Merge hdf5 1 10 8 (#1154)hdf5-1_10_8

 Merge HDF5 1.10.8 release files to 1.10/master

5 files changed, 404 insertions, 311 deletions

diff --git a/hl/c++/src/CMakeLists.txt b/hl/c++/src/CMakeLists.txt
index fbabc86..c516df1 100644
--- a/hl/c++/src/CMakeLists.txt
+++ b/hl/c++/src/CMakeLists.txt
@@ -9,9 +9,9 @@ set (HDF5_HL_CPP_SOURCES ${HDF5_HL_CPP_SRC_SOURCE_DIR}/H5PacketTable.cpp)
 set (HDF5_HL_CPP_HDRS ${HDF5_HL_CPP_SRC_SOURCE_DIR}/H5PacketTable.h)
 
 if (NOT ONLY_SHARED_LIBS)
-  add_library (${HDF5_HL_CPP_LIB_TARGET} STATIC ${HDF5_HL_CPP_SOURCES})
+  add_library (${HDF5_HL_CPP_LIB_TARGET} STATIC ${HDF5_HL_CPP_SOURCES} ${HDF5_HL_CPP_HDRS})
   target_include_directories (${HDF5_HL_CPP_LIB_TARGET}
-      PRIVATE "${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>"
+      PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>"
       INTERFACE "$<INSTALL_INTERFACE:$<INSTALL_PREFIX>/include>"
   )
   target_compile_options(${HDF5_HL_CPP_LIB_TARGET} PRIVATE "${HDF5_CMAKE_CXX_FLAGS}")
@@ -26,7 +26,7 @@ endif ()
 if (BUILD_SHARED_LIBS)
   add_library (${HDF5_HL_CPP_LIBSH_TARGET} SHARED ${HDF5_HL_CPP_SOURCES})
   target_include_directories (${HDF5_HL_CPP_LIBSH_TARGET}
-      PRIVATE "${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>"
+      PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>"
       INTERFACE "$<INSTALL_INTERFACE:$<INSTALL_PREFIX>/include>"
   )
   target_compile_options(${HDF5_HL_CPP_LIBSH_TARGET} PRIVATE "${HDF5_CMAKE_CXX_FLAGS}")
@@ -40,6 +40,17 @@ if (BUILD_SHARED_LIBS)
 endif ()
 
 #-----------------------------------------------------------------------------
+# Add Target to clang-format
+#-----------------------------------------------------------------------------
+if (HDF5_ENABLE_FORMATTERS)
+  if (NOT ONLY_SHARED_LIBS)
+    clang_format (HDF5_HL_CPP_SRC_FORMAT ${HDF5_HL_CPP_LIB_TARGET})
+  else ()
+    clang_format (HDF5_HL_CPP_SRC_FORMAT ${HDF5_HL_CPP_LIBSH_TARGET})
+  endif ()
+endif ()
+
+#-----------------------------------------------------------------------------
 # Add file(s) to CMake Install
 #-----------------------------------------------------------------------------
 install (
@@ -94,22 +105,26 @@ if (BUILD_SHARED_LIBS)
   set (_PKG_CONFIG_SH_LIBS "${_PKG_CONFIG_SH_LIBS} -l${HDF5_HL_CPP_LIB_CORENAME}")
 endif ()
 
-set (_PKG_CONFIG_REQUIRES "${HDF5_HL_LIB_CORENAME}")
-set (_PKG_CONFIG_REQUIRES_PRIVATE "${HDF5_HL_LIB_CORENAME}")
+set (_PKG_CONFIG_REQUIRES "${HDF5_HL_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}")
+set (_PKG_CONFIG_REQUIRES_PRIVATE "${HDF5_HL_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}")
 
 configure_file (
-    ${HDF_RESOURCES_DIR}/libhdf5.pc.in
-    ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_HL_CPP_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}.pc
+    ${HDF_CONFIG_DIR}/libhdf5.pc.in
+    ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_HL_CPP_LIB_CORENAME}.pc
     @ONLY
 )
 install (
-    FILES ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_HL_CPP_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}.pc
+    FILES ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_HL_CPP_LIB_CORENAME}.pc
     DESTINATION ${HDF5_INSTALL_LIB_DIR}/pkgconfig
     COMPONENT hlcpplibraries
 )
 
 if (NOT WIN32 AND NOT MINGW)
-  set (_PKG_CONFIG_COMPILER ${CMAKE_CXX_COMPILER})
+  if (HDF5_ENABLE_PARALLEL AND MPI_CXX_FOUND)
+    set (_PKG_CONFIG_COMPILER ${MPI_CXX_COMPILER})
+  else ()
+    set (_PKG_CONFIG_COMPILER ${CMAKE_CXX_COMPILER})
+  endif ()
   configure_file (
       ${HDF_RESOURCES_DIR}/libh5cc.in
       ${HDF5_BINARY_DIR}/CMakeFiles/h5hlc++
@@ -122,4 +137,3 @@ if (NOT WIN32 AND NOT MINGW)
       COMPONENT hlcpplibraries
   )
 endif ()
-
diff --git a/hl/c++/src/H5PacketTable.cpp b/hl/c++/src/H5PacketTable.cpp
index 544df0b..5f41e26 100644
--- a/hl/c++/src/H5PacketTable.cpp
+++ b/hl/c++/src/H5PacketTable.cpp
@@ -6,7 +6,7 @@
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
@@ -24,257 +24,286 @@
 
