Sync CMake and doxygen changes with develop (#3543)

* Sync CMake and doxygen changes from develop

* Add missing images

CMakeFilters.cmake

@@ -9,7 +9,7 @@
 # If you do not have access to either file, you may request a copy from
 # [email protected].
 #
-option (USE_LIBAEC "Use AEC library as SZip Filter" OFF)
+option (USE_LIBAEC "Use AEC library as SZip Filter" ON)
 option (USE_LIBAEC_STATIC "Use static AEC library " OFF)
 option (ZLIB_USE_EXTERNAL "Use External Library Building for ZLIB" 0)
 option (SZIP_USE_EXTERNAL "Use External Library Building for SZIP" 0)

CMakeInstallation.cmake

@@ -390,7 +390,9 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED AND NOT HDF5_NO_PACKAGES)
     set(CPACK_WIX_PROPERTY_ARPURLINFOABOUT "${HDF5_PACKAGE_URL}")
     set(CPACK_WIX_PROPERTY_ARPHELPLINK "${HDF5_PACKAGE_BUGREPORT}")
     if (BUILD_SHARED_LIBS)
-      set(CPACK_WIX_PATCH_FILE "${HDF_RESOURCES_DIR}/patch.xml")
+      set (WIX_CMP_NAME "${HDF5_LIB_NAME}${CMAKE_DEBUG_POSTFIX}")
+      configure_file (${HDF_RESOURCES_DIR}/patch.xml.in ${HDF5_BINARY_DIR}/patch.xml @ONLY)
+      set(CPACK_WIX_PATCH_FILE "${HDF5_BINARY_DIR}/patch.xml")
     endif ()
   elseif (APPLE)
     list (APPEND CPACK_GENERATOR "STGZ")

config/cmake/HDFFortranCompilerFlags.cmake

@@ -58,7 +58,7 @@ if (NOT MSVC AND NOT MINGW)
   # General flags
   if (CMAKE_Fortran_COMPILER_ID STREQUAL "Intel")
     ADD_H5_FLAGS (HDF5_CMAKE_Fortran_FLAGS "${HDF5_SOURCE_DIR}/config/intel-warnings/ifort-general")
-    list (APPEND HDF5_CMAKE_Fortran_FLAGS "-stand:f03" "-free")
+    list (APPEND HDF5_CMAKE_Fortran_FLAGS "-free")
   elseif (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
     ADD_H5_FLAGS (HDF5_CMAKE_Fortran_FLAGS "${HDF5_SOURCE_DIR}/config/gnu-warnings/gfort-general")
     if (HDF5_ENABLE_DEV_WARNINGS)

