C++ warning and build fixes (#707)

* Committing clang-format changes

* C++ build and warning updates

* Fixes all warnings on C++ (with gcc 9.3)
* Updates CMake and Autotools C++ builds

* Undo warning clobber

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

9 files changed, 30 insertions, 198 deletions

diff --git a/config/cmake/H5cxx_config.h.in b/config/cmake/H5cxx_config.h.in
deleted file mode 100644
index b5ae8ce..0000000
--- a/config/cmake/H5cxx_config.h.in
+++ /dev/null
@@ -1,16 +0,0 @@
-/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * Copyright by The HDF Group.                                               *
- * All rights reserved.                                                      *
- *                                                                           *
- * 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://www.hdfgroup.org/licenses.               *
- * If you do not have access to either file, you may request a copy from     *
- * help@hdfgroup.org.                                                        *
- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
-/* src/H5cxx_config.h.in Created manually. */
-
-/* Define if offsetof extension is present */
-#cmakedefine H5_HAVE_OFFSETOF ${H5_HAVE_OFFSETOF}
-
diff --git a/config/cmake/H5pubconf.h.in b/config/cmake/H5pubconf.h.in
index 0176c7a..45ab8b8 100644
--- a/config/cmake/H5pubconf.h.in
+++ b/config/cmake/H5pubconf.h.in
@@ -26,9 +26,6 @@
 /* Define if using a Windows compiler (i.e. Visual Studio) */
 #cmakedefine H5_HAVE_VISUAL_STUDIO @H5_HAVE_VISUAL_STUDIO@
 
-/* Define if C++ compiler recognizes offsetof */
-#cmakedefine H5_CXX_HAVE_OFFSETOF @CXX_HAVE_OFFSETOF@
-
 /* Define the default plugins path to compile */
 #cmakedefine H5_DEFAULT_PLUGINDIR "@H5_DEFAULT_PLUGINDIR@"
 
diff --git a/config/cmake/HDFCXXCompilerFlags.cmake b/config/cmake/HDFCXXCompilerFlags.cmake
index e2904ca..260bbe0 100644
--- a/config/cmake/HDFCXXCompilerFlags.cmake
+++ b/config/cmake/HDFCXXCompilerFlags.cmake
@@ -71,10 +71,6 @@ endif ()
 # HDF5 library compile options
 #-----------------------------------------------------------------------------
 
-#-----------------------------------------------------------------------------
-# CDash is configured to only allow 3000 warnings, so
-# break into groups (from the config/gnu-flags file)
-#-----------------------------------------------------------------------------
 if (NOT MSVC AND NOT MINGW)
   if (${CMAKE_SYSTEM_NAME} MATCHES "SunOS")
     list (APPEND HDF5_CMAKE_CXX_FLAGS "-erroff=%none -DBSD_COMP")
@@ -121,9 +117,9 @@ if (NOT MSVC AND NOT MINGW)
   #-----------------------------------------------------------------------------
   if (HDF5_ENABLE_DEV_WARNINGS)
     message (STATUS "....HDF5 developer group warnings are enabled")
-  #  if (CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-  #    list (APPEND H5_CXXFLAGS "-Winline -Wreorder -Wport -Wstrict-aliasing")
-  #  elseif (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+    #  if (CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+    #    list (APPEND H5_CXXFLAGS "-Winline -Wreorder -Wport -Wstrict-aliasing")
+    #  elseif (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
     if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
       # autotools always add the C flags with the CXX flags
       ADD_H5_FLAGS (H5_CXXFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/developer-general")
@@ -147,7 +143,7 @@ if (NOT MSVC AND NOT MINGW)
       ADD_H5_FLAGS (H5_CXXFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/4.8-4.last")
     endif ()
 
-    # Append more extra warning flags that only gcc 4.8+ know about
+    # Append more extra warning flags that only gcc 4.8+ knows about
     if (NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.8)
       ADD_H5_FLAGS (H5_CXXFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/4.8")
       if (HDF5_ENABLE_DEV_WARNINGS)
@@ -157,14 +153,14 @@ if (NOT MSVC AND NOT MINGW)
       endif ()
     endif ()
 