 #include "H5PacketTable.h"
 
-    /********************************/
-    /* PacketTable superclass       */
-    /********************************/
-
-    /* "Open" Constructor
-     * Opens an existing packet table, which can contain either fixed-length or
-     * variable-length packets.
-     */
-    PacketTable::PacketTable(hid_t fileID, const char* name)
-    {
-        table_id = H5PTopen( fileID, name);
-    }
-
-    /* "Open" Constructor - will be deprecated because of char* name */
-    PacketTable::PacketTable(hid_t fileID, char* name)
-    {
-        table_id = H5PTopen( fileID, name);
-    }
-
-    /* Destructor
-     * Cleans up the packet table
-     */
-    PacketTable::~PacketTable()
-    {
-        H5PTclose( table_id);
-    }
-
-    /* IsValid
-     * Returns true if this packet table is valid, false otherwise.
-     * Use this after the constructor to ensure HDF did not have
-     * any trouble making or opening the packet table.
-     */
-    bool PacketTable::IsValid()
-    {
-        if (H5PTis_valid(table_id) == 0)
-            return true;
-        else
-            return false;
-    }
-
-    /* IsVariableLength
-     * Return 1 if this packet table uses variable-length datatype,
-     * and 0, otherwise.  Returns -1 if the table is invalid (not open).
-     */
-    int PacketTable::IsVariableLength()
-    {
-        return H5PTis_varlen(table_id);
-    }
-
-    /* ResetIndex
-     * Sets the index to point to the first packet in the packet table
-     */
-    void PacketTable::ResetIndex()
-    {
-        H5PTcreate_index(table_id);
-    }
-
-    /* SetIndex
-     * Sets the index to point to the packet specified by index.
-     * Returns 0 on success, negative on failure (if index is out of bounds)
-     */
-    int PacketTable::SetIndex(hsize_t index)
-    {
-        return H5PTset_index(table_id, index);
-    }
-
-    /* SetIndex
-     * Sets the index to point to the packet specified by index.
-     * Returns 0 on success, negative on failure (if index is out of bounds)
-     */
-    hsize_t PacketTable::GetIndex(int &error)
-    {
-        hsize_t index;
-
-        error = H5PTget_index(table_id, &index);
-        if(error < 0)
-           return 0;
-        else
-           return index;
-    }
-
-    /* GetPacketCount
-     * Returns the number of packets in the packet table.  Error
-     * is set to 0 on success.  On failure, returns 0 and
-     * error is set to negative.
-     */
-    hsize_t PacketTable::GetPacketCount(int& error)
-    {
-        hsize_t npackets;
-
-        error = H5PTget_num_packets(table_id, &npackets);
-        return npackets;
-    }
-
-    /* GetTableId
-     * Returns the identifier of the packet table
-     */
-    hid_t PacketTable::GetTableId()
-    {
-        return table_id;
-    }
-
-    /* GetDatatype
-     * Returns the datatype identifier used by the packet table, on success,
-     * or H5I_INVALID_HID, on failure.
-     * Note: it is best to avoid using this identifier in applications, unless
-     * the desired functionality cannot be performed via the packet table ID.
-     */
-    hid_t PacketTable::GetDatatype()
-    {
-        return H5PTget_type(table_id);
-    }
-
-    /* GetDataset
-     * Returns the dataset identifier associated with the packet table, on
-     * success, or H5I_INVALID_HID, on failure.
-     * Note: it is best to avoid using this identifier in applications, unless
-     * the desired functionality cannot be performed via the packet table ID.
-     */
-    hid_t PacketTable::GetDataset()
-    {
-        return H5PTget_dataset(table_id);
-    }
-
-    /* FreeBuff
-     * Frees the buffers created when variable-length packets are read.
-     * Takes the number of hvl_t structs to be freed and a pointer to their
-     * location in memory.
-     * Returns 0 on success, negative on error.
-     */
-    int PacketTable::FreeBuff(size_t numStructs, hvl_t * buffer)
-    {
-        return H5PTfree_vlen_buff( table_id, numStructs, buffer);
-    }
-
-
-    /********************************/
-    /* Fixed-Length Packet Table    */
-    /********************************/
-
-    /* Constructor
-     * Creates a packet table to store either fixed- or variable-length packets.
-     * Takes the ID of the file the packet table will be created in, the ID of
-     * the property list to specify compression, the name of the packet table,
-     * the ID of the datatype, and the size of a memory chunk used in chunking.
-     */
-    FL_PacketTable::FL_PacketTable(hid_t fileID, const char* name, hid_t dtypeID, hsize_t chunkSize, hid_t plistID)
-    {
-        table_id = H5PTcreate(fileID, name, dtypeID, chunkSize, plistID);
-    }
-
-    /* Constructor - deprecated
-     * Creates a packet table to store either fixed- or variable-length packets.
-     * Takes the ID of the file the packet table will be created in, the ID of
-     * the property list to specify compression, the name of the packet table,
-     * the ID of the datatype, and the size of a memory chunk used in chunking.
-     * Note: The above constructor has a better prototype, which allows default
-     * values to be used.  This constructor was only released in 1.10.0.
-     */
-    FL_PacketTable::FL_PacketTable(hid_t fileID, hid_t plistID, const char* name, hid_t dtypeID, hsize_t chunkSize)
-    {
-        table_id = H5PTcreate(fileID, name, dtypeID, chunkSize, plistID);
-    }
-
-    /* Constructor
-     * Creates a packet table to store either fixed- or variable-length packets.
-     * Takes the ID of the file the packet table will be created in, the name of
-     * the packet table, the ID of the datatype of the set, and the size
-     * of a memory chunk used in chunking.
