** Special parameters for ScaleOffset filter*/
     public static final int H5Z_SO_INT_MINBITS_DEFAULT = H5Z_SO_INT_MINBITS_DEFAULT();
+    /** Special parameters for ScaleOffset filter*/
     public static final int H5Z_SO_FLOAT_DSCALE = H5Z_SO_FLOAT_DSCALE();
+    /** Special parameters for ScaleOffset filter*/
     public static final int H5Z_SO_FLOAT_ESCALE = H5Z_SO_FLOAT_ESCALE();
+    /** Special parameters for ScaleOffset filter*/
     public static final int H5Z_SO_INT = H5Z_SO_INT();
+    /** shuffle filter - Number of parameters that users can set */
     public static final int H5Z_SHUFFLE_USER_NPARMS = H5Z_SHUFFLE_USER_NPARMS();
+    /** shuffle filter - Total number of parameters for filter */
     public static final int H5Z_SHUFFLE_TOTAL_NPARMS = H5Z_SHUFFLE_TOTAL_NPARMS();
+    /** szip filter - Number of parameters that users can set */
     public static final int H5Z_SZIP_USER_NPARMS = H5Z_SZIP_USER_NPARMS();
+    /** szip filter - Total number of parameters for filter */
     public static final int H5Z_SZIP_TOTAL_NPARMS = H5Z_SZIP_TOTAL_NPARMS();
+    /** szip filter - "User" parameter for option mask */
     public static final int H5Z_SZIP_PARM_MASK = H5Z_SZIP_PARM_MASK();
+    /** szip filter - "User" parameter for pixels-per-block */
     public static final int H5Z_SZIP_PARM_PPB = H5Z_SZIP_PARM_PPB();
+    /** szip filter - "Local" parameter for bits-per-pixel */
     public static final int H5Z_SZIP_PARM_BPP = H5Z_SZIP_PARM_BPP();
+    /** szip filter - "Local" parameter for pixels-per-scanline */
     public static final int H5Z_SZIP_PARM_PPS = H5Z_SZIP_PARM_PPS();
+    /** nbit filter - Number of parameters that users can set */
     public static final int H5Z_NBIT_USER_NPARMS = H5Z_NBIT_USER_NPARMS();
+    /** scale offset filter - Number of parameters that users can set */
     public static final int H5Z_SCALEOFFSET_USER_NPARMS = H5Z_SCALEOFFSET_USER_NPARMS();
-    public static final int H5Z_FILTER_ALL = H5Z_FILTER_ALL();
 
     // /////////////////////////////////////////////////////////////////////////
     // List of private native variables to get constant values from C //
@@ -841,6 +1167,8 @@ public class HDF5Constants {
 
     private static native final long H5E_BADGROUP();
 
+    private static native final long H5E_BADITER();
+
     private static native final long H5E_BADMESG();
 
     private static native final long H5E_BADRANGE();
@@ -861,15 +1189,30 @@ public class HDF5Constants {
 
     private static native final long H5E_CANAPPLY();
 
-    // private static native final long H5E_CANTALLOC();
+    private static native final long H5E_CANTALLOC();
+
+    private static native final long H5E_CANTAPPEND();
+
+    private static native final long H5E_CANTATTACH();
+
+    private static native final long H5E_CANTCLEAN();
+
     private static native final long H5E_CANTCLIP();
 
     private static native final long H5E_CANTCLOSEFILE();
 
+    private static native final long H5E_CANTCLOSEOBJ();
+
+    private static native final long H5E_CANTCOMPARE();
+
+    private static native final long H5E_CANTCOMPUTE();
+
     private static native final long H5E_CANTCONVERT();
 
     private static native final long H5E_CANTCOPY();
 
+    private static native final long H5E_CANTCORK();
+
     private static native final long H5E_CANTCOUNT();
 
     private static native final long H5E_CANTCREATE();
@@ -882,18 +1225,36 @@ public class HDF5Constants {
 
     private static native final long H5E_CANTDELETEFILE();
 
+    private static native final long H5E_CANTDEPEND();
+
+    private static native final long H5E_CANTDIRTY();
+
     private static native final long H5E_CANTENCODE();
 
+    private static native final long H5E_CANTEXPUNGE();
+
+    private static native final long H5E_CANTEXTEND();
+
+    private static native final long H5E_CANTFILTER();
+
     private static native final long H5E_CANTFLUSH();
 
     private static native final long H5E_CANTFREE();
 
+    private static native final long H5E_CANTGATHER();
+
+    private static native final long H5E_CANTGC();
+
     private static native final long H5E_CANTGET();
 
+    private static native final long H5E_CANTGETSIZE();
+
     private static native final long H5E_CANTINC();
 
     private static native final long H5E_CANTINIT();
 
+    private static native final long H5E_CANTINS();
+
     private static native final long H5E_CANTINSERT();
 
     private static native final long H5E_CANTLIST();
@@ -902,29 +1263,96 @@ public class HDF5Constants {
 
     private static native final long H5E_CANTLOCK();
 
+    private static native final long H5E_CANTLOCKFILE();
+
+    private static native final long H5E_CANTMARKCLEAN();
+
+    private static native final long H5E_CANTMARKDIRTY();
+
+    private static native final long H5E_CANTMARKSERIALIZED();
+
+    private static native final long H5E_CANTMARKUNSERIALIZED();
+
+    private static native final long H5E_CANTMERGE();
+
+    private static native final long H5E_CANTMOVE();
+
+    private static native final long H5E_CANTMODIFY();
+
     private static native final long H5E_CANTNEXT();
 
+    private static native final long H5E_CANTNOTIFY();
+
     private static native final long H5E_CANTOPENFILE();
 
     private static native final long H5E_CANTOPENOBJ();
 
-    // private static native final long H5E_CANTRECV();
+    private static native final long H5E_CANTOPERATE();
+
+    private static native final long H5E_CANTPACK();
+
+    private static native final long H5E_CANTPIN();
+
+    private static native final long H5E_CANTPROTECT();
+
+    private static native final long H5E_CANTRECV();
+
+    private static native final long H5E_CANTREDISTRIBUTE();
+
     private static native final long H5E_CANTREGISTER();
 
     private static native final long H5E_CANTRELEASE();
 
+    private static native final long H5E_CANTREMOVE();
+
+    private static native final long H5E_CANTRENAME();
+
+    private static native final long H5E_CANTRESET();
+
+    private static native final long H5E_CANTRESIZE();
+
+    private static native final long H5E_CANTRESTORE();
+
+    private static native final long H5E_CANTREVIVE();
+
+    private static native final long H5E_CANTSHRINK();
+
     private static native final long H5E_CANTSELECT();
 
     private static native final long H5E_CANTSET();
 
+    private static native final long H5E_CANTSERIALIZE();
+
+    private static native final long H5E_CANTSORT();
+
     private static native final long H5E_CANTSPLIT();
 
+    private static native final long H5E_CANTSWAP();
+
+    private static native final long H5E_CANTTAG();
+
+    private static native final long H5E_CANTUNCORK();
+
+    private static native final long H5E_CANTUNDEPEND();
+
     private static native final long H5E_CANTUNLOCK();
 
+    private static native final long H5E_CANTUNLOCKFILE();
+
+    private static native final long H5E_CANTUNPIN();
+
+    private static native final long H5E_CANTUNPROTECT();
+
+    private static native final long H5E_CANTUNSERIALIZE();
+
+    private static native final long H5E_CANTUPDATE();
+
     private static native final long H5E_CLOSEERROR();
 
     private static native final long H5E_COMPLEN();
 
+    private static native final long H5E_CONTEXT();
+
     private static native final long H5E_DATASET();
 
     private static native final long H5E_DATASPACE();
@@ -935,10 +1363,16 @@ public class HDF5Constants {
 
     private static native final long H5E_DUPCLASS();
 
+    private static native final long H5E_EARRAY();
+
     private static native final long H5E_EFL();
 
+    private static native final long H5E_ERROR();
+
     private static native final long H5E_EXISTS();
 
+    private static native final long H5E_FARRAY();
+
     private static native final long H5E_FCNTL();
 
     private static native final long H5E_FILE();
@@ -947,10 +1381,14 @@ public class HDF5Constants {
 
     private static native final long H5E_FILEOPEN();
 
+    private static native final long H5E_FSPACE();
+
     private static native final long H5E_FUNC();
 
     private static native final long H5E_HEAP();
 
+    private static native final long H5E_INCONSISTENTSTATE();
+
     private static native final long H5E_INTERNAL();
 
     private static native final long H5E_IO();
@@ -959,8 +1397,12 @@ public class HDF5Constants {
 
     private static native final long H5E_LINKCOUNT();
 
+    private static native final long H5E_LOGGING();
+
     private static native final int H5E_MAJOR();
 
+    private static native final long H5E_MAP();
+
     private static native final int H5E_MINOR();
 
     private static native final long H5E_MOUNT();
@@ -969,6 +1411,12 @@ public class HDF5Constants {
 
     private static native final long H5E_MPIERRSTR();
 
+    private static native final long H5E_NLINKS();
+
+    private static native final long H5E_NO_INDEPENDENT();
+
+    private static native final long H5E_NOENCODER();
+
     private static native final long H5E_NOFILTER();
 
     private static native final long H5E_NOIDS();
@@ -985,14 +1433,26 @@ public class HDF5Constants {
 
     private static native final long H5E_NOTHDF5();
 
+    private static native final long H5E_NOTREGISTERED();
+
+    private static native final long H5E_OBJOPEN();
+
     private static native final long H5E_OHDR();
 
+    private static native final long H5E_OPENERROR();
+
     private static native final long H5E_OVERFLOW();
 
+    private static native final long H5E_PAGEBUF();
+
+    private static native final long H5E_PATH();
+
     private static native final long H5E_PLINE();
 
     private static native final long H5E_PLIST();
 
+    private static native final long H5E_PLUGIN();
+
     private static native final long H5E_PROTECT();
 
     private static native final long H5E_READERROR();
@@ -1005,12 +1465,24 @@ public class HDF5Constants {
 
     private static native final long H5E_SEEKERROR();
 
+    private static native final long H5E_SETDISALLOWED();
+
     private static native final long H5E_SETLOCAL();
 
+    private static native final long H5E_SLIST();
+
+    private static native final long H5E_SOHM();
+
     private static native final long H5E_STORAGE();
 
     private static native final long H5E_SYM();
 
+    private static native final long H5E_SYSERRSTR();
+
+    private static native final long H5E_SYSTEM();
+
+    private static native final long H5E_TRAVERSE();
+
     private static native final long H5E_TRUNCATED();
 
     private static native final long H5E_TST();
diff --git a/java/src/jni/h5Constants.c b/java/src/jni/h5Constants.c
index 38f0883..94d5b19 100644
--- a/java/src/jni/h5Constants.c
+++ b/java/src/jni/h5Constants.c
@@ -355,6 +355,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1BADGROUP(JNIEnv *env, jclass cls)
     return H5E_BADGROUP;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1BADITER(JNIEnv *env, jclass cls)
+{
+    return H5E_BADITER;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1BADMESG(JNIEnv *env, jclass cls)
 {
     return H5E_BADMESG;
@@ -404,8 +409,26 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANAPPLY(JNIEnv *env, jclass cls)
 {
     return H5E_CANAPPLY;
 }
-/*JNIEXPORT jlong JNICALL
-Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTALLOC(JNIEnv *env, jclass cls) { return H5E_CANTALLOC; }*/
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTALLOC(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTALLOC;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTAPPEND(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTAPPEND;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTATTACH(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTATTACH;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCLEAN(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTCLEAN;
+}
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCLIP(JNIEnv *env, jclass cls)
 {
@@ -417,6 +440,21 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCLOSEFILE(JNIEnv *env, jclass cls)
     return H5E_CANTCLOSEFILE;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCLOSEOBJ(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTCLOSEOBJ;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCOMPARE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTCOMPARE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCOMPUTE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTCOMPUTE;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCONVERT(JNIEnv *env, jclass cls)
 {
     return H5E_CANTCONVERT;
@@ -427,6 +465,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCOPY(JNIEnv *env, jclass cls)
     return H5E_CANTCOPY;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCORK(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTCORK;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCOUNT(JNIEnv *env, jclass cls)
 {
     return H5E_CANTCOUNT;
@@ -457,11 +500,36 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTDELETEFILE(JNIEnv *env, jclass cls)
     return H5E_CANTDELETEFILE;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTDEPEND(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTDEPEND;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTDIRTY(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTDIRTY;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTFILTER(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTFILTER;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTENCODE(JNIEnv *env, jclass cls)
 {
     return H5E_CANTENCODE;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTEXPUNGE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTEXPUNGE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTEXTEND(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTEXTEND;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTFLUSH(JNIEnv *env, jclass cls)
 {
     return H5E_CANTFLUSH;
@@ -472,11 +540,26 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTFREE(JNIEnv *env, jclass cls)
     return H5E_CANTFREE;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTGATHER(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTGATHER;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTGC(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTGC;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTGET(JNIEnv *env, jclass cls)
 {
     return H5E_CANTGET;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTGETSIZE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTGETSIZE;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTINC(JNIEnv *env, jclass cls)
 {
     return H5E_CANTINC;
@@ -487,6 +570,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTINIT(JNIEnv *env, jclass cls)
     return H5E_CANTINIT;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTINS(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTINS;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTINSERT(JNIEnv *env, jclass cls)
 {
     return H5E_CANTINSERT;
@@ -507,11 +595,56 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTLOCK(JNIEnv *env, jclass cls)
     return H5E_CANTLOCK;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTLOCKFILE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTLOCKFILE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMARKCLEAN(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTMARKCLEAN;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMARKDIRTY(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTMARKDIRTY;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMARKSERIALIZED(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTMARKSERIALIZED;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMARKUNSERIALIZED(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTMARKUNSERIALIZED;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMERGE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTMERGE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMODIFY(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTMODIFY;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMOVE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTMOVE;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTNEXT(JNIEnv *env, jclass cls)
 {
     return H5E_CANTNEXT;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTNOTIFY(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTNOTIFY;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTOPENFILE(JNIEnv *env, jclass cls)
 {
     return H5E_CANTOPENFILE;
@@ -521,8 +654,36 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTOPENOBJ(JNIEnv *env, jclass cls)
 {
     return H5E_CANTOPENOBJ;
 }
-/*JNIEXPORT jlong JNICALL
-Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRECV(JNIEnv *env, jclass cls) { return H5E_CANTRECV; }*/
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTOPERATE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTOPERATE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTPACK(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTPACK;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTPIN(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTPIN;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTPROTECT(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTPROTECT;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRECV(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTRECV;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTREDISTRIBUTE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTREDISTRIBUTE;
+}
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTREGISTER(JNIEnv *env, jclass cls)
 {
@@ -534,6 +695,41 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRELEASE(JNIEnv *env, jclass cls)
     return H5E_CANTRELEASE;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTREMOVE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTREMOVE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRENAME(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTRENAME;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRESET(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTRESET;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRESIZE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTRESIZE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRESTORE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTRESTORE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTREVIVE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTREVIVE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSHRINK(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTSHRINK;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSELECT(JNIEnv *env, jclass cls)
 {
     return H5E_CANTSELECT;
@@ -544,16 +740,71 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSET(JNIEnv *env, jclass cls)
     return H5E_CANTSET;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSERIALIZE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTSERIALIZE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSORT(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTSORT;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSPLIT(JNIEnv *env, jclass cls)
 {
     return H5E_CANTSPLIT;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSWAP(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTSWAP;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTTAG(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTTAG;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNCORK(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTUNCORK;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNDEPEND(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTUNDEPEND;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNLOCK(JNIEnv *env, jclass cls)
 {
     return H5E_CANTUNLOCK;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNLOCKFILE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTUNLOCKFILE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNPIN(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTUNPIN;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNPROTECT(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTUNPROTECT;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNSERIALIZE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTUNSERIALIZE;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUPDATE(JNIEnv *env, jclass cls)
+{
+    return H5E_CANTUPDATE;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CLOSEERROR(JNIEnv *env, jclass cls)
 {
     return H5E_CLOSEERROR;
@@ -564,6 +815,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1COMPLEN(JNIEnv *env, jclass cls)
     return H5E_COMPLEN;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1CONTEXT(JNIEnv *env, jclass cls)
+{
+    return H5E_CONTEXT;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1DATASET(JNIEnv *env, jclass cls)
 {
     return H5E_DATASET;
@@ -589,16 +845,31 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1DUPCLASS(JNIEnv *env, jclass cls)
     return H5E_DUPCLASS;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1EARRAY(JNIEnv *env, jclass cls)
+{
+    return H5E_EARRAY;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1EFL(JNIEnv *env, jclass cls)
 {
     return H5E_EFL;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1ERROR(JNIEnv *env, jclass cls)
+{
+    return H5E_ERROR;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1EXISTS(JNIEnv *env, jclass cls)
 {
     return H5E_EXISTS;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1FARRAY(JNIEnv *env, jclass cls)
+{
+    return H5E_FARRAY;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1FCNTL(JNIEnv *env, jclass cls)
 {
     return H5E_FCNTL;
@@ -619,6 +890,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1FILEOPEN(JNIEnv *env, jclass cls)
     return H5E_FILEOPEN;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1FSPACE(JNIEnv *env, jclass cls)
+{
+    return H5E_FSPACE;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1FUNC(JNIEnv *env, jclass cls)
 {
     return H5E_FUNC;
@@ -629,6 +905,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1HEAP(JNIEnv *env, jclass cls)
     return H5E_HEAP;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1INCONSISTENTSTATE(JNIEnv *env, jclass cls)
+{
+    return H5E_INCONSISTENTSTATE;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1INTERNAL(JNIEnv *env, jclass cls)
 {
     return H5E_INTERNAL;
@@ -648,11 +929,21 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1LINKCOUNT(JNIEnv *env, jclass cls)
 {
     return H5E_LINKCOUNT;
 }
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1LOGGING(JNIEnv *env, jclass cls)
+{
+    return H5E_LOGGING;
+}
 JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1MAJOR(JNIEnv *env, jclass cls)
 {
     return H5E_MAJOR;
 }
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1MAP(JNIEnv *env, jclass cls)
+{
+    return H5E_MAP;
+}
 JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1MINOR(JNIEnv *env, jclass cls)
 {
@@ -674,6 +965,21 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1MPIERRSTR(JNIEnv *env, jclass cls)
     return H5E_MPIERRSTR;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1NLINKS(JNIEnv *env, jclass cls)
+{
+    return H5E_NLINKS;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1NO_1INDEPENDENT(JNIEnv *env, jclass cls)
+{
+    return H5E_NO_INDEPENDENT;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1NOENCODER(JNIEnv *env, jclass cls)
+{
+    return H5E_NOENCODER;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1NOFILTER(JNIEnv *env, jclass cls)
 {
     return H5E_NOFILTER;
@@ -714,16 +1020,41 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1NOTHDF5(JNIEnv *env, jclass cls)
     return H5E_NOTHDF5;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1NOTREGISTERED(JNIEnv *env, jclass cls)
+{
+    return H5E_NOTREGISTERED;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1OBJOPEN(JNIEnv *env, jclass cls)
+{
+    return H5E_OBJOPEN;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1OHDR(JNIEnv *env, jclass cls)
 {
     return H5E_OHDR;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1OPENERROR(JNIEnv *env, jclass cls)
+{
+    return H5E_OPENERROR;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1OVERFLOW(JNIEnv *env, jclass cls)
 {
     return H5E_OVERFLOW;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1PAGEBUF(JNIEnv *env, jclass cls)
+{
+    return H5E_PAGEBUF;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1PATH(JNIEnv *env, jclass cls)
+{
+    return H5E_PATH;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1PLINE(JNIEnv *env, jclass cls)
 {
     return H5E_PLINE;
@@ -734,6 +1065,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1PLIST(JNIEnv *env, jclass cls)
     return H5E_PLIST;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1PLUGIN(JNIEnv *env, jclass cls)
+{
+    return H5E_PLUGIN;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1PROTECT(JNIEnv *env, jclass cls)
 {
     return H5E_PROTECT;
@@ -764,11 +1100,26 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1SEEKERROR(JNIEnv *env, jclass cls)
     return H5E_SEEKERROR;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1SETDISALLOWED(JNIEnv *env, jclass cls)
+{
+    return H5E_SETDISALLOWED;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1SETLOCAL(JNIEnv *env, jclass cls)
 {
     return H5E_SETLOCAL;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1SLIST(JNIEnv *env, jclass cls)
+{
+    return H5E_SLIST;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1SOHM(JNIEnv *env, jclass cls)
+{
+    return H5E_SOHM;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1STORAGE(JNIEnv *env, jclass cls)
 {
     return H5E_STORAGE;
@@ -779,6 +1130,21 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1SYM(JNIEnv *env, jclass cls)
     return H5E_SYM;
 }
 JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1SYSERRSTR(JNIEnv *env, jclass cls)
+{
+    return H5E_SYSERRSTR;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1SYSTEM(JNIEnv *env, jclass cls)
+{
+    return H5E_SYSTEM;
+}
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5E_1TRAVERSE(JNIEnv *env, jclass cls)
+{
+    return H5E_TRAVERSE;
+}
+JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1TRUNCATED(JNIEnv *env, jclass cls)
 {
     return H5E_TRUNCATED;
diff --git a/java/src/jni/h5sImp.c b/java/src/jni/h5sImp.c
index 2a9cff5..e29c2ec 100644
--- a/java/src/jni/h5sImp.c
+++ b/java/src/jni/h5sImp.c
@@ -1340,6 +1340,389 @@ done:
     return;
 } /* end Java_hdf_hdf5lib_H5_H5Sget_1regular_1hyperslab */
 