-    # Append more extra warning flags that only gcc 4.9+ know about
+    # Append more extra warning flags that only gcc 4.9+ knows about
     if (NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.9)
       # autotools always add the C flags with the CXX flags
       ADD_H5_FLAGS (H5_CXXFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/4.9")
       ADD_H5_FLAGS (H5_CXXFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/cxx-4.9")
     endif ()
 
-    # Append more extra warning flags that only gcc 5.1+ know about
+    # Append more extra warning flags that only gcc 5.1+ knows about
     if (NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.0)
       # autotools always add the C flags with the CXX flags
       ADD_H5_FLAGS (H5_CXXFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/cxx-5")
@@ -175,13 +171,13 @@ if (NOT MSVC AND NOT MINGW)
       endif ()
     endif ()
 
-    # Append more extra warning flags that only gcc 6.x+ know about
+    # Append more extra warning flags that only gcc 6.x+ knows about
     if (NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 6.0)
       # autotools always add the C flags with the CXX flags
       ADD_H5_FLAGS (H5_CXXFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/6")
     endif ()
 
-    # Append more extra warning flags that only gcc 7.x+ know about
+    # Append more extra warning flags that only gcc 7.x+ knows about
     if (NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 7.0)
       # autotools always add the C flags with the CXX flags
       ADD_H5_FLAGS (H5_CXxFLAGS2 "${HDF5_SOURCE_DIR}/config/gnu-warnings/7")
@@ -193,7 +189,7 @@ if (NOT MSVC AND NOT MINGW)
       endif ()
     endif ()
 
-    # Append more extra warning flags that only gcc 8.x+ know about
+    # Append more extra warning flags that only gcc 8.x+ knows about
     if (NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 8.0)
       # autotools always add the C flags with the CXX flags
       ADD_H5_FLAGS (H5_CXXFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/8")
@@ -211,10 +207,11 @@ if (NOT MSVC AND NOT MINGW)
       endif ()
     endif ()
 
-    # Append more extra warning flags that only gcc 9.x+ know about
+    # Append more extra warning flags that only gcc 9.x+ knows about
     if (NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9.0)
       # autotools always add the C flags with the CXX flags
       ADD_H5_FLAGS (H5_CXXFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/9")
+      ADD_H5_FLAGS (H5_CXXFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/cxx-9")
     endif ()
   endif ()
 else ()
diff --git a/config/cmake/HDFCompilerFlags.cmake b/config/cmake/HDFCompilerFlags.cmake
index bb6ad78..0775f59 100644
--- a/config/cmake/HDFCompilerFlags.cmake
+++ b/config/cmake/HDFCompilerFlags.cmake
@@ -81,10 +81,6 @@ endif ()
 # HDF5 library compile options
 #-----------------------------------------------------------------------------
 
-#-----------------------------------------------------------------------------
-# CDash is configured to only allow 3000 warnings, so
-# break into groups (from the config/gnu-flags file)
-#-----------------------------------------------------------------------------
 if (NOT MSVC AND NOT MINGW)
   #-----------------------------------------------------------------------------
   # Option to allow the user to interpret certain warnings as errors
@@ -178,7 +174,7 @@ if (NOT MSVC AND NOT MINGW)
       ADD_H5_FLAGS (H5_CFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/4.8-4.last")
     endif ()
 
-    # Append more extra warning flags that only gcc 4.8+ know about
+    # Append more extra warning flags that only gcc 4.8+ knows about
     if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 4.8)
       ADD_H5_FLAGS (H5_CFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/4.8")
       if (HDF5_ENABLE_DEV_WARNINGS)
@@ -188,12 +184,12 @@ if (NOT MSVC AND NOT MINGW)
       endif ()
     endif ()
 
