Various merges from develop (#3135)

* Merges from develop/1.14
* Fix doxygen warnings
* Fix spelling
* Fix doxygen ref
* Add braces
* Fix format
* Remove unused file

8 files changed, 38 insertions, 151 deletions

diff --git a/config/cmake/ConfigureChecks.cmake b/config/cmake/ConfigureChecks.cmake
index dbf395b..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
@@ -694,11 +695,6 @@ endif ()
 #-----------------------------------------------------------------------------
 set (${HDF_PREFIX}_CONVERT_DENORMAL_FLOAT 1)
 
-# ----------------------------------------------------------------------
-# Set a special flag when using memory sanity checkers like Valgrind.
-# This disables the free lists, as the memory reuse scheme they implement
-# can hide memory problems.
-#-----------------------------------------------------------------------------
 if (HDF5_ENABLE_USING_MEMCHECKER)
   set (${HDF_PREFIX}_USING_MEMCHECKER 1)
 endif ()
@@ -707,6 +703,7 @@ endif ()
 # Option for --enable-strict-format-checks
 #-----------------------------------------------------------------------------
 option (HDF5_STRICT_FORMAT_CHECKS "Whether to perform strict file format checks" OFF)
+mark_as_advanced (HDF5_STRICT_FORMAT_CHECKS)
 if (HDF5_STRICT_FORMAT_CHECKS)
   set (${HDF_PREFIX}_STRICT_FORMAT_CHECKS 1)
 endif ()
@@ -719,6 +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 (${HDF_PREFIX}_WANT_DATA_ACCURACY 1)
 endif ()
@@ -731,6 +729,7 @@ MARK_AS_ADVANCED (HDF5_WANT_DATA_ACCURACY)
 # actually benefit little.
 #-----------------------------------------------------------------------------
 option (HDF5_WANT_DCONV_EXCEPTION "exception handling functions is checked during data conversions" ON)
+mark_as_advanced (HDF5_WANT_DCONV_EXCEPTION)
 if (HDF5_WANT_DCONV_EXCEPTION)
   set (${HDF_PREFIX}_WANT_DCONV_EXCEPTION 1)
 endif ()
@@ -740,6 +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/HDF5UseFortran.cmake b/config/cmake/HDF5UseFortran.cmake
index 43e006c..fd09c51 100644
--- a/config/cmake/HDF5UseFortran.cmake
+++ b/config/cmake/HDF5UseFortran.cmake
@@ -17,6 +17,12 @@
 enable_language (Fortran)
 
 set (HDF_PREFIX "H5")
+
+# Force lowercase Fortran module file names
+if (CMAKE_Fortran_COMPILER_ID STREQUAL "Cray")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -ef")
+endif ()
+
 include (CheckFortranFunctionExists)
 
 if (NOT CMAKE_VERSION VERSION_LESS "3.14.0")
@@ -43,11 +49,16 @@ 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 +198,10 @@ 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 +241,10 @@ 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 +283,17 @@ 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,*) ${FC_SIZEOF_C}
+          WRITE(stdout,*) kind(c)
        END
   "
 )
diff --git a/config/cmake/HDFCompilerFlags.cmake b/config/cmake/HDFCompilerFlags.cmake
index 88670d7..b5c50b3 100644
--- a/config/cmake/HDFCompilerFlags.cmake
+++ b/config/cmake/HDFCompilerFlags.cmake
@@ -56,7 +56,9 @@ if (CMAKE_COMPILER_IS_GNUCC)
       set (CMAKE_C_FLAGS "${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)
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/HDFTests.c b/config/cmake/HDFTests.c
index 2d7e1b4..133540b 100644
--- a/config/cmake/HDFTests.c
+++ b/config/cmake/HDFTests.c
@@ -188,8 +188,8 @@ int main(void)
   for (currentArg = llwidthArgs; *currentArg != NULL; currentArg++)
     {
     char formatString[64];
-    sprintf(formatString, "%%%sd", *currentArg);
-    sprintf(s, formatString, x);
+    snprintf(formatString, sizeof(formatString), "%%%sd", *currentArg);
+    snprintf(s, 128, formatString, x);
     if (strcmp(s, "1099511627776") == 0)
       {
       printf("PRINTF_LL_WIDTH=[%s]\n", *currentArg);
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 ()
diff --git a/config/cmake/scripts/HDF5options.cmake b/config/cmake/scripts/HDF5options.cmake
index 92bfd37..ba5fc24 100644
--- a/config/cmake/scripts/HDF5options.cmake
+++ b/config/cmake/scripts/HDF5options.cmake
@@ -70,7 +70,7 @@ set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRIN
 ### disable using ext zlib
 #set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=OFF")
 ### disable using ext szip
-#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF")
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=ON")
 #set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_ENCODING:BOOL=OFF")
 
 ####      package examples       ####