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Sselect_copy
+ * Signature: (JJ)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Sselect_1copy(JNIEnv *env, jclass clss, jlong dst_id, jlong src_id)
+{
+    hssize_t retVal = -1;
+
+    UNUSED(clss);
+
+    if ((retVal = H5Sselect_copy((hid_t)dst_id, (hid_t)src_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return;
+} /* end Java_hdf_hdf5lib_H5_H5Sselect_1copy */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Sselect_shape_same
+ * Signature: (JJ)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Sselect_1shape_1same(JNIEnv *env, jclass clss, jlong space1_id, jlong space2_id)
+{
+    htri_t bval = JNI_FALSE;
+
+    UNUSED(clss);
+
+    if ((bval = H5Sselect_shape_same((hid_t)space1_id, (hid_t)space2_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    bval = (bval > 0) ? JNI_TRUE : JNI_FALSE;
+
+done:
+    return (jboolean)bval;
+} /* end Java_hdf_hdf5lib_H5_H5Sselect_1shape_1same */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Sselect_adjust
+ * Signature: (J[J)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Sselect_1adjust(JNIEnv *env, jclass clss, jlong space_id, jlongArray offset)
+{
+    jboolean  isCopy;
+    hssize_t *offst       = NULL;
+    jlong *   offsetP     = NULL;
+    jsize     offset_rank = -1;
+    int       i, rank = -1;
+    herr_t    status = FAIL;
+
+    UNUSED(clss);
+
+    if (space_id < 0)
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_adjust: invalid dataspace ID");
+
+    if ((rank = H5Sget_simple_extent_ndims(space_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    if (NULL == offset) {
+        offsetP = NULL;
+        offst   = (hssize_t *)offsetP;
+    }
+    else {
+        if ((offset_rank = ENVPTR->GetArrayLength(ENVONLY, offset)) < 0) {
+            CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_adjust: offset length < 0");
+        }
+
+        if (offset_rank != rank)
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_adjust: offset rank doesn't match dataspace rank!");
+
+        PIN_LONG_ARRAY(ENVONLY, offset, offsetP, &isCopy, "H5Sselect_adjust: offset not pinned");
+
+        if (NULL == (offst = (hssize_t *)HDmalloc((size_t)offset_rank * sizeof(hsize_t))))
+            H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_adjust: failed to allocate offset buffer");
+    }
+
+    if ((status = H5Sselect_adjust(space_id, (hssize_t *)offst)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    for (i = 0; i < offset_rank; i++) {
+        offsetP[i] = (jlong)offst[i];
+    } /* end for */
+
+done:
+    if (offst)
+        HDfree(offst);
+    if (offsetP)
+        UNPIN_LONG_ARRAY(ENVONLY, offset, offsetP, (status < 0) ? JNI_ABORT : 0);
+
+    return;
+} /* end Java_hdf_hdf5lib_H5_H5Sselect_1adjust */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Sselect_intersect_block
+ * Signature: (J[J[J)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Sselect_1intersect_1block(JNIEnv *env, jclass clss, jlong space_id, jlongArray start,
+                                                jlongArray end)
+{
+    htri_t   bval = JNI_FALSE;
+    jboolean isCopy;
+    hsize_t *strt = NULL, *nd = NULL;
+    jlong *  startP = NULL, *endP = NULL;
+    jsize    start_rank = -1, end_rank = -1;
+    int      i, rank                   = -1;
+
+    UNUSED(clss);
+
+    if (space_id < 0)
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_intersect_block: invalid dataspace ID");
+
+    if ((rank = H5Sget_simple_extent_ndims(space_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    if (NULL == start) {
+        startP = NULL;
+        strt   = (hsize_t *)startP;
+    }
+    else {
+        if ((start_rank = ENVPTR->GetArrayLength(ENVONLY, start)) < 0) {
+            CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_intersect_block: start length < 0");
+        }
+
+        if (start_rank != rank)
+            H5_BAD_ARGUMENT_ERROR(ENVONLY,
+                                  "H5Sselect_intersect_block: start rank doesn't match dataspace rank!");
+
+        PIN_LONG_ARRAY(ENVONLY, start, startP, &isCopy, "H5Sselect_intersect_block: start not pinned");
+
+        if (NULL == (strt = (hsize_t *)HDmalloc((size_t)start_rank * sizeof(hsize_t))))
+            H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_intersect_block: failed to allocate start buffer");
+    }
+
+    if (NULL == end) {
+        endP = NULL;
+        nd   = (hsize_t *)endP;
+    }
+    else {
+        if ((end_rank = ENVPTR->GetArrayLength(ENVONLY, end)) < 0) {
+            CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_intersect_block: end array length < 0");
+        }
+
+        if (end_rank != rank)
+            H5_BAD_ARGUMENT_ERROR(ENVONLY,
+                                  "H5Sselect_intersect_block: end rank doesn't match dataspace rank!");
+
+        PIN_LONG_ARRAY(ENVONLY, end, endP, &isCopy, "H5Sselect_intersect_block: end not pinned");
+
+        if (NULL == (nd = (hsize_t *)HDmalloc((size_t)end_rank * sizeof(hsize_t))))
+            H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_intersect_block: failed to allocate end buffer");
+    }
+
+    if ((bval = H5Sselect_intersect_block(space_id, (hsize_t *)strt, (hsize_t *)nd)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    bval = (bval > 0) ? JNI_TRUE : JNI_FALSE;
+
+    for (i = 0; i < start_rank; i++) {
+        startP[i] = (jlong)strt[i];
+        endP[i]   = (jlong)nd[i];
+    } /* end for */
+
+done:
+    if (strt)
+        HDfree(strt);
+    if (startP)
+        UNPIN_LONG_ARRAY(ENVONLY, start, startP, (bval < 0) ? JNI_ABORT : 0);
+    if (nd)
+        HDfree(nd);
+    if (endP)
+        UNPIN_LONG_ARRAY(ENVONLY, end, endP, (bval < 0) ? JNI_ABORT : 0);
+
+    return (jboolean)bval;
+} /* end Java_hdf_hdf5lib_H5_H5Sselect_1intersect_1block */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Sselect_project_intersection
+ * Signature: (JJJ)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5Sselect_1project_1intersection(JNIEnv *env, jclass clss, jlong src_space_id,
+                                                     jlong dst_space_id, jlong src_intersect_space_id)
+{
+    hid_t sid = H5I_INVALID_HID;
+
+    UNUSED(clss);
+
+    if ((sid = H5Sselect_project_intersection(src_space_id, dst_space_id, src_intersect_space_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+
+    return (jlong)sid;
+} /* end Java_hdf_hdf5lib_H5_H5Sselect_1project_1intersection */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Scombine_hyperslab
+ * Signature: (JI[J[J[J[J)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5Scombine_1hyperslab(JNIEnv *env, jclass clss, jlong space_id, jint op, jlongArray start,
+                                          jlongArray stride, jlongArray count, jlongArray block)
+{
+    jboolean isCopy;
+    hsize_t *strt = NULL, *strd = NULL, *cnt = NULL, *blk = NULL;
+    hsize_t *lp     = NULL;
+    jlong *  startP = NULL, *strideP = NULL, *countP = NULL, *blockP = NULL;
+    jlong *  jlp = NULL;
+    jsize    start_rank, stride_rank, count_rank, block_rank;
+    int      i;
+    hid_t    sid = H5I_INVALID_HID;
+
+    UNUSED(clss);
+
+    if (NULL == start)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Sselect_hyperslab: start is NULL");
+    if (NULL == count)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Sselect_hyperslab: count is NULL");
+
+    if ((start_rank = ENVPTR->GetArrayLength(ENVONLY, start)) < 0) {
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_hyperslab: start array length < 0");
+    }
+    if ((count_rank = ENVPTR->GetArrayLength(ENVONLY, count)) < 0) {
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_hyperslab: count array length < 0");
+    }
+
+    if (start_rank != count_rank)
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_hyperslab: count and start have different rank!");
+
+    PIN_LONG_ARRAY(ENVONLY, start, startP, &isCopy, "H5Sselect_hyperslab: start not pinned");
+
+    if (NULL == (strt = lp = (hsize_t *)HDmalloc((size_t)start_rank * sizeof(hsize_t))))
+        H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_hyperslab: failed to allocate start buffer");
+
+    jlp = (jlong *)startP;
+    for (i = 0; i < start_rank; i++) {
+        *lp = (hsize_t)*jlp;
+        lp++;
+        jlp++;
+    } /* end if */
+
+    PIN_LONG_ARRAY(ENVONLY, count, countP, &isCopy, "H5Sselect_hyperslab: count not pinned");
+
+    if (NULL == (cnt = lp = (hsize_t *)HDmalloc((size_t)count_rank * sizeof(hsize_t))))
+        H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_hyperslab: failed to allocate count buffer");
+
+    jlp = (jlong *)countP;
+    for (i = 0; i < count_rank; i++) {
+        *lp = (hsize_t)*jlp;
+        lp++;
+        jlp++;
+    } /* end if */
+
+    if (NULL == stride) {
+        strideP = NULL;
+        strd    = (hsize_t *)strideP;
+    }
+    else {
+        if ((stride_rank = ENVPTR->GetArrayLength(ENVONLY, stride)) < 0) {
+            CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_hyperslab: stride array length < 0");
+        }
+
+        if (stride_rank != start_rank)
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_hyperslab: stride and start have different rank!");
+
+        PIN_LONG_ARRAY(ENVONLY, stride, strideP, &isCopy, "H5Sselect_hyperslab: stride not pinned");
+
+        if (NULL == (strd = lp = (hsize_t *)HDmalloc((size_t)stride_rank * sizeof(hsize_t))))
+            H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_hyperslab: failed to allocate stride buffer");
+
+        jlp = (jlong *)strideP;
+        for (i = 0; i < stride_rank; i++) {
+            *lp = (hsize_t)*jlp;
+            lp++;
+            jlp++;
+        } /* end if */
+    }
+
+    if (NULL == block) {
+        blockP = NULL;
+        blk    = (hsize_t *)blockP;
+    }
+    else {
+        if ((block_rank = ENVPTR->GetArrayLength(ENVONLY, block)) < 0) {
+            CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_hyperslab: block array length < 0");
+        }
+
+        if (block_rank != start_rank)
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_hyperslab: block and start have different rank!");
+
+        PIN_LONG_ARRAY(ENVONLY, block, blockP, &isCopy, "H5Sselect_hyperslab: block not pinned");
+
+        if (NULL == (blk = lp = (hsize_t *)HDmalloc((size_t)block_rank * sizeof(hsize_t))))
+            H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_hyperslab: failed to allocate block buffer");
+
+        jlp = (jlong *)blockP;
+        for (i = 0; i < block_rank; i++) {
+            *lp = (hsize_t)*jlp;
+            lp++;
+            jlp++;
+        } /* end for */
+    }
+
+    if ((sid = H5Scombine_hyperslab(space_id, (H5S_seloper_t)op, (const hsize_t *)strt, (const hsize_t *)strd,
+                                    (const hsize_t *)cnt, (const hsize_t *)blk)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    if (blk)
+        HDfree(blk);
+    if (blockP)
+        UNPIN_LONG_ARRAY(ENVONLY, block, blockP, JNI_ABORT);
+    if (strd)
+        HDfree(strd);
+    if (strideP)
+        UNPIN_LONG_ARRAY(ENVONLY, stride, strideP, JNI_ABORT);
+    if (cnt)
+        HDfree(cnt);
+    if (countP)
+        UNPIN_LONG_ARRAY(ENVONLY, count, countP, JNI_ABORT);
+    if (strt)
+        HDfree(strt);
+    if (startP)
+        UNPIN_LONG_ARRAY(ENVONLY, start, startP, JNI_ABORT);
+
+    return (jlong)sid;
+} /* end Java_hdf_hdf5lib_H5_H5Sselect_1hyperslab */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Smodify_select
+ * Signature: (JIJ)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Smodify_1select(JNIEnv *env, jclass clss, jlong space1_id, jint op, jlong space2_id)
+{
+    hssize_t retVal = -1;
+
+    UNUSED(clss);
+
+    if ((retVal = H5Smodify_select((hid_t)space1_id, (H5S_seloper_t)op, (hid_t)space2_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return;
+} /* end Java_hdf_hdf5lib_H5_H5Smodify_1select */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Scombine_select
+ * Signature: (JIJ)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5Scombine_1select(JNIEnv *env, jclass clss, jlong space1_id, jint op, jlong space2_id)
+{
+    hid_t sid = H5I_INVALID_HID;
+
+    UNUSED(clss);
+
+    if ((sid = H5Scombine_select((hid_t)space1_id, (H5S_seloper_t)op, (hid_t)space2_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+
+    return (jlong)sid;
+} /* end Java_hdf_hdf5lib_H5_H5Scombine_1select */
+
 #ifdef __cplusplus
 } /* end extern "C" */
 #endif /* __cplusplus */
diff --git a/java/src/jni/h5sImp.h b/java/src/jni/h5sImp.h
index ee28b39..83255c1 100644
--- a/java/src/jni/h5sImp.h
+++ b/java/src/jni/h5sImp.h
@@ -259,6 +259,65 @@ JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5Sis_1regular_1hyperslab(JNIEnv
 JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Sget_1regular_1hyperslab(JNIEnv *, jclass, jlong, jlongArray,
                                                                       jlongArray, jlongArray, jlongArray);
 
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Sselect_copy
+ * Signature: (JJ)V
+ */
+JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Sselect_1copy(JNIEnv *, jclass, jlong, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Sselect_shape_same
+ * Signature: (JJ)Z
+ */
+JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5Sselect_1shape_1same(JNIEnv *, jclass, jlong, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Sselect_adjust
+ * Signature: (J[J)V
+ */
+JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Sselect_1adjust(JNIEnv *, jclass, jlong, jlongArray);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Sselect_intersect_block
+ * Signature: (J[J[J)Z
+ */
+JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5Sselect_1intersect_1block(JNIEnv *, jclass, jlong,
+                                                                           jlongArray, jlongArray);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Sselect_project_intersection
+ * Signature: (JJJ)J
+ */
+JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Sselect_1project_1intersection(JNIEnv *, jclass, jlong, jlong,
+                                                                             jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Scombine_hyperslab
+ * Signature: (JI[J[J[J[J)J
+ */
+JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Scombine_1hyperslab(JNIEnv *, jclass, jlong, jint, jlongArray,
+                                                                  jlongArray, jlongArray, jlongArray);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Smodify_select
+ * Signature: (JIJ)V
+ */
+JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Smodify_1select(JNIEnv *, jclass, jlong, jint, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Scombine_select
+ * Signature: (JIJ)J
+ */
+JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Scombine_1select(JNIEnv *, jclass, jlong, jint, jlong);
+
 #ifdef __cplusplus
 } /* end extern "C" */
 #endif /* __cplusplus */
diff --git a/java/test/TestH5Sbasic.java b/java/test/TestH5Sbasic.java
index 2173647..9874584 100644
--- a/java/test/TestH5Sbasic.java
+++ b/java/test/TestH5Sbasic.java
@@ -242,4 +242,142 @@ public class TestH5Sbasic {
         H5.H5Sdecode(null);
     }
 
+    @Test(expected = IllegalArgumentException.class)
+    public void testH5Sget_regular_hyperslab_invalid() throws Throwable {
+        long q_start[] = new long[2];
+        long q_stride[] = new long[2];
+        long q_count[] = new long[2];
+        long q_block[] = new long[2];
+
+        H5.H5Sget_regular_hyperslab(-1, q_start, q_stride, q_count, q_block);
+    }
+
+    @Test(expected = hdf.hdf5lib.exceptions.HDF5FunctionArgumentException.class)
+    public void testH5Sselect_copy_invalid() throws Throwable {
+        H5.H5Sselect_copy(-1, -1);
+    }
+
+    @Test(expected = hdf.hdf5lib.exceptions.HDF5DataspaceInterfaceException.class)
+    public void testH5Sselect_shape_same_invalid() throws Throwable {
+        H5.H5Sselect_shape_same(-1, -1);
+    }
+
+    @Test(expected = IllegalArgumentException.class)
+    public void testH5Sselect_adjust_invalid() throws Throwable {
+        long offset[][] = {{0,1},{2,4},{5,6}};
+        H5.H5Sselect_adjust(-1, offset);
+    }
+
+    @Test(expected = IllegalArgumentException.class)
+    public void testH5Sselect_adjust_rank_offset() throws Throwable {
+        long sid = -1;
+        long offset[][] = {{0,1},{2,4},{5,6}};
+
+        try {
+            sid = H5.H5Screate(HDF5Constants.H5S_SIMPLE);
+            assertTrue("H5.H5Screate_simple_extent",sid > 0);
+            H5.H5Sselect_adjust(sid, offset);
+        }
+        finally {
+            try {H5.H5Sclose(sid);} catch (Exception ex) {}
+        }
+    }
+
+    @Test(expected = IllegalArgumentException.class)
+    public void testH5Sselect_intersect_block_invalid() throws Throwable {
+        long start[] = new long[2];
+        long end[] = new long[2];
+        H5.H5Sselect_intersect_block(-1, start, end);
+    }
+
+    @Test(expected = IllegalArgumentException.class)
+    public void testH5Sselect_intersect_block_rank_start() throws Throwable {
+        long sid = -1;
+        long start[] = new long[2];
+        long end[] = null;
+
+        try {
+            sid = H5.H5Screate(HDF5Constants.H5S_SIMPLE);
+            assertTrue("H5.H5Screate_simple_extent",sid > 0);
+            H5.H5Sselect_intersect_block(sid, start, end);
+        }
+        finally {
+            try {H5.H5Sclose(sid);} catch (Exception ex) {}
+        }
+    }
+
+    @Test(expected = IllegalArgumentException.class)
+    public void testH5Sselect_intersect_block_rank_end() throws Throwable {
+        long sid = -1;
+        long start[] = null;
+        long end[] = new long[2];
+
+        try {
+            sid = H5.H5Screate(HDF5Constants.H5S_SIMPLE);
+            assertTrue("H5.H5Screate_simple_extent",sid > 0);
+            H5.H5Sselect_intersect_block(sid, start, end);
+        }
+        finally {
+            try {H5.H5Sclose(sid);} catch (Exception ex) {}
+        }
+    }
+
+    @Test(expected = hdf.hdf5lib.exceptions.HDF5DataspaceInterfaceException.class)
+    public void testH5Sselect_project_intersection_invalid() throws Throwable {
+        H5.H5Sselect_project_intersection(-1, -1, -1);
+    }
+
+    @Test(expected = hdf.hdf5lib.exceptions.HDF5FunctionArgumentException.class)
+    public void testH5Scombine_hyperslab_invalid() throws Throwable {
+        long start[] = new long[2];
+        long count[] = new long[2];
+        H5.H5Scombine_hyperslab(-1, 0, start, null, count, null);
+    }
+
+    @Test(expected = NullPointerException.class)
+    public void testH5Scombine_hyperslab_null_start() throws Throwable {
+        long sid = -1;
+        long start[] = null;
+        long stride[] = null;
+        long count[] = new long[2];
+        long block[] = null;
+
+        try {
+            sid = H5.H5Screate(HDF5Constants.H5S_SIMPLE);
+            assertTrue("H5.H5Screate_simple_extent",sid > 0);
+            H5.H5Scombine_hyperslab(sid, 0, start, stride, count, block);
+        }
+        finally {
+            try {H5.H5Sclose(sid);} catch (Exception ex) {}
+        }
+    }
+
+    @Test(expected = NullPointerException.class)
+    public void testH5Scombine_hyperslab_null_count() throws Throwable {
+        long sid = -1;
+        long start[] = new long[2];
+        long stride[] = null;
+        long count[] = null;
+        long block[] = null;
+
+        try {
+            sid = H5.H5Screate(HDF5Constants.H5S_SIMPLE);
+            assertTrue("H5.H5Screate_simple_extent",sid > 0);
+            H5.H5Scombine_hyperslab(sid, 0, start, stride, count, block);
+        }
+        finally {
+            try {H5.H5Sclose(sid);} catch (Exception ex) {}
+        }
+    }
+
+    @Test(expected = hdf.hdf5lib.exceptions.HDF5FunctionArgumentException.class)
+    public void testH5Smodify_select_invalid() throws Throwable {
+        H5.H5Smodify_select(-1, 0, -1);
+    }
+
+    @Test(expected = hdf.hdf5lib.exceptions.HDF5FunctionArgumentException.class)
+    public void testH5Scombine_select_invalid() throws Throwable {
+        H5.H5Scombine_select(-1, 0, -1);
+    }
+
 }
diff --git a/java/test/testfiles/JUnit-TestH5Sbasic.txt b/java/test/testfiles/JUnit-TestH5Sbasic.txt
index 707878e..3422442 100644
--- a/java/test/testfiles/JUnit-TestH5Sbasic.txt
+++ b/java/test/testfiles/JUnit-TestH5Sbasic.txt
@@ -5,18 +5,32 @@ JUnit version 4.11
 .testH5Sdecode_null
 .testH5Screate_simple_dims_exceed
 .testH5Screate_simple_unlimted_1d
+.testH5Sselect_intersect_block_rank_start
+.testH5Sget_regular_hyperslab_invalid
+.testH5Sselect_adjust_rank_offset
 .testH5Screate_simple_dims_invalid
 .testH5Screate_scalar
 .testH5Screate_simple
+.testH5Sselect_project_intersection_invalid
 .testH5Screate_simple_rank_invalid
 .testH5Sget_simple_extent_type_invalid
+.testH5Scombine_hyperslab_invalid
+.testH5Scombine_hyperslab_null_count
+.testH5Scombine_hyperslab_null_start
 .testH5Sencode_invalid
 .testH5Screate_null
 .testH5Screate_simple_extent
 .testH5Screate_invalid
+.testH5Sselect_intersect_block_invalid
+.testH5Sselect_adjust_invalid
 .testH5Screate_simple_unlimted
+.testH5Sselect_shape_same_invalid
+.testH5Smodify_select_invalid
+.testH5Scombine_select_invalid
+.testH5Sselect_copy_invalid
+.testH5Sselect_intersect_block_rank_end
 
 Time:  XXXX
 
-OK (16 tests)
+OK (30 tests)
 
-- 
cgit v0.12


From e5f792cf12cd246fbf7d9f54e6675738d7c5ccd5 Mon Sep 17 00:00:00 2001
From: Binh-Minh Ribler 
Date: Tue, 27 Oct 2020 22:18:52 -0500
Subject: Added test for the fix HDFFV-10590

---
 tools/test/h5repack/h5repack.sh.in                 |  32 +++++++++++++++++++++
 .../testfiles/HDFFV-10590_CVE-2018-17432.h5        | Bin 0 -> 7648 bytes
 2 files changed, 32 insertions(+)
 create mode 100644 tools/test/h5repack/testfiles/HDFFV-10590_CVE-2018-17432.h5

diff --git a/tools/test/h5repack/h5repack.sh.in b/tools/test/h5repack/h5repack.sh.in
index a95a22e..a3676af 100644
--- a/tools/test/h5repack/h5repack.sh.in
+++ b/tools/test/h5repack/h5repack.sh.in
@@ -865,6 +865,34 @@ TOOLTESTV()
    rm -f $outfile
 }
 
+# Same as TOOLTEST, but expects h5repack fails
+#
+TOOLTEST_FAIL()
+{
+    infile=$1
+    outfile=$2
+    expect="$TESTDIR/$2-$1.ddl"
+    actual="$TESTDIR/$2-$1.out"
+    actual_err="$TESTDIR/$2-$1.err"
+    shift
+    shift
+
+    # Run test.
+    TESTING $H5REPACK $@
+    (
+        cd $TESTDIR
+        $ENVCMD $RUNSERIAL $H5REPACK_BIN "$@" $infile $outfile
+    ) >$actual
+    RET=$?
+    if [ $RET == 0 ] ; then
+        nerrors="`expr $nerrors + 1`"
+        echo " FAILED"
+    else
+        echo " PASSED"
+    fi
+    rm -f $outfile
+}
+
 # This is same as TOOLTESTV() with comparing display output
 # with actual filename swapped
 #
@@ -1681,6 +1709,10 @@ TOOLTEST HDFFV-5932 h5repack_attr_refs.h5
 # Note: this test is experimental for sharing test file among tools
 TOOLTEST HDFFV-7840 h5diff_attr1.h5
 
+# test HDFFV-10590
+arg="HDFFV-10590_CVE-2018-17432.h5 HDFFV-10590_CVE-2018-17432_out.h5 --low=1 --high=2 -f GZIP=8 -l dset1:CHUNK=5x6"
+TOOLTEST_FAIL $arg
+
 # tests for metadata block size option
 TOOLTEST_META meta_short h5repack_layout.h5 -M 8192
 TOOLTEST_META meta_long h5repack_layout.h5 --metadata_block_size=8192
diff --git a/tools/test/h5repack/testfiles/HDFFV-10590_CVE-2018-17432.h5 b/tools/test/h5repack/testfiles/HDFFV-10590_CVE-2018-17432.h5
new file mode 100644
index 0000000..7a815ba
Binary files /dev/null and b/tools/test/h5repack/testfiles/HDFFV-10590_CVE-2018-17432.h5 differ
-- 
cgit v0.12


From ba00760d7a078c25bfc2108060320e7d96ffdd4e Mon Sep 17 00:00:00 2001
From: Allen Byrne 
Date: Wed, 28 Oct 2020 07:06:01 -0500
Subject: HDFFV-10868 - add note

---
 release_docs/RELEASE.txt | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 1c5d96d..e3a1dd4 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -717,6 +717,15 @@ New Features
 
     Java Library:
     ----------------
+    - Added new H5S functions.
+
+      H5Sselect_copy, H5Sselect_shape_same, H5Sselect_adjust,
+      H5Sselect_intersect_block, H5Sselect_project_intersection,
+      H5Scombine_hyperslab, H5Smodify_select, H5Scombine_select
+      wrapper functions added.
+
+      (ADB - 2020/10/27, HDFFV-10868)
+
     - Added ability to test java library with VOLs.
 
