Merge examples and workflows from develop (#3918)

10 files changed, 249 insertions, 74 deletions

diff --git a/config/cmake-presets/hidden-presets.json b/config/cmake-presets/hidden-presets.json
index 901e83c..ab8fdf1 100644
--- a/config/cmake-presets/hidden-presets.json
+++ b/config/cmake-presets/hidden-presets.json
@@ -88,8 +88,16 @@
     {
       "name": "ci-Intel",
       "hidden": true,
+      "toolset": {
+        "value": "host=x64",
+        "strategy": "external"
+      }
+    },
+    {
+      "name": "ci-Fortran",
+      "hidden": true,
       "cacheVariables": {
-        "CMAKE_TOOLCHAIN_FILE": "config/toolchain/intel.cmake"
+        "HDF5_BUILD_FORTRAN": "ON"
       },
       "toolset": {
         "value": "host=x64",
@@ -99,6 +107,7 @@
     {
       "name": "ci-Fortran-Clang",
       "hidden": true,
+      "inherits": "ci-Fortran",
       "cacheVariables": {
         "CMAKE_Fortran_COMPILER":  {"type": "FILEPATH", "value": "gfortran"}
       },
@@ -109,18 +118,6 @@
       }
     },
     {
-      "name": "ci-Fortran",
-      "hidden": true,
-      "inherits": "ci-Fortran-Clang",
-      "cacheVariables": {
-        "HDF5_BUILD_FORTRAN": "ON"
-      },
-      "toolset": {
-        "value": "host=x64",
-        "strategy": "external"
-      }
-    },
-    {
       "name": "ci-CPP",
       "hidden": true,
       "cacheVariables": {
diff --git a/config/cmake/HDF5ExampleCache.cmake b/config/cmake/HDF5ExampleCache.cmake
new file mode 100644
index 0000000..6ac9cc0
--- /dev/null
+++ b/config/cmake/HDF5ExampleCache.cmake
@@ -0,0 +1,74 @@
+# CMake cache file for examples
+
+#########################
+# EXTERNAL cache entries
+#########################
+
+# set example options to match build options
+set (H5EX_BUILD_TESTING ${BUILD_TESTING} CACHE BOOL "Enable examples testing" FORCE)
+set (H5EX_BUILD_EXAMPLES ${HDF5_BUILD_EXAMPLES} CACHE BOOL "Build Examples" FORCE)
+set (HDF_BUILD_FORTRAN ${HDF5_BUILD_FORTRAN} CACHE BOOL "Build examples FORTRAN support" FORCE)
+set (HDF_BUILD_JAVA ${HDF5_BUILD_JAVA} CACHE BOOL "Build examples JAVA support" FORCE)
+set (HDF_BUILD_FILTERS ${HDF5_ENABLE_PLUGIN_SUPPORT} CACHE BOOL "Build examples PLUGIN filter support" FORCE)
+set (HDF_BUILD_CPP_LIB ${HDF5_BUILD_CPP_LIB} CACHE BOOL "Build HDF5 C++ Library" FORCE)
+set (HDF_BUILD_HL_LIB ${HDF5_BUILD_HL_LIB} CACHE BOOL "Build HIGH Level examples" FORCE)
+set (HDF_ENABLE_THREADSAFE ${HDF5_ENABLE_THREADSAFE} CACHE BOOL "Enable examples thread-safety" FORCE)
+set (HDF_ENABLE_PARALLEL ${HDF5_ENABLE_PARALLEL} CACHE BOOL "Enable examples parallel build (requires MPI)" FORCE)
+set (H5EX_USE_GNU_DIRS ${HDF5_USE_GNU_DIRS} CACHE BOOL "TRUE to use GNU Coding Standard install directory variables, FALSE to use historical settings" FORCE)
+
+#preset HDF5 cache vars to this projects libraries instead of searching
+set (H5EX_HDF5_HEADER "H5pubconf.h" CACHE STRING "Name of HDF5 header" FORCE)
+#set (H5EX_HDF5_INCLUDE_DIRS $<TARGET_PROPERTY:${HDF5_LIBSH_TARGET},INCLUDE_DIRECTORIES> CACHE PATH "HDF5 include dirs" FORCE)
+set (H5EX_HDF5_INCLUDE_DIRS "${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR}" CACHE PATH "HDF5 include dirs" FORCE)
