Merges from develop/1.14 (#3118)

* Fix release action that allows files to be uploaded.
Add autotools h5copy help test.
Update cmake tools.cmake file for clang-tidy.
CMake build is missing H5FDsubfiling.h
macros improved for configure output capture.
Remove obsolete files

* Revert parallel config with TS

* Fix doxygen warnings

7 files changed, 36 insertions, 149 deletions

diff --git a/config/cmake/ConfigureChecks.cmake b/config/cmake/ConfigureChecks.cmake
index c72f415..8900d4c 100644
--- a/config/cmake/ConfigureChecks.cmake
+++ b/config/cmake/ConfigureChecks.cmake
@@ -272,6 +272,7 @@ if (MINGW OR NOT WINDOWS)
     set (HDF_EXTRA_C_FLAGS ${HDF_EXTRA_C_FLAGS} -D_GNU_SOURCE)
 
     option (HDF_ENABLE_LARGE_FILE "Enable support for large (64-bit) files on Linux." ON)
+    mark_as_advanced (HDF_ENABLE_LARGE_FILE)
     if (HDF_ENABLE_LARGE_FILE AND NOT DEFINED TEST_LFS_WORKS_RUN)
       set (msg "Performing TEST_LFS_WORKS")
       try_run (TEST_LFS_WORKS_RUN   TEST_LFS_WORKS_COMPILE
@@ -702,6 +703,7 @@ endif ()
 # Option for --enable-strict-format-checks
 #-----------------------------------------------------------------------------
 option (HDF5_STRICT_FORMAT_CHECKS "Whether to perform strict file format checks" OFF)
+mark_as_advanced (HDF5_STRICT_FORMAT_CHECKS)
 if (HDF5_STRICT_FORMAT_CHECKS)
   set (${HDF_PREFIX}_STRICT_FORMAT_CHECKS 1)
 endif ()
@@ -714,6 +716,7 @@ MARK_AS_ADVANCED (HDF5_STRICT_FORMAT_CHECKS)
 # support denormalized floating values) to maximize speed.
 #-----------------------------------------------------------------------------
 option (HDF5_WANT_DATA_ACCURACY "IF data accuracy is guaranteed during data conversions" ON)
+mark_as_advanced (HDF5_WANT_DATA_ACCURACY)
 if (HDF5_WANT_DATA_ACCURACY)
   set (${HDF_PREFIX}_WANT_DATA_ACCURACY 1)
 endif ()
@@ -726,6 +729,7 @@ MARK_AS_ADVANCED (HDF5_WANT_DATA_ACCURACY)
 # actually benefit little.
 #-----------------------------------------------------------------------------
 option (HDF5_WANT_DCONV_EXCEPTION "exception handling functions is checked during data conversions" ON)
+mark_as_advanced (HDF5_WANT_DCONV_EXCEPTION)
 if (HDF5_WANT_DCONV_EXCEPTION)
   set (${HDF_PREFIX}_WANT_DCONV_EXCEPTION 1)
 endif ()
@@ -735,6 +739,7 @@ MARK_AS_ADVANCED (HDF5_WANT_DCONV_EXCEPTION)
 # Check if they would like the function stack support compiled in
 #-----------------------------------------------------------------------------
 option (HDF5_ENABLE_CODESTACK "Enable the function stack tracing (for developer debugging)." OFF)
+mark_as_advanced (HDF5_ENABLE_CODESTACK)
 if (HDF5_ENABLE_CODESTACK)
   set (${HDF_PREFIX}_HAVE_CODESTACK 1)
 endif ()
diff --git a/config/cmake/FindSZIP.cmake b/config/cmake/FindSZIP.cmake
deleted file mode 100644
index 846a3d1..0000000
--- a/config/cmake/FindSZIP.cmake
+++ /dev/null
@@ -1,129 +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.
-#
-#########################################################################
-
-# - Derived from the FindTiff.cmake and FindJPEG.cmake that is included with cmake
-# FindSZIP
-
-# Find the native SZIP includes and library
-
-# Imported targets
-##################
-
-# This module defines the following :prop_tgt:`IMPORTED` targets:
-#
-# SZIP::SZIP
-#  The SZIP library, if found.
-#
-# Result variables
-###################
-
-# This module will set the following variables in your project:
-
-#  SZIP_FOUND, true if the SZIP headers and libraries were found.
-#  SZIP_INCLUDE_DIR, the directory containing the SZIP headers.