       Created new CMake script that combines the java and vol test scripts.
-- 
cgit v0.12


From 2266ee56c38685910e9cb7517307448bc8f68a23 Mon Sep 17 00:00:00 2001
From: Dana Robinson 
Date: Wed, 28 Oct 2020 15:34:51 -0700
Subject: Fixes minor issues in various virtual file drivers

- HDFS VFD files now ignored in the Autotools when the HDFS VFD is not
  being built.
- All VFD init code uses idiomatic H5I_INVALID_HID instead of -1
  or FAIL.
- The HDFS VFD now includes H5FDdrvr_module.h in the right place.
- The HDFS tests in test/hdfs.c no longer pass NULL to VERIFY macros, which
  raised warnings.
- Minor tweaks to fix const, unused variables, etc. warnings in
  several VFDs.
---
 configure.ac       |  3 +++
 src/H5FDdirect.c   | 14 +++++++-------
 src/H5FDdirect.h   |  2 +-
 src/H5FDhdfs.c     |  8 ++++----
 src/H5FDhdfs.h     |  2 +-
 src/H5FDmirror.c   |  2 +-
 src/H5FDmpio.c     | 29 -----------------------------
 src/H5FDmpio.h     |  2 +-
 src/H5FDros3.c     |  3 +--
 src/H5FDsplitter.c |  2 +-
 src/Makefile.am    |  9 +++++++--
 test/hdfs.c        | 14 +++++++-------
 test/vfd.c         |  2 --
 13 files changed, 34 insertions(+), 58 deletions(-)

diff --git a/configure.ac b/configure.ac
index e7a65ce..3dbf73b 100644
--- a/configure.ac
+++ b/configure.ac
@@ -3124,6 +3124,9 @@ if test "x$HAVE_LIBHDFS" = "xyes"; then
             [Proceed to build with libhdfs])
 fi
 
+## Read-only HDFS files are not built if not required.
+AM_CONDITIONAL([HDFS_VFD_CONDITIONAL], [test "X$HAVE_LIBHDFS" = "Xyes"])
+
 ## Checkpoint the cache
 AC_CACHE_SAVE
 
diff --git a/src/H5FDdirect.c b/src/H5FDdirect.c
index ac7720f..4c2d251 100644
--- a/src/H5FDdirect.c
+++ b/src/H5FDdirect.c
@@ -384,14 +384,13 @@ static void *
 H5FD__direct_fapl_get(H5FD_t *_file)
 {
     H5FD_direct_t *file = (H5FD_direct_t *)_file;
-    void *         ret_value; /* Return value */
+    void          *ret_value = NULL; /* Return value */
 
-    FUNC_ENTER_STATIC
+    FUNC_ENTER_STATIC_NOERR
 
     /* Set return value */
     ret_value = H5FD__direct_fapl_copy(&(file->fa));
 
-done:
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5FD__direct_fapl_get() */
 
@@ -447,7 +446,7 @@ H5FD__direct_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxad
     int                 o_flags;
     int                 fd   = (-1);
     H5FD_direct_t *     file = NULL;
-    H5FD_direct_fapl_t *fa;
+    const H5FD_direct_fapl_t *fa;
 #ifdef H5_HAVE_WIN32_API
     HFILE                              filehandle;
     struct _BY_HANDLE_FILE_INFORMATION fileinfo;
@@ -496,7 +495,7 @@ H5FD__direct_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxad
     /* Get the driver specific information */
     if (NULL == (plist = H5P_object_verify(fapl_id, H5P_FILE_ACCESS)))
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a file access property list")
-    if (NULL == (fa = (H5FD_direct_fapl_t *)H5P_peek_driver_info(plist)))
+    if (NULL == (fa = (const H5FD_direct_fapl_t *)H5P_peek_driver_info(plist)))
         HGOTO_ERROR(H5E_PLIST, H5E_BADVALUE, NULL, "bad VFL driver info")
 
     file->fd = fd;
@@ -546,7 +545,8 @@ H5FD__direct_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxad
         }
         else {
             file->fa.must_align = FALSE;
-            HDftruncate(file->fd, (HDoff_t)0);
+            if (-1 == HDftruncate(file->fd, (HDoff_t)0))
+                HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, NULL, "unable to truncate file")
         }
     }
     else {
@@ -793,7 +793,7 @@ H5FD__direct_get_eof(const H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type)
 {
     const H5FD_direct_t *file = (const H5FD_direct_t *)_file;
 
-    FUNC_ENTER_STATIC
+    FUNC_ENTER_STATIC_NOERR
 
     FUNC_LEAVE_NOAPI(file->eof)
 }
diff --git a/src/H5FDdirect.h b/src/H5FDdirect.h
index 2d88a69..ea2b3f2 100644
--- a/src/H5FDdirect.h
+++ b/src/H5FDdirect.h
@@ -23,7 +23,7 @@
 #ifdef H5_HAVE_DIRECT
 #define H5FD_DIRECT (H5FD_direct_init())
 #else
-#define H5FD_DIRECT (-1)
+#define H5FD_DIRECT (H5I_INVALID_HID)
 #endif /* H5_HAVE_DIRECT */
 
 #ifdef H5_HAVE_DIRECT
diff --git a/src/H5FDhdfs.c b/src/H5FDhdfs.c
index a7c6aae..b4aecfd 100644
--- a/src/H5FDhdfs.c
+++ b/src/H5FDhdfs.c
@@ -20,6 +20,9 @@
  *             File System (HDFS).
  */
 
+/* This source code file is part of the H5FD driver module */
+#include "H5FDdrvr_module.h"
+
 #include "H5private.h"   /* Generic Functions        */
 #include "H5Eprivate.h"  /* Error handling           */
 #include "H5FDprivate.h" /* File drivers             */
@@ -30,9 +33,6 @@
 
 #ifdef H5_HAVE_LIBHDFS
 
-/* This source code file is part of the H5FD driver module */
-#include "H5FDdrvr_module.h"
-
 /* HDFS routines */
 #include "hdfs.h"
 
@@ -356,7 +356,7 @@ done:
 hid_t
 H5FD_hdfs_init(void)
 {
-    hid_t ret_value = H5I_INVALID_HID; /* Return value */
+    hid_t ret_value = H5I_INVALID_HID;
 #if HDFS_STATS
     unsigned int bin_i;
 #endif
diff --git a/src/H5FDhdfs.h b/src/H5FDhdfs.h
index 9d14e9a..abe7682 100644
--- a/src/H5FDhdfs.h
+++ b/src/H5FDhdfs.h
@@ -25,7 +25,7 @@
 #ifdef H5_HAVE_LIBHDFS
 #define H5FD_HDFS (H5FD_hdfs_init())
 #else /* H5_HAVE_LIBHDFS */
-#define H5FD_HDFS (-1)
+#define H5FD_HDFS (H5I_INVALID_HID)
 #endif /* H5_HAVE_LIBHDFS */
 
 #ifdef H5_HAVE_LIBHDFS
diff --git a/src/H5FDmirror.c b/src/H5FDmirror.c
index 3895b42..8f1d25c 100644
--- a/src/H5FDmirror.c
+++ b/src/H5FDmirror.c
@@ -242,7 +242,7 @@ H5FD_mirror_init(void)
 {
     hid_t ret_value = H5I_INVALID_HID;
 
-    FUNC_ENTER_NOAPI(FAIL)
+    FUNC_ENTER_NOAPI(H5I_INVALID_HID)
 
     LOG_OP_CALL(FUNC);
 
diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c
index 6042776..c16e01e 100644
--- a/src/H5FDmpio.c
+++ b/src/H5FDmpio.c
@@ -1746,33 +1746,4 @@ H5FD__mpio_communicator(const H5FD_t *_file)
     FUNC_LEAVE_NOAPI(file->comm)
 } /* end H5FD__mpio_communicator() */
 
-/*-------------------------------------------------------------------------
- * Function:       H5FD__mpio_get_info
- *
- * Purpose:        Returns the file info of MPIO file driver.
- *
- * Returns:        Non-negative if succeed or negative if fails.
- *
- * Programmer:     John Mainzer
- *                 April 4, 2017
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5FD__mpio_get_info(H5FD_t *_file, void **mpi_info)
-{
-    H5FD_mpio_t *file      = (H5FD_mpio_t *)_file;
-    herr_t       ret_value = SUCCEED;
-
-    FUNC_ENTER_STATIC
-
-    if (!mpi_info)
-        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "mpi info not valid")
-
-    *mpi_info = &(file->info);
-
-done:
-    FUNC_LEAVE_NOAPI(ret_value)
-} /* H5FD__mpio_get_info() */
-
 #endif /* H5_HAVE_PARALLEL */
diff --git a/src/H5FDmpio.h b/src/H5FDmpio.h
index c9280c7..0773d9e 100644
--- a/src/H5FDmpio.h
+++ b/src/H5FDmpio.h
@@ -25,7 +25,7 @@
 #ifdef H5_HAVE_PARALLEL
 #define H5FD_MPIO (H5FD_mpio_init())
 #else
-#define H5FD_MPIO (-1)
+#define H5FD_MPIO (H5I_INVALID_HID)
 #endif /* H5_HAVE_PARALLEL */
 
 #ifdef H5_HAVE_PARALLEL
diff --git a/src/H5FDros3.c b/src/H5FDros3.c
index fa41b6f..cc27fd0 100644
--- a/src/H5FDros3.c
+++ b/src/H5FDros3.c
@@ -320,7 +320,7 @@ H5FD_ros3_init(void)
     unsigned int bin_i;
 #endif
 
-    FUNC_ENTER_NOAPI(FAIL)
+    FUNC_ENTER_NOAPI(H5I_INVALID_HID)
 
 #if ROS3_DEBUG
     HDfprintf(stdout, "H5FD_ros3_init() called.\n");
@@ -340,7 +340,6 @@ H5FD_ros3_init(void)
     }
 #endif
 
-    /* Set return value */
     ret_value = H5FD_ROS3_g;
 
 done:
diff --git a/src/H5FDsplitter.c b/src/H5FDsplitter.c
index 5ba1a27..698ae7e 100644
--- a/src/H5FDsplitter.c
+++ b/src/H5FDsplitter.c
@@ -210,7 +210,7 @@ H5FD_splitter_init(void)
 {
     hid_t ret_value = H5I_INVALID_HID;
 
-    FUNC_ENTER_NOAPI(FAIL)
+    FUNC_ENTER_NOAPI(H5I_INVALID_HID)
 
     H5FD_SPLITTER_LOG_CALL(FUNC);
 
diff --git a/src/Makefile.am b/src/Makefile.am
index cbecccd..a333220 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -39,7 +39,7 @@ DISTCLEANFILES=H5pubconf.h
 
 # library sources
 libhdf5_la_SOURCES= H5.c H5checksum.c H5dbg.c H5lib_settings.c H5system.c \
-	H5timer.c H5trace.c \
+		H5timer.c H5trace.c \
         H5A.c H5Abtree2.c H5Adense.c H5Adeprec.c H5Aint.c H5Atest.c \
         H5AC.c H5ACdbg.c H5ACproxy_entry.c \
         H5B.c H5Bcache.c H5Bdbg.c \
@@ -61,7 +61,7 @@ libhdf5_la_SOURCES= H5.c H5checksum.c H5dbg.c H5lib_settings.c H5system.c \
         H5Fsuper.c H5Fsuper_cache.c H5Ftest.c \
         H5FA.c H5FAcache.c H5FAdbg.c H5FAdblock.c H5FAdblkpage.c H5FAhdr.c \
         H5FAint.c H5FAstat.c H5FAtest.c \
-        H5FD.c H5FDcore.c H5FDfamily.c H5FDhdfs.c H5FDint.c H5FDlog.c \
+        H5FD.c H5FDcore.c H5FDfamily.c H5FDint.c H5FDlog.c \
         H5FDmulti.c H5FDsec2.c H5FDspace.c \
         H5FDsplitter.c H5FDstdio.c H5FDtest.c \
         H5FL.c H5FO.c H5FS.c H5FScache.c H5FSdbg.c H5FSint.c H5FSsection.c \
@@ -126,6 +126,11 @@ if DIRECT_VFD_CONDITIONAL
     libhdf5_la_SOURCES += H5FDdirect.c
 endif
 
+# Only compile the read-only HDFS VFD if necessary
+if HDFS_VFD_CONDITIONAL
+    libhdf5_la_SOURCES += H5FDhdfs.c
+endif
+
 # Only compile the mirror VFD if necessary
 if MIRROR_VFD_CONDITIONAL
     libhdf5_la_SOURCES += H5FDmirror.c
diff --git a/test/hdfs.c b/test/hdfs.c
index 701df47..a59cdb6 100644
--- a/test/hdfs.c
+++ b/test/hdfs.c
@@ -564,9 +564,9 @@ test_fapl_config_validation(void)
             JSVERIFY(config.version, fa_fetch.version, "version number mismatch")
             JSVERIFY(config.namenode_port, fa_fetch.namenode_port, "namenode port mismatch")
             JSVERIFY(config.stream_buffer_size, fa_fetch.stream_buffer_size, "streambuffer size mismatch")
-            JSVERIFY_STR(config.namenode_name, fa_fetch.namenode_name, NULL)
-            JSVERIFY_STR(config.user_name, fa_fetch.user_name, NULL)
-            JSVERIFY_STR(config.kerberos_ticket_cache, fa_fetch.kerberos_ticket_cache, NULL)
+            JSVERIFY_STR(config.namenode_name, fa_fetch.namenode_name, "node name mismatch")
+            JSVERIFY_STR(config.user_name, fa_fetch.user_name, "user name mismatch")
+            JSVERIFY_STR(config.kerberos_ticket_cache, fa_fetch.kerberos_ticket_cache, "kerberos ticket cache mismatch")
         }
 
         /*-----------------------------
@@ -996,7 +996,7 @@ test_eof_eoa(void)
 
     /* verify as found
      */
-    JSVERIFY(5458199, H5FDget_eof(fd_shakespeare, H5FD_MEM_DEFAULT), NULL)
+    JSVERIFY(5458199, H5FDget_eof(fd_shakespeare, H5FD_MEM_DEFAULT), "EOF mismatch")
     JSVERIFY(H5FDget_eof(fd_shakespeare, H5FD_MEM_DEFAULT), H5FDget_eof(fd_shakespeare, H5FD_MEM_DRAW),
              "mismatch between DEFAULT and RAW memory types")
     JSVERIFY(0, H5FDget_eoa(fd_shakespeare, H5FD_MEM_DEFAULT), "EoA should be unset by H5FDopen")
@@ -1272,7 +1272,7 @@ test_read(void)
                           HADDR_UNDEF); /* Demonstrate success with "automatic" value */
     FAIL_IF(NULL == file_raven)
 
-    JSVERIFY(6464, H5FDget_eof(file_raven, H5FD_MEM_DEFAULT), NULL)
+    JSVERIFY(6464, H5FDget_eof(file_raven, H5FD_MEM_DEFAULT), "EOF mismatch")
 
     /*********
      * TESTS *
@@ -1432,8 +1432,8 @@ test_noops_and_autofails(void)
     /* no-op calls to `lock()` and `unlock()`
      */
     JSVERIFY(SUCCEED, H5FDlock(file, TRUE), "lock always succeeds; has no effect")
-    JSVERIFY(SUCCEED, H5FDlock(file, FALSE), NULL)
-    JSVERIFY(SUCCEED, H5FDunlock(file), NULL)
+    JSVERIFY(SUCCEED, H5FDlock(file, FALSE), "lock issue")
+    JSVERIFY(SUCCEED, H5FDunlock(file), "unlock issue")
     /* Lock/unlock with null file or similar error crashes tests.
      * HDassert in calling heirarchy, `H5FD[un]lock()` and `H5FD_[un]lock()`
      */
diff --git a/test/vfd.c b/test/vfd.c
index ae4921c..4ba0422 100644
--- a/test/vfd.c
+++ b/test/vfd.c
@@ -2168,8 +2168,6 @@ test_ros3(void)
     hid_t            driver_id    = -1;     /* ID for this VFD              */
     unsigned long    driver_flags = 0;      /* VFD feature flags            */
     char             filename[1024];        /* filename                     */
-    void *           os_file_handle = NULL; /* OS file handle               */
-    hsize_t          file_size;             /* file size                    */
     H5FD_ros3_fapl_t test_ros3_fa;
     H5FD_ros3_fapl_t ros3_fa_0 = {
         /* version      = */ H5FD_CURR_ROS3_FAPL_T_VERSION,
-- 
cgit v0.12


From a4cbd51db61868d6190d7c10764b0c9e9666b6ee Mon Sep 17 00:00:00 2001
From: Allen Byrne 
Date: Thu, 29 Oct 2020 13:14:51 -0500
Subject: HDFFV-10868 Corrections from review

---
 java/src/hdf/hdf5lib/H5.java |  2 +-
 java/src/jni/h5sImp.c        | 42 +++++++++++++++++++++---------------------
 2 files changed, 22 insertions(+), 22 deletions(-)

diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index 6ad7cf2..1f6d0dc 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -5370,7 +5370,6 @@ public class H5 implements java.io.Serializable {
      **/
     public synchronized static native long H5Iget_file_id(long obj_id) throws HDF5LibraryException;
 
-
     /**
      * H5Iget_name_long retrieves the name of an object specified by the identifier, obj_id.
      * @deprecated
@@ -5387,6 +5386,7 @@ public class H5 implements java.io.Serializable {
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
+    @Deprecated
     public synchronized static native long H5Iget_name_long(long obj_id, String[] name, long size)
             throws HDF5LibraryException, NullPointerException;
     /**
diff --git a/java/src/jni/h5sImp.c b/java/src/jni/h5sImp.c
index e29c2ec..f7b65d9 100644
--- a/java/src/jni/h5sImp.c
+++ b/java/src/jni/h5sImp.c
@@ -1348,11 +1348,11 @@ done:
 JNIEXPORT void JNICALL
 Java_hdf_hdf5lib_H5_H5Sselect_1copy(JNIEnv *env, jclass clss, jlong dst_id, jlong src_id)
 {
-    hssize_t retVal = -1;
+    herr_t    status = FAIL;
 
     UNUSED(clss);
 
-    if ((retVal = H5Sselect_copy((hid_t)dst_id, (hid_t)src_id)) < 0)
+    if ((status = H5Sselect_copy((hid_t)dst_id, (hid_t)src_id)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
 done:
@@ -1567,26 +1567,26 @@ Java_hdf_hdf5lib_H5_H5Scombine_1hyperslab(JNIEnv *env, jclass clss, jlong space_
     UNUSED(clss);
 
     if (NULL == start)
-        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Sselect_hyperslab: start is NULL");
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: start is NULL");
     if (NULL == count)
-        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Sselect_hyperslab: count is NULL");
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: count is NULL");
 
     if ((start_rank = ENVPTR->GetArrayLength(ENVONLY, start)) < 0) {
         CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
-        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_hyperslab: start array length < 0");
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: start array length < 0");
     }
     if ((count_rank = ENVPTR->GetArrayLength(ENVONLY, count)) < 0) {
         CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
-        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_hyperslab: count array length < 0");
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: count array length < 0");
     }
 
     if (start_rank != count_rank)
-        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_hyperslab: count and start have different rank!");
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: count and start have different rank!");
 
-    PIN_LONG_ARRAY(ENVONLY, start, startP, &isCopy, "H5Sselect_hyperslab: start not pinned");
+    PIN_LONG_ARRAY(ENVONLY, start, startP, &isCopy, "H5Scombine_hyperslab: start not pinned");
 
     if (NULL == (strt = lp = (hsize_t *)HDmalloc((size_t)start_rank * sizeof(hsize_t))))
-        H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_hyperslab: failed to allocate start buffer");
+        H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Scombine_hyperslab: failed to allocate start buffer");
 
     jlp = (jlong *)startP;
     for (i = 0; i < start_rank; i++) {
@@ -1595,10 +1595,10 @@ Java_hdf_hdf5lib_H5_H5Scombine_1hyperslab(JNIEnv *env, jclass clss, jlong space_
         jlp++;
     } /* end if */
 
-    PIN_LONG_ARRAY(ENVONLY, count, countP, &isCopy, "H5Sselect_hyperslab: count not pinned");
+    PIN_LONG_ARRAY(ENVONLY, count, countP, &isCopy, "H5Scombine_hyperslab: count not pinned");
 
     if (NULL == (cnt = lp = (hsize_t *)HDmalloc((size_t)count_rank * sizeof(hsize_t))))
-        H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_hyperslab: failed to allocate count buffer");
+        H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Scombine_hyperslab: failed to allocate count buffer");
 
     jlp = (jlong *)countP;
     for (i = 0; i < count_rank; i++) {
@@ -1614,16 +1614,16 @@ Java_hdf_hdf5lib_H5_H5Scombine_1hyperslab(JNIEnv *env, jclass clss, jlong space_
     else {
         if ((stride_rank = ENVPTR->GetArrayLength(ENVONLY, stride)) < 0) {
             CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
-            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_hyperslab: stride array length < 0");
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: stride array length < 0");
         }
 
         if (stride_rank != start_rank)
-            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_hyperslab: stride and start have different rank!");
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: stride and start have different rank!");
 
-        PIN_LONG_ARRAY(ENVONLY, stride, strideP, &isCopy, "H5Sselect_hyperslab: stride not pinned");
+        PIN_LONG_ARRAY(ENVONLY, stride, strideP, &isCopy, "H5Scombine_hyperslab: stride not pinned");
 
         if (NULL == (strd = lp = (hsize_t *)HDmalloc((size_t)stride_rank * sizeof(hsize_t))))
-            H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_hyperslab: failed to allocate stride buffer");
+            H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Scombine_hyperslab: failed to allocate stride buffer");
 
         jlp = (jlong *)strideP;
         for (i = 0; i < stride_rank; i++) {
@@ -1640,16 +1640,16 @@ Java_hdf_hdf5lib_H5_H5Scombine_1hyperslab(JNIEnv *env, jclass clss, jlong space_
     else {
         if ((block_rank = ENVPTR->GetArrayLength(ENVONLY, block)) < 0) {
             CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
-            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_hyperslab: block array length < 0");
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: block array length < 0");
         }
 
         if (block_rank != start_rank)
-            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_hyperslab: block and start have different rank!");
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: block and start have different rank!");
 
-        PIN_LONG_ARRAY(ENVONLY, block, blockP, &isCopy, "H5Sselect_hyperslab: block not pinned");
+        PIN_LONG_ARRAY(ENVONLY, block, blockP, &isCopy, "H5Scombine_hyperslab: block not pinned");
 
         if (NULL == (blk = lp = (hsize_t *)HDmalloc((size_t)block_rank * sizeof(hsize_t))))
-            H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_hyperslab: failed to allocate block buffer");
+            H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Scombine_hyperslab: failed to allocate block buffer");
 
         jlp = (jlong *)blockP;
         for (i = 0; i < block_rank; i++) {
@@ -1692,11 +1692,11 @@ done:
 JNIEXPORT void JNICALL
 Java_hdf_hdf5lib_H5_H5Smodify_1select(JNIEnv *env, jclass clss, jlong space1_id, jint op, jlong space2_id)
 {
-    hssize_t retVal = -1;
+    herr_t    status = FAIL;
 
     UNUSED(clss);
 