+set (H5EX_HDF5_DIR ${CMAKE_CURRENT_BINARY_DIR} CACHE STRING "HDF5 build folder" FORCE)
+set (EXAMPLES_EXTERNALLY_CONFIGURED ON CACHE BOOL "Examples build is used in another project" FORCE)
+
+set (EXAMPLE_VARNAME "H5")
+set (H5EX_RESOURCES_DIR ${HDF_RESOURCES_DIR})
+message (STATUS "HDF5 Example H5EX_RESOURCES_DIR: ${H5EX_RESOURCES_DIR}")
+if (DEFAULT_API_VERSION MATCHES "v16")
+  set (H5_USE_16_API ON)
+elseif (DEFAULT_API_VERSION MATCHES "v18")
+  set (H5_USE_18_API ON)
+elseif (DEFAULT_API_VERSION MATCHES "v110")
+  set (H5_USE_110_API ON)
+elseif (DEFAULT_API_VERSION MATCHES "v112")
+  set (H5_USE_112_API ON)
+elseif (DEFAULT_API_VERSION MATCHES "v114")
+  set (H5_USE_114_API ON)
+elseif (DEFAULT_API_VERSION MATCHES "v116")
+  set (H5_USE_116_API ON)
+endif ()
+message (STATUS "HDF5 H5_LIBVER_DIR: ${H5_LIBVER_DIR} HDF5_API_VERSION: ${DEFAULT_API_VERSION}")
+
+if (NOT BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
+  set (USE_SHARED_LIBS OFF CACHE BOOL "Use Shared Libraries for Examples" FORCE)
+  set (H5EX_HDF5_LINK_LIBS ${HDF5_LIB_TARGET} CACHE STRING "HDF5 target" FORCE)
+  if (HDF5_BUILD_FORTRAN)
+    set (H5EX_HDF5_LINK_LIBS ${H5EX_HDF5_LINK_LIBS} ${HDF5_F90_LIB_TARGET})
+    set (HDF_MOD_EXT "/static" CACHE STRING "Use Static Modules for Examples" FORCE)
+  endif ()
+else ()
+  set (USE_SHARED_LIBS ON CACHE BOOL "Use Shared Libraries for Examples" FORCE)
+  set (H5EX_HDF5_LINK_LIBS ${HDF5_LIBSH_TARGET} CACHE STRING "HDF5 target" FORCE)
+  if (HDF5_BUILD_FORTRAN)
+    set (H5EX_HDF5_LINK_LIBS ${H5EX_HDF5_LINK_LIBS} ${HDF5_F90_LIBSH_TARGET})
+    set (HDF_MOD_EXT "/shared" CACHE STRING "Use Shared Modules for Examples" FORCE)
+  endif ()
+  if (HDF5_BUILD_JAVA)
+    set (HDF5_JAVA_INCLUDE_DIRS ${HDF5_JAVA_JARS} ${HDF5_JAVA_LOGGING_JAR})
+    set (H5EX_JAVA_LIBRARY ${HDF5_JAVA_JNI_LIB_TARGET})
+    set (H5EX_JAVA_LIBRARIES ${HDF5_JAVA_HDF5_LIB_TARGET} ${HDF5_JAVA_JNI_LIB_TARGET})
+    set (HDF5_LIBRARY_PATH ${CMAKE_TEST_OUTPUT_DIRECTORY})
+    message (STATUS "HDF5 Example java lib: ${H5EX_JAVA_LIBRARY} jars: ${HDF5_JAVA_INCLUDE_DIRS}")
+  endif ()
+  if (HDF5_ENABLE_PLUGIN_SUPPORT)
+    set (H5EX_HDF5_PLUGIN_PATH "${CMAKE_BINARY_DIR}/plugins")
+  endif ()
+endif ()
+message (STATUS "HDF5 Example link libs: ${H5EX_HDF5_LINK_LIBS} Includes: ${H5EX_HDF5_INCLUDE_DIRS}")
+
+set (HDF5_TOOLS_DIR ${CMAKE_TEST_OUTPUT_DIRECTORY} CACHE STRING "HDF5 Directory for all Executables" FORCE)
+set (H5EX_HDF5_DUMP_EXECUTABLE $<TARGET_FILE:h5dump${tgt_file_ext}> CACHE STRING "HDF5 h5dump target" FORCE)
+set (H5EX_HDF5_REPACK_EXECUTABLE $<TARGET_FILE:h5repack${tgt_file_ext}> CACHE STRING "HDF5 h5repack target" FORCE)
+
diff --git a/config/cmake/HDF5PluginCache.cmake b/config/cmake/HDF5PluginCache.cmake
index 1407561..d299d9f 100644
--- a/config/cmake/HDF5PluginCache.cmake
+++ b/config/cmake/HDF5PluginCache.cmake
@@ -22,12 +22,17 @@ if (NOT DEFINED H5PL_ALLOW_EXTERNAL_SUPPORT)
   set (H5PL_ALLOW_EXTERNAL_SUPPORT "${HDF5_ALLOW_EXTERNAL_SUPPORT}" CACHE STRING "Allow External Library Building (NO GIT TGZ)" FORCE)
 endif ()
 