-     * Note: this overload will be deprecated in favor of the constructor above.
-     */
-    FL_PacketTable::FL_PacketTable(hid_t fileID, char* name, hid_t dtypeID, hsize_t chunkSize, int compression)
-    {
-        table_id = H5PTcreate_fl(fileID, name, dtypeID, chunkSize, compression);
-    }
-
-    /* "Open" Constructor
-     * Opens an existing fixed-length packet table.
-     * Fails if the packet table specified is variable-length.
-     */
-    FL_PacketTable::FL_PacketTable(hid_t fileID, const char* name) : PacketTable(fileID, name) {}
-
-    /* "Open" Constructor - will be deprecated because of char* name */
-    FL_PacketTable::FL_PacketTable(hid_t fileID, char* name) : PacketTable(fileID, name) {}
-
-    /* AppendPacket
-     * Adds a single packet to the packet table.  Takes a pointer
-     * to the location of the data in memory.
-     * Returns 0 on success, negative on failure
-     */
-    int FL_PacketTable::AppendPacket(void * data)
-    {
-        return H5PTappend(table_id, 1, data);
-    }
-
-    /* AppendPackets (multiple packets)
-     * Adds multiple packets to the packet table.  Takes the number of packets
-     * to be added and a pointer to their location in memory.
-     * Returns 0 on success, -1 on failure.
-     */
-    int FL_PacketTable::AppendPackets(size_t numPackets, void * data)
-    {
-        return H5PTappend(table_id, numPackets, data);
-    }
-
-    /* GetPacket (indexed)
-     * Gets a single packet from the packet table.  Takes the index
-     * of the packet (with 0 being the first packet) and a pointer
-     * to memory where the data should be stored.
-     * Returns 0 on success, negative on failure
-     */
-    int FL_PacketTable::GetPacket(hsize_t index, void * data)
-    {
-        return H5PTread_packets(table_id, index, 1, data);
-    }
-
-    /* GetPackets (multiple packets)
-     * Gets multiple packets at once, all packets between
-     * startIndex and endIndex inclusive.  Also takes a pointer to
-     * the memory where these packets should be stored.
-     * Returns 0 on success, negative on failure.
-     */
-    int FL_PacketTable::GetPackets(hsize_t startIndex, hsize_t endIndex, void * data)
-    {
-        // Make sure the range of indexes is valid
-        if (startIndex > endIndex)
-            return -1;
-
-        return  H5PTread_packets(table_id, startIndex, (size_t)(endIndex-startIndex+1), data);
-    }
-
-    /* GetNextPacket (single packet)
-     * Gets the next packet in the packet table.  Takes a pointer to
-     * memory where the packet should be stored.
-     * Returns 0 on success, negative on failure.  Index
-     * is not advanced to the next packet on failure.
-     */
-    int FL_PacketTable::GetNextPacket(void * data)
-    {
-        return H5PTget_next(table_id, 1, data);
-    }
-
-    /* GetNextPackets (multiple packets)
-     * Gets the next numPackets packets in the packet table.  Takes a
-     * pointer to memory where these packets should be stored.
-     * Returns 0 on success, negative on failure.  Index
-     * is not advanced on failure.
-     */
-    int FL_PacketTable::GetNextPackets(size_t numPackets, void * data)
-    {
-        return H5PTget_next(table_id, numPackets, data);
-    }
+/********************************/
+/* PacketTable superclass       */
+/********************************/
+
+/* Null constructor
+ * Sets table_id to "invalid"
+ */
+PacketTable::PacketTable()
+{
+    table_id = H5I_INVALID_HID;
+}
+
+/* "Open" Constructor
+ * Opens an existing packet table, which can contain either fixed-length or
+ * variable-length packets.
+ */
+PacketTable::PacketTable(hid_t fileID, const char *name)
+{
+    table_id = H5PTopen(fileID, name);
+}
+
+/* "Open" Constructor - will be deprecated because of char* name */
+PacketTable::PacketTable(hid_t fileID, char *name)
+{
+    table_id = H5PTopen(fileID, name);
+}
+
+/* Destructor
+ * Cleans up the packet table
+ */
+PacketTable::~PacketTable()
+{
+    H5PTclose(table_id);
+}
+
+/* IsValid
+ * Returns true if this packet table is valid, false otherwise.
+ * Use this after the constructor to ensure HDF did not have
+ * any trouble making or opening the packet table.
+ */
+bool
+PacketTable::IsValid()
+{
+    if (H5PTis_valid(table_id) == 0)
+        return true;
+    else
+        return false;
+}
+
+/* IsVariableLength
+ * Return 1 if this packet table uses variable-length datatype,
+ * and 0, otherwise.  Returns -1 if the table is invalid (not open).
+ */
+int
+PacketTable::IsVariableLength()
+{
+    return H5PTis_varlen(table_id);
+}
+
+/* ResetIndex
+ * Sets the index to point to the first packet in the packet table
+ */
+void
+PacketTable::ResetIndex()
+{
+    H5PTcreate_index(table_id);
+}
+
+/* SetIndex
+ * Sets the index to point to the packet specified by index.
+ * Returns 0 on success, negative on failure (if index is out of bounds)
+ */
+int
+PacketTable::SetIndex(hsize_t index)
+{
+    return H5PTset_index(table_id, index);
+}
+
+/* SetIndex
+ * Sets the index to point to the packet specified by index.
+ * Returns 0 on success, negative on failure (if index is out of bounds)
+ */
+hsize_t
+PacketTable::GetIndex(int &error)
+{
+    hsize_t index;
+
+    error = H5PTget_index(table_id, &index);
+    if (error < 0)
+        return 0;
+    else
+        return index;
+}
+
+/* GetPacketCount
+ * Returns the number of packets in the packet table.  Error
+ * is set to 0 on success.  On failure, returns 0 and
+ * error is set to negative.
+ */
+hsize_t
+PacketTable::GetPacketCount(int &error)
+{
+    hsize_t npackets;
+
+    error = H5PTget_num_packets(table_id, &npackets);
+    return npackets;
+}
+
+/* GetTableId
+ * Returns the identifier of the packet table
+ */
+hid_t
+PacketTable::GetTableId()