-    if ((retVal = H5Smodify_select((hid_t)space1_id, (H5S_seloper_t)op, (hid_t)space2_id)) < 0)
+    if ((status = H5Smodify_select((hid_t)space1_id, (H5S_seloper_t)op, (hid_t)space2_id)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
 done:
-- 
cgit v0.12


From 1e93bbc183fcaebb451a39ff4c489b83f66694cd Mon Sep 17 00:00:00 2001
From: Dana Robinson 
Date: Thu, 29 Oct 2020 16:28:38 -0700
Subject: Fixes a bit shift issue in an MPI constant

Redefines TWO_GIG_LIMIT to be INT32_MAX instead of 1 << 31, which
fixes an issue revealed by compiling with -Wshift-overflow.
---
 src/H5mpi.c | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/src/H5mpi.c b/src/H5mpi.c
index c1f9132..613a4bf 100644
--- a/src/H5mpi.c
+++ b/src/H5mpi.c
@@ -25,7 +25,7 @@
 /****************/
 /* Local Macros */
 /****************/
-#define TWO_GIG_LIMIT (1 << 31)
+#define TWO_GIG_LIMIT INT32_MAX
 #ifndef H5_MAX_MPI_COUNT
 #define H5_MAX_MPI_COUNT (1 << 30)
 #endif
@@ -33,7 +33,7 @@
 /*******************/
 /* Local Variables */
 /*******************/
-static hsize_t bigio_count = H5_MAX_MPI_COUNT;
+static hsize_t bigio_count_g = H5_MAX_MPI_COUNT;
 
 /*-------------------------------------------------------------------------
  * Function:  H5_mpi_set_bigio_count
@@ -42,7 +42,7 @@ static hsize_t bigio_count = H5_MAX_MPI_COUNT;
  *            when we utilize derived datatypes.  This is of
  *            particular interest for allowing nightly testing
  *
- * Return:    The current/previous value of bigio_count.
+ * Return:    The current/previous value of bigio_count_g.
  *
  * Programmer: Richard Warren,  March 10, 2017
  *
@@ -51,10 +51,10 @@ static hsize_t bigio_count = H5_MAX_MPI_COUNT;
 hsize_t
 H5_mpi_set_bigio_count(hsize_t new_count)
 {
-    hsize_t orig_count = bigio_count;
+    hsize_t orig_count = bigio_count_g;
 
     if ((new_count > 0) && (new_count < (hsize_t)TWO_GIG_LIMIT)) {
-        bigio_count = new_count;
+        bigio_count_g = new_count;
     }
     return orig_count;
 } /* end H5_mpi_set_bigio_count() */
@@ -63,9 +63,9 @@ H5_mpi_set_bigio_count(hsize_t new_count)
  * Function:  H5_mpi_get_bigio_count
  *
  * Purpose:   Allow other HDF5 library functions to access
- *            the current value for bigio_count.
+ *            the current value for bigio_count_g.
  *
- * Return:    The current/previous value of bigio_count.
+ * Return:    The current/previous value of bigio_count_g.
  *
  * Programmer: Richard Warren,  October 7, 2019
  *
@@ -74,7 +74,7 @@ H5_mpi_set_bigio_count(hsize_t new_count)
 hsize_t
 H5_mpi_get_bigio_count(void)
 {
-    return bigio_count;
+    return bigio_count_g;
 }
 
 /*-------------------------------------------------------------------------
@@ -471,8 +471,8 @@ H5_mpio_create_large_type(hsize_t num_elements, MPI_Aint stride_bytes, MPI_Datat
     FUNC_ENTER_NOAPI(FAIL)
 
     /* Calculate how many Big MPI datatypes are needed to represent the buffer */
-    num_big_types = (int)(num_elements / bigio_count);
-    leftover      = (hsize_t)num_elements - (hsize_t)num_big_types * bigio_count;
+    num_big_types = (int)(num_elements / bigio_count_g);
+    leftover      = (hsize_t)num_elements - (hsize_t)num_big_types * bigio_count_g;
     H5_CHECKED_ASSIGN(remaining_bytes, int, leftover, hsize_t);
 
     /* Create a contiguous datatype of size equal to the largest
@@ -481,11 +481,11 @@ H5_mpio_create_large_type(hsize_t num_elements, MPI_Aint stride_bytes, MPI_Datat
      * use type_hvector to create the type with the displacement provided
      */
     if (0 == stride_bytes) {
-        if (MPI_SUCCESS != (mpi_code = MPI_Type_contiguous((int)bigio_count, old_type, &inner_type)))
+        if (MPI_SUCCESS != (mpi_code = MPI_Type_contiguous((int)bigio_count_g, old_type, &inner_type)))
             HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code)
     } /* end if */
     else if (MPI_SUCCESS !=
-             (mpi_code = MPI_Type_create_hvector((int)bigio_count, 1, stride_bytes, old_type, &inner_type)))
+             (mpi_code = MPI_Type_create_hvector((int)bigio_count_g, 1, stride_bytes, old_type, &inner_type)))
         HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hvector failed", mpi_code)
 
     /* Create a contiguous datatype of the buffer (minus the remaining < 2GB part)
@@ -510,7 +510,7 @@ H5_mpio_create_large_type(hsize_t num_elements, MPI_Aint stride_bytes, MPI_Datat
                 HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code)
         } /* end if */
         else if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hvector(
-                                     (int)(num_elements - (hsize_t)num_big_types * bigio_count), 1,
+                                     (int)(num_elements - (hsize_t)num_big_types * bigio_count_g), 1,
                                      stride_bytes, old_type, &leftover_type)))
             HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hvector failed", mpi_code)
 
@@ -529,7 +529,7 @@ H5_mpio_create_large_type(hsize_t num_elements, MPI_Aint stride_bytes, MPI_Datat
         block_len[0] = 1;
         block_len[1] = 1;
         disp[0]      = 0;
-        disp[1]      = (old_extent + stride_bytes) * num_big_types * (MPI_Aint)bigio_count;
+        disp[1]      = (old_extent + stride_bytes) * num_big_types * (MPI_Aint)bigio_count_g;
 
         if (MPI_SUCCESS != (mpi_code = MPI_Type_create_struct(2, block_len, disp, type, new_type)))
             HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code)
-- 
cgit v0.12


From 16eab69bcd5219bef52cf9de88d8e1fa7557fc48 Mon Sep 17 00:00:00 2001
From: Dana Robinson 
Date: Thu, 29 Oct 2020 17:17:15 -0700
Subject: Replaces C std library calls with H5MM equivalents

Mostly H5MM_memcpy in newer VFDs
---
 src/H5FDhdfs.c     |  8 ++++----
 src/H5FDmirror.c   | 22 +++++++++++-----------
 src/H5FDros3.c     |  8 ++++----
 src/H5FDs3comms.c  | 30 +++++++++++++++---------------
 src/H5FDsplitter.c |  6 +++---
 src/H5Tref.c       |  4 ++--
 6 files changed, 39 insertions(+), 39 deletions(-)

diff --git a/src/H5FDhdfs.c b/src/H5FDhdfs.c
index b4aecfd..38145d0 100644
--- a/src/H5FDhdfs.c
+++ b/src/H5FDhdfs.c
@@ -674,7 +674,7 @@ H5Pget_fapl_hdfs(hid_t fapl_id, H5FD_hdfs_fapl_t *fa_out)
         HGOTO_ERROR(H5E_PLIST, H5E_BADVALUE, FAIL, "bad VFL driver info")
 
     /* Copy the hdfs fapl data out */
-    HDmemcpy(fa_out, fa, sizeof(H5FD_hdfs_fapl_t));
+    H5MM_memcpy(fa_out, fa, sizeof(H5FD_hdfs_fapl_t));
 
 done:
     FUNC_LEAVE_API(ret_value)
@@ -709,7 +709,7 @@ H5FD__hdfs_fapl_get(H5FD_t *_file)
         HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, NULL, "memory allocation failed")
 
     /* Copy the fields of the structure */
-    HDmemcpy(fa, &(file->fa), sizeof(H5FD_hdfs_fapl_t));
+    H5MM_memcpy(fa, &(file->fa), sizeof(H5FD_hdfs_fapl_t));
 
     ret_value = fa;
 
@@ -747,7 +747,7 @@ H5FD__hdfs_fapl_copy(const void *_old_fa)
     if (new_fa == NULL)
         HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, NULL, "memory allocation failed")
 
-    HDmemcpy(new_fa, old_fa, sizeof(H5FD_hdfs_fapl_t));
+    H5MM_memcpy(new_fa, old_fa, sizeof(H5FD_hdfs_fapl_t));
     ret_value = new_fa;
 
 done:
@@ -904,7 +904,7 @@ H5FD__hdfs_open(const char *path, unsigned flags, hid_t fapl_id, haddr_t maxaddr
     if (file == NULL)
         HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, NULL, "unable to allocate file struct")
     file->hdfs_handle = handle;
-    HDmemcpy(&(file->fa), &fa, sizeof(H5FD_hdfs_fapl_t));
+    H5MM_memcpy(&(file->fa), &fa, sizeof(H5FD_hdfs_fapl_t));
 
 #if HDFS_STATS
     if (FAIL == hdfs__reset_stats(file))
diff --git a/src/H5FDmirror.c b/src/H5FDmirror.c
index 8f1d25c..7ea9609 100644
--- a/src/H5FDmirror.c
+++ b/src/H5FDmirror.c
@@ -298,7 +298,7 @@ H5FD__mirror_xmit_decode_uint16(uint16_t *out, const unsigned char *_buf)
 
     HDassert(_buf && out);
 
-    HDmemcpy(&n, _buf, sizeof(n));
+    H5MM_memcpy(&n, _buf, sizeof(n));
     *out = (uint16_t)HDntohs(n);
 
     return 2; /* number of bytes eaten */
@@ -326,7 +326,7 @@ H5FD__mirror_xmit_decode_uint32(uint32_t *out, const unsigned char *_buf)
 
     HDassert(_buf && out);
 
-    HDmemcpy(&n, _buf, sizeof(n));
+    H5MM_memcpy(&n, _buf, sizeof(n));
     *out = (uint32_t)HDntohl(n);
 
     return 4; /* number of bytes eaten */
@@ -385,7 +385,7 @@ H5FD__mirror_xmit_decode_uint64(uint64_t *out, const unsigned char *_buf)
 
     HDassert(_buf && out);
 
-    HDmemcpy(&n, _buf, sizeof(n));
+    H5MM_memcpy(&n, _buf, sizeof(n));
     if (TRUE == is_host_little_endian())
         *out = BSWAP_64(n);
     else
@@ -412,7 +412,7 @@ H5FD__mirror_xmit_decode_uint8(uint8_t *out, const unsigned char *_buf)
 
     HDassert(_buf && out);
 
-    HDmemcpy(out, _buf, sizeof(uint8_t));
+    H5MM_memcpy(out, _buf, sizeof(uint8_t));
 
     return 1; /* number of bytes eaten */
 } /* end H5FD__mirror_xmit_decode_uint8() */
@@ -439,7 +439,7 @@ H5FD__mirror_xmit_encode_uint16(unsigned char *_dest, uint16_t v)
     HDassert(_dest);
 
     n = (uint16_t)HDhtons(v);
-    HDmemcpy(_dest, &n, sizeof(n));
+    H5MM_memcpy(_dest, &n, sizeof(n));
 
     return 2;
 } /* end H5FD__mirror_xmit_encode_uint16() */
@@ -466,7 +466,7 @@ H5FD__mirror_xmit_encode_uint32(unsigned char *_dest, uint32_t v)
     HDassert(_dest);
 
     n = (uint32_t)HDhtonl(v);
-    HDmemcpy(_dest, &n, sizeof(n));
+    H5MM_memcpy(_dest, &n, sizeof(n));
 
     return 4;
 } /* end H5FD__mirror_xmit_encode_uint32() */
@@ -494,7 +494,7 @@ H5FD__mirror_xmit_encode_uint64(unsigned char *_dest, uint64_t v)
 
     if (TRUE == is_host_little_endian())
         n = BSWAP_64(v);
-    HDmemcpy(_dest, &n, sizeof(n));
+    H5MM_memcpy(_dest, &n, sizeof(n));
 
     return 8;
 } /* H5FD__mirror_xmit_encode_uint64() */
@@ -519,7 +519,7 @@ H5FD__mirror_xmit_encode_uint8(unsigned char *dest, uint8_t v)
 
     HDassert(dest);
 
-    HDmemcpy(dest, &v, sizeof(v));
+    H5MM_memcpy(dest, &v, sizeof(v));
 
     return 1;
 } /* end H5FD__mirror_xmit_encode_uint8() */
@@ -1188,7 +1188,7 @@ H5FD__mirror_fapl_get(H5FD_t *_file)
     if (NULL == fa)
         HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, NULL, "calloc failed");
 
-    HDmemcpy(fa, &(file->fa), sizeof(H5FD_mirror_fapl_t));
+    H5MM_memcpy(fa, &(file->fa), sizeof(H5FD_mirror_fapl_t));
 
     ret_value = fa;
 
@@ -1224,7 +1224,7 @@ H5FD__mirror_fapl_copy(const void *_old_fa)
     if (new_fa == NULL)
         HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, NULL, "memory allocation failed");
 
-    HDmemcpy(new_fa, old_fa, sizeof(H5FD_mirror_fapl_t));
+    H5MM_memcpy(new_fa, old_fa, sizeof(H5FD_mirror_fapl_t));
     ret_value = new_fa;
 
 done:
@@ -1298,7 +1298,7 @@ H5Pget_fapl_mirror(hid_t fapl_id, H5FD_mirror_fapl_t *fa_out)
 
     HDassert(fa->magic == H5FD_MIRROR_FAPL_MAGIC); /* sanity check */
 
-    HDmemcpy(fa_out, fa, sizeof(H5FD_mirror_fapl_t));
+    H5MM_memcpy(fa_out, fa, sizeof(H5FD_mirror_fapl_t));
 
 done:
     FUNC_LEAVE_API(ret_value);
diff --git a/src/H5FDros3.c b/src/H5FDros3.c
index cc27fd0..a557f1d 100644
--- a/src/H5FDros3.c
+++ b/src/H5FDros3.c
@@ -500,7 +500,7 @@ H5Pget_fapl_ros3(hid_t fapl_id, H5FD_ros3_fapl_t *fa_out)
         HGOTO_ERROR(H5E_PLIST, H5E_BADVALUE, FAIL, "bad VFL driver info")
 
     /* Copy the ros3 fapl data out */
-    HDmemcpy(fa_out, fa, sizeof(H5FD_ros3_fapl_t));
+    H5MM_memcpy(fa_out, fa, sizeof(H5FD_ros3_fapl_t));
 
 done:
     FUNC_LEAVE_API(ret_value)
@@ -535,7 +535,7 @@ H5FD__ros3_fapl_get(H5FD_t *_file)
         HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
 
     /* Copy the fields of the structure */
-    HDmemcpy(fa, &(file->fa), sizeof(H5FD_ros3_fapl_t));
+    H5MM_memcpy(fa, &(file->fa), sizeof(H5FD_ros3_fapl_t));
 
     /* Set return value */
     ret_value = fa;
@@ -575,7 +575,7 @@ H5FD__ros3_fapl_copy(const void *_old_fa)
     if (new_fa == NULL)
         HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed");
 
-    HDmemcpy(new_fa, old_fa, sizeof(H5FD_ros3_fapl_t));
+    H5MM_memcpy(new_fa, old_fa, sizeof(H5FD_ros3_fapl_t));
     ret_value = new_fa;
 
 done:
@@ -768,7 +768,7 @@ H5FD__ros3_open(const char *url, unsigned flags, hid_t fapl_id, haddr_t maxaddr)
         HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "unable to allocate file struct")
 
     file->s3r_handle = handle;
-    HDmemcpy(&(file->fa), &fa, sizeof(H5FD_ros3_fapl_t));
+    H5MM_memcpy(&(file->fa), &fa, sizeof(H5FD_ros3_fapl_t));
 
 #if ROS3_STATS
     if (FAIL == ros3_reset_stats(file))
diff --git a/src/H5FDs3comms.c b/src/H5FDs3comms.c
index 92921ad..ac58f67 100644
--- a/src/H5FDs3comms.c
+++ b/src/H5FDs3comms.c
@@ -144,7 +144,7 @@ curlwritecallback(char *ptr, size_t size, size_t nmemb, void *userdata)
         return written;
 
     if (size > 0) {
-        HDmemcpy(&(sds->data[sds->size]), ptr, product);
+        H5MM_memcpy(&(sds->data[sds->size]), ptr, product);
         sds->size += product;
         written = product;
     }
@@ -263,12 +263,12 @@ H5FD_s3comms_hrb_node_set(hrb_node_t **L, const char *name, const char *value)
         namecpy = (char *)H5MM_malloc(sizeof(char) * (namelen + 1));
         if (namecpy == NULL)
             HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "cannot make space for name copy.");
-        HDmemcpy(namecpy, name, (namelen + 1));
+        H5MM_memcpy(namecpy, name, (namelen + 1));
 
         valuecpy = (char *)H5MM_malloc(sizeof(char) * (valuelen + 1));
         if (valuecpy == NULL)
             HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "cannot make space for value copy.");
-        HDmemcpy(valuecpy, value, (valuelen + 1));
+        H5MM_memcpy(valuecpy, value, (valuelen + 1));
 
         nvcat = (char *)H5MM_malloc(sizeof(char) * catwrite);
         if (nvcat == NULL)
@@ -701,14 +701,14 @@ H5FD_s3comms_hrb_init_request(const char *_verb, const char *_resource, const ch
         res = (char *)H5MM_malloc(sizeof(char) * (reslen + 1));
         if (res == NULL)
             HGOTO_ERROR(H5E_ARGS, H5E_CANTALLOC, NULL, "no space for resource string");
-        HDmemcpy(res, _resource, (reslen + 1));
+        H5MM_memcpy(res, _resource, (reslen + 1));
     }
     else {
         res = (char *)H5MM_malloc(sizeof(char) * (reslen + 2));
         if (res == NULL)
             HGOTO_ERROR(H5E_ARGS, H5E_CANTALLOC, NULL, "no space for resource string");
         *res = '/';
-        HDmemcpy((&res[1]), _resource, (reslen + 1));
+        H5MM_memcpy((&res[1]), _resource, (reslen + 1));
         HDassert((reslen + 1) == HDstrlen(res));
     } /* end if (else resource string not starting with '/') */
 
@@ -910,7 +910,7 @@ H5FD_s3comms_s3r_getsize(s3r_t *handle)
     handle->httpverb = (char *)H5MM_malloc(sizeof(char) * 16);
     if (handle->httpverb == NULL)
         HGOTO_ERROR(H5E_ARGS, H5E_CANTALLOC, FAIL, "unable to allocate space for S3 request HTTP verb");
-    HDmemcpy(handle->httpverb, "HEAD", 5);
+    H5MM_memcpy(handle->httpverb, "HEAD", 5);
 
     headerresponse = (char *)H5MM_malloc(sizeof(char) * CURL_MAX_HTTP_HEADER);
     if (headerresponse == NULL)
@@ -1078,19 +1078,19 @@ H5FD_s3comms_s3r_open(const char *url, const char *region, const char *id, const
         handle->region = (char *)H5MM_malloc(sizeof(char) * tmplen);
         if (handle->region == NULL)
             HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, NULL, "could not malloc space for handle region copy.");
-        HDmemcpy(handle->region, region, tmplen);
+        H5MM_memcpy(handle->region, region, tmplen);
 
         tmplen            = HDstrlen(id) + 1;
         handle->secret_id = (char *)H5MM_malloc(sizeof(char) * tmplen);
         if (handle->secret_id == NULL)
             HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, NULL, "could not malloc space for handle ID copy.");
-        HDmemcpy(handle->secret_id, id, tmplen);
+        H5MM_memcpy(handle->secret_id, id, tmplen);
 
         tmplen              = SHA256_DIGEST_LENGTH;
         handle->signing_key = (unsigned char *)H5MM_malloc(sizeof(unsigned char) * tmplen);
         if (handle->signing_key == NULL)
             HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, NULL, "could not malloc space for handle key copy.");
-        HDmemcpy(handle->signing_key, signing_key, tmplen);
+        H5MM_memcpy(handle->signing_key, signing_key, tmplen);
     } /* if authentication information provided */
 
     /************************
@@ -1138,7 +1138,7 @@ H5FD_s3comms_s3r_open(const char *url, const char *region, const char *id, const
      *********************/
 
     HDassert(handle->httpverb != NULL);
-    HDmemcpy(handle->httpverb, "GET", 4);
+    H5MM_memcpy(handle->httpverb, "GET", 4);
 
     ret_value = handle;
 
@@ -2150,7 +2150,7 @@ H5FD_s3comms_nlowercase(char *dest, const char *s, size_t len)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "destination cannot be null.");
 
     if (len > 0) {
-        HDmemcpy(dest, s, len);
+        H5MM_memcpy(dest, s, len);
         do {
             len--;
             dest[len] = (char)HDtolower((int)dest[len]);
@@ -2686,14 +2686,14 @@ H5FD_s3comms_tostringtosign(char *dest, const char *req, const char *now, const
     if (ret <= 0 || ret >= 127)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "problem adding day and region to string")
 
-    HDmemcpy((dest + d), "AWS4-HMAC-SHA256\n", 17);
+    H5MM_memcpy((dest + d), "AWS4-HMAC-SHA256\n", 17);
     d = 17;
 
-    HDmemcpy((dest + d), now, HDstrlen(now));
+    H5MM_memcpy((dest + d), now, HDstrlen(now));
     d += HDstrlen(now);
     dest[d++] = '\n';
 
-    HDmemcpy((dest + d), tmp, HDstrlen(tmp));
+    H5MM_memcpy((dest + d), tmp, HDstrlen(tmp));
     d += HDstrlen(tmp);
     dest[d++] = '\n';
 
@@ -2777,7 +2777,7 @@ H5FD_s3comms_trim(char *dest, char *s, size_t s_len, size_t *n_written)
             s_len++;
 
             /* write output into dest */
-            HDmemcpy(dest, s, s_len);
+            H5MM_memcpy(dest, s, s_len);
         }
     }
 
diff --git a/src/H5FDsplitter.c b/src/H5FDsplitter.c
index 698ae7e..6ecafe0 100644
--- a/src/H5FDsplitter.c
+++ b/src/H5FDsplitter.c
@@ -585,7 +585,7 @@ H5FD__splitter_fapl_copy(const void *_old_fa)
     if (NULL == new_fa_ptr)
         HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, NULL, "unable to allocate log file FAPL")
 
-    HDmemcpy(new_fa_ptr, old_fa_ptr, sizeof(H5FD_splitter_fapl_t));
+    H5MM_memcpy(new_fa_ptr, old_fa_ptr, sizeof(H5FD_splitter_fapl_t));
     HDstrncpy(new_fa_ptr->wo_path, old_fa_ptr->wo_path, H5FD_SPLITTER_PATH_MAX);
     HDstrncpy(new_fa_ptr->log_file_path, old_fa_ptr->log_file_path, H5FD_SPLITTER_PATH_MAX);
 
@@ -1300,14 +1300,14 @@ H5FD__splitter_log_error(const H5FD_splitter_t *file, const char *atfunc, const
         char * s;
 
         size = HDstrlen(atfunc) + HDstrlen(msg) + 3; /* ':', ' ', '\n' */
-        s    = (char *)HDmalloc(sizeof(char) * (size + 1));
+        s    = (char *)H5MM_malloc(sizeof(char) * (size + 1));
         if (NULL == s)
             ret_value = FAIL;
         else if (size < (size_t)HDsnprintf(s, size + 1, "%s: %s\n", atfunc, msg))
             ret_value = FAIL;
         else if (size != HDfwrite(s, 1, size, file->logfp))
             ret_value = FAIL;
-        HDfree(s);
+        H5MM_free(s);
     }
 