+if (H5PL_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT")
+  set (ENABLE_JPEG OFF CACHE BOOL "" FORCE)
+  set (ENABLE_LZF OFF CACHE BOOL "" FORCE)
+endif ()
+
 if (NOT DEFINED H5PL_TGZPATH)
   set (H5PL_TGZPATH "${TGZPATH}" CACHE PATH "PATH for finding plugin tgz file" FORCE)
 endif ()
 
-set (H5PL_GIT_URL "https://github.com/HDFGroup/hdf5_plugins.git" CACHE STRING "Use plugins from HDF Group repository" FORCE)
-set (H5PL_GIT_BRANCH "master" CACHE STRING "" FORCE)
+set (H5PL_GIT_URL "${PLUGIN_GIT_URL}" CACHE STRING "Use plugins from HDF Group repository" FORCE)
+set (H5PL_GIT_BRANCH "${PLUGIN_GIT_BRANCH}" CACHE STRING "" FORCE)
 
 set (H5PL_TGZ_NAME "${PLUGIN_TGZ_NAME}" CACHE STRING "Use plugins from compressed file" FORCE)
 
diff --git a/config/cmake/HDFMacros.cmake b/config/cmake/HDFMacros.cmake
index f0b6f03..30c16e6 100644
--- a/config/cmake/HDFMacros.cmake
+++ b/config/cmake/HDFMacros.cmake
@@ -11,6 +11,55 @@
 #
 
 #-------------------------------------------------------------------------------
+# Setup output Directories
+#-----------------------------------------------------------------------------
+macro (SET_HDF_OUTPUT_DIRS package_prefix)
+  if (NOT ${package_prefix}_EXTERNALLY_CONFIGURED)
+    set (CMAKE_RUNTIME_OUTPUT_DIRECTORY
+        ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all Executables."
+    )
+    set (CMAKE_LIBRARY_OUTPUT_DIRECTORY
+        ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all Libraries"
+    )
+    set (CMAKE_ARCHIVE_OUTPUT_DIRECTORY
+        ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all static libraries."
+    )
+    set (CMAKE_Fortran_MODULE_DIRECTORY
+        ${PROJECT_BINARY_DIR}/mod CACHE PATH "Single Directory for all fortran modules."
+    )
+    get_property(_isMultiConfig GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
+    if(_isMultiConfig)
+      set (CMAKE_TEST_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${HDF_CFG_NAME})
+      set (CMAKE_PDB_OUTPUT_DIRECTORY
+          ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all pdb files."
+      )
+    else ()
+      set (CMAKE_TEST_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
+    endif ()
+  else ()
+    # if we are externally configured, but the project uses old cmake scripts
+    # this may not be set and utilities like H5detect will fail
+    if (NOT CMAKE_RUNTIME_OUTPUT_DIRECTORY)
+      set (CMAKE_RUNTIME_OUTPUT_DIRECTORY ${EXECUTABLE_OUTPUT_PATH})
+    endif ()
+  endif ()
+
+  if (NOT ${package_prefix}_EXTERNALLY_CONFIGURED AND CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+    if (CMAKE_HOST_UNIX)
+      set (CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}/HDF_Group/${HDF5_PACKAGE_NAME}/${HDF5_PACKAGE_VERSION}"
+        CACHE PATH "Install path prefix, prepended onto install directories." FORCE)
+    else ()
+      GetDefaultWindowsPrefixBase(CMAKE_GENERIC_PROGRAM_FILES)
+      set (CMAKE_INSTALL_PREFIX
+        "${CMAKE_GENERIC_PROGRAM_FILES}/HDF_Group/${HDF5_PACKAGE_NAME}/${HDF5_PACKAGE_VERSION}"
+        CACHE PATH "Install path prefix, prepended onto install directories." FORCE)
+      set (CMAKE_GENERIC_PROGRAM_FILES)
+    endif ()
+    set (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT 0 CACHE PATH "" FORCE)
+  endif ()
+endmacro ()
+
+#-------------------------------------------------------------------------------
 macro (SET_HDF_BUILD_TYPE)
   get_property (_isMultiConfig GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
   if (_isMultiConfig)
@@ -434,52 +483,7 @@ macro (HDF_DIR_PATHS package_prefix)
 