+{
+    return table_id;
+}
+
+/* GetDatatype
+ * Returns the datatype identifier used by the packet table, on success,
+ * or H5I_INVALID_HID, on failure.
+ * Note: it is best to avoid using this identifier in applications, unless
+ * the desired functionality cannot be performed via the packet table ID.
+ */
+hid_t
+PacketTable::GetDatatype()
+{
+    return H5PTget_type(table_id);
+}
+
+/* GetDataset
+ * Returns the dataset identifier associated with the packet table, on
+ * success, or H5I_INVALID_HID, on failure.
+ * Note: it is best to avoid using this identifier in applications, unless
+ * the desired functionality cannot be performed via the packet table ID.
+ */
+hid_t
+PacketTable::GetDataset()
+{
+    return H5PTget_dataset(table_id);
+}
+
+/* FreeBuff
+ * Frees the buffers created when variable-length packets are read.
+ * Takes the number of hvl_t structs to be freed and a pointer to their
+ * location in memory.
+ * Returns 0 on success, negative on error.
+ */
+int
+PacketTable::FreeBuff(size_t numStructs, hvl_t *buffer)
+{
+    return H5PTfree_vlen_buff(table_id, numStructs, buffer);
+}
+
+/********************************/
+/* Fixed-Length Packet Table    */
+/********************************/
+
+/* Constructor
+ * Creates a packet table to store either fixed- or variable-length packets.
+ * Takes the ID of the file the packet table will be created in, the ID of
+ * the property list to specify compression, the name of the packet table,
+ * the ID of the datatype, and the size of a memory chunk used in chunking.
+ */
+FL_PacketTable::FL_PacketTable(hid_t fileID, const char *name, hid_t dtypeID, hsize_t chunkSize,
+                               hid_t plistID)
+{
+    table_id = H5PTcreate(fileID, name, dtypeID, chunkSize, plistID);
+}
+
+/* Constructor - deprecated
+ * Creates a packet table to store either fixed- or variable-length packets.
+ * Takes the ID of the file the packet table will be created in, the ID of
+ * the property list to specify compression, the name of the packet table,
+ * the ID of the datatype, and the size of a memory chunk used in chunking.
+ * Note: The above constructor has a better prototype, which allows default
+ * values to be used.  This constructor was only released in 1.10.0.
+ */
+FL_PacketTable::FL_PacketTable(hid_t fileID, hid_t plistID, const char *name, hid_t dtypeID,
+                               hsize_t chunkSize)
+{
+    table_id = H5PTcreate(fileID, name, dtypeID, chunkSize, plistID);
+}
+
+/* Constructor
+ * Creates a packet table to store either fixed- or variable-length packets.
+ * Takes the ID of the file the packet table will be created in, the name of
+ * the packet table, the ID of the datatype of the set, and the size
+ * of a memory chunk used in chunking.
+ * Note: this overload will be deprecated in favor of the constructor above.
+ */
+FL_PacketTable::FL_PacketTable(hid_t fileID, char *name, hid_t dtypeID, hsize_t chunkSize, int compression)
+{
+    table_id = H5PTcreate_fl(fileID, name, dtypeID, chunkSize, compression);
+}
+
+/* "Open" Constructor
+ * Opens an existing fixed-length packet table.
+ * Fails if the packet table specified is variable-length.
+ */
+FL_PacketTable::FL_PacketTable(hid_t fileID, const char *name) : PacketTable(fileID, name)
+{
+}
+
+/* "Open" Constructor - will be deprecated because of char* name */
+FL_PacketTable::FL_PacketTable(hid_t fileID, char *name) : PacketTable(fileID, name)
+{
+}
+
+/* AppendPacket
+ * Adds a single packet to the packet table.  Takes a pointer
+ * to the location of the data in memory.
+ * Returns 0 on success, negative on failure
+ */
+int
+FL_PacketTable::AppendPacket(void *data)
+{
+    return H5PTappend(table_id, 1, data);
+}
+
+/* AppendPackets (multiple packets)
+ * Adds multiple packets to the packet table.  Takes the number of packets
+ * to be added and a pointer to their location in memory.
+ * Returns 0 on success, -1 on failure.
+ */
+int
+FL_PacketTable::AppendPackets(size_t numPackets, void *data)
+{
+    return H5PTappend(table_id, numPackets, data);
+}
+
+/* GetPacket (indexed)
+ * Gets a single packet from the packet table.  Takes the index
+ * of the packet (with 0 being the first packet) and a pointer
+ * to memory where the data should be stored.
+ * Returns 0 on success, negative on failure
+ */
+int
+FL_PacketTable::GetPacket(hsize_t index, void *data)
+{
+    return H5PTread_packets(table_id, index, 1, data);
+}
+
+/* GetPackets (multiple packets)
+ * Gets multiple packets at once, all packets between
+ * startIndex and endIndex inclusive.  Also takes a pointer to
+ * the memory where these packets should be stored.
+ * Returns 0 on success, negative on failure.
+ */
+int
+FL_PacketTable::GetPackets(hsize_t startIndex, hsize_t endIndex, void *data)
+{
+    // Make sure the range of indexes is valid
+    if (startIndex > endIndex)
+        return -1;
+
+    return H5PTread_packets(table_id, startIndex, (size_t)(endIndex - startIndex + 1), data);
+}
+
+/* GetNextPacket (single packet)
+ * Gets the next packet in the packet table.  Takes a pointer to
+ * memory where the packet should be stored.
+ * Returns 0 on success, negative on failure.  Index
+ * is not advanced to the next packet on failure.
+ */
+int
+FL_PacketTable::GetNextPacket(void *data)
+{
+    return H5PTget_next(table_id, 1, data);
+}
+
+/* GetNextPackets (multiple packets)
+ * Gets the next numPackets packets in the packet table.  Takes a
+ * pointer to memory where these packets should be stored.
+ * Returns 0 on success, negative on failure.  Index
+ * is not advanced on failure.
+ */
+int
+FL_PacketTable::GetNextPackets(size_t numPackets, void *data)
+{
+    return H5PTget_next(table_id, numPackets, data);
+}
 