     FUNC_LEAVE_NOAPI(ret_value)
diff --git a/src/H5Tref.c b/src/H5Tref.c
index ccb5232..c71724f 100644
--- a/src/H5Tref.c
+++ b/src/H5Tref.c
@@ -513,7 +513,7 @@ H5T__ref_mem_read(H5VL_object_t H5_ATTR_UNUSED *src_file, const void *src_buf, s
 
     /* Memory-to-memory conversion to support vlen conversion */
     if (NULL == dst_file) {
-        HDmemcpy(dst_buf, src_buf, dst_size);
+        H5MM_memcpy(dst_buf, src_buf, dst_size);
         HGOTO_DONE(ret_value);
     }
 
@@ -602,7 +602,7 @@ H5T__ref_mem_write(H5VL_object_t *src_file, const void *src_buf, size_t src_size
 
     /* Memory-to-memory conversion to support vlen conversion */
     if (NULL == src_file) {
-        HDmemcpy(dst_buf, src_buf, src_size);
+        H5MM_memcpy(dst_buf, src_buf, src_size);
         HGOTO_DONE(ret_value);
     }
 
-- 
cgit v0.12


From 0e9981aa59054cccd30154f22c01903a02f8d670 Mon Sep 17 00:00:00 2001
From: Michel Zou 
Date: Fri, 30 Oct 2020 10:32:34 +0100
Subject: CMake: Set specific INSTALL_DATA_DIR only on MSVC

For MinGW we want INSTALL_DATA_DIR to be set to share instead of .
to properly install files in a standard package layout.
---
 config/cmake_ext_mod/HDFMacros.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/cmake_ext_mod/HDFMacros.cmake b/config/cmake_ext_mod/HDFMacros.cmake
index eb0392e..1a1c571 100644
--- a/config/cmake_ext_mod/HDFMacros.cmake
+++ b/config/cmake_ext_mod/HDFMacros.cmake
@@ -343,7 +343,7 @@ macro (HDF_DIR_PATHS package_prefix)
     set (${package_prefix}_INSTALL_INCLUDE_DIR include)
   endif ()
   if (NOT ${package_prefix}_INSTALL_DATA_DIR)
-    if (NOT WIN32)
+    if (NOT MSVC)
       if (APPLE)
         if (${package_prefix}_BUILD_FRAMEWORKS)
           set (${package_prefix}_INSTALL_EXTRA_DIR ../SharedSupport)
-- 
cgit v0.12


From de4ccdfd630cc1edfac9f9b82c20ad120340ed4b Mon Sep 17 00:00:00 2001
From: Michel Zou 
Date: Fri, 30 Oct 2020 10:36:32 +0100
Subject: CMake: Add an option to opt-out MSVC naming convention

We might want to keep the default mingw import name, see:
https://github.com/msys2/MINGW-packages/blob/master/mingw-w64-hdf5/hdf5-default-import-suffix.patch
---
 config/cmake_ext_mod/HDFMacros.cmake | 4 ++--
 release_docs/INSTALL_CMake.txt       | 1 +
 release_docs/RELEASE.txt             | 7 +++++++
 3 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/config/cmake_ext_mod/HDFMacros.cmake b/config/cmake_ext_mod/HDFMacros.cmake
index eb0392e..74dd35b 100644
--- a/config/cmake_ext_mod/HDFMacros.cmake
+++ b/config/cmake_ext_mod/HDFMacros.cmake
@@ -143,8 +143,8 @@ macro (HDF_SET_LIB_OPTIONS libtarget libname libtype)
     endif ()
   endif ()
 
-  #----- Use MSVC Naming conventions for Shared Libraries
-  if (MINGW AND ${libtype} MATCHES "SHARED")
+  option (HDF5_MSVC_NAMING_CONVENTION "Use MSVC Naming conventions for Shared Libraries" OFF)
+  if (HDF5_MSVC_NAMING_CONVENTION AND MINGW AND ${libtype} MATCHES "SHARED")
     set_target_properties (${libtarget} PROPERTIES
         IMPORT_SUFFIX ".lib"
         IMPORT_PREFIX ""
diff --git a/release_docs/INSTALL_CMake.txt b/release_docs/INSTALL_CMake.txt
index 0d35b3f..ed27bb2 100644
--- a/release_docs/INSTALL_CMake.txt
+++ b/release_docs/INSTALL_CMake.txt
@@ -777,6 +777,7 @@ HDF5_USE_FOLDERS               "Enable folder grouping of projects in IDEs."
 HDF5_WANT_DATA_ACCURACY        "IF data accuracy is guaranteed during data conversions"       ON
 HDF5_WANT_DCONV_EXCEPTION      "exception handling functions is checked during data conversions" ON
 HDF5_ENABLE_THREADSAFE         "Enable Threadsafety"                                          OFF
+HDF5_MSVC_NAMING_CONVENTION    "Use MSVC Naming conventions for Shared Libraries"             OFF
 if (APPLE)
     HDF5_BUILD_WITH_INSTALL_NAME "Build with library install_name set to the installation path"  OFF
 if (CMAKE_BUILD_TYPE MATCHES Debug)
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index e3a1dd4..70af053 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -48,6 +48,13 @@ New Features
 
     Configuration:
     -------------
+    - CMake option to use MSVC naming conventions with MinGW
+
+      HDF5_MSVC_NAMING_CONVENTION option enable to use MSVC naming conventions
+      when using a MinGW toolchain
+
+      (xan - 2020/10/30)
+
     - CMake option to build the HDF filter plugins project as an external project
 
       The HDF filter plugins project is a collection of registered compression
-- 
cgit v0.12


From 0db1fe81d58e6926b3e5982dd0329fc95faf2c8e Mon Sep 17 00:00:00 2001
From: Michel Zou 
Date: Fri, 30 Oct 2020 13:09:23 +0100
Subject: CMake: MINGW implies WIN32

---
 CMakeInstallation.cmake                | 14 +++++++-------
 CMakeLists.txt                         | 11 ++++++-----
 config/cmake/jrunTest.cmake            |  6 +++---
 config/cmake/jvolTest.cmake            |  6 +++---
 config/cmake_ext_mod/grepTest.cmake    |  4 ++--
 config/cmake_ext_mod/runTest.cmake     |  6 +++---
 java/examples/datasets/CMakeLists.txt  |  2 +-
 java/examples/datatypes/CMakeLists.txt |  2 +-
 java/examples/groups/CMakeLists.txt    |  2 +-
 java/examples/intro/CMakeLists.txt     |  2 +-
 java/test/CMakeLists.txt               |  2 +-
 test/CMakeTests.cmake                  |  4 ++--
 test/flushrefreshTest.cmake            |  2 +-
 tools/test/h5dump/CMakeTests.cmake     |  2 +-
 14 files changed, 33 insertions(+), 32 deletions(-)

diff --git a/CMakeInstallation.cmake b/CMakeInstallation.cmake
index 799c117..ccd4fbc 100644
--- a/CMakeInstallation.cmake
+++ b/CMakeInstallation.cmake
@@ -189,7 +189,7 @@ HDF_README_PROPERTIES(HDF5_BUILD_FORTRAN)
 #-----------------------------------------------------------------------------
 # Configure the COPYING.txt file for the windows binary package
 #-----------------------------------------------------------------------------
-if (WIN32 OR MINGW)
+if (WIN32)
   configure_file (${HDF5_SOURCE_DIR}/COPYING ${HDF5_BINARY_DIR}/COPYING.txt @ONLY)
 endif ()
 
@@ -208,7 +208,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED)
         ${HDF5_SOURCE_DIR}/release_docs/COPYING
         ${HDF5_SOURCE_DIR}/release_docs/RELEASE.txt
     )
-    if (WIN32 OR MINGW)
+    if (WIN32)
       set (release_files
           ${release_files}
           ${HDF5_SOURCE_DIR}/release_docs/USING_HDF5_VS.txt
@@ -222,7 +222,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED)
           ${HDF5_SOURCE_DIR}/release_docs/HISTORY-1_8.txt
           ${HDF5_SOURCE_DIR}/release_docs/INSTALL
       )
-      if (WIN32 OR MINGW)
+      if (WIN32)
         set (release_files
             ${release_files}
             ${HDF5_SOURCE_DIR}/release_docs/INSTALL_Windows.txt
@@ -290,7 +290,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED AND NOT HDF5_NO_PACKAGES)
   set (CPACK_PACKAGE_ICON "${HDF_RESOURCES_EXT_DIR}/hdf.bmp")
 
   set (CPACK_GENERATOR "TGZ")
-  if (WIN32 OR MINGW)
+  if (WIN32)
     set (CPACK_GENERATOR "ZIP")
 
     if (NSIS_EXECUTABLE)
@@ -455,7 +455,7 @@ The HDF5 data model, file format, API, library, and tools are open and distribut
   if (HDF5_PACKAGE_EXTLIBS)
     if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ")
       if (ZLIB_FOUND AND ZLIB_USE_EXTERNAL)
-        if (WIN32 OR MINGW)
+        if (WIN32)
           set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ZLIB_INCLUDE_DIR_GEN};ZLIB;ALL;/")
         else ()
           set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ZLIB_INCLUDE_DIR_GEN};ZLIB;libraries;/")
@@ -464,7 +464,7 @@ The HDF5 data model, file format, API, library, and tools are open and distribut
         endif ()
       endif ()
       if (SZIP_FOUND AND SZIP_USE_EXTERNAL)
-        if (WIN32 OR MINGW)
+        if (WIN32)
           set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${SZIP_INCLUDE_DIR_GEN};SZIP;ALL;/")
         else ()
           set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${SZIP_INCLUDE_DIR_GEN};SZIP;libraries;/")
@@ -473,7 +473,7 @@ The HDF5 data model, file format, API, library, and tools are open and distribut
         endif ()
       endif ()
       if (PLUGIN_FOUND AND PLUGIN_USE_EXTERNAL)
-        if (WIN32 OR MINGW)
+        if (WIN32)
           set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${PLUGIN_BINARY_DIR};PLUGIN;ALL;/")
         else ()
           set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${PLUGIN_BINARY_DIR};PLUGIN;libraries;/")
diff --git a/CMakeLists.txt b/CMakeLists.txt
index d0eebad..01355dd 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -572,10 +572,11 @@ endif ()
 # Certain systems may add /Debug or /Release to output paths
 # and we need to call the executable from inside the CMake configuration
 #-----------------------------------------------------------------------------
-set (EXE_EXT "")
-if (WIN32 OR MINGW)
-  set (EXE_EXT ".exe")
-  add_compile_definitions (_BIND_TO_CURRENT_VCLIBS_VERSION=1 _CRT_SECURE_NO_WARNINGS _CONSOLE)
+if (WIN32)
+  add_compile_definitions (_CRT_SECURE_NO_WARNINGS)
+  if (MSVC)
+    add_compile_definitions (_BIND_TO_CURRENT_VCLIBS_VERSION=1 _CONSOLE)
+  endif ()
 endif ()
 
 if (MSVC)
@@ -777,7 +778,7 @@ endif ()
 option (HDF5_ENABLE_THREADSAFE "Enable thread-safety" OFF)
 if (HDF5_ENABLE_THREADSAFE)
   # check for unsupported options
-  if (WIN32 OR MINGW)
+  if (WIN32)
     message (STATUS " **** thread-safety option not supported with static library **** ")
     message (STATUS " **** thread-safety option will not be used building static library **** ")
   endif ()
diff --git a/config/cmake/jrunTest.cmake b/config/cmake/jrunTest.cmake
index 41570eb..7d59ce5 100644
--- a/config/cmake/jrunTest.cmake
+++ b/config/cmake/jrunTest.cmake
@@ -49,7 +49,7 @@ endif ()
 
 message (STATUS "COMMAND: ${TEST_TESTER} -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=${LOG_LEVEL} -Djava.library.path=\"${TEST_LIBRARY_DIRECTORY}\" -cp \"${TEST_CLASSPATH}\" ${TEST_ARGS} ${TEST_PROGRAM} ${ARGN}")
 
-if (WIN32 OR MINGW)
+if (WIN32)
   set (ENV{PATH} "$ENV{PATH}\\;${TEST_LIBRARY_DIRECTORY}")
 else ()
   set (ENV{LD_LIBRARY_PATH} "$ENV{LD_LIBRARY_PATH}:${TEST_LIBRARY_DIRECTORY}")
@@ -131,7 +131,7 @@ if (NOT TEST_SKIP_COMPARE)
     file (READ ${TEST_FOLDER}/${TEST_REFERENCE} TEST_STREAM)
     list (LENGTH TEST_STREAM test_len)
     if (test_len GREATER 0)
-      if (WIN32 OR MINGW)
+      if (WIN32)
         configure_file(${TEST_FOLDER}/${TEST_REFERENCE} ${TEST_FOLDER}/${TEST_REFERENCE}.tmp NEWLINE_STYLE CRLF)
         if (EXISTS "${TEST_FOLDER}/${TEST_REFERENCE}.tmp")
           file(RENAME ${TEST_FOLDER}/${TEST_REFERENCE}.tmp ${TEST_FOLDER}/${TEST_REFERENCE})
@@ -202,7 +202,7 @@ if (NOT TEST_SKIP_COMPARE)
     file (READ ${TEST_FOLDER}/${TEST_ERRREF} TEST_STREAM)
     list (LENGTH TEST_STREAM test_len)
     if (test_len GREATER 0)
-      if (WIN32 OR MINGW)
+      if (WIN32)
         configure_file(${TEST_FOLDER}/${TEST_ERRREF} ${TEST_FOLDER}/${TEST_ERRREF}.tmp NEWLINE_STYLE CRLF)
         if (EXISTS "${TEST_FOLDER}/${TEST_ERRREF}.tmp")
           file(RENAME ${TEST_FOLDER}/${TEST_ERRREF}.tmp ${TEST_FOLDER}/${TEST_ERRREF})
diff --git a/config/cmake/jvolTest.cmake b/config/cmake/jvolTest.cmake
index 3a3877b..bcd9dbd 100644
--- a/config/cmake/jvolTest.cmake
+++ b/config/cmake/jvolTest.cmake
@@ -54,7 +54,7 @@ message (STATUS "USING ${TEST_VOL} ON COMMAND: ${TEST_TESTER} -Xmx1024M -Dorg.sl
 
 set (ENV{HDF5_VOL_CONNECTOR} "${TEST_VOL}")
 
-if (WIN32 OR MINGW)
+if (WIN32)
   set (ENV{PATH} "$ENV{PATH}\\;${TEST_LIBRARY_DIRECTORY}")
 else ()
   set (ENV{LD_LIBRARY_PATH} "$ENV{LD_LIBRARY_PATH}:${TEST_LIBRARY_DIRECTORY}")
@@ -136,7 +136,7 @@ if (NOT TEST_SKIP_COMPARE)
     file (READ ${TEST_FOLDER}/${TEST_REFERENCE} TEST_STREAM)
     list(LENGTH TEST_STREAM test_len)
     if (test_len GREATER 0)
-      if (WIN32 OR MINGW)
+      if (WIN32)
         configure_file(${TEST_FOLDER}/${TEST_REFERENCE} ${TEST_FOLDER}/${TEST_REFERENCE}.tmp NEWLINE_STYLE CRLF)
         if (EXISTS "${TEST_FOLDER}/${TEST_REFERENCE}.tmp")
           file(RENAME ${TEST_FOLDER}/${TEST_REFERENCE}.tmp ${TEST_FOLDER}/${TEST_REFERENCE})
@@ -207,7 +207,7 @@ if (NOT TEST_SKIP_COMPARE)
     file (READ ${TEST_FOLDER}/${TEST_ERRREF} TEST_STREAM)
     list(LENGTH TEST_STREAM test_len)
     if (test_len GREATER 0)
-      if (WIN32 OR MINGW)
+      if (WIN32)
         configure_file(${TEST_FOLDER}/${TEST_ERRREF} ${TEST_FOLDER}/${TEST_ERRREF}.tmp NEWLINE_STYLE CRLF)
         if (EXISTS "${TEST_FOLDER}/${TEST_ERRREF}.tmp")
           file(RENAME ${TEST_FOLDER}/${TEST_ERRREF}.tmp ${TEST_FOLDER}/${TEST_ERRREF})
diff --git a/config/cmake_ext_mod/grepTest.cmake b/config/cmake_ext_mod/grepTest.cmake
index b011ae8..758b62b 100644
--- a/config/cmake_ext_mod/grepTest.cmake
+++ b/config/cmake_ext_mod/grepTest.cmake
@@ -46,7 +46,7 @@ endif ()
 message (STATUS "COMMAND: ${TEST_EMULATOR} ${TEST_PROGRAM} ${TEST_ARGS}")
 
 if (TEST_LIBRARY_DIRECTORY)
-  if (WIN32 OR MINGW)
+  if (WIN32)
     set (ENV{PATH} "$ENV{PATH};${TEST_LIBRARY_DIRECTORY}")
   else ()
     set (ENV{LD_LIBRARY_PATH} "$ENV{LD_LIBRARY_PATH}:${TEST_LIBRARY_DIRECTORY}")
@@ -105,7 +105,7 @@ if (TEST_ERRREF)
       file (READ ${TEST_FOLDER}/${TEST_REFERENCE} TEST_STREAM)
       list (LENGTH TEST_STREAM test_len)
       if (test_len GREATER 0)
-        if (WIN32 OR MINGW)
+        if (WIN32)
           configure_file(${TEST_FOLDER}/${TEST_REFERENCE} ${TEST_FOLDER}/${TEST_REFERENCE}.tmp NEWLINE_STYLE CRLF)
           if (EXISTS "${TEST_FOLDER}/${TEST_REFERENCE}.tmp")
             file(RENAME ${TEST_FOLDER}/${TEST_REFERENCE}.tmp ${TEST_FOLDER}/${TEST_REFERENCE})
diff --git a/config/cmake_ext_mod/runTest.cmake b/config/cmake_ext_mod/runTest.cmake
index 2b8b6b0..baf15c0 100644
--- a/config/cmake_ext_mod/runTest.cmake
+++ b/config/cmake_ext_mod/runTest.cmake
@@ -38,7 +38,7 @@ endif ()
 message (STATUS "COMMAND: ${TEST_EMULATOR} ${TEST_PROGRAM} ${TEST_ARGS}")
 
 if (TEST_LIBRARY_DIRECTORY)
-  if (WIN32 OR MINGW)
+  if (WIN32)
     set (ENV{PATH} "$ENV{PATH};${TEST_LIBRARY_DIRECTORY}")
   else ()
     set (ENV{LD_LIBRARY_PATH} "$ENV{LD_LIBRARY_PATH}:${TEST_LIBRARY_DIRECTORY}")
@@ -212,7 +212,7 @@ if (NOT TEST_SKIP_COMPARE)
     file (READ ${TEST_FOLDER}/${TEST_REFERENCE} TEST_STREAM)
     list (LENGTH TEST_STREAM test_len)
     if (test_len GREATER 0)
-      if (WIN32 OR MINGW)
+      if (WIN32)
         configure_file(${TEST_FOLDER}/${TEST_REFERENCE} ${TEST_FOLDER}/${TEST_REFERENCE}.tmp NEWLINE_STYLE CRLF)
         if (EXISTS "${TEST_FOLDER}/${TEST_REFERENCE}.tmp")
           file(RENAME ${TEST_FOLDER}/${TEST_REFERENCE}.tmp ${TEST_FOLDER}/${TEST_REFERENCE})
@@ -283,7 +283,7 @@ if (NOT TEST_SKIP_COMPARE)
     file (READ ${TEST_FOLDER}/${TEST_ERRREF} TEST_STREAM)
     list (LENGTH TEST_STREAM test_len)
     if (test_len GREATER 0)
-      if (WIN32 OR MINGW)
+      if (WIN32)
         configure_file(${TEST_FOLDER}/${TEST_ERRREF} ${TEST_FOLDER}/${TEST_ERRREF}.tmp NEWLINE_STYLE CRLF)
         if (EXISTS "${TEST_FOLDER}/${TEST_ERRREF}.tmp")
           file(RENAME ${TEST_FOLDER}/${TEST_ERRREF}.tmp ${TEST_FOLDER}/${TEST_ERRREF})
diff --git a/java/examples/datasets/CMakeLists.txt b/java/examples/datasets/CMakeLists.txt
index fc4acc4..8198135 100644
--- a/java/examples/datasets/CMakeLists.txt
+++ b/java/examples/datasets/CMakeLists.txt
@@ -39,7 +39,7 @@ set (HDF_JAVA_SZIP_EXAMPLES
     set (${HDF_JAVA_EXAMPLES} ${HDF_JAVA_EXAMPLES} ${HDF_JAVA_SZIP_EXAMPLES})
   endif (H5_HAVE_FILTER_SZIP)
 
-if (WIN32 OR MINGW)
+if (WIN32)
   set (CMAKE_JAVA_INCLUDE_FLAG_SEP ";")
 else ()
   set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":")
diff --git a/java/examples/datatypes/CMakeLists.txt b/java/examples/datatypes/CMakeLists.txt
index bd4f483..6997b2e 100644
--- a/java/examples/datatypes/CMakeLists.txt
+++ b/java/examples/datatypes/CMakeLists.txt
@@ -24,7 +24,7 @@ set (HDF_JAVA_EXAMPLES
     H5Ex_T_VLString
 )
 
-if (WIN32 OR MINGW)
+if (WIN32)
   set (CMAKE_JAVA_INCLUDE_FLAG_SEP ";")
 else ()
   set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":")
diff --git a/java/examples/groups/CMakeLists.txt b/java/examples/groups/CMakeLists.txt
index c2c7d0f..6483f91 100644
--- a/java/examples/groups/CMakeLists.txt
+++ b/java/examples/groups/CMakeLists.txt
@@ -13,7 +13,7 @@ set (HDF_JAVA_EXAMPLES
     H5Ex_G_Visit
 )
 
-if (WIN32 OR MINGW)
+if (WIN32)
   set (CMAKE_JAVA_INCLUDE_FLAG_SEP ";")
 else ()
   set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":")
diff --git a/java/examples/intro/CMakeLists.txt b/java/examples/intro/CMakeLists.txt
index 6cb1e16..867740b 100644
--- a/java/examples/intro/CMakeLists.txt
+++ b/java/examples/intro/CMakeLists.txt
@@ -13,7 +13,7 @@ set (HDF_JAVA_EXAMPLES
     H5_ReadWrite
 )
 
-if (WIN32 OR MINGW)
+if (WIN32)
   set (CMAKE_JAVA_INCLUDE_FLAG_SEP ";")
 else ()
   set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":")
diff --git a/java/test/CMakeLists.txt b/java/test/CMakeLists.txt
index b97ad26..b0a0d53 100644
--- a/java/test/CMakeLists.txt
+++ b/java/test/CMakeLists.txt
@@ -96,7 +96,7 @@ HDFTEST_COPY_FILE("${PROJECT_SOURCE_DIR}/h5ex_g_iterate.orig" "${PROJECT_BINARY_
 
 add_custom_target(${HDF5_JAVA_TEST_LIB_TARGET}_files ALL COMMENT "Copying files needed by ${HDF5_JAVA_TEST_LIB_TARGET} tests" DEPENDS ${${HDF5_JAVA_TEST_LIB_TARGET}_files_list})
 
