Add python testing for examples (#4628)

HDF5Examples/CMakeLists.txt

@@ -27,6 +27,11 @@ if (NOT EXAMPLES_EXTERNALLY_CONFIGURED)
   #-----------------------------------------------------------------------------
   HDF5_SUPPORT (TRUE)
   APIVersion(${HDF5_VERSION} H5_LIBVER_DIR)
+
+  #-----------------------------------------------------------------------------
+  # Python support check
+  #-----------------------------------------------------------------------------
+  PYTHON_SUPPORT ()
 endif ()
 message (STATUS "HDF5 link libs: ${H5EX_HDF5_LINK_LIBS}")
 message (STATUS "HDF5 H5_LIBVER_DIR: ${H5_LIBVER_DIR} HDF5_VERSION_MAJOR: ${HDF5_VERSION_MAJOR}")
@@ -230,4 +235,7 @@ endif ()
 if (HDF_BUILD_CPP_LIB AND HDF5_BUILD_CPP_LIB)
   add_subdirectory (CXX)
 endif ()
+if (HDF_BUILD_PYTHON)
+  add_subdirectory (PYTHON)
+endif ()
 

HDF5Examples/PYTHON/CMakeLists.txt

@@ -0,0 +1,72 @@
+cmake_minimum_required (VERSION 3.18)
+project (HDF5Examples_PYTHON)
+
+#-----------------------------------------------------------------------------
+# Define Sources
+#-----------------------------------------------------------------------------
+include (Py_sourcefiles.cmake)
+
+if (H5EX_BUILD_TESTING)
+  set (${EXAMPLE_VARNAME}_PY_CLEANFILES
+    compound.h5
+    dset.h5
+    gzip.h5
+    hype.h5
+    links.h5
+    objref.h5
+    regref.h5
+    copy1.h5
+    copy2.h5
+    string.h5
+    unlim.h5
+    vlstring.h5
+  )
+
+   # Remove any output file left over from previous test run
+  add_test (
+      NAME ${EXAMPLE_VARNAME}_PY-clear-objects
+      COMMAND    ${CMAKE_COMMAND} -E remove ${${EXAMPLE_VARNAME}_PY_CLEANFILES}
+  )
+  set_tests_properties (${EXAMPLE_VARNAME}_PY-clear-objects PROPERTIES
+      FIXTURES_SETUP clear_${EXAMPLE_VARNAME}_PY
+      WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
+  )
+
+  add_custom_target(${EXAMPLE_VARNAME}_PY-copy-objects ALL COMMENT "Copying Python source files")
+  foreach (example_name ${examples})
+    add_custom_command (
+        TARGET     ${EXAMPLE_VARNAME}_PY-copy-objects
+        POST_BUILD
+        COMMAND    ${CMAKE_COMMAND}
+        ARGS       -E copy_if_different ${PROJECT_SOURCE_DIR}/${example_name}.py ${PROJECT_BINARY_DIR}/${example_name}.py
+    )
+  endforeach ()
+
+  add_test (
+      NAME ${EXAMPLE_VARNAME}_PY-clean-objects
+      COMMAND    ${CMAKE_COMMAND} -E remove ${${EXAMPLE_VARNAME}_PY_CLEANFILES}
+  )
+  set_tests_properties (${EXAMPLE_VARNAME}_PY-clean-objects PROPERTIES
+      FIXTURES_CLEANUP clear_${EXAMPLE_VARNAME}_PY
+      WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
+  )
+
+  macro (ADD_H5_TEST testname)
+    if (NOT HDF5_USING_ANALYSIS_TOOL)
+      add_test (
+          NAME ${EXAMPLE_VARNAME}_PY_${testname}
+          COMMAND ${Python3_EXECUTABLE} ${testname}.py
+          WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
+      )
+      set_tests_properties (${EXAMPLE_VARNAME}_PY_${testname} PROPERTIES FIXTURES_REQUIRED clear_${EXAMPLE_VARNAME}_PY)
+      if (last_test)
+        set_tests_properties (${EXAMPLE_VARNAME}_PY_${testname} PROPERTIES DEPENDS ${last_test})
+      endif ()
+      set (last_test "${EXAMPLE_VARNAME}_PY_${testname}")
+    endif ()
+  endmacro ()
+
+  foreach (example_name ${examples})
+    ADD_H5_TEST (${example_name})
+  endforeach ()
+endif ()

HDF5Examples/PYTHON/Py_sourcefiles.cmake

@@ -0,0 +1,20 @@
+#-----------------------------------------------------------------------------
+# Define Sources, one file per application
+#-----------------------------------------------------------------------------
+set (examples
+    h5_compound
+    h5_crtdat
+    h5_gzip
+    h5_hype
+    h5_hypeb
+    h5_links
+    h5_objref
+    h5_readtofloat
+    h5_regref
+    h5_selecelem
+    h5_string
+    h5_unlim
+    h5_visit
+    h5_visita
+    h5_vlstring
+)

HDF5Examples/PYTHON/h5_vlstring.py

@@ -10,7 +10,7 @@
 #
 # Create a dataset under the Root group using variable-length string type.
 #
-str_type = h5py.new_vlen(str)
+str_type = h5py.special_dtype(vlen=str)
 dataset = file.create_dataset("DSvariable",(4,), dtype=str_type)
 data = ("Parting", " is such", " sweet", " sorrow...")
 dataset[...] = data
@@ -22,7 +22,7 @@
 dataset = file['DSvariable']
 data_out = dataset[...]
 for i in range(4):	
-    print("DSvariable[",i,"]", "'"+data_out[i]+"'", "has length", len(data_out[i]))
+    print("DSvariable[",i,"]", "'"+data_out[i].decode('utf-8')+"'", "has length", len(data_out[i]))
 
 print(data_out)
 file.close()

HDF5Examples/config/cmake/HDFExampleMacros.cmake

@@ -105,6 +105,29 @@ macro (BASIC_SETTINGS varname)
   )
 endmacro ()
 
+macro (PYTHON_SUPPORT)
+  option (HDF_BUILD_PYTHON "Test Python3 support" OFF)
+  if (HDF_BUILD_PYTHON)
+    find_package (Python3 COMPONENTS Interpreter Development NumPy)
+    if (Python3_FOUND AND Python3_NumPy_FOUND)
+      include (ExternalProject)
+      EXTERNALPROJECT_ADD (h5py
+          GIT_REPOSITORY https://github.com/h5py/h5py.git
+          GIT_TAG master
+          UPDATE_COMMAND      ""
+          PATCH_COMMAND       ""
+          CONFIGURE_COMMAND   ""
+          BUILD_COMMAND       "${CMAKE_COMMAND}" -E env HDF5_DIR=${HDF5_ROOT} "${Python3_EXECUTABLE}" setup.py build
+          BUILD_IN_SOURCE     1
+          INSTALL_COMMAND     python3 -m pip --no-cache-dir install -v .
+      )
+    else ()
+      set (HDF_BUILD_PYTHON OFF CACHE BOOL "Test Python3 support" FORCE)
+      message (STATUS "Python3:${Python3_FOUND} or numpy:${Python3_NumPy_FOUND} not found - disable test of Python examples")
+    endif ()
+  endif ()
+endmacro ()
+
 macro (HDF5_SUPPORT)
   set (CMAKE_MODULE_PATH ${H5EX_RESOURCES_DIR} ${CMAKE_MODULE_PATH})
   option (USE_SHARED_LIBS "Use Shared Libraries" ON)