-#  SZIP_INCLUDE_DIRS, the directory containing the SZIP headers.
-#  SZIP_LIBRARIES, libraries to link against to use SZIP.
-
-# Cache variables
-#################
-
-# The following variables may also be set:
-
-#  SZIP_LIBRARY, where to find the SZIP library.
-#  SZIP_LIBRARY_DEBUG - Debug version of SZIP library
-#  SZIP_LIBRARY_RELEASE - Release Version of SZIP library
-
-# message (STATUS "Finding SZIP library and headers..." )
-#########################################################################
-
-
-find_path(SZIP_INCLUDE_DIR szlib.h)
-
-set(szip_names ${SZIP_NAMES} sz szip szip-static libsz libszip libszip-static)
-foreach(name ${szip_names})
-  list (APPEND szip_names_debug "${name}d")
-endforeach()
-
-if(NOT SZIP_LIBRARY)
-  find_library(SZIP_LIBRARY_RELEASE NAMES ${szip_names})
-  find_library(SZIP_LIBRARY_DEBUG NAMES ${szip_names_debug})
-  include(SelectLibraryConfigurations)
-  select_library_configurations(SZIP)
-  mark_as_advanced(SZIP_LIBRARY_RELEASE SZIP_LIBRARY_DEBUG)
-endif()
-unset(szip_names)
-unset(szip_names_debug)
-
-if(SZIP_INCLUDE_DIR AND EXISTS "${SZIP_INCLUDE_DIR}/SZconfig.h")
-    file(STRINGS "${SZIP_INCLUDE_DIR}/SZconfig.h" szip_version_str
-         REGEX "^#define[\t ]+SZIP_PACKAGE_VERSION[\t ]+.*")
-
-    string(REGEX REPLACE "^#define[\t ]+SZIP_PACKAGE_VERSION[\t ]+([0-9]+).*"
-           "\\1" SZIP_VERSION "${szip_version_str}")
-    unset(szip_version_str)
-endif()
-
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(SZIP
-  REQUIRED_VARS SZIP_LIBRARY SZIP_INCLUDE_DIR
-  VERSION_VAR SZIP_VERSION)
-
-if(SZIP_FOUND)
-  set(SZIP_LIBRARIES ${SZIP_LIBRARY})
-  set(SZIP_INCLUDE_DIRS "${SZIP_INCLUDE_DIR}")
-
-  if(NOT TARGET SZIP::SZIP)
-    add_library(SZIP::SZIP UNKNOWN IMPORTED)
-    if(SZIP_INCLUDE_DIRS)
-      set_target_properties(SZIP::SZIP PROPERTIES
-        INTERFACE_INCLUDE_DIRECTORIES "${SZIP_INCLUDE_DIRS}")
-    endif()
-    if(EXISTS "${SZIP_LIBRARY}")
-      set_target_properties(SZIP::SZIP PROPERTIES
-        IMPORTED_LINK_INTERFACE_LANGUAGES "C"
-        IMPORTED_LOCATION "${SZIP_LIBRARY}")
-    endif()
-    if(EXISTS "${SZIP_LIBRARY_RELEASE}")
-      set_property(TARGET SZIP::SZIP APPEND PROPERTY
-        IMPORTED_CONFIGURATIONS RELEASE)
-      set_target_properties(SZIP::SZIP PROPERTIES
-        IMPORTED_LINK_INTERFACE_LANGUAGES_RELEASE "C"
-        IMPORTED_LOCATION_RELEASE "${SZIP_LIBRARY_RELEASE}")
-    endif()
-    if(EXISTS "${SZIP_LIBRARY_DEBUG}")
-      set_property(TARGET SZIP::SZIP APPEND PROPERTY
-        IMPORTED_CONFIGURATIONS DEBUG)
-      set_target_properties(SZIP::SZIP PROPERTIES
-        IMPORTED_LINK_INTERFACE_LANGUAGES_DEBUG "C"
-        IMPORTED_LOCATION_DEBUG "${SZIP_LIBRARY_DEBUG}")
-    endif()
-  endif()
-endif()
-
-mark_as_advanced(SZIP_LIBRARY SZIP_INCLUDE_DIR)
-
-# Report the results.
-if (NOT SZIP_FOUND)
-  set (SZIP_DIR_MESSAGE
-      "SZip was not found. Make sure SZIP_LIBRARY and SZIP_INCLUDE_DIR are set or set the SZIP_INSTALL environment variable."
-  )
-  if (NOT SZIP_FIND_QUIETLY)
-    if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-      message (VERBOSE "${SZIP_DIR_MESSAGE}")
-    endif ()
-  else ()
-    if (SZIP_FIND_REQUIRED)
-      message (FATAL_ERROR "SZip was NOT found and is Required by this project")
-    endif ()
-  endif ()
-endif ()
diff --git a/config/cmake/HDF5Macros.cmake b/config/cmake/HDF5Macros.cmake
index 8b8b334..710c28b 100644
--- a/config/cmake/HDF5Macros.cmake
+++ b/config/cmake/HDF5Macros.cmake
@@ -75,23 +75,23 @@ macro (H5_SET_VFD_LIST)
   )
 