-if (WIN32 OR MINGW)
+if (WIN32)
   set (CMAKE_JAVA_INCLUDE_FLAG_SEP ";")
 else ()
   set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":")
diff --git a/test/CMakeTests.cmake b/test/CMakeTests.cmake
index 462e9d5..013189c 100644
--- a/test/CMakeTests.cmake
+++ b/test/CMakeTests.cmake
@@ -844,7 +844,7 @@ endif ()
 ###    F I L T E R  P L U G I N  T E S T S
 ##############################################################################
 if (BUILD_SHARED_LIBS)
-  if (WIN32 OR MINGW)
+  if (WIN32)
     set (CMAKE_SEP "\;")
     set (BIN_REL_PATH "../../")
   else ()
@@ -940,7 +940,7 @@ endif ()
 ###    V O L  P L U G I N  T E S T S
 ##############################################################################
 if (BUILD_SHARED_LIBS)
-  if (WIN32 OR MINGW)
+  if (WIN32)
     set (CMAKE_SEP "\;")
     set (BIN_REL_PATH "../../")
   else ()
diff --git a/test/flushrefreshTest.cmake b/test/flushrefreshTest.cmake
index 6faf37b..e280b8b 100644
--- a/test/flushrefreshTest.cmake
+++ b/test/flushrefreshTest.cmake
@@ -41,7 +41,7 @@ endif ()
 message (STATUS "COMMAND: ${TEST_PROGRAM} ${TEST_ARGS}")
 
 if (TEST_LIBRARY_DIRECTORY)
-  if (WIN32 OR MINGW)
+  if (WIN32)
     set (ENV{PATH} "$ENV{PATH};${TEST_LIBRARY_DIRECTORY}")
   else ()
     set (ENV{LD_LIBRARY_PATH} "$ENV{LD_LIBRARY_PATH}:${TEST_LIBRARY_DIRECTORY}")
diff --git a/tools/test/h5dump/CMakeTests.cmake b/tools/test/h5dump/CMakeTests.cmake
index 91d3ea9..a664e6f 100644
--- a/tools/test/h5dump/CMakeTests.cmake
+++ b/tools/test/h5dump/CMakeTests.cmake
@@ -405,7 +405,7 @@
   # --------------------------------------------------------------------
   HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/tbin1.ddl" "${PROJECT_BINARY_DIR}/testfiles/std/tbin1LE.ddl" "h5dump_std_files")
 
-  if (WIN32 OR MINGW)
+  if (WIN32)
     configure_file(${HDF5_TOOLS_DIR}/testfiles/tbinregR.exp ${PROJECT_BINARY_DIR}/testfiles/std/tbinregR.exp NEWLINE_STYLE CRLF)
     #file (READ ${HDF5_TOOLS_DIR}/testfiles/tbinregR.exp TEST_STREAM)
     #file (WRITE ${PROJECT_BINARY_DIR}/testfiles/std/tbinregR.exp "${TEST_STREAM}")
-- 
cgit v0.12


From 7259b5eb7ac291f00cc989a44c5fe4964759efaf Mon Sep 17 00:00:00 2001
From: Michel Zou 
Date: Fri, 30 Oct 2020 10:44:24 +0100
Subject: CMake: Add an option to opt-out static libgcc

With sjlj exception model, statically link to libgcc/libstdc++
prevents exceptions to be caught from other dynamic libraries.
---
 CMakeLists.txt                 | 2 ++
 c++/examples/CMakeLists.txt    | 4 ++--
 c++/src/CMakeLists.txt         | 2 +-
 c++/test/CMakeLists.txt        | 2 +-
 config/cmake/cacheinit.cmake   | 2 ++
 release_docs/INSTALL_CMake.txt | 1 +
 release_docs/RELEASE.txt       | 7 +++++++
 7 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index d0eebad..dc2cf1a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -578,6 +578,8 @@ if (WIN32 OR MINGW)
   add_compile_definitions (_BIND_TO_CURRENT_VCLIBS_VERSION=1 _CRT_SECURE_NO_WARNINGS _CONSOLE)
 endif ()
 
+option (HDF5_MINGW_STATIC_GCC_LIBS "Statically link libgcc/libstdc++" OFF)
+
 if (MSVC)
   set (CMAKE_MFC_FLAG 0)
   set (WIN_COMPILE_FLAGS "")
diff --git a/c++/examples/CMakeLists.txt b/c++/examples/CMakeLists.txt
index 3035841..c50315f 100644
--- a/c++/examples/CMakeLists.txt
+++ b/c++/examples/CMakeLists.txt
@@ -41,7 +41,7 @@ foreach (example ${examples})
   else ()
     TARGET_C_PROPERTIES (cpp_ex_${example} SHARED)
     target_link_libraries (cpp_ex_${example} PRIVATE ${HDF5_CPP_LIBSH_TARGET} ${HDF5_LIBSH_TARGET})
-    if (MINGW)
+    if (MINGW AND HDF5_MINGW_STATIC_GCC_LIBS)
       target_link_options (${HDF5_CPP_LIBSH_TARGET}
           PRIVATE -static-libgcc -static-libstdc++
       )
@@ -66,7 +66,7 @@ foreach (example ${tutr_examples})
   else ()
     TARGET_C_PROPERTIES (cpp_ex_${example} SHARED)
     target_link_libraries (cpp_ex_${example} PRIVATE ${HDF5_CPP_LIBSH_TARGET} ${HDF5_LIBSH_TARGET})
-    if (MINGW)
+    if (MINGW AND HDF5_MINGW_STATIC_GCC_LIBS)
       target_link_options (${HDF5_CPP_LIBSH_TARGET}
           PRIVATE -static-libgcc -static-libstdc++
       )
diff --git a/c++/src/CMakeLists.txt b/c++/src/CMakeLists.txt
index 04822cf..de2306e 100644
--- a/c++/src/CMakeLists.txt
+++ b/c++/src/CMakeLists.txt
@@ -117,7 +117,7 @@ if (BUILD_SHARED_LIBS)
   target_link_libraries (${HDF5_CPP_LIBSH_TARGET}
       PUBLIC ${HDF5_LIBSH_TARGET}
   )
-  if (MINGW)
+  if (MINGW AND HDF5_MINGW_STATIC_GCC_LIBS)
     target_link_options (${HDF5_CPP_LIBSH_TARGET}
         PRIVATE -static-libgcc -static-libstdc++
     )
diff --git a/c++/test/CMakeLists.txt b/c++/test/CMakeLists.txt
index 550b7ea..1255e39 100644
--- a/c++/test/CMakeLists.txt
+++ b/c++/test/CMakeLists.txt
@@ -49,7 +49,7 @@ if (NOT BUILD_SHARED_LIBS)
 else ()
   TARGET_C_PROPERTIES (cpp_testhdf5 SHARED)
   target_link_libraries (cpp_testhdf5 PRIVATE ${HDF5_CPP_LIBSH_TARGET} ${HDF5_LIBSH_TARGET} ${HDF5_TEST_LIBSH_TARGET})
-  if (MINGW)
+  if (MINGW AND HDF5_MINGW_STATIC_GCC_LIBS)
     target_link_options (${HDF5_CPP_LIBSH_TARGET}
         PRIVATE -static-libgcc -static-libstdc++
     )
diff --git a/config/cmake/cacheinit.cmake b/config/cmake/cacheinit.cmake
index f8ab3a2..71c8b4a 100644
--- a/config/cmake/cacheinit.cmake
+++ b/config/cmake/cacheinit.cmake
@@ -40,6 +40,8 @@ set (HDF5_ENABLE_ALL_WARNINGS ON CACHE BOOL "Enable all warnings" FORCE)
 
 set (HDF_TEST_EXPRESS "2" CACHE STRING "Control testing framework (0-3)" FORCE)
 
+set (HDF5_MINGW_STATIC_GCC_LIBS ON CACHE BOOL "Statically link libgcc/libstdc++" FORCE)
+
 set (HDF5_ALLOW_EXTERNAL_SUPPORT "NO" CACHE STRING "Allow External Library Building (NO GIT TGZ)" FORCE)
 set_property (CACHE HDF5_ALLOW_EXTERNAL_SUPPORT PROPERTY STRINGS NO GIT TGZ)
 
diff --git a/release_docs/INSTALL_CMake.txt b/release_docs/INSTALL_CMake.txt
index ed27bb2..89d3ac0 100644
--- a/release_docs/INSTALL_CMake.txt
+++ b/release_docs/INSTALL_CMake.txt
@@ -778,6 +778,7 @@ HDF5_WANT_DATA_ACCURACY        "IF data accuracy is guaranteed during data conve
 HDF5_WANT_DCONV_EXCEPTION      "exception handling functions is checked during data conversions" ON
 HDF5_ENABLE_THREADSAFE         "Enable Threadsafety"                                          OFF
 HDF5_MSVC_NAMING_CONVENTION    "Use MSVC Naming conventions for Shared Libraries"             OFF
+HDF5_MINGW_STATIC_GCC_LIBS     "Statically link libgcc/libstdc++"                             OFF
 if (APPLE)
     HDF5_BUILD_WITH_INSTALL_NAME "Build with library install_name set to the installation path"  OFF
 if (CMAKE_BUILD_TYPE MATCHES Debug)
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 70af053..43356527 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -54,6 +54,13 @@ New Features
       when using a MinGW toolchain
 
       (xan - 2020/10/30)
+    
+    - CMake option to statically link gcc libs with MinGW
+
+      HDF5_MINGW_STATIC_GCC_LIBS allows to statically link libg/libstdc++
+      with the MinGW toolchain
+
+      (xan - 2020/10/30)
 
     - CMake option to build the HDF filter plugins project as an external project
 
-- 
cgit v0.12


From 0b6067574b673908c09dd9d487e0592103c828e4 Mon Sep 17 00:00:00 2001
From: Jordan Henderson 
Date: Mon, 2 Nov 2020 21:03:46 -0600
Subject: Change H5R__copy to not assume destination reference storage is
 initialized

---
 src/H5Rint.c | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/H5Rint.c b/src/H5Rint.c
index 8f3163a..60f8131 100644
--- a/src/H5Rint.c
+++ b/src/H5Rint.c
@@ -746,8 +746,10 @@ H5R__copy(const H5R_ref_priv_t *src_ref, H5R_ref_priv_t *dst_ref)
         dst_ref->info.obj.filename = NULL;
 
         /* Set location ID and hold reference to it */
-        if (H5R__set_loc_id(dst_ref, src_ref->loc_id, TRUE, TRUE) < 0)
-            HGOTO_ERROR(H5E_REFERENCE, H5E_CANTSET, FAIL, "cannot set reference location ID")
+        dst_ref->loc_id = src_ref->loc_id;
+        if (H5I_inc_ref(dst_ref->loc_id, TRUE) < 0)
+            HGOTO_ERROR(H5E_REFERENCE, H5E_CANTINC, FAIL, "incrementing location ID failed")
+        dst_ref->app_ref = TRUE;
     }
 
 done:
-- 
cgit v0.12


From c812f3fea2c9bacfc0f2d2bcad6960e9aa640dcd Mon Sep 17 00:00:00 2001
From: Allen Byrne 
Date: Tue, 3 Nov 2020 10:42:09 -0600
Subject: Add doxygen auotoconf and cmake support

---
 CMakeLists.txt                      |   15 +
 Makefile.am                         |   10 +
 config/doxygen.am                   |  156 +++
 configure.ac                        |   67 +-
 doxygen/Doxyfile.in                 | 2542 +++++++++++++++++++++++++++++++++++
 doxygen/Makefile                    |   20 +
 doxygen/aliases                     |  184 +++
 doxygen/dox/H5Acreate.dox           |    9 +
 doxygen/dox/H5Aiterate.dox          |    9 +
 doxygen/dox/H5Fget_info.dox         |   47 +
 doxygen/dox/H5Lget_info.dox         |   18 +
 doxygen/dox/H5Lget_info_by_idx.dox  |   18 +
 doxygen/dox/H5Literate.dox          |   22 +
 doxygen/dox/H5Literate_by_name.dox  |   23 +
 doxygen/dox/H5Lvisit.dox            |   22 +
 doxygen/dox/H5Lvisit_by_name.dox    |   22 +
 doxygen/dox/H5Oget_info.dox         |  121 ++
 doxygen/dox/H5Oget_info_by_idx.dox  |   92 ++
 doxygen/dox/H5Oget_info_by_name.dox |   99 ++
 doxygen/dox/H5Ovisit.dox            |   92 ++
 doxygen/dox/H5Ovisit_by_name.dox    |   92 ++
 doxygen/dox/H5Sencode.dox           |    5 +
 doxygen/dox/mainpage.dox            |   36 +
 doxygen/dox/rm-template.dox         |   72 +
 doxygen/examples/H5Fclose.c         |   12 +
 doxygen/examples/H5Fcreate.c        |   12 +
 doxygen/examples/hello_hdf5.c       |   12 +
 doxygen/img/HDFG-logo.png           |  Bin 0 -> 4541 bytes
 m4/ax_prog_doxygen.m4               |  532 ++++++++
 src/CMakeLists.txt                  |   32 +
 src/Makefile.am                     |   13 +-
 31 files changed, 4400 insertions(+), 6 deletions(-)
 create mode 100644 config/doxygen.am
 create mode 100644 doxygen/Doxyfile.in
 create mode 100644 doxygen/Makefile
 create mode 100644 doxygen/aliases
 create mode 100644 doxygen/dox/H5Acreate.dox
 create mode 100644 doxygen/dox/H5Aiterate.dox
 create mode 100644 doxygen/dox/H5Fget_info.dox
 create mode 100644 doxygen/dox/H5Lget_info.dox
 create mode 100644 doxygen/dox/H5Lget_info_by_idx.dox
 create mode 100644 doxygen/dox/H5Literate.dox
 create mode 100644 doxygen/dox/H5Literate_by_name.dox
 create mode 100644 doxygen/dox/H5Lvisit.dox
 create mode 100644 doxygen/dox/H5Lvisit_by_name.dox
 create mode 100644 doxygen/dox/H5Oget_info.dox
 create mode 100644 doxygen/dox/H5Oget_info_by_idx.dox
 create mode 100644 doxygen/dox/H5Oget_info_by_name.dox
 create mode 100644 doxygen/dox/H5Ovisit.dox
 create mode 100644 doxygen/dox/H5Ovisit_by_name.dox
 create mode 100644 doxygen/dox/H5Sencode.dox
 create mode 100644 doxygen/dox/mainpage.dox
 create mode 100644 doxygen/dox/rm-template.dox
 create mode 100644 doxygen/examples/H5Fclose.c
 create mode 100644 doxygen/examples/H5Fcreate.c
 create mode 100644 doxygen/examples/hello_hdf5.c
 create mode 100644 doxygen/img/HDFG-logo.png
 create mode 100644 m4/ax_prog_doxygen.m4

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 43088b0..8283fbc 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -225,6 +225,7 @@ set (HDF5_JAVA_LIB_DIR             ${HDF5_SOURCE_DIR}/java/lib)
 set (HDF5_JAVA_LOGGING_JAR         ${HDF5_SOURCE_DIR}/java/lib/slf4j-api-1.7.25.jar)
 set (HDF5_JAVA_LOGGING_NOP_JAR     ${HDF5_SOURCE_DIR}/java/lib/ext/slf4j-nop-1.7.25.jar)
 set (HDF5_JAVA_LOGGING_SIMPLE_JAR  ${HDF5_SOURCE_DIR}/java/lib/ext/slf4j-simple-1.7.25.jar)
+set (HDF5_DOXYGEN_DIR              ${HDF5_SOURCE_DIR}/doxygen)
 
 #-----------------------------------------------------------------------------
 # parse the full version number from H5public.h and include in H5_VERS_INFO
@@ -532,6 +533,20 @@ endif ()
 # endif ()
 
 #-----------------------------------------------------------------------------
+# Option to build documentation
+#-----------------------------------------------------------------------------
+option (HDF5_BUILD_DOC "Build documentation" ON)
+if (HDF5_BUILD_DOC AND EXISTS "${HDF5_DOXYGEN_DIR}" AND IS_DIRECTORY "${HDF5_DOXYGEN_DIR}")
+# check if Doxygen is installed
+  find_package(Doxygen)
+  if (DOXYGEN_FOUND)
+    message(STATUS "Doxygen version: ${DOXYGEN_VERSION}")
+  else ()
+    message(STATUS "Doxygen needs to be installed to generate the doxygen documentation")
+  endif ()
+endif ()
+
+#-----------------------------------------------------------------------------
 # Option to indicate using a memory checker
 #-----------------------------------------------------------------------------
 option (HDF5_ENABLE_USING_MEMCHECKER "Indicate that a memory checker is used" OFF)
diff --git a/Makefile.am b/Makefile.am
index 9cb5d02..21bc550 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -187,6 +187,16 @@ check-all-install:
 trace:
 	@(cd src && $(MAKE) $(AM_MAKEFLAGS) $@) || exit 1;
 
+# Run doxygen across source files.
+# Currently, only invoke doxygen in the src directory.
+doxygen:
+	@echo Invoking doxygen
+	for d in src; do                                                \
+	  if test $$d != .; then                                        \
+	    (cd $$d && $(MAKE) $(AM_MAKEFLAGS) $@) || exit 1;           \
+	  fi;                                                           \
+	done
+
 # Run tests with different Virtual File Drivers.
 # Currently, only invoke check-vfd in the test directory.
 check-vfd:
diff --git a/config/doxygen.am b/config/doxygen.am
new file mode 100644
index 0000000..cf37f1a
--- /dev/null
+++ b/config/doxygen.am
@@ -0,0 +1,156 @@
+## --------------------------------- ##
+## Format-independent Doxygen rules. ##
+## --------------------------------- ##
+
+if DX_COND_doc
+
+## ------------------------------- ##
+## Rules specific for HTML output. ##
+## ------------------------------- ##
+
+if DX_COND_html
+
+DX_CLEAN_HTML = @DX_DOCDIR@/html
+
+endif DX_COND_html
+
+## ------------------------------ ##
+## Rules specific for CHM output. ##
+## ------------------------------ ##
+
+if DX_COND_chm
+
+DX_CLEAN_CHM = @DX_DOCDIR@/chm
+
+if DX_COND_chi
+
+DX_CLEAN_CHI = @DX_DOCDIR@/@PACKAGE@.chi
+
+endif DX_COND_chi
+
+endif DX_COND_chm
+
+## ------------------------------ ##
+## Rules specific for MAN output. ##
+## ------------------------------ ##
+
+if DX_COND_man
+
+DX_CLEAN_MAN = @DX_DOCDIR@/man
+
+endif DX_COND_man
+
+## ------------------------------ ##
+## Rules specific for RTF output. ##
+## ------------------------------ ##
+
+if DX_COND_rtf
+
+DX_CLEAN_RTF = @DX_DOCDIR@/rtf
+
+endif DX_COND_rtf
+
+## ------------------------------ ##
+## Rules specific for XML output. ##
+## ------------------------------ ##
+
+if DX_COND_xml
+
+DX_CLEAN_XML = @DX_DOCDIR@/xml
+
+endif DX_COND_xml
+
+## ----------------------------- ##
+## Rules specific for PS output. ##
+## ----------------------------- ##
+
+if DX_COND_ps
+
+DX_CLEAN_PS = @DX_DOCDIR@/@PACKAGE@.ps
+
+DX_PS_GOAL = doxygen-ps
+
+doxygen-ps: @DX_DOCDIR@/@PACKAGE@.ps
+
+@DX_DOCDIR@/@PACKAGE@.ps: @DX_DOCDIR@/@PACKAGE@.tag
+	cd @DX_DOCDIR@/latex; \
+	rm -f *.aux *.toc *.idx *.ind *.ilg *.log *.out; \
+	$(DX_LATEX) refman.tex; \
+	$(MAKEINDEX_PATH) refman.idx; \
+	$(DX_LATEX) refman.tex; \
+	countdown=5; \
+	while $(DX_EGREP) 'Rerun (LaTeX|to get cross-references right)' \
+	                  refman.log > /dev/null 2>&1 \
+	   && test $$countdown -gt 0; do \
+	    $(DX_LATEX) refman.tex; \
+	    countdown=`expr $$countdown - 1`; \
+	done; \
+	$(DX_DVIPS) -o ../@PACKAGE@.ps refman.dvi
+
+endif DX_COND_ps
+
+## ------------------------------ ##
+## Rules specific for PDF output. ##
+## ------------------------------ ##
+
+if DX_COND_pdf
+
+DX_CLEAN_PDF = @DX_DOCDIR@/@PACKAGE@.pdf
+
+DX_PDF_GOAL = doxygen-pdf
+
+doxygen-pdf: @DX_DOCDIR@/@PACKAGE@.pdf
+
+@DX_DOCDIR@/@PACKAGE@.pdf: @DX_DOCDIR@/@PACKAGE@.tag
+	cd @DX_DOCDIR@/latex; \
+	rm -f *.aux *.toc *.idx *.ind *.ilg *.log *.out; \
+	$(DX_PDFLATEX) refman.tex; \
+	$(DX_MAKEINDEX) refman.idx; \
+	$(DX_PDFLATEX) refman.tex; \
+	countdown=5; \
+	while $(DX_EGREP) 'Rerun (LaTeX|to get cross-references right)' \
+	                  refman.log > /dev/null 2>&1 \
+	   && test $$countdown -gt 0; do \
+	    $(DX_PDFLATEX) refman.tex; \
+	    countdown=`expr $$countdown - 1`; \
+	done; \
+	mv refman.pdf ../@PACKAGE@.pdf
+
+endif DX_COND_pdf
+
+## ------------------------------------------------- ##
+## Rules specific for LaTeX (shared for PS and PDF). ##
+## ------------------------------------------------- ##
+
+if DX_COND_latex
+
+DX_CLEAN_LATEX = @DX_DOCDIR@/latex
+
+endif DX_COND_latex
+
+.PHONY: doxygen-run doxygen-doc $(DX_PS_GOAL) $(DX_PDF_GOAL)
+
+.INTERMEDIATE: doxygen-run $(DX_PS_GOAL) $(DX_PDF_GOAL)
+
+doxygen-run: @DX_DOCDIR@/@PACKAGE@.tag
+
+doxygen-doc: doxygen-run $(DX_PS_GOAL) $(DX_PDF_GOAL)
+
+@DX_DOCDIR@/@PACKAGE@.tag: $(DX_CONFIG) $(pkginclude_HEADERS)
+	rm -rf @DX_DOCDIR@
+	$(DX_ENV) $(DX_DOXYGEN) $(srcdir)/$(DX_CONFIG)
+
+DX_CLEANFILES = \
+	@DX_DOCDIR@/@PACKAGE@.tag \
+	-r \
+	$(DX_CLEAN_HTML) \
+	$(DX_CLEAN_CHM) \
+	$(DX_CLEAN_CHI) \
+	$(DX_CLEAN_MAN) \
+	$(DX_CLEAN_RTF) \
+	$(DX_CLEAN_XML) \
+	$(DX_CLEAN_PS) \
+	$(DX_CLEAN_PDF) \
+	$(DX_CLEAN_LATEX)
+
+endif DX_COND_doc
diff --git a/configure.ac b/configure.ac
index 3dbf73b..e5041c6 100644
--- a/configure.ac
+++ b/configure.ac
@@ -296,7 +296,7 @@ AC_MSG_CHECKING([for clang sanitizer checks])
 AC_ARG_ENABLE([sanitize-checks],
               [AS_HELP_STRING([--enable-sanitize-checks=address],
                               [(clang/clang++ compilers only) Enable sanitize checks.
-                               Address is useful for detecting issues dealing with 
+                               Address is useful for detecting issues dealing with
                                memory. See AddressSanitizer in config/sanitizer/README.md
                                for more information.
                                [default=none]
@@ -311,7 +311,7 @@ fi
 if test "X$CC_BASENAME" = "Xclang"; then
   AC_SUBST([CLANG_SANITIZE_CHECKS])
 
