ENH: When using cmake > 3.12 use FindPython3 module

The FindPython3 module is more robust for ensuring that python 3 or greater is found. The FindPythonInterp and FindPythonLib modules are deprecated in cmake greater than 3.12.0 The GoogleTest framework uses the deprecated FindPythonInterp, so this patch uses the FindPython3 module, and then uses that more robust information to set the FindPythonInterp cmake variables so that wrapping, google tests, documentation generation, etc.. all use the same found version of Python 3.
InsightSoftwareConsortium · Jan 6, 2020 · 75fbf66 · 75fbf66
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diff --git a/CMake/ITKModuleDoxygen.cmake b/CMake/ITKModuleDoxygen.cmake
@@ -6,7 +6,23 @@
 # python is needed to verify the presence of the module name in the doxygen header
 # Don't require it to not force the developers to install python to be able to build
 # ITK. The tests will simply not be run if python is not available.
-find_package(PythonInterp)
+# Prefer to use more robust FindPython3 module if greater than cmake 3.12.0
+if("${CMAKE_VERSION}" VERSION_LESS_EQUAL "3.12.0")
+  # Use of PythonInterp and PythonLibs is dprecated since cmake version 3.12.0
+
+  # configure python (find PythonInterp first, as of cmake 3.1)
+  find_package(PythonInterp)
+  # Check for supported python versions
+  if(PYTHON_VERSION_STRING VERSION_LESS 3.5)
+    message(FATAL_ERROR "Python versions less than 3.5 are not supported. Python version: \"${PYTHON_VERSION_STRING}\".")
+  endif()
+
+  ## For forward compatibility with cmake 3.12.0 or greater
+  set(Python3_EXECUTABLE ${PYTHON_EXECUTABLE})
+else()
+  find_package(Python3 COMPONENTS Interpreter REQUIRED)
+endif()
+
 
 macro( itk_module_doxygen _name )
 
@@ -43,8 +59,8 @@ macro( itk_module_doxygen _name )
   endif()
 
   if(NOT ${_name}_THIRD_PARTY AND EXISTS ${${_name}_SOURCE_DIR}/include)
-    if(PYTHON_EXECUTABLE AND BUILD_TESTING AND NOT DISABLE_MODULE_TESTS)
-      itk_add_test(NAME ${_name}InDoxygenGroup COMMAND ${PYTHON_EXECUTABLE} "${ITK_CMAKE_DIR}/../Utilities/Doxygen/mcdoc.py" check ${_name} ${${_name}_SOURCE_DIR}/include)
+    if(Python3_EXECUTABLE AND BUILD_TESTING AND NOT DISABLE_MODULE_TESTS)
+      itk_add_test(NAME ${_name}InDoxygenGroup COMMAND ${Python3_EXECUTABLE} "${ITK_CMAKE_DIR}/../Utilities/Doxygen/mcdoc.py" check ${_name} ${${_name}_SOURCE_DIR}/include)
       itk_memcheck_ignore(${_name}InDoxygenGroup)
     endif()
   endif()

diff --git a/CMake/ITKModuleHeaderTest.cmake b/CMake/ITKModuleHeaderTest.cmake
@@ -6,7 +6,22 @@
 
 # This does not force the developer to install python to be able to build ITK.
 # The tests will simply not be run if python is unavailable.
-find_package(PythonInterp)
+# Prefer to use more robust FindPython3 module if greater than cmake 3.12.0
+if("${CMAKE_VERSION}" VERSION_LESS_EQUAL "3.12.0")
+  # Use of PythonInterp and PythonLibs is dprecated since cmake version 3.12.0
+
+  # configure python (find PythonInterp first, as of cmake 3.1)
+  find_package(PythonInterp)
+  # Check for supported python versions
+  if(PYTHON_VERSION_STRING VERSION_LESS 3.5)
+    message(FATAL_ERROR "Python versions less than 3.5 are not supported. Python version: \"${PYTHON_VERSION_STRING}\".")
+  endif()
+
+  ## For forward compatibility with cmake 3.12.0 or greater
+  set(Python3_EXECUTABLE ${PYTHON_EXECUTABLE})
+else()
+  find_package(Python3 COMPONENTS Interpreter REQUIRED)
+endif()
 