   SET_HDF_BUILD_TYPE()
 
-#-----------------------------------------------------------------------------
-# Setup output Directories
-#-----------------------------------------------------------------------------
-  if (NOT ${package_prefix}_EXTERNALLY_CONFIGURED)
-    set (CMAKE_RUNTIME_OUTPUT_DIRECTORY
-        ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all Executables."
-    )
-    set (CMAKE_LIBRARY_OUTPUT_DIRECTORY
-        ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all Libraries"
-    )
-    set (CMAKE_ARCHIVE_OUTPUT_DIRECTORY
-        ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all static libraries."
-    )
-    set (CMAKE_Fortran_MODULE_DIRECTORY
-        ${PROJECT_BINARY_DIR}/mod CACHE PATH "Single Directory for all fortran modules."
-    )
-    get_property(_isMultiConfig GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
-    if(_isMultiConfig)
-      set (CMAKE_TEST_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${HDF_CFG_NAME})
-      set (CMAKE_PDB_OUTPUT_DIRECTORY
-          ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all pdb files."
-      )
-    else ()
-      set (CMAKE_TEST_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
-    endif ()
-  else ()
-    # if we are externally configured, but the project uses old cmake scripts
-    # this may not be set and utilities like H5detect will fail
-    if (NOT CMAKE_RUNTIME_OUTPUT_DIRECTORY)
-      set (CMAKE_RUNTIME_OUTPUT_DIRECTORY ${EXECUTABLE_OUTPUT_PATH})
-    endif ()
-  endif ()
-
-  if (NOT ${package_prefix}_EXTERNALLY_CONFIGURED AND CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
-    if (CMAKE_HOST_UNIX)
-      set (CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}/HDF_Group/${HDF5_PACKAGE_NAME}/${HDF5_PACKAGE_VERSION}"
-        CACHE PATH "Install path prefix, prepended onto install directories." FORCE)
-    else ()
-      GetDefaultWindowsPrefixBase(CMAKE_GENERIC_PROGRAM_FILES)
-      set (CMAKE_INSTALL_PREFIX
-        "${CMAKE_GENERIC_PROGRAM_FILES}/HDF_Group/${HDF5_PACKAGE_NAME}/${HDF5_PACKAGE_VERSION}"
-        CACHE PATH "Install path prefix, prepended onto install directories." FORCE)
-      set (CMAKE_GENERIC_PROGRAM_FILES)
-    endif ()
-    set (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT 0 CACHE PATH "" FORCE)
-  endif ()
+  SET_HDF_OUTPUT_DIRS(${package_prefix})
 
   include (FetchContent)
 endmacro ()
@@ -504,4 +508,3 @@ macro (ADD_H5_FLAGS h5_flag_var infile)
   endif ()
   #message (TRACE "h5_flag_var=${${h5_flag_var}}")
 endmacro ()
-
diff --git a/config/cmake/UseJava.cmake b/config/cmake/UseJava.cmake
index 2783cb6..12e324c 100644
--- a/config/cmake/UseJava.cmake
+++ b/config/cmake/UseJava.cmake
@@ -6,7 +6,7 @@ UseJava
 
 This file provides support for ``Java``.  It is assumed that
 :module:`FindJava` has already been loaded.  See :module:`FindJava` for
-information on how to load Java into your ``CMake`` project.
+information on how to load Java into your CMake project.
 