config/cmake/hdf5-config.cmake.in

@@ -38,20 +38,22 @@ set (${HDF5_PACKAGE_NAME}_BUILD_CPP_LIB   @HDF5_BUILD_CPP_LIB@)
 set (${HDF5_PACKAGE_NAME}_BUILD_JAVA      @HDF5_BUILD_JAVA@)
 set (${HDF5_PACKAGE_NAME}_BUILD_TOOLS     @HDF5_BUILD_TOOLS@)
 set (${HDF5_PACKAGE_NAME}_BUILD_HL_LIB    @HDF5_BUILD_HL_LIB@)
-set (${HDF5_PACKAGE_NAME}_BUILD_HL_TOOLS  @HDF5_BUILD_HL_TOOLS@)
+set (${HDF5_PACKAGE_NAME}_BUILD_HL_GIF_TOOLS  @HDF5_BUILD_HL_GIF_TOOLS@)
 set (${HDF5_PACKAGE_NAME}_ENABLE_THREADSAFE @HDF5_ENABLE_THREADSAFE@)
 set (${HDF5_PACKAGE_NAME}_ENABLE_PLUGIN_SUPPORT @HDF5_ENABLE_PLUGIN_SUPPORT@)
 set (${HDF5_PACKAGE_NAME}_ENABLE_Z_LIB_SUPPORT @HDF5_ENABLE_Z_LIB_SUPPORT@)
 set (${HDF5_PACKAGE_NAME}_ENABLE_SZIP_SUPPORT  @HDF5_ENABLE_SZIP_SUPPORT@)
 set (${HDF5_PACKAGE_NAME}_ENABLE_SZIP_ENCODING @HDF5_ENABLE_SZIP_ENCODING@)
+set (${HDF5_PACKAGE_NAME}_ENABLE_ROS3_VFD      @HDF5_ENABLE_ROS3_VFD@)
 set (${HDF5_PACKAGE_NAME}_BUILD_SHARED_LIBS    @H5_ENABLE_SHARED_LIB@)
 set (${HDF5_PACKAGE_NAME}_BUILD_STATIC_LIBS    @H5_ENABLE_STATIC_LIB@)
 set (${HDF5_PACKAGE_NAME}_PACKAGE_EXTLIBS      @HDF5_PACKAGE_EXTLIBS@)
 set (${HDF5_PACKAGE_NAME}_EXPORT_LIBRARIES @HDF5_LIBRARIES_TO_EXPORT@)
 set (${HDF5_PACKAGE_NAME}_ARCHITECTURE "@CMAKE_GENERATOR_ARCHITECTURE@")
 set (${HDF5_PACKAGE_NAME}_TOOLSET "@CMAKE_GENERATOR_TOOLSET@")
 set (${HDF5_PACKAGE_NAME}_DEFAULT_API_VERSION "@DEFAULT_API_VERSION@")
-set (${HDF5_PACKAGE_NAME}_PARALLEL_FILTERED_WRITES "@PARALLEL_FILTERED_WRITES@")
+set (${HDF5_PACKAGE_NAME}_PARALLEL_FILTERED_WRITES @PARALLEL_FILTERED_WRITES@)
+set (${HDF5_PACKAGE_NAME}_INSTALL_MOD_FORTRAN "@HDF5_INSTALL_MOD_FORTRAN@")
 
 #-----------------------------------------------------------------------------
 # Dependencies
@@ -67,11 +69,16 @@ if (${HDF5_PACKAGE_NAME}_ENABLE_PARALLEL)
   find_package(MPI QUIET REQUIRED)
 endif ()
 
+if (${HDF5_PACKAGE_NAME}_ENABLE_THREADSAFE)
+  set(THREADS_PREFER_PTHREAD_FLAG ON)
+  find_package(Threads QUIET REQUIRED)
+endif ()
+
 if (${HDF5_PACKAGE_NAME}_BUILD_JAVA)
   set (${HDF5_PACKAGE_NAME}_JAVA_INCLUDE_DIRS
       @PACKAGE_CURRENT_BUILD_DIR@/lib/jarhdf5-@[email protected]
-      @PACKAGE_CURRENT_BUILD_DIR@/lib/slf4j-api-1.7.33.jar
-      @PACKAGE_CURRENT_BUILD_DIR@/lib/slf4j-nop-1.7.33.jar
+      @PACKAGE_CURRENT_BUILD_DIR@/lib/slf4j-api-2.0.6.jar
+      @PACKAGE_CURRENT_BUILD_DIR@/lib/slf4j-nop-2.0.6.jar
   )
   set (${HDF5_PACKAGE_NAME}_JAVA_LIBRARY "@PACKAGE_CURRENT_BUILD_DIR@/lib")
   set (${HDF5_PACKAGE_NAME}_JAVA_LIBRARIES "${${HDF5_PACKAGE_NAME}_JAVA_LIBRARY}")
@@ -143,14 +150,14 @@ foreach (comp IN LISTS ${HDF5_PACKAGE_NAME}_FIND_COMPONENTS)
     list (REMOVE_ITEM ${HDF5_PACKAGE_NAME}_FIND_COMPONENTS ${comp})
     set (${HDF5_PACKAGE_NAME}_LIB_TYPE ${${HDF5_PACKAGE_NAME}_LIB_TYPE} ${comp})
 
-    if (${HDF5_PACKAGE_NAME}_BUILD_FORTRAN)
+    if (${HDF5_PACKAGE_NAME}_BUILD_FORTRAN AND ${HDF5_PACKAGE_NAME}_INSTALL_MOD_FORTRAN STREQUAL "SHARED")
       set (${HDF5_PACKAGE_NAME}_INCLUDE_DIR_FORTRAN "@PACKAGE_INCLUDE_INSTALL_DIR@/shared")
     endif ()
   elseif (comp STREQUAL "static")
     list (REMOVE_ITEM ${HDF5_PACKAGE_NAME}_FIND_COMPONENTS ${comp})
     set (${HDF5_PACKAGE_NAME}_LIB_TYPE ${${HDF5_PACKAGE_NAME}_LIB_TYPE} ${comp})
 