 # Improve performance of MSVC GUI, by reducing number of header tests.
 set( MAXIMUM_NUMBER_OF_HEADERS_default 35 )
@@ -29,7 +44,7 @@ endif()
 macro( itk_module_headertest _name )
   if( NOT ${_name}_THIRD_PARTY
       AND EXISTS ${${_name}_SOURCE_DIR}/include
-      AND PYTHON_EXECUTABLE
+      AND Python3_EXECUTABLE
       AND NOT (${_name} STREQUAL ITKTestKernel)
       AND NOT (CMAKE_GENERATOR MATCHES "^Visual Studio 10.*"))
 
@@ -81,7 +96,7 @@ macro( itk_module_headertest _name )
       get_filename_component( _test_name ${_header_test_src} NAME_WE )
       add_custom_command(
         OUTPUT ${_header_test_src}
-        COMMAND ${PYTHON_EXECUTABLE} ${ITK_CMAKE_DIR}/../Utilities/Maintenance/BuildHeaderTest.py
+        COMMAND ${Python3_EXECUTABLE} ${ITK_CMAKE_DIR}/../Utilities/Maintenance/BuildHeaderTest.py
         ${_name}
         ${${_name}_SOURCE_DIR}
         ${${_name}_BINARY_DIR}

diff --git a/CMake/ITKModuleTest.cmake b/CMake/ITKModuleTest.cmake
@@ -176,7 +176,7 @@ function(itk_python_add_test)
   set(multiValueArgs TEST_DRIVER_ARGS COMMAND)
   cmake_parse_arguments(PYTHON_ADD_TEST "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
 
-  set(command "${PYTHON_EXECUTABLE}")
+  set(command "${Python3_EXECUTABLE}")
   # add extra command which may be needed on some systems
   if(CMAKE_OSX_ARCHITECTURES)
     list(GET CMAKE_OSX_ARCHITECTURES 0 test_arch)

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -235,6 +235,8 @@ set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} ${ITK_REQUIRED_LINK_
 if(NOT CMAKE_POSITION_INDEPENDENT_CODE)
   set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 endif()
+# Because GoogleTest uses deprecated FindPythonInterp
+set(Python_ADDITIONAL_VERSIONS 3.9 3.8 3.7 3.6 3.5)
 # Because GoogleTest sets CMAKE_DEBUG_POSTFIX CMake CACHE variable to "d" when it is
 # built in debug, we preemptively set it to an empty string to avoid having a postfix
 # added to the ITK library names.
@@ -512,6 +514,51 @@ endif()
 
 install(FILES "LICENSE" "NOTICE" "README.md" DESTINATION ${ITK_INSTALL_DOC_DIR} COMPONENT Runtime)
 
+if(BUILD_TESTNG OR ITK_WRAP_PYTHON)
+  # Python3 is required if testing (for google tests) or wrapping for python is requested.
+  # Because GoogleTest uses deprecated FindPythonInterp
+  # Prefer to use more robust FindPython3 module if greater than cmake 3.12.0
+  if("${CMAKE_VERSION}" VERSION_LESS_EQUAL "3.12.0")
+    # Use of PythonInterp and PythonLibs is dprecated since cmake version 3.12.0
+
+    # configure python (find PythonInterp first, as of cmake 3.1)
+    find_package(PythonInterp REQUIRED)
+    set(Python3_EXECUTABLE ${PYTHON_EXECUTABLE})
+
+    if(ITK_WRAP_PYTHON)
+      find_package(PythonLibs REQUIRED)
+
+      # check for version mismatch.
+      if(PYTHONLIBS_FOUND AND PYTHONINTERP_FOUND
+          AND NOT(PYTHON_VERSION_STRING VERSION_EQUAL PYTHONLIBS_VERSION_STRING))
+        message(WARNING "Python executable (\"${PYTHON_VERSION_STRING}\") and library (\"${PYTHONLIBS_VERSION_STRING}\") version mismatch.")
+      endif()
+      # Check for supported python versions
+      if(PYTHON_VERSION_STRING VERSION_LESS 3.5)
+        message(FATAL_ERROR "Python versions less than 3.5 are not supported. Python version: \"${PYTHON_VERSION_STRING}\".")
+      endif()
+
+      ## For forward compatibility with cmake 3.12.0 or greater
+      set(Python3_INCLUDE_DIRS ${PYTHON_INCLUDE_DIRS})
+    endif()
+  else()
+    if(ITK_WRAP_PYTHON)
+      find_package(Python3 COMPONENTS Interpreter Development REQUIRED)
+
+    else()
+      find_package(Python3 COMPONENTS Interpreter REQUIRED)
+    endif()
+    # For GoogleTest to force use of same python interpreter as found by the Python3 package
+    # as is looked for by the FindPythonInterp from the incluced GoogleTest package.
+    set(PYTHON_EXECUTABLE ${Python3_EXECUTABLE})
+    set(PYTHONINTERP_FOUND ${Python3_Interpreter_FOUND})
+    set(PYTHON_VERSION ${Python3_VERSION})
+    set(PYTHON_VERSION_MAJOR ${Python3_VERSION_MAJOR})
+    set(PYTHON_VERSION_MINOR ${Python3_VERSION_MINOR})
+    set(PYTHON_VERSION_PATCH ${Python3_VERSION_PATCH})
+  endif()
+endif()
+
 if(BUILD_TESTING)
   # If building the testing, write the test costs (i.e. time to run)
   # analysis to disk to more easily review long-running test times