 Synopsis
 ^^^^^^^^
@@ -42,6 +42,7 @@ Creating And Installing JARs
 
     add_jar(<target_name>
             [SOURCES] <source1> [<source2>...] [<resource1>...]
+            [RESOURCES NAMESPACE <ns1> <resource1>... [NAMESPACE <nsX> <resourceX>...]... ]
             [INCLUDE_JARS <jar1> [<jar2>...]]
             [ENTRY_POINT <entry>]
             [VERSION <version>]
@@ -64,6 +65,34 @@ Creating And Installing JARs
     .. versionadded:: 3.4
       Support for response files, prefixed by ``@``.
 
+  ``RESOURCES``
+    .. versionadded:: 3.21
+
+    Adds the named ``<resource>`` files to the jar by stripping the source file
+    path and placing the file beneath ``<ns>`` within the jar.
+
+    For example::
+
+      RESOURCES NAMESPACE "/com/my/namespace" "a/path/to/resource.txt"
+
+    results in a resource accessible via ``/com/my/namespace/resource.txt``
+    within the jar.
+
+    Resources may be added without adjusting the namespace by adding them to
+    the list of ``SOURCES`` (original behavior), in this case, resource
+    paths must be relative to ``CMAKE_CURRENT_SOURCE_DIR``.  Adding resources
+    without using the ``RESOURCES`` parameter in out of source builds will
+    almost certainly result in confusion.
+
+    .. note::
+
+      Adding resources via the ``SOURCES`` parameter relies upon a hard-coded
+      list of file extensions which are tested to determine whether they
+      compile (e.g. File.java). ``SOURCES`` files which match the extensions
+      are compiled. Files which do not match are treated as resources. To
+      include uncompiled resources matching those file extensions use
+      the ``RESOURCES`` parameter.
+
   ``INCLUDE_JARS``
     The list of jars are added to the classpath when compiling the java sources
     and also to the dependencies of the target. ``INCLUDE_JARS`` also accepts
@@ -264,7 +293,7 @@ Header Generation
 
   .. deprecated:: 3.11
     This command will no longer be supported starting with version 10 of the JDK
-    due to the `suppression of javah tool <http://openjdk.java.net/jeps/313>`_.
+    due to the `suppression of javah tool <https://openjdk.org/jeps/313>`_.
     The :ref:`add_jar(GENERATE_NATIVE_HEADERS) <add_jar>` command should be
     used instead.
 
@@ -526,6 +555,7 @@ function (__java_copy_file src dest comment)
                 ${dest}
         DEPENDS ${src}
         COMMENT ${comment}
+        VERBATIM
         )
 endfunction ()
 
@@ -552,6 +582,58 @@ function(__java_export_jar VAR TARGET PATH)
     set(${VAR} "${${VAR}}" PARENT_SCOPE)
 endfunction()
 
+function(__java_copy_resource_namespaces VAR DEST JAVA_RESOURCE_FILES JAVA_RESOURCE_FILES_RELATIVE)
+
+    set(_ns_ID "")
+    set(_ns_VAL "")
+
+    foreach(_item IN LISTS VAR)
+        if(NOT _ns_ID)
+            if(NOT _item STREQUAL "NAMESPACE")
+                message(FATAL_ERROR "UseJava: Expecting \"NAMESPACE\", got\t\"${_item}\"")
+                return()
+            endif()
+        endif()
+
+        if(_item STREQUAL "NAMESPACE")
+            set(_ns_VAL "")               # Prepare for next namespace
+            set(_ns_ID "${_item}")
+            continue()
+        endif()
+
+        if( NOT _ns_VAL)
+            # we're expecting the next token to be a namespace value
+            # whatever it is, we're treating it like a namespace
+            set(_ns_VAL "${_item}")
+            continue()
+        endif()
+
+        if(_ns_ID AND _ns_VAL)
+            # We're expecting a file name, check to see if we got one
+            cmake_path(ABSOLUTE_PATH _item OUTPUT_VARIABLE _test_file_name)
+            if (NOT EXISTS "${_test_file_name}")
+                message(FATAL_ERROR "UseJava: File does not exist:\t${_item}")
+                return()
+            endif()
+        endif()
+
+        cmake_path(ABSOLUTE_PATH _item OUTPUT_VARIABLE _abs_file_name)
+        cmake_path(GET _item FILENAME _resource_file_name)
+        set(_dest_resource_file_name "${_ns_VAL}/${_resource_file_name}" )
+
+        __java_copy_file( ${_abs_file_name}
+                          ${DEST}/${_dest_resource_file_name}
+                          "Copying ${_item} to the build directory")
+
+        list(APPEND RESOURCE_FILES_LIST           ${DEST}/${_dest_resource_file_name})
+        list(APPEND RELATIVE_RESOURCE_FILES_LIST  ${_dest_resource_file_name})
+
+    endforeach()
+
+    set(${JAVA_RESOURCE_FILES} "${RESOURCE_FILES_LIST}" PARENT_SCOPE)
+    set(${JAVA_RESOURCE_FILES_RELATIVE} "${RELATIVE_RESOURCE_FILES_LIST}" PARENT_SCOPE)
+endfunction()
+
 # define helper scripts
 set(_JAVA_EXPORT_TARGETS_SCRIPT ${CMAKE_CURRENT_LIST_DIR}/javaTargets.cmake.in)
 set(_JAVA_CLASS_FILELIST_SCRIPT ${CMAKE_CURRENT_LIST_DIR}/UseJavaClassFilelist.cmake)
@@ -746,6 +828,13 @@ function(add_jar _TARGET_NAME)
         endif ()
     endforeach()
 