-    if (${HDF5_PACKAGE_NAME}_BUILD_FORTRAN)
+    if (${HDF5_PACKAGE_NAME}_BUILD_FORTRAN AND ${HDF5_PACKAGE_NAME}_INSTALL_MOD_FORTRAN STREQUAL "STATIC")
       set (${HDF5_PACKAGE_NAME}_INCLUDE_DIR_FORTRAN "@PACKAGE_INCLUDE_INSTALL_DIR@/static")
     endif ()
   endif ()

config/cmake/mccacheinit.cmake

@@ -11,9 +11,9 @@
 #
 # This is the CMakeCache file.
 
-########################
+#########################
 # EXTERNAL cache entries
-########################
+#########################
 
 set (CMAKE_INSTALL_FRAMEWORK_PREFIX "Library/Frameworks" CACHE STRING "Frameworks installation directory" FORCE)
 
@@ -25,14 +25,14 @@ set (HDF_PACKAGE_NAMESPACE "hdf5::" CACHE STRING "Name for HDF package namespace
 
 set (HDF5_BUILD_CPP_LIB ON CACHE BOOL "Build HDF5 C++ Library" FORCE)
 
-set (HDF5_BUILD_EXAMPLES ON CACHE BOOL "Build HDF5 Library Examples" FORCE)
-
 set (HDF5_BUILD_FORTRAN ON CACHE BOOL "Build FORTRAN support" FORCE)
 
 set (HDF5_BUILD_HL_LIB ON CACHE BOOL "Build HIGH Level HDF5 Library" FORCE)
 
 set (HDF5_BUILD_TOOLS ON CACHE BOOL "Build HDF5 Tools" FORCE)
 
+set (HDF5_BUILD_EXAMPLES ON CACHE BOOL "Build HDF5 Library Examples" FORCE)
+
 set (HDF5_ENABLE_Z_LIB_SUPPORT ON CACHE BOOL "Enable Zlib Filters" FORCE)
 
 set (HDF5_ENABLE_SZIP_SUPPORT ON CACHE BOOL "Use SZip Filter" FORCE)

config/cmake/patch.xml → config/cmake/patch.xml.in

@@ -1,5 +1,5 @@
 <CPackWiXPatch>
-    <CPackWiXFragment Id="CM_CP_libraries.bin.hdf5.dll">
+    <CPackWiXFragment Id="CM_CP_libraries.bin.@WIX_CMP_NAME@.dll">
         <Environment Id="PATH" 
              Name="PATH" 
              Value="[CM_DP_libraries.bin]" 

config/cmake/runTest.cmake

@@ -122,6 +122,10 @@ if (NOT TEST_RESULT EQUAL TEST_EXPECT)
       file (READ ${TEST_FOLDER}/${TEST_OUTPUT} TEST_STREAM)
       message (STATUS "Output :\n${TEST_STREAM}")
     endif ()
+    if (EXISTS "${TEST_FOLDER}/${TEST_OUTPUT}.err")
+      file (READ ${TEST_FOLDER}/${TEST_OUTPUT}.err TEST_STREAM)
+      message (STATUS "Error Output :\n${TEST_STREAM}")
+    endif ()
   endif ()
   message (FATAL_ERROR "Failed: Test program ${TEST_PROGRAM} exited != ${TEST_EXPECT}.\n${TEST_ERROR}")
 endif ()

config/toolchain/build32.cmake

@@ -42,7 +42,7 @@ elseif(MINGW)
   set (CMAKE_CROSSCOMPILING_EMULATOR wine)
 
   include_directories(/usr/${TOOLCHAIN_PREFIX}/include)
-  set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS On CACHE BOOL "Export windows symbols")
+  set (CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS On CACHE BOOL "Export windows symbols")
 else ()
   set (CMAKE_SYSTEM_NAME Linux)
 

config/toolchain/clang.cmake

@@ -1,16 +1,16 @@
 # Uncomment the following to use cross-compiling
-#set(CMAKE_SYSTEM_NAME Linux)
+#set (CMAKE_SYSTEM_NAME Linux)
 