diff --git a/Documentation/Maintenance/Release.md b/Documentation/Maintenance/Release.md
@@ -516,7 +516,7 @@ virtualenv itk-venv
 git clone https://github.com/InsightSoftwareConsortium/ITKExamples
 mkdir ITKExamples-build
 cd ITKExamples-build
-cmake -DITK_DIR=/path/to/ITK-build -DPYTHON_EXECUTABLE=../itk-venv/bin/python ../ITKExamples
+cmake -DITK_DIR=/path/to/ITK-build -DPython3_ROOT_DIR=../itk-venv/bin/python -DPython3_FIND_VIRTUALENV=ONLY ../ITKExamples
 ctest -R Python
 ```
 

diff --git a/Modules/Bridge/NumPy/wrapping/test/CMakeLists.txt b/Modules/Bridge/NumPy/wrapping/test/CMakeLists.txt
@@ -1,4 +1,4 @@
-execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "import numpy"
+execute_process(COMMAND ${Python3_EXECUTABLE} -c "import numpy"
   RESULT_VARIABLE _have_numpy_return_code
   OUTPUT_QUIET
   ERROR_QUIET

diff --git a/Modules/Core/Common/wrapping/test/CMakeLists.txt b/Modules/Core/Common/wrapping/test/CMakeLists.txt
@@ -7,7 +7,7 @@ itk_python_add_test(NAME itkDirectoryPythonTest COMMAND itkDirectoryTest.py)
 itk_python_expression_add_test(NAME itkObjectPythonTest EXPRESSION "itkObject = itk.Object.New()")
 itk_python_add_test(NAME itkIndexOffsetPythonTest COMMAND itkIndexOffsetTest.py)
 itk_python_add_test(NAME itkImageDuplicatorPythonTest COMMAND itkImageDuplicatorTest.py)
-execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "import numpy"
+execute_process(COMMAND ${Python3_EXECUTABLE} -c "import numpy"
   RESULT_VARIABLE _have_numpy_return_code
   OUTPUT_QUIET
   ERROR_QUIET

diff --git a/Modules/Filtering/ImageIntensity/wrapping/test/CMakeLists.txt b/Modules/Filtering/ImageIntensity/wrapping/test/CMakeLists.txt
@@ -17,7 +17,7 @@ if(ITK_WRAP_unsigned_char AND wrap_2_index GREATER -1)
 endif()
 itk_python_expression_add_test(NAME itkSymmetricEigenAnalysisImageFilterPythonTest
   EXPRESSION "filt = itk.SymmetricEigenAnalysisImageFilter.New()")
-execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "import numpy"
+execute_process(COMMAND ${Python3_EXECUTABLE} -c "import numpy"
   RESULT_VARIABLE _have_numpy_return_code
   OUTPUT_QUIET
   ERROR_QUIET

diff --git a/Testing/ContinuousIntegration/AzurePipelinesLinuxPython.yml b/Testing/ContinuousIntegration/AzurePipelinesLinuxPython.yml
@@ -46,12 +46,14 @@ jobs:
 
     - bash: |
         python_executable=`which python3`
+        python_root_dir=$(dirname $(dirname ${python_executable}))
         cat > dashboard.cmake << EOF
         set(CTEST_BUILD_CONFIGURATION "MinSizeRel")
         set(CTEST_CMAKE_GENERATOR "Ninja")
         set(BUILD_NAME_SUFFIX "-Python")
         set(dashboard_cache "
-          PYTHON_EXECUTABLE:FILEPATH=${python_executable}
+          Python3_ROOT_DIR:PATH=${python_root_dir}
+          Python3_EXECUTABLE:FILEPATH=${python_executable}
           DISABLE_MODULE_TESTS:BOOL=ON