+    if(_add_jar_RESOURCES)         # Process RESOURCES if it exists
+        __java_copy_resource_namespaces("${_add_jar_RESOURCES}"
+                                        ${CMAKE_JAVA_CLASS_OUTPUT_PATH}
+                                        _JAVA_RESOURCE_FILES
+                                        _JAVA_RESOURCE_FILES_RELATIVE)
+    endif()
+
     foreach(_JAVA_INCLUDE_JAR IN LISTS _add_jar_INCLUDE_JARS)
         if (TARGET ${_JAVA_INCLUDE_JAR})
             get_target_property(_JAVA_JAR_PATH ${_JAVA_INCLUDE_JAR} JAR_FILE)
@@ -792,9 +881,10 @@ function(add_jar _TARGET_NAME)
                 ${_GENERATE_NATIVE_HEADERS}
                 ${_JAVA_SOURCES_FILELISTS}
             COMMAND ${CMAKE_COMMAND} -E touch ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_compiled_${_TARGET_NAME}
-            DEPENDS ${_JAVA_COMPILE_FILES} ${_JAVA_COMPILE_FILELISTS} ${_JAVA_COMPILE_DEPENDS}
+            DEPENDS ${_JAVA_COMPILE_FILES} ${_JAVA_COMPILE_FILELISTS} ${_JAVA_COMPILE_DEPENDS} ${_JAVA_SOURCES_FILE}
             WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
             COMMENT "Building Java objects for ${_TARGET_NAME}.jar"
+            VERBATIM
         )
         add_custom_command(
             OUTPUT ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_class_filelist
@@ -804,6 +894,7 @@ function(add_jar _TARGET_NAME)
                 -P ${_JAVA_CLASS_FILELIST_SCRIPT}
             DEPENDS ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_compiled_${_TARGET_NAME}
             WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+            VERBATIM
         )
     else ()
         # create an empty java_class_filelist
@@ -834,6 +925,7 @@ function(add_jar _TARGET_NAME)
             DEPENDS ${_JAVA_RESOURCE_FILES} ${_JAVA_DEPENDS} ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_class_filelist
             WORKING_DIRECTORY ${CMAKE_JAVA_CLASS_OUTPUT_PATH}
             COMMENT "Creating Java archive ${_JAVA_TARGET_OUTPUT_NAME}"
+            VERBATIM
         )
     else ()
         add_custom_command(
@@ -849,6 +941,7 @@ function(add_jar _TARGET_NAME)
             WORKING_DIRECTORY ${CMAKE_JAVA_CLASS_OUTPUT_PATH}
             DEPENDS ${_JAVA_RESOURCE_FILES} ${_JAVA_DEPENDS} ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_class_filelist
             COMMENT "Creating Java archive ${_JAVA_TARGET_OUTPUT_NAME}"
+            VERBATIM
         )
     endif ()
 