-    # Append more extra warning flags that only gcc 4.9+ know about
+    # Append more extra warning flags that only gcc 4.9+ knows about
     if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 4.9)
       ADD_H5_FLAGS (H5_CFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/4.9")
     endif ()
 
-    # Append more extra warning flags that only gcc 5.x+ know about
+    # Append more extra warning flags that only gcc 5.x+ knows about
     if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 5.0)
       ADD_H5_FLAGS (H5_CFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/5")
       if (HDF5_ENABLE_WARNINGS_AS_ERRORS)
@@ -203,12 +199,12 @@ if (NOT MSVC AND NOT MINGW)
       endif ()
     endif ()
 
-    # Append more extra warning flags that only gcc 6.x+ know about
+    # Append more extra warning flags that only gcc 6.x+ knows about
     if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 6.0)
       ADD_H5_FLAGS (H5_CFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/6")
     endif ()
 
-    # Append more extra warning flags that only gcc 7.x+ know about
+    # Append more extra warning flags that only gcc 7.x+ knows about
     if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 7.0)
       ADD_H5_FLAGS (H5_CFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/7")
       if (HDF5_ENABLE_DEV_WARNINGS)
@@ -218,7 +214,7 @@ if (NOT MSVC AND NOT MINGW)
       endif ()
     endif ()
 
-    # Append more extra warning flags that only gcc 8.x+ know about
+    # Append more extra warning flags that only gcc 8.x+ knows about
     if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 8.0)
       ADD_H5_FLAGS (H5_CFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/8")
       if (HDF5_ENABLE_WARNINGS_AS_ERRORS)
@@ -231,17 +227,17 @@ if (NOT MSVC AND NOT MINGW)
       endif ()
     endif ()
 
-    # Append more extra warning flags that only gcc 9.x+ know about
+    # Append more extra warning flags that only gcc 9.x+ knows about
     if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 9.0)
       ADD_H5_FLAGS (H5_CFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/9")
     endif ()
 
-    # Append more extra warning flags that only gcc 9.3+ know about
+    # Append more extra warning flags that only gcc 9.3+ knows about
     if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 9.3)
       ADD_H5_FLAGS (H5_CFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/9.3")
     endif ()
 
-    # Append more extra warning flags that only gcc 10.x+ know about
+    # Append more extra warning flags that only gcc 10.x+ knows about
     if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 10.0)
       if (HDF5_ENABLE_DEV_WARNINGS)
         ADD_H5_FLAGS (H5_CFLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/developer-10")
diff --git a/config/cmake/HDFFortranCompilerFlags.cmake b/config/cmake/HDFFortranCompilerFlags.cmake
index 8b631ad..18ab621 100644
--- a/config/cmake/HDFFortranCompilerFlags.cmake
+++ b/config/cmake/HDFFortranCompilerFlags.cmake
@@ -80,37 +80,37 @@ if (NOT MSVC AND NOT MINGW)
 
   if (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
 
-    # Append more extra warning flags that only gcc 4.8+ know about
+    # Append more extra warning flags that only gcc 4.8+ knows about
     if (NOT CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 4.8)
       ADD_H5_FLAGS (HDF5_CMAKE_Fortran_FLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/gfort-4.8")
     endif ()
 
-    # Append more extra warning flags that only gcc 4.9+ know about
+    # Append more extra warning flags that only gcc 4.9+ knows about
     #if (NOT CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 4.9)
     #  ADD_H5_FLAGS (HDF5_CMAKE_Fortran_FLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/gfort-4.9")
     #endif ()
 
-    # Append more extra warning flags that only gcc 5.x+ know about
+    # Append more extra warning flags that only gcc 5.x+ knows about
     if (NOT CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 5.0)
       ADD_H5_FLAGS (HDF5_CMAKE_Fortran_FLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/gfort-5")
     endif ()
 
-    # Append more extra warning flags that only gcc 6.x+ know about
+    # Append more extra warning flags that only gcc 6.x+ knows about
     if (NOT CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 6.0)
       ADD_H5_FLAGS (HDF5_CMAKE_Fortran_FLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/gfort-6")
     endif ()
 