 /* Removed "ifdef VLPT_REMOVED" block. 03/08/2016, -BMR */
diff --git a/hl/c++/src/H5PacketTable.h b/hl/c++/src/H5PacketTable.h
index 2665984..eae66f1 100644
--- a/hl/c++/src/H5PacketTable.h
+++ b/hl/c++/src/H5PacketTable.h
@@ -6,7 +6,7 @@
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
@@ -28,22 +28,21 @@
 #include "H5PTpublic.h"
 #include "H5api_adpt.h"
 
-class H5_HLCPPDLL  PacketTable
-{
-public:
+class H5_HLCPPDLL PacketTable {
+  public:
     /* Null constructor
-     * Sets table_id to "invalid"
+     * Sets table_id to H5I_INVALID_HID
      */
-    PacketTable() {table_id = H5I_BADID;}
+    PacketTable();
 
     /* "Open" Constructor
      * Opens an existing packet table, which can contain either fixed-length or
      * variable-length packets.
      */
-    PacketTable(hid_t fileID, const char* name);
+    PacketTable(hid_t fileID, const char *name);
 
     /* "Open" Constructor - will be deprecated because of char* name */
-    PacketTable(hid_t fileID, char* name);
+    PacketTable(hid_t fileID, char *name);
 
     /* Destructor
      * Cleans up the packet table
@@ -80,16 +79,17 @@ public:
      * Returns the position of the current packet.
      * On failure, returns 0 and error is set to negative.
      */
-    hsize_t GetIndex(int& error);
+    hsize_t GetIndex(int &error);
 
     /* GetPacketCount
      * Returns the number of packets in the packet table.  Error
      * is set to 0 on success.  On failure, returns 0 and
      * error is set to negative.
      */
-    hsize_t GetPacketCount(int& error);
+    hsize_t GetPacketCount(int &error);
 
-    hsize_t GetPacketCount()
+    hsize_t
+    GetPacketCount()
     {
         int ignoreError;
         return GetPacketCount(ignoreError);
@@ -122,22 +122,22 @@ public:
      * location in memory.
      * Returns 0 on success, negative on error.
      */
-    int FreeBuff(size_t numStructs, hvl_t * buffer);
+    int FreeBuff(size_t numStructs, hvl_t *buffer);
 
-protected:
+  protected:
     hid_t table_id;
 };
 