diff --git a/config/cmake/cacheinit.cmake b/config/cmake/cacheinit.cmake
index c8f5d06..6a3526f 100644
--- a/config/cmake/cacheinit.cmake
+++ b/config/cmake/cacheinit.cmake
@@ -50,11 +50,15 @@ set (ZLIB_PACKAGE_NAME "zlib" CACHE STRING "Name of ZLIB package" FORCE)
 set (ZLIB_TGZ_NAME "zlib-1.3.tar.gz" CACHE STRING "Use HDF5_ZLib from compressed file" FORCE)
 set (ZLIB_TGZ_ORIGPATH "https://github.com/madler/zlib/releases/download/v1.3" CACHE STRING "Use ZLIB from original location" FORCE)
 set (ZLIB_USE_LOCALCONTENT ON CACHE BOOL "Use local file for ZLIB FetchContent" FORCE)
+set (ZLIB_GIT_URL "https://github.com/madler/zlib.git" CACHE STRING "Use ZLIB from  GitHub repository" FORCE)
+set (ZLIB_GIT_BRANCH "develop" CACHE STRING "" FORCE)
 
 set (LIBAEC_PACKAGE_NAME "libaec" CACHE STRING "Name of AEC SZIP package" FORCE)
 set (LIBAEC_TGZ_NAME "libaec-1.0.6.tar.gz" CACHE STRING "Use SZip AEC from compressed file" FORCE)
 set (LIBAEC_TGZ_ORIGPATH "https://github.com/MathisRosenhauer/libaec/releases/download/v1.0.6" CACHE STRING "Use LIBAEC from original location" FORCE)
 set (LIBAEC_USE_LOCALCONTENT ON CACHE BOOL "Use local file for LIBAEC FetchContent" FORCE)
+set (LIBAEC_GIT_URL "https://github.com/MathisRosenhauer/libaec.git" CACHE STRING "Use LIBAEC from  GitHub repository" FORCE)
+set (LIBAEC_GIT_BRANCH "v1.0.6" CACHE STRING "" FORCE)
 
 ########################
 # API test options
@@ -71,6 +75,8 @@ set (PLUGIN_TGZ_ORIGPATH "https://github.com/HDFGroup/hdf5_plugins/releases/down
 set (PLUGIN_TGZ_NAME "hdf5_plugins-master.tar.gz" CACHE STRING "Use PLUGINS from compressed file" FORCE)
 set (PLUGIN_USE_LOCALCONTENT ON CACHE BOOL "Use local file for PLUGIN FetchContent" FORCE)
 set (PLUGIN_PACKAGE_NAME "pl" CACHE STRING "Name of PLUGIN package" FORCE)
+set (PLUGIN_GIT_URL "https://github.com/HDFGroup/hdf5_plugins.git" CACHE STRING "Use plugins from HDF Group repository" FORCE)
+set (PLUGIN_GIT_BRANCH "master" CACHE STRING "" FORCE)
 set (H5PL_VERS_MAJOR "1" CACHE STRING "Major version of hdf5 package for PLUGIN package" FORCE)
 set (H5PL_VERS_MINOR "14" CACHE STRING "Minor version of hdf5 package for PLUGIN package" FORCE)
 set (H5PL_VERS_RELEASE "4" CACHE STRING "Release version of hdf5 package for PLUGIN package" FORCE)
@@ -112,7 +118,7 @@ set (BLOSC_ZLIB_PACKAGE_NAME "zlib" CACHE STRING "Name of BLOSC_ZLIB package" FO
 ########
 
 set (BZ2_GIT_URL "https://github.com/libarchive/bzip2.git" CACHE STRING "Use BZ2 from  GitHub repository" FORCE)
-set (BZ2_GIT_BRANCH "master" CACHE STRING "" FORCE)
+set (BZ2_GIT_BRANCH "bzip2-1.0.8" CACHE STRING "" FORCE)
 
 set (BZ2_TGZ_ORIGPATH "https://github.com/libarchive/bzip2/archive/refs/tags" CACHE STRING "Use PLUGINS from original location" FORCE)
 set (BZ2_TGZ_NAME "bzip2-bzip2-1.0.8.tar.gz" CACHE STRING "Use BZ2 from compressed file" FORCE)
@@ -135,8 +141,8 @@ set (FPZIP_PACKAGE_NAME "fpzip" CACHE STRING "Name of FPZIP package" FORCE)
 # jpeg
 #######
 