   if (H5_HAVE_DIRECT)
-    set (VFD_LIST ${VFD_LIST} direct)
+    list (APPEND VFD_LIST direct)
   endif ()
   if (H5_HAVE_PARALLEL)
     # MPI I/O VFD is currently incompatible with too many tests in the VFD test set
-    # set (VFD_LIST ${VFD_LIST} mpio)
+    # list (APPEND VFD_LIST mpio)
   endif ()
   if (H5_HAVE_MIRROR_VFD)
-    set (VFD_LIST ${VFD_LIST} mirror)
+    list (APPEND VFD_LIST mirror)
   endif ()
   if (H5_HAVE_ROS3_VFD)
-    set (VFD_LIST ${VFD_LIST} ros3)
+    list (APPEND VFD_LIST ros3)
   endif ()
   if (H5_HAVE_LIBHDFS)
-    set (VFD_LIST ${VFD_LIST} hdfs)
+    list (APPEND VFD_LIST hdfs)
   endif ()
   if (H5_HAVE_WINDOWS)
-    set (VFD_LIST ${VFD_LIST} windows)
+    list (APPEND VFD_LIST windows)
   endif ()
 endmacro ()
 
diff --git a/config/cmake/HDF5UseFortran.cmake b/config/cmake/HDF5UseFortran.cmake
index 43e006c..5cf5088 100644
--- a/config/cmake/HDF5UseFortran.cmake
+++ b/config/cmake/HDF5UseFortran.cmake
@@ -43,11 +43,16 @@ macro (FORTRAN_RUN FUNCTION_NAME SOURCE_CODE RUN_RESULT_VAR1 COMPILE_RESULT_VAR1
         ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/testFortranCompiler1.f90
         "${SOURCE_CODE}"
     )
+    if (CMAKE_VERSION VERSION_LESS 3.25)
+      set (_RUN_OUTPUT_VARIABLE "RUN_OUTPUT_VARIABLE")
+    else ()
+      set (_RUN_OUTPUT_VARIABLE  "RUN_OUTPUT_STDOUT_VARIABLE")
+    endif()
     TRY_RUN (RUN_RESULT_VAR COMPILE_RESULT_VAR
         ${CMAKE_BINARY_DIR}
         ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/testFortranCompiler1.f90
         LINK_LIBRARIES "${HDF5_REQUIRED_LIBRARIES}"
-        RUN_OUTPUT_VARIABLE OUTPUT_VAR
+        ${_RUN_OUTPUT_VARIABLE} OUTPUT_VAR
     )
     set (${RETURN_OUTPUT_VAR} ${OUTPUT_VAR})
 