-class H5_HLCPPDLL FL_PacketTable : virtual public PacketTable
-{
-public:
+class H5_HLCPPDLL FL_PacketTable : virtual public PacketTable {
+  public:
     /* Constructor
      * Creates a packet table to store either fixed- or variable-length packets.
      * Takes the ID of the file the packet table will be created in, the ID of
      * the property list to specify compression, the name of the packet table,
      * the ID of the datatype, and the size of a memory chunk used in chunking.
      */
-    FL_PacketTable(hid_t fileID, const char* name, hid_t dtypeID, hsize_t chunkSize = 0, hid_t plistID = H5P_DEFAULT);
+    FL_PacketTable(hid_t fileID, const char *name, hid_t dtypeID, hsize_t chunkSize = 0,
+                   hid_t plistID = H5P_DEFAULT);
 
     /* Constructors - deprecated
      * Creates a packet table in which to store fixed length packets.
@@ -148,36 +148,38 @@ public:
      * Note: these overloaded constructors will be deprecated in favor of the
      * constructor above.
      */
-    FL_PacketTable(hid_t fileID, hid_t plist_id, const char* name, hid_t dtypeID, hsize_t chunkSize);
-    FL_PacketTable(hid_t fileID, char* name, hid_t dtypeID, hsize_t chunkSize, int compression = 0);
+    FL_PacketTable(hid_t fileID, hid_t plist_id, const char *name, hid_t dtypeID, hsize_t chunkSize);
+    FL_PacketTable(hid_t fileID, char *name, hid_t dtypeID, hsize_t chunkSize, int compression = 0);
 
     /* "Open" Constructor
      * Opens an existing fixed-length packet table.
      * Fails if the packet table specified is variable-length.
      */
-    FL_PacketTable(hid_t fileID, const char* name);
+    FL_PacketTable(hid_t fileID, const char *name);
 
     /* "Open" Constructor - will be deprecated because of char* name */
-    FL_PacketTable(hid_t fileID, char* name);
+    FL_PacketTable(hid_t fileID, char *name);
 
     /* Destructor
      * Cleans up the packet table
      */
-    virtual ~FL_PacketTable() {};
+    virtual ~FL_PacketTable()
+    {
+    }
 
     /* AppendPacket
      * Adds a single packet to the packet table.  Takes a pointer
      * to the location of the data in memory.
      * Returns 0 on success, negative on failure
      */
-    int AppendPacket(void * data);
+    int AppendPacket(void *data);
 
     /* AppendPackets (multiple packets)
      * Adds multiple packets to the packet table.  Takes the number of packets
      * to be added and a pointer to their location in memory.
      * Returns 0 on success, -1 on failure.
      */
-    int AppendPackets(size_t numPackets, void * data);
+    int AppendPackets(size_t numPackets, void *data);
 
     /* GetPacket (indexed)
      * Gets a single packet from the packet table.  Takes the index
@@ -185,7 +187,7 @@ public:
      * to memory where the data should be stored.
      * Returns 0 on success, negative on failure
      */
-    int GetPacket(hsize_t index, void * data);
+    int GetPacket(hsize_t index, void *data);
 
     /* GetPackets (multiple packets)
      * Gets multiple packets at once, all packets between
@@ -193,7 +195,7 @@ public:
      * the memory where these packets should be stored.
      * Returns 0 on success, negative on failure.
      */
-    int GetPackets(hsize_t startIndex, hsize_t endIndex, void * data);
+    int GetPackets(hsize_t startIndex, hsize_t endIndex, void *data);
 
     /* GetNextPacket (single packet)
      * Gets the next packet in the packet table.  Takes a pointer to
@@ -201,7 +203,7 @@ public:
      * Returns 0 on success, negative on failure.  Index
      * is not advanced to the next packet on failure.
      */
-    int GetNextPacket(void * data);
+    int GetNextPacket(void *data);
 
     /* GetNextPackets (multiple packets)
      * Gets the next numPackets packets in the packet table.  Takes a
@@ -209,7 +211,7 @@ public:
      * Returns 0 on success, negative on failure.  Index
      * is not advanced on failure.
      */
-    int GetNextPackets(size_t numPackets, void * data);
+    int GetNextPackets(size_t numPackets, void *data);
 };
 
 /* Removed "#ifdef VLPT_REMOVED" block.  03/08/2016, -BMR */
diff --git a/hl/c++/src/Makefile.am b/hl/c++/src/Makefile.am
index 363ba3b..f10ee19 100644
--- a/hl/c++/src/Makefile.am
+++ b/hl/c++/src/Makefile.am
@@ -6,7 +6,7 @@
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
 # the COPYING file, which can be found at the root of the source code
-# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# distribution tree, or in https://www.hdfgroup.org/licenses.
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 ##
diff --git a/hl/c++/src/Makefile.in b/hl/c++/src/Makefile.in
index e8cbabf..f52c771 100644
--- a/hl/c++/src/Makefile.in
+++ b/hl/c++/src/Makefile.in
@@ -22,7 +22,7 @@
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
 # the COPYING file, which can be found at the root of the source code
-# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# distribution tree, or in https://www.hdfgroup.org/licenses.
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 #
@@ -115,6 +115,7 @@ am__aclocal_m4_deps = $(top_srcdir)/m4/aclocal_cxx.m4 \
 	$(top_srcdir)/m4/ax_check_junit.m4 \
 	$(top_srcdir)/m4/ax_java_options.m4 \
 	$(top_srcdir)/m4/ax_jni_include_dir.m4 \
+	$(top_srcdir)/m4/ax_prog_doxygen.m4 \
 	$(top_srcdir)/m4/ax_prog_jar.m4 \
 	$(top_srcdir)/m4/ax_prog_java.m4 \
 	$(top_srcdir)/m4/ax_prog_java_works.m4 \
@@ -422,12 +423,12 @@ AMTAR = @AMTAR@
 # AM_CFLAGS is an automake construct which should be used by Makefiles
 # instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
 # This applies to FCFLAGS, CXXFLAGS, CPPFLAGS, and LDFLAGS as well.
-AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@ @H5_ECFLAGS@
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
 