-  # There are several sanitizer tools.  At present we are testing 
+  # There are several sanitizer tools.  At present we are testing
   # and describing only -fsanitizer=address with autotools.
   case "X-$CLANG_SANITIZE_CHECKS" in
     X-no|X-none)
@@ -328,8 +328,8 @@ if test "X$CC_BASENAME" = "Xclang"; then
   # The clang compiler doesn't support some of them; they should be
   # checked before adding them to the list in the help message.
   # The sanitizers/sanitizers.cmake file lists these options:
-  # address, memory, memoryWithOrigins, undefined, thread, leak, 
-  # 'address;undefined'.  Which and which combinations of these are 
+  # address, memory, memoryWithOrigins, undefined, thread, leak,
+  # 'address;undefined'.  Which and which combinations of these are
   #  supported varies by compiler version, but unsupported options
   # or combinations will result in configure errors reported in config.log.
   # Comma separated lists of sanitize options wil be entered intact in
@@ -1049,6 +1049,64 @@ if test "X$HDF5_TOOLS" = "Xno"; then
 fi
 
 ## ----------------------------------------------------------------------
+## Check if they would like to enable building doxygen files
+##
+
+## This needs to be exposed for the library info file.
+AC_SUBST([HDF5_DOXYGEN])
+
+## Default is to build DOXYGEN
+HDF5_DOXYGEN=yes
+
+AC_MSG_CHECKING([if building doxygen is disabled])
+
+AC_ARG_ENABLE([doxygen],
+              [AS_HELP_STRING([--enable-doxygen],
+                              [Compile the HDF5 doxygen files [default=yes]])],
+              [HDF5_DOXYGEN=$enableval])
+
+if test "X$HDF5_DOXYGEN" = "Xyes"; then
+  DX_DOXYGEN_FEATURE(ON)
+  DX_DOT_FEATURE(OFF)
+  DX_HTML_FEATURE(ON)
+  DX_CHM_FEATURE(OFF)
+  DX_CHI_FEATURE(OFF)
+  DX_MAN_FEATURE(OFF)
+  DX_RTF_FEATURE(OFF)
+  DX_XML_FEATURE(OFF)
+  DX_PDF_FEATURE(ON)
+  DX_PS_FEATURE(OFF)
+
+  AC_SUBST([DOXYGEN_PACKAGE])
+  AC_SUBST([DOXYGEN_VERSION_STRING])
+  AC_SUBST([DOXYGEN_INCLUDE_ALIASES])
+  AC_SUBST([DOXYGEN_PROJECT_LOGO])
+  AC_SUBST([DOXYGEN_PROJECT_BRIEF])
+  AC_SUBST([DOXYGEN_INPUT_DIRECTORY])
+  AC_SUBST([DOXYGEN_OPTIMIZE_OUTPUT_FOR_C])
+  AC_SUBST([DOXYGEN_MACRO_EXPANSION])
+  AC_SUBST([DOXYGEN_OUTPUT_DIR])
+
+  DOXYGEN_PACKAGE=${PACKAGE_NAME}
+  DOXYGEN_VERSION_STRING=${PACKAGE_VERSION}
+  DOXYGEN_INCLUDE_ALIASES='$(SRCDIR)/doxygen/aliases'
+  DOXYGEN_PROJECT_LOGO='$(SRCDIR)/doxygen/img/HDFG-logo.png'
+  DOXYGEN_PROJECT_BRIEF="HDF5 (Hierarchical Data Format 5) Software Library and Utilities"
+  DOXYGEN_INPUT_DIRECTORY='$(SRCDIR) $(SRCDIR)/doxygen/dox'
+  DOXYGEN_OPTIMIZE_OUTPUT_FOR_C=YES
+  DOXYGEN_MACRO_EXPANSION=YES
+  DOXYGEN_OUTPUT_DIR=hdf5lib_docs
+
+  DX_INIT_DOXYGEN([HDF5], [doxygen/Doxyfile], [hdf5lib_docs])
+
+  #AC_SUBST([DOXYGEN_OUTPUT_DIR], [hdf5lib_docs])
+
+else
+  AC_MSG_RESULT([no])
+fi
+
+
+## ----------------------------------------------------------------------
 ## Create libtool.  If shared/static libraries are going to be enabled
 ## or disabled, it should happen before these macros.
 LT_PREREQ([2.2])
@@ -3866,6 +3924,7 @@ AM_CONDITIONAL([HAVE_SHARED_CONDITIONAL], [test "X$enable_shared" = "Xyes"])
 