-set (JPEG_GIT_URL "No repo www.ijg.org/files" CACHE STRING "Use JPEG from ILG" FORCE)
-set (JPEG_GIT_BRANCH "v9e" CACHE STRING "" FORCE)
+set (JPEG_GIT_URL "https://github.com/libjpeg-turbo/libjpeg-turbo.git" CACHE STRING "Use JPEG from TurboJPEG" FORCE)
+set (JPEG_GIT_BRANCH "jpeg-9e" CACHE STRING "" FORCE)
 
 set (JPEG_TGZ_ORIGPATH "https://www.ijg.org/files" CACHE STRING "Use PLUGINS from original location" FORCE)
 set (JPEG_TGZ_NAME "jpegsrc.v9e.tar.gz" CACHE STRING "Use JPEG from compressed file" FORCE)
diff --git a/config/cmake/examples/HDF5_Examples.cmake.in b/config/cmake/examples/HDF5_Examples.cmake.in
index 9c99719..d5a6051 100644
--- a/config/cmake/examples/HDF5_Examples.cmake.in
+++ b/config/cmake/examples/HDF5_Examples.cmake.in
@@ -55,7 +55,7 @@ if(NOT DEFINED INSTALLDIR)
   if(WIN32)
     set(INSTALLDIR "\"%ProgramFiles%/HDF_Group/@HDF5_PACKAGE_NAME@/@HDF5_PACKAGE_VERSION@\"")
   else()
-    set(INSTALLDIR "@CMAKE_INSTALL_PREFIX@")
+    set(INSTALLDIR "/opt/HDF_Group/@HDF5_PACKAGE_NAME@/@HDF5_PACKAGE_VERSION@")
   endif()
 endif()
 
diff --git a/config/cmake/hdf5-config.cmake.in b/config/cmake/hdf5-config.cmake.in
index c20e18f..186ae67 100644
--- a/config/cmake/hdf5-config.cmake.in
+++ b/config/cmake/hdf5-config.cmake.in
@@ -92,8 +92,6 @@ if (${HDF5_PACKAGE_NAME}_BUILD_JAVA)
       @PACKAGE_CURRENT_BUILD_DIR@/lib/slf4j-api-2.0.6.jar
       @PACKAGE_CURRENT_BUILD_DIR@/lib/slf4j-nop-2.0.6.jar
   )
-  set (${HDF5_PACKAGE_NAME}_JAVA_LIBRARY "@PACKAGE_CURRENT_BUILD_DIR@/lib")
-  set (${HDF5_PACKAGE_NAME}_JAVA_LIBRARIES "${${HDF5_PACKAGE_NAME}_JAVA_LIBRARY}")
 endif ()
 
 #-----------------------------------------------------------------------------
diff --git a/config/cmake/javaTargets.cmake.in b/config/cmake/javaTargets.cmake.in
index 6e14256..f3670c2 100644
--- a/config/cmake/javaTargets.cmake.in
+++ b/config/cmake/javaTargets.cmake.in
@@ -1,6 +1,5 @@
-cmake_minimum_required(VERSION 2.8.12)
 cmake_policy(PUSH)
-cmake_policy(VERSION 2.8)
+cmake_policy(VERSION 2.8.12...3.27)
 
 #----------------------------------------------------------------
 # Generated CMake Java target import file.
diff --git a/config/cmake/mccacheinit.cmake b/config/cmake/mccacheinit.cmake
index b499371..2fe3b6b 100644
--- a/config/cmake/mccacheinit.cmake
+++ b/config/cmake/mccacheinit.cmake
@@ -19,7 +19,7 @@ set (CMAKE_INSTALL_FRAMEWORK_PREFIX "Library/Frameworks" CACHE STRING "Framework
 
 set (HDF_PACKAGE_EXT "" CACHE STRING "Name of HDF package extension" FORCE)
 
-set (HDF_PACKAGE_NAMESPACE "hdf5::" CACHE STRING "Name for HDF package namespace" FORCE)
+set (HDF_PACKAGE_NAMESPACE "hdf5::" CACHE STRING "Name for HDF package namespace (can be empty)" FORCE)
 
 set (HDF5_BUILD_CPP_LIB ON CACHE BOOL "Build HDF5 C++ Library" FORCE)