 # Include src directory
 AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@ -I$(top_srcdir)/src \
 	-I$(top_srcdir)/hl/src
-AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@ @H5_ECXXFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
 AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
 AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
 AM_JAVACFLAGS = @AM_JAVACFLAGS@
@@ -465,11 +466,56 @@ DEFS = @DEFS@
 DEPDIR = @DEPDIR@
 DEPRECATED_SYMBOLS = @DEPRECATED_SYMBOLS@
 DESIRED_FILE_LOCKING = @DESIRED_FILE_LOCKING@
-DEV_WARNINGS = @DEV_WARNINGS@
+DIAGS = @DIAGS@
 DIRECT_VFD = @DIRECT_VFD@
 DLLTOOL = @DLLTOOL@
+DOXYGEN_EXAMPLES_DIRECTORY = @DOXYGEN_EXAMPLES_DIRECTORY@
+DOXYGEN_EXTERNAL_SEARCH = @DOXYGEN_EXTERNAL_SEARCH@
+DOXYGEN_HTML_EXTRA_FILES = @DOXYGEN_HTML_EXTRA_FILES@
+DOXYGEN_HTML_EXTRA_STYLESHEET = @DOXYGEN_HTML_EXTRA_STYLESHEET@
+DOXYGEN_HTML_FOOTER = @DOXYGEN_HTML_FOOTER@
+DOXYGEN_HTML_HEADER = @DOXYGEN_HTML_HEADER@
+DOXYGEN_INCLUDE_ALIASES = @DOXYGEN_INCLUDE_ALIASES@
+DOXYGEN_INPUT_DIRECTORY = @DOXYGEN_INPUT_DIRECTORY@
+DOXYGEN_LAYOUT_FILE = @DOXYGEN_LAYOUT_FILE@
+DOXYGEN_MACRO_EXPANSION = @DOXYGEN_MACRO_EXPANSION@
+DOXYGEN_OPTIMIZE_OUTPUT_FOR_C = @DOXYGEN_OPTIMIZE_OUTPUT_FOR_C@
+DOXYGEN_OUTPUT_DIRECTORY = @DOXYGEN_OUTPUT_DIRECTORY@
+DOXYGEN_PACKAGE = @DOXYGEN_PACKAGE@
+DOXYGEN_PAPER_SIZE = @DOXYGEN_PAPER_SIZE@
+DOXYGEN_PREDEFINED = @DOXYGEN_PREDEFINED@
+DOXYGEN_PROJECT_BRIEF = @DOXYGEN_PROJECT_BRIEF@
+DOXYGEN_PROJECT_LOGO = @DOXYGEN_PROJECT_LOGO@
+DOXYGEN_SEARCHENGINE_URL = @DOXYGEN_SEARCHENGINE_URL@
+DOXYGEN_SERVER_BASED_SEARCH = @DOXYGEN_SERVER_BASED_SEARCH@
+DOXYGEN_STRIP_FROM_PATH = @DOXYGEN_STRIP_FROM_PATH@
+DOXYGEN_TAG_FILE = @DOXYGEN_TAG_FILE@
+DOXYGEN_VERSION_STRING = @DOXYGEN_VERSION_STRING@
 DSYMUTIL = @DSYMUTIL@
 DUMPBIN = @DUMPBIN@
+DX_CONFIG = @DX_CONFIG@
+DX_DOCDIR = @DX_DOCDIR@
+DX_DOT = @DX_DOT@
+DX_DOXYGEN = @DX_DOXYGEN@
+DX_DVIPS = @DX_DVIPS@
+DX_EGREP = @DX_EGREP@
+DX_ENV = @DX_ENV@
+DX_FLAG_chi = @DX_FLAG_chi@
+DX_FLAG_chm = @DX_FLAG_chm@
+DX_FLAG_doc = @DX_FLAG_doc@
+DX_FLAG_dot = @DX_FLAG_dot@
+DX_FLAG_html = @DX_FLAG_html@
+DX_FLAG_man = @DX_FLAG_man@
+DX_FLAG_pdf = @DX_FLAG_pdf@
+DX_FLAG_ps = @DX_FLAG_ps@
+DX_FLAG_rtf = @DX_FLAG_rtf@
+DX_FLAG_xml = @DX_FLAG_xml@
+DX_HHC = @DX_HHC@
+DX_LATEX = @DX_LATEX@
+DX_MAKEINDEX = @DX_MAKEINDEX@
+DX_PDFLATEX = @DX_PDFLATEX@
+DX_PERL = @DX_PERL@
+DX_PROJECT = @DX_PROJECT@
 ECHO_C = @ECHO_C@
 ECHO_N = @ECHO_N@
 ECHO_T = @ECHO_T@
@@ -501,8 +547,6 @@ H5_CFLAGS = @H5_CFLAGS@
 H5_CLASSPATH = @H5_CLASSPATH@
 H5_CPPFLAGS = @H5_CPPFLAGS@
 H5_CXXFLAGS = @H5_CXXFLAGS@
-H5_ECFLAGS = @H5_ECFLAGS@
-H5_ECXXFLAGS = @H5_ECXXFLAGS@
 H5_FCFLAGS = @H5_FCFLAGS@
 H5_FORTRAN_SHARED = @H5_FORTRAN_SHARED@
 H5_IS_DARWIN = @H5_IS_DARWIN@
@@ -516,7 +560,9 @@ HAVE_DMALLOC = @HAVE_DMALLOC@
 HAVE_Fortran_INTEGER_SIZEOF_16 = @HAVE_Fortran_INTEGER_SIZEOF_16@
 HAVE_LIBHDFS = @HAVE_LIBHDFS@
 HAVE_PTHREAD = @HAVE_PTHREAD@
+HDF5_DOXYGEN = @HDF5_DOXYGEN@
 HDF5_HL = @HDF5_HL@
+HDF5_HL_TOOLS = @HDF5_HL_TOOLS@
 HDF5_INTERFACES = @HDF5_INTERFACES@
 HDF5_TESTS = @HDF5_TESTS@
 HDF5_TOOLS = @HDF5_TOOLS@
@@ -526,6 +572,7 @@ HDF_JAVA = @HDF_JAVA@
 HID_T = @HID_T@
 HL = @HL@
 HL_FOR = @HL_FOR@
+HL_TOOLS = @HL_TOOLS@
 HSIZE_T = @HSIZE_T@
 HSSIZE_T = @HSSIZE_T@
 IGNORE_DISABLED_FILE_LOCKS = @IGNORE_DISABLED_FILE_LOCKS@
@@ -719,7 +766,7 @@ LIBH5F_HL = $(top_builddir)/hl/fortran/src/libhdf5hl_fortran.la
 LIBH5CPP_HL = $(top_builddir)/hl/c++/src/libhdf5_hl_cpp.la
 