@@ -187,10 +192,10 @@ foreach (KIND ${VAR})
   "
        PROGRAM main
           USE ISO_C_BINDING
-          USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : stderr=>ERROR_UNIT
+          USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : stdout=>OUTPUT_UNIT
           IMPLICIT NONE
           INTEGER (KIND=${KIND}) a
-          WRITE(stderr,'(I0)') ${FC_SIZEOF_A}
+          WRITE(stdout,'(I0)') ${FC_SIZEOF_A}
        END
    "
   )
@@ -230,10 +235,10 @@ foreach (KIND ${VAR} )
   "
        PROGRAM main
           USE ISO_C_BINDING
-          USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : stderr=>ERROR_UNIT
+          USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : stdout=>OUTPUT_UNIT
           IMPLICIT NONE
           REAL (KIND=${KIND}) a
-          WRITE(stderr,'(I0)') ${FC_SIZEOF_A}
+          WRITE(stdout,'(I0)') ${FC_SIZEOF_A}
        END
   "
   )
@@ -272,17 +277,17 @@ set (PROG_SRC3
   "
        PROGRAM main
           USE ISO_C_BINDING
-          USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : stderr=>ERROR_UNIT
+          USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : stdout=>OUTPUT_UNIT
           IMPLICIT NONE
           INTEGER a
           REAL b
           DOUBLE PRECISION c
-          WRITE(stderr,*) ${FC_SIZEOF_A}
-          WRITE(stderr,*) kind(a)
-          WRITE(stderr,*) ${FC_SIZEOF_B}
-          WRITE(stderr,*) kind(b)
-          WRITE(stderr,*) ${FC_SIZEOF_C}
-          WRITE(stderr,*) kind(c)
+          WRITE(stdout,*) ${FC_SIZEOF_A}
+          WRITE(stdout,*) kind(a)
+          WRITE(stdout,*) ${FC_SIZEOF_B}
+          WRITE(stdout,*) kind(b)
+          WRITE(stdout,*) ${FC_SIZEOF_C}
+          WRITE(stdout,*) kind(c)
        END
   "
 )
diff --git a/config/cmake/HDFCompilerFlags.cmake b/config/cmake/HDFCompilerFlags.cmake
index 15b158d..1560bbd 100644
--- a/config/cmake/HDFCompilerFlags.cmake
+++ b/config/cmake/HDFCompilerFlags.cmake
@@ -56,7 +56,9 @@ if (CMAKE_COMPILER_IS_GNUCC)
       set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Og -ftrapv -fno-common")
     endif ()
   else ()
-    if (CMAKE_C_COMPILER_ID STREQUAL "GNU" AND NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 5.0)
+    if (CMAKE_C_COMPILER_ID STREQUAL "GNU" AND NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 5.0 AND
+        NOT CMAKE_C_CLANG_TIDY)
+      # `clang-tidy` does not understand -fstdarg-opt
       set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fstdarg-opt")
     endif ()
     if (CMAKE_C_COMPILER_ID STREQUAL "GNU" AND NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 10.0)
@@ -66,6 +68,7 @@ if (CMAKE_COMPILER_IS_GNUCC)
       # This should NOT be on by default as it can cause process issues.
       #-----------------------------------------------------------------------------
       option (HDF5_ENABLE_BUILD_DIAGS "Enable color and URL extended diagnostic messages" OFF)
+      mark_as_advanced (HDF5_ENABLE_BUILD_DIAGS)
       if (HDF5_ENABLE_BUILD_DIAGS)
         message (STATUS "... default color and URL extended diagnostic messages enabled")
       else ()
diff --git a/config/cmake/HDFLibMacros.cmake b/config/cmake/HDFLibMacros.cmake
index 6d77ab5..752d817 100644
--- a/config/cmake/HDFLibMacros.cmake
+++ b/config/cmake/HDFLibMacros.cmake
@@ -17,13 +17,14 @@ macro (ORIGINAL_ZLIB_LIBRARY compress_type)
         GIT_TAG ${ZLIB_BRANCH}
     )
   elseif (${compress_type} MATCHES "TGZ")
+    message (VERBOSE "Filter ZLIB file ${ZLIB_URL}")
     FetchContent_Declare (HDF5_ZLIB
         URL ${ZLIB_URL}
         URL_HASH ""
     )
   endif ()
   FetchContent_GetProperties(HDF5_ZLIB)
-  if(NOT zlib_POPULATED)
+  if(NOT hdf5_zlib_POPULATED)
     FetchContent_Populate(HDF5_ZLIB)
 
     # Copy an additional/replacement files into the populated source
@@ -51,6 +52,7 @@ macro (ORIGINAL_SZIP_LIBRARY compress_type encoding)
         GIT_TAG ${SZIP_BRANCH}
     )
   elseif (${compress_type} MATCHES "TGZ")
+    message (VERBOSE "Filter SZIP file ${SZIP_URL}")
     FetchContent_Declare (SZIP
         URL ${SZIP_URL}
         URL_HASH ""
diff --git a/config/cmake/UserMacros/Windows_MT.cmake b/config/cmake/UserMacros/Windows_MT.cmake
index 15cffba..c8edbe4 100644
--- a/config/cmake/UserMacros/Windows_MT.cmake
+++ b/config/cmake/UserMacros/Windows_MT.cmake
@@ -47,6 +47,7 @@ endmacro ()
 
 #-----------------------------------------------------------------------------
 option (BUILD_STATIC_CRT_LIBS "Build With Static CRT Libraries" OFF)
+mark_as_advanced (BUILD_STATIC_CRT_LIBS)
 if (BUILD_STATIC_CRT_LIBS)
   TARGET_STATIC_CRT_FLAGS ()
 endif ()