-    # Append more extra warning flags that only gcc 7.x+ know about
+    # Append more extra warning flags that only gcc 7.x+ knows about
     #if (NOT CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 7.0)
     #  ADD_H5_FLAGS (HDF5_CMAKE_Fortran_FLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/gfort-7")
     #endif ()
 
-    # Append more extra warning flags that only gcc 8.x+ know about
+    # Append more extra warning flags that only gcc 8.x+ knows about
     if (NOT CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 8.0)
       ADD_H5_FLAGS (HDF5_CMAKE_Fortran_FLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/gfort-8")
     endif ()
 
-    # Append more extra warning flags that only gcc 9.x+ know about
+    # Append more extra warning flags that only gcc 9.x+ knows about
     #if (NOT CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 9.0)
     #  ADD_H5_FLAGS (HDF5_CMAKE_Fortran_FLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/gfort-9")
     #endif ()
diff --git a/config/cmake_ext_mod/HDFCXXTests.cpp b/config/cmake_ext_mod/HDFCXXTests.cpp
deleted file mode 100644
index 08ccb34..0000000
--- a/config/cmake_ext_mod/HDFCXXTests.cpp
+++ /dev/null
@@ -1,46 +0,0 @@
-/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * Copyright by The HDF Group.                                               *
- * All rights reserved.                                                      *
- *                                                                           *
- * 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://www.hdfgroup.org/licenses.               *
- * If you do not have access to either file, you may request a copy from     *
- * help@hdfgroup.org.                                                        *
- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
-
-#ifdef CXX_HAVE_OFFSETOF
-
-#include <stdio.h>
-#include <stddef.h>
-
-#ifdef FC_DUMMY_MAIN
-#ifndef FC_DUMMY_MAIN_EQ_F77
-#  ifdef __cplusplus
-extern "C"
-#  endif
-int FC_DUMMY_MAIN()
-{ return 1;}
-#endif
-#endif
-int
-main ()
-{
-
-  struct index_st
-  {
-    unsigned char type;
-    unsigned char num;
-    unsigned int len;
-  };
-  typedef struct index_st index_t;
-  int x,y;
-  x = offsetof(struct index_st, len);
-  y = offsetof(index_t, num)
-
-  ;
-  return 0;
-}
-
-#endif
diff --git a/config/cmake_ext_mod/HDFUseCXX.cmake b/config/cmake_ext_mod/HDFUseCXX.cmake
deleted file mode 100644
index 423f74a..0000000
--- a/config/cmake_ext_mod/HDFUseCXX.cmake
+++ /dev/null
@@ -1,99 +0,0 @@
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# 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://www.hdfgroup.org/licenses.
-# If you do not have access to either file, you may request a copy from
-# help@hdfgroup.org.
-#
-#
-# This file provides functions for C++ support.
-#
-#-------------------------------------------------------------------------------
-ENABLE_LANGUAGE (CXX)
-set (HDF_PREFIX "H5")
-
-#-------------------------------------------------------------------------------
-#  Fix CXX flags if we are compiling staticly on Windows using
-#  Windows_MT.cmake from config/cmake/UserMacros
-#-------------------------------------------------------------------------------
-if (BUILD_STATIC_CRT_LIBS)
-  TARGET_STATIC_CRT_FLAGS ()
-endif ()
-
-#-----------------------------------------------------------------------------