 # Note that in svn revision 19400 the '/' after DESTDIR in H5* variables below
-# has been removed. According to the official description of DESTDIR by Gnu at
+# has been removed. According to the official description of DESTDIR by GNU at
 # http://www.gnu.org/prep/standards/html_node/DESTDIR.html, DESTDIR is
 # prepended to the normal and complete install path that it precedes for the
 # purpose of installing in a temporary directory which is useful for building
@@ -747,28 +794,28 @@ TRACE = perl $(top_srcdir)/bin/trace
 # *.clog and *.clog2 are from the MPE option.
 CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.clog2
 LT_VERS_INTERFACE = 106
-LT_VERS_REVISION = 0
+LT_VERS_REVISION = 1
 LT_VERS_AGE = 3
-LT_CXX_VERS_INTERFACE = 106
+LT_CXX_VERS_INTERFACE = 107
 LT_CXX_VERS_REVISION = 0
-LT_CXX_VERS_AGE = 3
+LT_CXX_VERS_AGE = 4
 LT_F_VERS_INTERFACE = 103
-LT_F_VERS_REVISION = 0
+LT_F_VERS_REVISION = 1
 LT_F_VERS_AGE = 1
 LT_HL_VERS_INTERFACE = 101
-LT_HL_VERS_REVISION = 4
+LT_HL_VERS_REVISION = 5
 LT_HL_VERS_AGE = 1
 LT_HL_CXX_VERS_INTERFACE = 101
-LT_HL_CXX_VERS_REVISION = 5
+LT_HL_CXX_VERS_REVISION = 6
 LT_HL_CXX_VERS_AGE = 1
 LT_HL_F_VERS_INTERFACE = 100
-LT_HL_F_VERS_REVISION = 6
+LT_HL_F_VERS_REVISION = 7
 LT_HL_F_VERS_AGE = 0
-LT_JAVA_VERS_INTERFACE = 105
+LT_JAVA_VERS_INTERFACE = 106
 LT_JAVA_VERS_REVISION = 0
-LT_JAVA_VERS_AGE = 5
+LT_JAVA_VERS_AGE = 6
 LT_TOOLS_VERS_INTERFACE = 102
-LT_TOOLS_VERS_REVISION = 0
+LT_TOOLS_VERS_REVISION = 1
 LT_TOOLS_VERS_AGE = 0
 
 # This is our main target
@@ -1304,8 +1351,9 @@ uninstall-am: uninstall-includeHEADERS uninstall-libLTLIBRARIES
 # commands that should be executed even if a file with the same name already
 # exists.
 .PHONY: build-check-clean build-check-p build-check-s build-lib build-progs \
-        build-tests check-clean check-install check-p check-s check-vfd \
-        install-doc lib progs tests uninstall-doc _exec_check-s _test help
+	build-tests check-clean check-install check-p check-s check-vfd \
+	install-doc lib progs tests uninstall-doc \
+	_exec_check-s _test help trace doxygen
 
 help:
 	@$(top_srcdir)/bin/makehelp