-set(CMAKE_COMPILER_VENDOR "clang")
+set (CMAKE_COMPILER_VENDOR "clang")
 
 if(WIN32)
-  set(CMAKE_C_COMPILER clang-cl)
-  set(CMAKE_CXX_COMPILER clang-cl)
+  set (CMAKE_C_COMPILER clang-cl)
+  set (CMAKE_CXX_COMPILER clang-cl)
 else()
-  set(CMAKE_C_COMPILER clang)
-  set(CMAKE_CXX_COMPILER clang++)
+  set (CMAKE_C_COMPILER clang)
+  set (CMAKE_CXX_COMPILER clang++)
 endif()
-set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+set (CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
 # the following is used if cross-compiling
-set(CMAKE_CROSSCOMPILING_EMULATOR "")
+set (CMAKE_CROSSCOMPILING_EMULATOR "")

config/toolchain/crayle.cmake

@@ -1,10 +1,10 @@
 # The following line will use cross-compiling
-set(CMAKE_SYSTEM_NAME Linux)
+set (CMAKE_SYSTEM_NAME Linux)
 
-set(CMAKE_COMPILER_VENDOR "CrayLinuxEnvironment")
+set (CMAKE_COMPILER_VENDOR "CrayLinuxEnvironment")
 
-set(CMAKE_C_COMPILER cc)
-set(CMAKE_Fortran_COMPILER ftn)
+set (CMAKE_C_COMPILER cc)
+set (CMAKE_Fortran_COMPILER ftn)
 
 # the following is used if cross-compiling
-set(CMAKE_CROSSCOMPILING_EMULATOR "")
+set (CMAKE_CROSSCOMPILING_EMULATOR "")

config/toolchain/gcc.cmake

@@ -1,11 +1,11 @@
 # Uncomment the following line and the correct system name to use cross-compiling
-#set(CMAKE_SYSTEM_NAME Linux)
+#set (CMAKE_SYSTEM_NAME Linux)
 
-set(CMAKE_COMPILER_VENDOR "GCC")
+set (CMAKE_COMPILER_VENDOR "GCC")
 
-set(CMAKE_C_COMPILER cc)
-set(CMAKE_CXX_COMPILER c++)
-set(CMAKE_Fortran_COMPILER gfortran)
+set (CMAKE_C_COMPILER cc)
+set (CMAKE_CXX_COMPILER c++)
+set (CMAKE_Fortran_COMPILER gfortran)
 
 # the following is used if cross-compiling
-set(CMAKE_CROSSCOMPILING_EMULATOR "")
+set (CMAKE_CROSSCOMPILING_EMULATOR "")

config/toolchain/mingw64.cmake

@@ -11,4 +11,4 @@ set (CMAKE_FIND_ROOT_PATH_MODE_INCLUDE ONLY)
 set (CMAKE_CROSSCOMPILING_EMULATOR wine64)
 
 include_directories(/usr/${TOOLCHAIN_PREFIX}/include)
-set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS On CACHE BOOL "Export windows symbols")
+set (CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS On CACHE BOOL "Export windows symbols")

config/toolchain/pgi.cmake

@@ -1,11 +1,11 @@
 # Uncomment the following to use cross-compiling
-#set(CMAKE_SYSTEM_NAME Linux)
+#set (CMAKE_SYSTEM_NAME Linux)
 
-set(CMAKE_COMPILER_VENDOR "PGI")
+set (CMAKE_COMPILER_VENDOR "PGI")
 
-set(CMAKE_C_COMPILER pgcc)
-set(CMAKE_CXX_COMPILER pgc++)
-set(CMAKE_Fortran_COMPILER pgf90)
+set (CMAKE_C_COMPILER pgcc)
+set (CMAKE_CXX_COMPILER pgc++)
+set (CMAKE_Fortran_COMPILER pgf90)
 
 # the following is used if cross-compiling
-set(CMAKE_CROSSCOMPILING_EMULATOR "")
+set (CMAKE_CROSSCOMPILING_EMULATOR "")