-# Configure Checks which require CXX compilation must go in here
-# not in the main ConfigureChecks.cmake files, because if the user has
-# no CXX compiler, problems arise.
-#-----------------------------------------------------------------------------
-include (CheckIncludeFileCXX)
-include (TestForSTDNamespace)
-
-# For other CXX specific tests, use this MACRO.
-macro (HDF_CXX_FUNCTION_TEST OTHER_TEST)
-  if (NOT DEFINED ${OTHER_TEST})
-    set (MACRO_CHECK_FUNCTION_DEFINITIONS "-D${OTHER_TEST} ${CMAKE_REQUIRED_FLAGS}")
-    set (OTHER_TEST_ADD_LIBRARIES)
-    if (HDF5_REQUIRED_LIBRARIES)
-      set (OTHER_TEST_ADD_LIBRARIES "-DLINK_LIBRARIES:STRING=${HDF5_REQUIRED_LIBRARIES}")
-    endif ()
-
-    foreach (def
-        HAVE_SYS_TIME_H
-        HAVE_UNISTD_H
-        HAVE_SYS_TYPES_H
-        HAVE_SYS_SOCKET_H
-        HAVE_SYS_FILE_H
-    )
-      if ("${${HDF_PREFIX}_${def}}")
-        set (MACRO_CHECK_FUNCTION_DEFINITIONS "${MACRO_CHECK_FUNCTION_DEFINITIONS} -D${def}")
-      endif ()
-    endforeach ()
-
-    if (LARGEFILE)
-      set (MACRO_CHECK_FUNCTION_DEFINITIONS
-          "${MACRO_CHECK_FUNCTION_DEFINITIONS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE"
-      )
-    endif ()
-
-    if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-      message (TRACE "Performing ${OTHER_TEST}")
-    endif ()
-    TRY_COMPILE (${OTHER_TEST}
-        ${CMAKE_BINARY_DIR}
-        ${HDF_RESOURCES_EXT_DIR}/HDFCXXTests.cpp
-        CMAKE_FLAGS -DCOMPILE_DEFINITIONS:STRING=${MACRO_CHECK_FUNCTION_DEFINITIONS}
-        "${OTHER_TEST_ADD_LIBRARIES}"
-        OUTPUT_VARIABLE OUTPUT
-    )
-    if (${OTHER_TEST} EQUAL 0)
-      set (${OTHER_TEST} 1 CACHE INTERNAL "CXX test ${FUNCTION}")
-      if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-        message (VERBOSE "Performing CXX Test ${OTHER_TEST} - Success")
-      endif ()
-    else ()
-      if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-        message (VERBOSE "Performing CXX Test ${OTHER_TEST} - Failed")
-      endif ()
-      set (${OTHER_TEST} "" CACHE INTERNAL "CXX test ${FUNCTION}")
-      file (APPEND ${CMAKE_BINARY_DIR}/CMakeFiles/CMakeError.log
-          "Performing CXX Test ${OTHER_TEST} failed with the following output:\n"
-          "${OUTPUT}\n"
-      )
-    endif ()
-  endif ()
-endmacro ()
-
-#-----------------------------------------------------------------------------
-# Check a bunch of cxx functions
-#-----------------------------------------------------------------------------
-if (CMAKE_CXX_COMPILER_LOADED)
-  foreach (cxx_test
-      CXX_HAVE_OFFSETOF
-  )
-    HDF_CXX_FUNCTION_TEST (${cxx_test})
-  endforeach ()
-endif ()
diff --git a/config/gnu-cxxflags b/config/gnu-cxxflags
index 0a7c63e..4fe5782 100644
--- a/config/gnu-cxxflags
+++ b/config/gnu-cxxflags
@@ -260,6 +260,7 @@ if test "X-g++" = "X-$cxx_vendor"; then
     # gcc 9
     if test $cxx_vers_major -ge 9; then
         H5_CXXFLAGS="$H5_CXXFLAGS $(load_gnu_arguments 9)"
+        H5_CXXFLAGS="$H5_CXXFLAGS $(load_gnu_arguments cxx-9)"
     fi
 
     #################
diff --git a/config/gnu-warnings/cxx-9 b/config/gnu-warnings/cxx-9
new file mode 100644
index 0000000..d897de2
--- /dev/null
+++ b/config/gnu-warnings/cxx-9
@@ -0,0 +1,2 @@
+# Turn this on when the C++ wrappers obey the Rule of Five
+-Wno-deprecated-copy