 AC_CONFIG_FILES([src/libhdf5.settings
                  Makefile
+                 doxygen/Doxyfile
                  src/Makefile
                  test/Makefile
                  test/H5srcdir_str.h
diff --git a/doxygen/Doxyfile.in b/doxygen/Doxyfile.in
new file mode 100644
index 0000000..22a16e9
--- /dev/null
+++ b/doxygen/Doxyfile.in
@@ -0,0 +1,2542 @@
+# Doxyfile 1.8.18
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project.
+#
+# All text after a double hash (##) is considered a comment and is placed in
+# front of the TAG it is preceding.
+#
+# All text after a single hash (#) is considered a comment and will be ignored.
+# The format is:
+# TAG = value [value, ...]
+# For lists, items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (\" \").
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# This tag specifies the encoding used for all characters in the configuration
+# file that follow. The default is UTF-8 which is also the encoding used for all
+# text before the first occurrence of this tag. Doxygen uses libiconv (or the
+# iconv built into libc) for the transcoding. See
+# https://www.gnu.org/software/libiconv/ for the list of possible encodings.
+# The default value is: UTF-8.
+
+DOXYFILE_ENCODING      = UTF-8
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
+# double-quotes, unless you are using Doxywizard) that should identify the
+# project for which the documentation is generated. This name is used in the
+# title of most generated pages and in a few other places.
+# The default value is: My Project.
+
+PROJECT_NAME           = @DOXYGEN_PACKAGE@
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
+# could be handy for archiving the generated documentation or if some version
+# control system is used.
+
+PROJECT_NUMBER         = @DOXYGEN_VERSION_STRING@
+
+# Using the PROJECT_BRIEF tag one can provide an optional one line description
+# for a project that appears at the top of each page and should give viewer a
+# quick idea about the purpose of the project. Keep the description short.
+
+PROJECT_BRIEF          = @DOXYGEN_PROJECT_BRIEF@
+
+# With the PROJECT_LOGO tag one can specify a logo or an icon that is included
+# in the documentation. The maximum height of the logo should not exceed 55
+# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
+# the logo to the output directory.
+
+PROJECT_LOGO           = @DOXYGEN_PROJECT_LOGO@
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
+# into which the generated documentation will be written. If a relative path is
+# entered, it will be relative to the location where doxygen was started. If
+# left blank the current directory will be used.
+
+OUTPUT_DIRECTORY       = @DOXYGEN_OUTPUT_DIRECTORY@
+
+# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
+# directories (in 2 levels) under the output directory of each output format and
+# will distribute the generated files over these directories. Enabling this
+# option can be useful when feeding doxygen a huge amount of source files, where
+# putting all generated files in the same directory would otherwise causes
+# performance problems for the file system.
+# The default value is: NO.
+
+CREATE_SUBDIRS         = NO
+
+# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
+# characters to appear in the names of generated files. If set to NO, non-ASCII
+# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
+# U+3044.
+# The default value is: NO.
+
+ALLOW_UNICODE_NAMES    = NO
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all constant output in the proper language.
+# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
+# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
+# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
+# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
+# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
+# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
+# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
+# Ukrainian and Vietnamese.
+# The default value is: English.
+
+OUTPUT_LANGUAGE        = English
+
+# The OUTPUT_TEXT_DIRECTION tag is used to specify the direction in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all generated output in the proper direction.
+# Possible values are: None, LTR, RTL and Context.
+# The default value is: None.
+
+OUTPUT_TEXT_DIRECTION  = None
+
+# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
+# descriptions after the members that are listed in the file and class
+# documentation (similar to Javadoc). Set to NO to disable this.
+# The default value is: YES.
+
+BRIEF_MEMBER_DESC      = YES
+
+# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief
+# description of a member or function before the detailed description
+#
+# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
+# brief descriptions will be completely suppressed.
+# The default value is: YES.
+
+REPEAT_BRIEF           = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator that is
+# used to form the text in various listings. Each string in this list, if found
+# as the leading text of the brief description, will be stripped from the text
+# and the result, after processing the whole list, is used as the annotated
+# text. Otherwise, the brief description is used as-is. If left blank, the
+# following values are used ($name is automatically replaced with the name of
+# the entity):The $name class, The $name widget, The $name file, is, provides,
+# specifies, contains, represents, a, an and the.
+
+ABBREVIATE_BRIEF       = "The $name class" \
+                         "The $name widget" \
+                         "The $name file" \
+                         is \
+                         provides \
+                         specifies \
+                         contains \
+                         represents \
+                         a \
+                         an \
+                         the
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
+# doxygen will generate a detailed section even if there is only a brief
+# description.
+# The default value is: NO.
+
+ALWAYS_DETAILED_SEC    = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
+# inherited members of a class in the documentation of that class as if those
+# members were ordinary class members. Constructors, destructors and assignment
+# operators of the base classes will not be shown.
+# The default value is: NO.
+
+INLINE_INHERITED_MEMB  = NO
+
+# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path
+# before files name in the file list and in the header files. If set to NO the
+# shortest path that makes the file name unique will be used
+# The default value is: YES.
+
+FULL_PATH_NAMES        = YES
+
+# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
+# Stripping is only done if one of the specified strings matches the left-hand
+# part of the path. The tag can be used to show relative paths in the file list.
+# If left blank the directory from which doxygen is run is used as the path to
+# strip.
+#
+# Note that you can specify absolute paths here, but also relative paths, which
+# will be relative from the directory where doxygen is started.
+# This tag requires that the tag FULL_PATH_NAMES is set to YES.
+
+STRIP_FROM_PATH        =
+
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
+# path mentioned in the documentation of a class, which tells the reader which
+# header file to include in order to use a class. If left blank only the name of
+# the header file containing the class definition is used. Otherwise one should
+# specify the list of include paths that are normally passed to the compiler
+# using the -I flag.
+
+STRIP_FROM_INC_PATH    =
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
+# less readable) file names. This can be useful is your file systems doesn't
+# support long names like on DOS, Mac, or CD-ROM.
+# The default value is: NO.
+
+SHORT_NAMES            = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
+# first line (until the first dot) of a Javadoc-style comment as the brief
+# description. If set to NO, the Javadoc-style will behave just like regular Qt-
+# style comments (thus requiring an explicit @brief command for a brief
+# description.)
+# The default value is: NO.
+
+JAVADOC_AUTOBRIEF      = NO
+
+# If the JAVADOC_BANNER tag is set to YES then doxygen will interpret a line
+# such as
+# /***************
+# as being the beginning of a Javadoc-style comment "banner". If set to NO, the
+# Javadoc-style will behave just like regular comments and it will not be
+# interpreted by doxygen.
+# The default value is: NO.
+
+JAVADOC_BANNER         = NO
+
+# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
+# line (until the first dot) of a Qt-style comment as the brief description. If
+# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
+# requiring an explicit \brief command for a brief description.)
+# The default value is: NO.
+
+QT_AUTOBRIEF           = NO
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
+# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
+# a brief description. This used to be the default behavior. The new default is
+# to treat a multi-line C++ comment block as a detailed description. Set this
+# tag to YES if you prefer the old behavior instead.
+#
+# Note that setting this tag to YES also means that rational rose comments are
+# not recognized any more.
+# The default value is: NO.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
+# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
+# documentation from any documented member that it re-implements.
+# The default value is: YES.
+
+INHERIT_DOCS           = YES
+
+# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new
+# page for each member. If set to NO, the documentation of a member will be part
+# of the file/class/namespace that contains it.
+# The default value is: NO.
+
+SEPARATE_MEMBER_PAGES  = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
+# uses this value to replace tabs by spaces in code fragments.
+# Minimum value: 1, maximum value: 16, default value: 4.
+
+TAB_SIZE               = 4
+
+# This tag can be used to specify a number of aliases that act as commands in
+# the documentation. An alias has the form:
+# name=value
+# For example adding
+# "sideeffect=@par Side Effects:\n"
+# will allow you to put the command \sideeffect (or @sideeffect) in the
+# documentation, which will result in a user-defined paragraph with heading
+# "Side Effects:". You can put \n's in the value part of an alias to insert
+# newlines (in the resulting output). You can put ^^ in the value part of an
+# alias to insert a newline as if a physical newline was in the original file.
+# When you need a literal { or } or , in the value part of an alias you have to
+# escape them by means of a backslash (\), this can lead to conflicts with the
+# commands \{ and \} for these it is advised to use the version @{ and @} or use
+# a double escape (\\{ and \\})
+
+ALIASES                =
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
+# only. Doxygen will then generate output that is more tailored for C. For
+# instance, some of the names that are used will be different. The list of all
+# members will be omitted, etc.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_FOR_C  = YES
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
+# Python sources only. Doxygen will then generate output that is more tailored
+# for that language. For instance, namespaces will be presented as packages,
+# qualified scopes will look different, etc.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_JAVA   = NO
+
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+# sources. Doxygen will then generate output that is tailored for Fortran.
+# The default value is: NO.
+
+OPTIMIZE_FOR_FORTRAN   = NO
+
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
+# sources. Doxygen will then generate output that is tailored for VHDL.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_VHDL   = NO
+
+# Set the OPTIMIZE_OUTPUT_SLICE tag to YES if your project consists of Slice
+# sources only. Doxygen will then generate output that is more tailored for that
+# language. For instance, namespaces will be presented as modules, types will be
+# separated into more groups, etc.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_SLICE  = NO
+
+# Doxygen selects the parser to use depending on the extension of the files it
+# parses. With this tag you can assign which parser to use for a given
+# extension. Doxygen has a built-in mapping, but you can override or extend it
+# using this tag. The format is ext=language, where ext is a file extension, and
+# language is one of the parsers supported by doxygen: IDL, Java, JavaScript,
+# Csharp (C#), C, C++, D, PHP, md (Markdown), Objective-C, Python, Slice, VHDL,
+# Fortran (fixed format Fortran: FortranFixed, free formatted Fortran:
+# FortranFree, unknown formatted Fortran: Fortran. In the later case the parser
+# tries to guess whether the code is fixed or free formatted code, this is the
+# default for Fortran type files). For instance to make doxygen treat .inc files
+# as Fortran files (default is PHP), and .f files as C (default is Fortran),
+# use: inc=Fortran f=C.
+#
+# Note: For files without extension you can use no_extension as a placeholder.
+#
+# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
+# the files are not read by doxygen.
+
+EXTENSION_MAPPING      =
+
+# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
+# according to the Markdown format, which allows for more readable
+# documentation. See https://daringfireball.net/projects/markdown/ for details.
+# The output of markdown processing is further processed by doxygen, so you can
+# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
+# case of backward compatibilities issues.
+# The default value is: YES.
+
+MARKDOWN_SUPPORT       = YES
+
+# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up
+# to that level are automatically included in the table of contents, even if
+# they do not have an id attribute.
+# Note: This feature currently applies only to Markdown headings.
+# Minimum value: 0, maximum value: 99, default value: 5.
+# This tag requires that the tag MARKDOWN_SUPPORT is set to YES.
+
+TOC_INCLUDE_HEADINGS   = 5
+
+# When enabled doxygen tries to link words that correspond to documented
+# classes, or namespaces to their corresponding documentation. Such a link can
+# be prevented in individual cases by putting a % sign in front of the word or
+# globally by setting AUTOLINK_SUPPORT to NO.
+# The default value is: YES.
+
+AUTOLINK_SUPPORT       = YES
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should set this
+# tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string);
+# versus func(std::string) {}). This also make the inheritance and collaboration
+# diagrams that involve STL classes more complete and accurate.
+# The default value is: NO.
+
+BUILTIN_STL_SUPPORT    = NO
+
+# If you use Microsoft's C++/CLI language, you should set this option to YES to
+# enable parsing support.
+# The default value is: NO.
+
+CPP_CLI_SUPPORT        = NO
+
+# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
+# https://www.riverbankcomputing.com/software/sip/intro) sources only. Doxygen
+# will parse them like normal C++ but will assume all classes use public instead
+# of private inheritance when no explicit protection keyword is present.
+# The default value is: NO.
+
+SIP_SUPPORT            = NO
+
+# For Microsoft's IDL there are propget and propput attributes to indicate
+# getter and setter methods for a property. Setting this option to YES will make
+# doxygen to replace the get and set methods by a property in the documentation.
+# This will only work if the methods are indeed getting or setting a simple
+# type. If this is not the case, or you want to show the methods anyway, you
+# should set this option to NO.
+# The default value is: YES.
+
+IDL_PROPERTY_SUPPORT   = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
+# all members of a group must be documented explicitly.
+# The default value is: NO.
+
+DISTRIBUTE_GROUP_DOC   = NO
+
+# If one adds a struct or class to a group and this option is enabled, then also
+# any nested class or struct is added to the same group. By default this option
+# is disabled and one has to add nested compounds explicitly via \ingroup.
+# The default value is: NO.
+
+GROUP_NESTED_COMPOUNDS = NO
+
+# Set the SUBGROUPING tag to YES to allow class member groups of the same type
+# (for instance a group of public functions) to be put as a subgroup of that
+# type (e.g. under the Public Functions section). Set it to NO to prevent
+# subgrouping. Alternatively, this can be done per class using the
+# \nosubgrouping command.
+# The default value is: YES.
+
+SUBGROUPING            = YES
+
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
+# are shown inside the group in which they are included (e.g. using \ingroup)
+# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
+# and RTF).
+#
+# Note that this feature does not work in combination with
+# SEPARATE_MEMBER_PAGES.
+# The default value is: NO.
+
+INLINE_GROUPED_CLASSES = NO
+
+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
+# with only public data fields or simple typedef fields will be shown inline in
+# the documentation of the scope in which they are defined (i.e. file,
+# namespace, or group documentation), provided this scope is documented. If set
+# to NO, structs, classes, and unions are shown on a separate page (for HTML and
+# Man pages) or section (for LaTeX and RTF).
+# The default value is: NO.
+
+INLINE_SIMPLE_STRUCTS  = NO
+
+# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
+# enum is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically be
+# useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+# The default value is: NO.
+
+TYPEDEF_HIDES_STRUCT   = YES
+
+# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
+# cache is used to resolve symbols given their name and scope. Since this can be
+# an expensive process and often the same symbol appears multiple times in the
+# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
+# doxygen will become slower. If the cache is too large, memory is wasted. The
+# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
+# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
+# symbols. At the end of a run doxygen will report the cache usage and suggest
+# the optimal cache size from a speed point of view.
+# Minimum value: 0, maximum value: 9, default value: 0.
+
+LOOKUP_CACHE_SIZE      = 0
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
+# documentation are documented, even if no documentation was available. Private
+# class members and static file members will be hidden unless the
+# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
+# Note: This will also disable the warnings about undocumented members that are
+# normally produced when WARNINGS is set to YES.
+# The default value is: NO.
+
+EXTRACT_ALL            = YES
+
+# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
+# be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PRIVATE        = NO
+
+# If the EXTRACT_PRIV_VIRTUAL tag is set to YES, documented private virtual
+# methods of a class will be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PRIV_VIRTUAL   = NO
+
+# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
+# scope will be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PACKAGE        = NO
+
+# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
+# included in the documentation.
+# The default value is: NO.
+
+EXTRACT_STATIC         = YES
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
+# locally in source files will be included in the documentation. If set to NO,
+# only classes defined in header files are included. Does not have any effect
+# for Java sources.
+# The default value is: YES.
+
+EXTRACT_LOCAL_CLASSES  = YES
+
+# This flag is only useful for Objective-C code. If set to YES, local methods,
+# which are defined in the implementation section but not in the interface are
+# included in the documentation. If set to NO, only methods in the interface are
+# included.
+# The default value is: NO.
+
+EXTRACT_LOCAL_METHODS  = NO
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base name of
+# the file that contains the anonymous namespace. By default anonymous namespace
+# are hidden.
+# The default value is: NO.
+
+EXTRACT_ANON_NSPACES   = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
+# undocumented members inside documented classes or files. If set to NO these
+# members will be included in the various overviews, but no documentation
+# section is generated. This option has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_MEMBERS     = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy. If set
+# to NO, these classes will be included in the various overviews. This option
+# has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_CLASSES     = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
+# declarations. If set to NO, these declarations will be included in the
+# documentation.
+# The default value is: NO.
+
+HIDE_FRIEND_COMPOUNDS  = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
+# documentation blocks found inside the body of a function. If set to NO, these
+# blocks will be appended to the function's detailed documentation block.
+# The default value is: NO.
+
+HIDE_IN_BODY_DOCS      = NO
+
+# The INTERNAL_DOCS tag determines if documentation that is typed after a
+# \internal command is included. If the tag is set to NO then the documentation
+# will be excluded. Set it to YES to include the internal documentation.
+# The default value is: NO.
+
+INTERNAL_DOCS          = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
+# names in lower-case letters. If set to YES, upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# (including Cygwin) ands Mac users are advised to set this option to NO.
+# The default value is: system dependent.
+
+CASE_SENSE_NAMES       = NO
+
+# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
+# their full class and namespace scopes in the documentation. If set to YES, the
+# scope will be hidden.
+# The default value is: NO.
+
+HIDE_SCOPE_NAMES       = YES
+
+# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
+# append additional text to a page's title, such as Class Reference. If set to
+# YES the compound reference will be hidden.
+# The default value is: NO.
+
+HIDE_COMPOUND_REFERENCE= NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
+# the files that are included by a file in the documentation of that file.
+# The default value is: YES.
+
+SHOW_INCLUDE_FILES     = YES
+
+# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
+# grouped member an include statement to the documentation, telling the reader
+# which file to include in order to use the member.
+# The default value is: NO.
+
+SHOW_GROUPED_MEMB_INC  = NO
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
+# files with double quotes in the documentation rather than with sharp brackets.
+# The default value is: NO.
+
+FORCE_LOCAL_INCLUDES   = NO
+
+# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
+# documentation for inline members.
+# The default value is: YES.
+
+INLINE_INFO            = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
+# (detailed) documentation of file and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order.
+# The default value is: YES.
+
+SORT_MEMBER_DOCS       = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
+# descriptions of file, namespace and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order. Note that
+# this will also influence the order of the classes in the class list.
+# The default value is: NO.
+
+SORT_BRIEF_DOCS        = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
+# (brief and detailed) documentation of class members so that constructors and
+# destructors are listed first. If set to NO the constructors will appear in the
+# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
+# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
+# member documentation.
+# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
+# detailed member documentation.
+# The default value is: NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
+# of group names into alphabetical order. If set to NO the group names will
+# appear in their defined order.
+# The default value is: NO.
+
+SORT_GROUP_NAMES       = YES
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
+# fully-qualified names, including namespaces. If set to NO, the class list will
+# be sorted only by class name, not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the alphabetical
+# list.
+# The default value is: NO.
+
+SORT_BY_SCOPE_NAME     = NO
+
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
+# type resolution of all parameters of a function it will reject a match between
+# the prototype and the implementation of a member function even if there is
+# only one candidate or it is obvious which candidate to choose by doing a
+# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
+# accept a match between prototype and implementation in such cases.
+# The default value is: NO.
+
+STRICT_PROTO_MATCHING  = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
+# list. This list is created by putting \todo commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TODOLIST      = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
+# list. This list is created by putting \test commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TESTLIST      = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
+# list. This list is created by putting \bug commands in the documentation.
+# The default value is: YES.
+
+GENERATE_BUGLIST       = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
+# the deprecated list. This list is created by putting \deprecated commands in
+# the documentation.
+# The default value is: YES.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional documentation
+# sections, marked by \if  ... \endif and \cond 
+# ... \endcond blocks.
+
+ENABLED_SECTIONS       =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
+# initial value of a variable or macro / define can have for it to appear in the
+# documentation. If the initializer consists of more lines than specified here
+# it will be hidden. Use a value of 0 to hide initializers completely. The
+# appearance of the value of individual variables and macros / defines can be
+# controlled using \showinitializer or \hideinitializer command in the
+# documentation regardless of this setting.
+# Minimum value: 0, maximum value: 10000, default value: 30.
+
+MAX_INITIALIZER_LINES  = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
+# the bottom of the documentation of classes and structs. If set to YES, the
+# list will mention the files that were used to generate the documentation.
+# The default value is: YES.
+
+SHOW_USED_FILES        = YES
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
+# will remove the Files entry from the Quick Index and from the Folder Tree View
+# (if specified).
+# The default value is: YES.
+
+SHOW_FILES             = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
+# page. This will remove the Namespaces entry from the Quick Index and from the
+# Folder Tree View (if specified).
+# The default value is: YES.
+
+SHOW_NAMESPACES        = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command command input-file, where command is the value of the
+# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
+# by doxygen. Whatever the program writes to standard output is used as the file
+# version. For an example see the documentation.
+
+FILE_VERSION_FILTER    =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. To create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option. You can
+# optionally specify a file name after the option, if omitted DoxygenLayout.xml
+# will be used as the name of the layout file.
+#
+# Note that if you run doxygen from a directory containing a file called
+# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
+# tag is left empty.
+
+LAYOUT_FILE            =
+
+# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
+# the reference definitions. This must be a list of .bib files. The .bib
+# extension is automatically appended if omitted. This requires the bibtex tool
+# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info.
+# For LaTeX the style of the bibliography can be controlled using
+# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
+# search path. See also \cite for info how to create references.
+
+CITE_BIB_FILES         =
+
+#---------------------------------------------------------------------------
+# Configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated to
+# standard output by doxygen. If QUIET is set to YES this implies that the
+# messages are off.
+# The default value is: NO.
+
+QUIET                  = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
+# this implies that the warnings are on.
+#
+# Tip: Turn warnings on while writing the documentation.
+# The default value is: YES.
+
+WARNINGS               = YES
+
+# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
+# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
+# will automatically be disabled.
+# The default value is: YES.
+
+WARN_IF_UNDOCUMENTED   = YES
+
+# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some parameters
+# in a documented function, or documenting parameters that don't exist or using
+# markup commands wrongly.
+# The default value is: YES.
+
+WARN_IF_DOC_ERROR      = YES
+
+# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
+# are documented, but have no documentation for their parameters or return
+# value. If set to NO, doxygen will only warn about wrong or incomplete
+# parameter documentation, but not about the absence of documentation. If
+# EXTRACT_ALL is set to YES then this flag will automatically be disabled.
+# The default value is: NO.
+
+WARN_NO_PARAMDOC       = NO
+
+# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
+# a warning is encountered.
+# The default value is: NO.
+
+WARN_AS_ERROR          = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that doxygen
+# can produce. The string should contain the $file, $line, and $text tags, which
+# will be replaced by the file and line number from which the warning originated
+# and the warning text. Optionally the format may contain $version, which will
+# be replaced by the version of the file (if it could be obtained via
+# FILE_VERSION_FILTER)
+# The default value is: $file:$line: $text.
+
+WARN_FORMAT            = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning and error
+# messages should be written. If left blank the output is written to standard
+# error (stderr).
+
+WARN_LOGFILE           =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag is used to specify the files and/or directories that contain
+# documented source files. You may enter file names like myfile.cpp or
+# directories like /usr/src/myproject. Separate the files or directories with
+# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
+# Note: If this tag is empty the current directory is searched.
+
+INPUT                  = @DOXYGEN_INPUT_DIRECTORY@
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
+# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
+# documentation (see: https://www.gnu.org/software/libiconv/) for the list of
+# possible encodings.
+# The default value is: UTF-8.
+
+INPUT_ENCODING         = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
+# *.h) to filter out the source-files in the directories.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# read by doxygen.
+#
+# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
+# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
+# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
+# *.m, *.markdown, *.md, *.mm, *.dox (to be provided as doxygen C comment),
+# *.doc (to be provided as doxygen C comment), *.txt (to be provided as doxygen
+# C comment), *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, *.f18, *.f, *.for, *.vhd,
+# *.vhdl, *.ucf, *.qsf and *.ice.
+
+FILE_PATTERNS          = H5*public.h \
+                         H5*module.h \
+                         H5VLconnector.h \
+                         H5VLconnector_passthru.h \
+                         H5VLnative.h \
+                         H5version.h \
+                         *.dox
+
+# The RECURSIVE tag can be used to specify whether or not subdirectories should
+# be searched for input files as well.
+# The default value is: NO.
+
+RECURSIVE              = YES
+
+# The EXCLUDE tag can be used to specify files and/or directories that should be
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+#
+# Note that relative paths are relative to the directory from which doxygen is
+# run.
+
+EXCLUDE                = examples
+
+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
+# directories that are symbolic links (a Unix file system feature) are excluded
+# from the input.
+# The default value is: NO.
+
+EXCLUDE_SYMLINKS       = NO
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories.
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories for example use the pattern */test/*
+
+EXCLUDE_PATTERNS       =
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories use the pattern */test/*
+
+EXCLUDE_SYMBOLS        =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or directories
+# that contain example code fragments that are included (see the \include
+# command).
+
+EXAMPLE_PATH           = ../src ../examples ../test examples
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
+# *.h) to filter out the source-files in the directories. If left blank all
+# files are included.
+
+EXAMPLE_PATTERNS       = *.c
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude commands
+# irrespective of the value of the RECURSIVE tag.
+# The default value is: NO.
+
+EXAMPLE_RECURSIVE      = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or directories
+# that contain images that are to be included in the documentation (see the
+# \image command).
+
+IMAGE_PATH             =
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command:
+#
+#  
+#
+# where  is the value of the INPUT_FILTER tag, and  is the
+# name of an input file. Doxygen will then use the output that the filter
+# program writes to standard output. If FILTER_PATTERNS is specified, this tag
+# will be ignored.
+#
+# Note that the filter must not add or remove lines; it is applied before the
+# code is scanned, but not when the output code is generated. If lines are added
+# or removed, the anchors will not be placed correctly.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
+
+INPUT_FILTER           =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis. Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match. The filters are a list of the form: pattern=filter
+# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
+# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
+# patterns match the file name, INPUT_FILTER is applied.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
+
+FILTER_PATTERNS        =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will also be used to filter the input files that are used for
+# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# The default value is: NO.
+
+FILTER_SOURCE_FILES    = NO
+
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
+# it is also possible to disable source filtering for a specific pattern using
+# *.ext= (so without naming a filter).
+# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
+
+FILTER_SOURCE_PATTERNS =
+
+# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page
+# (index.html). This can be useful if you have a project on for instance GitHub
+# and want to reuse the introduction page also for the doxygen output.
+
+USE_MDFILE_AS_MAINPAGE =
+
+#---------------------------------------------------------------------------
+# Configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
+# generated. Documented entities will be cross-referenced with these sources.
+#
+# Note: To get rid of all source code in the generated output, make sure that
+# also VERBATIM_HEADERS is set to NO.
+# The default value is: NO.
+
+SOURCE_BROWSER         = NO
+
+# Setting the INLINE_SOURCES tag to YES will include the body of functions,
+# classes and enums directly into the documentation.
+# The default value is: NO.
+
+INLINE_SOURCES         = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
+# special comment blocks from generated source code fragments. Normal C, C++ and
+# Fortran comments will always remain visible.
+# The default value is: YES.
+
+STRIP_CODE_COMMENTS    = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
+# entity all documented functions referencing it will be listed.
+# The default value is: NO.
+
+REFERENCED_BY_RELATION = NO
+
+# If the REFERENCES_RELATION tag is set to YES then for each documented function
+# all documented entities called/used by that function will be listed.
+# The default value is: NO.
+
+REFERENCES_RELATION    = NO
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
+# to YES then the hyperlinks from functions in REFERENCES_RELATION and
+# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
+# link to the documentation.
+# The default value is: YES.
+
+REFERENCES_LINK_SOURCE = NO
+
+# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
+# source code will show a tooltip with additional information such as prototype,
+# brief description and links to the definition and documentation. Since this
+# will make the HTML file larger and loading of large files a bit slower, you
+# can opt to disable this feature.
+# The default value is: YES.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+SOURCE_TOOLTIPS        = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code will
+# point to the HTML generated by the htags(1) tool instead of doxygen built-in
+# source browser. The htags tool is part of GNU's global source tagging system
+# (see https://www.gnu.org/software/global/global.html). You will need version
+# 4.8.6 or higher.
+#
+# To use it do the following:
+# - Install the latest version of global
+# - Enable SOURCE_BROWSER and USE_HTAGS in the configuration file
+# - Make sure the INPUT points to the root of the source tree
+# - Run doxygen as normal
+#
+# Doxygen will invoke htags (and that will in turn invoke gtags), so these
+# tools must be available from the command line (i.e. in the search path).
+#
+# The result: instead of the source browser generated by doxygen, the links to
+# source code will now point to the output of htags.
+# The default value is: NO.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+USE_HTAGS              = NO
+
+# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
+# verbatim copy of the header file for each class for which an include is
+# specified. Set to NO to disable this.
+# See also: Section \class.
+# The default value is: YES.
+
+VERBATIM_HEADERS       = NO
+
+# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the
+# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the
+# cost of reduced performance. This can be particularly helpful with template
+# rich C++ code for which doxygen's built-in parser lacks the necessary type
+# information.
+# Note: The availability of this option depends on whether or not doxygen was
+# generated with the -Duse_libclang=ON option for CMake.
+# The default value is: NO.
+
+CLANG_ASSISTED_PARSING = NO
+
+# If clang assisted parsing is enabled you can provide the compiler with command
+# line options that you would normally use when invoking the compiler. Note that
+# the include paths will already be set by doxygen for the files and directories
+# specified with INPUT and INCLUDE_PATH.
+# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
+
+CLANG_OPTIONS          =
+
+# If clang assisted parsing is enabled you can provide the clang parser with the
+# path to the compilation database (see:
+# http://clang.llvm.org/docs/HowToSetupToolingForLLVM.html) used when the files
+# were built. This is equivalent to specifying the "-p" option to a clang tool,
+# such as clang-check. These options will then be passed to the parser.
+# Note: The availability of this option depends on whether or not doxygen was
+# generated with the -Duse_libclang=ON option for CMake.
+
+CLANG_DATABASE_PATH    =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
+# compounds will be generated. Enable this if the project contains a lot of
+# classes, structs, unions or interfaces.
+# The default value is: YES.
+
+ALPHABETICAL_INDEX     = YES
+
+# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
+# which the alphabetical index list will be split.
+# Minimum value: 1, maximum value: 20, default value: 5.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+COLS_IN_ALPHA_INDEX    = 5
+
+# In case all classes in a project start with a common prefix, all classes will
+# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
+# can be used to specify a prefix (or a list of prefixes) that should be ignored
+# while generating the index headers.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+IGNORE_PREFIX          = H5
+
+#---------------------------------------------------------------------------
+# Configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
+# The default value is: YES.
+
+GENERATE_HTML          = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_OUTPUT            = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
+# generated HTML page (for example: .htm, .php, .asp).
+# The default value is: .html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FILE_EXTENSION    = .html
+
+# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
+# each generated HTML page. If the tag is left blank doxygen will generate a
+# standard header.
+#
+# To get valid HTML the header file that includes any scripts and style sheets
+# that doxygen needs, which is dependent on the configuration options used (e.g.
+# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
+# default header using
+# doxygen -w html new_header.html new_footer.html new_stylesheet.css
+# YourConfigFile
+# and then modify the file new_header.html. See also section "Doxygen usage"
+# for information on how to generate the default header that doxygen normally
+# uses.
+# Note: The header is subject to change so you typically have to regenerate the
+# default header when upgrading to a newer version of doxygen. For a description
+# of the possible markers and block names see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_HEADER            =
+
+# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
+# generated HTML page. If the tag is left blank doxygen will generate a standard
+# footer. See HTML_HEADER for more information on how to generate a default
+# footer and what special commands can be used inside the footer. See also
+# section "Doxygen usage" for information on how to generate the default footer
+# that doxygen normally uses.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FOOTER            =
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
+# sheet that is used by each HTML page. It can be used to fine-tune the look of
+# the HTML output. If left blank doxygen will generate a default style sheet.
+# See also section "Doxygen usage" for information on how to generate the style
+# sheet that doxygen normally uses.
+# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
+# it is more robust and this tag (HTML_STYLESHEET) will in the future become
+# obsolete.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_STYLESHEET        =
+
+# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# cascading style sheets that are included after the standard style sheets
+# created by doxygen. Using this option one can overrule certain style aspects.
+# This is preferred over using HTML_STYLESHEET since it does not replace the
+# standard style sheet and is therefore more robust against future updates.
+# Doxygen will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list). For an example see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_STYLESHEET  =
+
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
+# files will be copied as-is; there are no commands or markers available.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_FILES       =
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
+# will adjust the colors in the style sheet and background images according to
+# this color. Hue is specified as an angle on a colorwheel, see
+# https://en.wikipedia.org/wiki/Hue for more information. For instance the value
+# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
+# purple, and 360 is red again.
+# Minimum value: 0, maximum value: 359, default value: 220.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_HUE    = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
+# in the HTML output. For a value of 0 the output will use grayscales only. A
+# value of 255 will produce the most vivid colors.
+# Minimum value: 0, maximum value: 255, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_SAT    = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
+# luminance component of the colors in the HTML output. Values below 100
+# gradually make the output lighter, whereas values above 100 make the output
+# darker. The value divided by 100 is the actual gamma applied, so 80 represents
+# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
+# change the gamma.
+# Minimum value: 40, maximum value: 240, default value: 80.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_GAMMA  = 80
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting this
+# to YES can help to show when doxygen was last run and thus if the
+# documentation is up to date.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_TIMESTAMP         = YES
+
+# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML
+# documentation will contain a main index with vertical navigation menus that
+# are dynamically created via JavaScript. If disabled, the navigation index will
+# consists of multiple levels of tabs that are statically embedded in every HTML
+# page. Disable this option to support browsers that do not have JavaScript,
+# like the Qt help browser.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_DYNAMIC_MENUS     = NO
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_DYNAMIC_SECTIONS  = NO
+
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
+# shown in the various tree structured indices initially; the user can expand
+# and collapse entries dynamically later on. Doxygen will expand the tree to
+# such a level that at most the specified number of entries are visible (unless
+# a fully collapsed tree already exceeds this amount). So setting the number of
+# entries 1 will produce a full collapsed tree by default. 0 is a special value
+# representing an infinite number of entries and will result in a full expanded
+# tree by default.
+# Minimum value: 0, maximum value: 9999, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files will be
+# generated that can be used as input for Apple's Xcode 3 integrated development
+# environment (see: https://developer.apple.com/xcode/), introduced with OSX
+# 10.5 (Leopard). To create a documentation set, doxygen will generate a
+# Makefile in the HTML output directory. Running make will produce the docset in
+# that directory and running make install will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
+# startup. See https://developer.apple.com/library/archive/featuredarticles/Doxy
+# genXcode/_index.html for more information.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_DOCSET        = NO
+
+# This tag determines the name of the docset feed. A documentation feed provides
+# an umbrella under which multiple documentation sets from a single provider
+# (such as a company or product suite) can be grouped.
+# The default value is: Doxygen generated docs.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_FEEDNAME        = "Doxygen generated docs"
+
+# This tag specifies a string that should uniquely identify the documentation
+# set bundle. This should be a reverse domain-name style string, e.g.
+# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_BUNDLE_ID       = org.doxygen.Project
+
+# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
+# string, e.g. com.mycompany.MyDocSet.documentation.
+# The default value is: org.doxygen.Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
+
+# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
+# The default value is: Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_NAME  = Publisher
+
+# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
+# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
+# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
+# (see: https://www.microsoft.com/en-us/download/details.aspx?id=21138) on
+# Windows.
+#
+# The HTML Help Workshop contains a compiler that can convert all HTML output
+# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
+# files are now used as the Windows 98 help format, and will replace the old
+# Windows help format (.hlp) on all Windows platforms in the future. Compressed
+# HTML files also contain an index, a table of contents, and you can search for
+# words in the documentation. The HTML workshop also contains a viewer for
+# compressed HTML files.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_HTMLHELP      = NO
+
+# The CHM_FILE tag can be used to specify the file name of the resulting .chm
+# file. You can add a path in front of the file if the result should not be
+# written to the html output directory.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_FILE               =
+
+# The HHC_LOCATION tag can be used to specify the location (absolute path
+# including file name) of the HTML help compiler (hhc.exe). If non-empty,
+# doxygen will try to run the HTML help compiler on the generated index.hhp.
+# The file has to be specified with full path.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+HHC_LOCATION           =
+
+# The GENERATE_CHI flag controls if a separate .chi index file is generated
+# (YES) or that it should be included in the master .chm file (NO).
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+GENERATE_CHI           = NO
+
+# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
+# and project file content.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_INDEX_ENCODING     =
+
+# The BINARY_TOC flag controls whether a binary table of contents is generated
+# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
+# enables the Previous and Next buttons.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+BINARY_TOC             = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members to
+# the table of contents of the HTML help documentation and to the tree view.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+TOC_EXPAND             = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
+# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
+# (.qch) of the generated HTML documentation.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_QHP           = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
+# the file name of the resulting .qch file. The path specified is relative to
+# the HTML output folder.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QCH_FILE               =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
+# Project output. For more information please see Qt Help Project / Namespace
+# (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#namespace).
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_NAMESPACE          = org.doxygen.Project
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
+# Help Project output. For more information please see Qt Help Project / Virtual
+# Folders (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#virtual-
+# folders).
+# The default value is: doc.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_VIRTUAL_FOLDER     = doc
+
+# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
+# filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_NAME   =
+
+# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_ATTRS  =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's filter section matches. Qt Help Project / Filter Attributes (see:
+# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#filter-attributes).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_SECT_FILTER_ATTRS  =
+
+# The QHG_LOCATION tag can be used to specify the location of Qt's
+# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
+# generated .qhp file.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHG_LOCATION           =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
+# generated, together with the HTML files, they form an Eclipse help plugin. To
+# install this plugin and make it available under the help contents menu in
+# Eclipse, the contents of the directory containing the HTML and XML files needs
+# to be copied into the plugins directory of eclipse. The name of the directory
+# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
+# After copying Eclipse needs to be restarted before the help appears.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_ECLIPSEHELP   = NO
+
+# A unique identifier for the Eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have this
+# name. Each documentation set should have its own identifier.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
+
+ECLIPSE_DOC_ID         = org.doxygen.Project
+
+# If you want full control over the layout of the generated HTML pages it might
+# be necessary to disable the index and replace it with your own. The
+# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
+# of each HTML page. A value of NO enables the index and the value YES disables
+# it. Since the tabs in the index contain the same information as the navigation
+# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+DISABLE_INDEX          = NO
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information. If the tag
+# value is set to YES, a side panel will be generated containing a tree-like
+# index structure (just like the one that is generated for HTML Help). For this
+# to work a browser that supports JavaScript, DHTML, CSS and frames is required
+# (i.e. any modern browser). Windows users are probably better off using the
+# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
+# further fine-tune the look of the index. As an example, the default style
+# sheet generated by doxygen has an example that shows how to put an image at
+# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
+# the same information as the tab index, you could consider setting
+# DISABLE_INDEX to YES when enabling this option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_TREEVIEW      = YES
+
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
+# doxygen will group on one line in the generated HTML documentation.
+#
+# Note that a value of 0 will completely suppress the enum values from appearing
+# in the overview section.
+# Minimum value: 0, maximum value: 20, default value: 4.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+ENUM_VALUES_PER_LINE   = 4
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
+# to set the initial width (in pixels) of the frame in which the tree is shown.
+# Minimum value: 0, maximum value: 1500, default value: 250.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+TREEVIEW_WIDTH         = 250
+
+# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
+# external symbols imported via tag files in a separate window.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+EXT_LINKS_IN_WINDOW    = NO
+
+# If the HTML_FORMULA_FORMAT option is set to svg, doxygen will use the pdf2svg
+# tool (see https://github.com/dawbarton/pdf2svg) or inkscape (see
+# https://inkscape.org) to generate formulas as SVG images instead of PNGs for
+# the HTML output. These images will generally look nicer at scaled resolutions.
+# Possible values are: png The default and svg Looks nicer but requires the
+# pdf2svg tool.
+# The default value is: png.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FORMULA_FORMAT    = png
+
+# Use this tag to change the font size of LaTeX formulas included as images in
+# the HTML documentation. When you change the font size after a successful
+# doxygen run you need to manually remove any form_*.png images from the HTML
+# output directory to force them to be regenerated.
+# Minimum value: 8, maximum value: 50, default value: 10.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_FONTSIZE       = 10
+
+# Use the FORMULA_TRANSPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are not
+# supported properly for IE 6.0, but are supported on all modern browsers.
+#
+# Note that when changing this option you need to delete any form_*.png files in
+# the HTML output directory before the changes have effect.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_TRANSPARENT    = YES
+
+# The FORMULA_MACROFILE can contain LaTeX \newcommand and \renewcommand commands
+# to create new LaTeX commands to be used in formulas as building blocks. See
+# the section "Including formulas" for details.
+
+FORMULA_MACROFILE      =
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
+# https://www.mathjax.org) which uses client side JavaScript for the rendering
+# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
+# installed or if you want to formulas look prettier in the HTML output. When
+# enabled you may also need to install MathJax separately and configure the path
+# to it using the MATHJAX_RELPATH option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+USE_MATHJAX            = NO
+
+# When MathJax is enabled you can set the default output format to be used for
+# the MathJax output. See the MathJax site (see:
+# http://docs.mathjax.org/en/latest/output.html) for more details.
+# Possible values are: HTML-CSS (which is slower, but has the best
+# compatibility), NativeMML (i.e. MathML) and SVG.
+# The default value is: HTML-CSS.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_FORMAT         = HTML-CSS
+
+# When MathJax is enabled you need to specify the location relative to the HTML
+# output directory using the MATHJAX_RELPATH option. The destination directory
+# should contain the MathJax.js script. For instance, if the mathjax directory
+# is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
+# Content Delivery Network so you can quickly see the result without installing
+# MathJax. However, it is strongly recommended to install a local copy of
+# MathJax from https://www.mathjax.org before deployment.
+# The default value is: https://cdn.jsdelivr.net/npm/mathjax@2.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_RELPATH        = https://cdn.jsdelivr.net/npm/mathjax@2
+
+# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
+# extension names that should be enabled during MathJax rendering. For example
+# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_EXTENSIONS     =
+
+# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
+# of code that will be used on startup of the MathJax code. See the MathJax site
+# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
+# example see the documentation.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_CODEFILE       =
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
+# the HTML output. The underlying search engine uses javascript and DHTML and
+# should work on any modern browser. Note that when using HTML help
+# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
+# there is already a search function so this one should typically be disabled.
+# For large projects the javascript based search engine can be slow, then
+# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
+# search using the keyboard; to jump to the search box use  + S
+# (what the  is depends on the OS and browser, but it is typically
+# , /