           BUILD_SHARED_LIBS:BOOL=OFF
           BUILD_EXAMPLES:BOOL=OFF

diff --git a/Testing/ContinuousIntegration/AzurePipelinesMacOSPython.yml b/Testing/ContinuousIntegration/AzurePipelinesMacOSPython.yml
@@ -44,12 +44,14 @@ jobs:
 
     - bash: |
         python_executable=`which python3`
+        python_root_dir=$(dirname $(dirname ${python_executable}))
         cat > dashboard.cmake << EOF
         set(CTEST_BUILD_CONFIGURATION "Release")
         set(CTEST_CMAKE_GENERATOR "Ninja")
         set(BUILD_NAME_SUFFIX "-Python")
         set(dashboard_cache "
-          PYTHON_EXECUTABLE:FILEPATH=${python_executable}
+          Python3_ROOT_DIR:PATH=${python_root_dir}
+          Python3_EXECUTABLE:FILEPATH=${python_executable}
           DISABLE_MODULE_TESTS:BOOL=ON
           BUILD_SHARED_LIBS:BOOL=OFF
           BUILD_EXAMPLES:BOOL=OFF

diff --git a/Wrapping/Generators/Doc/CMakeLists.txt b/Wrapping/Generators/Doc/CMakeLists.txt
@@ -105,7 +105,7 @@ macro(itk_end_wrap_submodule_DOC)
     set(swig_doc_interface_file ${WRAPPER_MASTER_INDEX_OUTPUT_DIR}/${WRAPPER_MODULE_NAME}_doc.i)
     add_custom_command(
       OUTPUT ${swig_doc_interface_file}
-      COMMAND ${PYTHON_EXECUTABLE} ${itk_doxy2swig_py} ${doxy2swig_config_file} ${swig_doc_interface_file}
+      COMMAND ${Python3_EXECUTABLE} ${itk_doxy2swig_py} ${doxy2swig_config_file} ${swig_doc_interface_file}
       #DEPENDS ${ITK_WRAP_DOC_DOXYGEN_XML_FILES} ${doxy2swig_config_file} ${itk_doxy2swig_py}
       DEPENDS ${WRAPPER_LIBRARY_NAME}Doxygen ${doxy2swig_config_file} ${itk_doxy2swig_py}
   #    COMMENT "-- Wrapping library ${WRAPPER_MODULE_NAME}: Generating swig interface for inline documentation."

diff --git a/Wrapping/Generators/Perl/ConfigureWrapping.cmake b/Wrapping/Generators/Perl/ConfigureWrapping.cmake
@@ -1,5 +1,4 @@
 find_package(PerlLibs)
 find_package(Perl)
-# mark_as_advanced(PYTHON_EXECUTABLE)
 
 include_directories(${PERL_INCLUDE_PATH})
diff --git a/Wrapping/Generators/Python/CMakeLists.txt b/Wrapping/Generators/Python/CMakeLists.txt
@@ -1,21 +1,6 @@
 ###############################################################################
-# configure python (find PythonInterp first, as of cmake 3.1)
-find_package(PythonInterp)
-find_package(PythonLibs)
 
-# Check for supported python versions
-if(PYTHON_VERSION_STRING VERSION_LESS 3.5)
-  message(WARNING "Python versions less than 3.5 are not supported. Python version: \"${PYTHON_VERSION_STRING}\".")
-endif()
-
-# check for version mismatch.
-if(PYTHONLIBS_FOUND AND PYTHONINTERP_FOUND
-    AND NOT(PYTHON_VERSION_STRING VERSION_EQUAL PYTHONLIBS_VERSION_STRING))
-  message(WARNING "Python executable (\"${PYTHON_VERSION_STRING}\") and library (\"${PYTHONLIBS_VERSION_STRING}\") version mismatch.")
-endif()
-
-mark_as_advanced(PYTHON_EXECUTABLE)
-include_directories("${PYTHON_INCLUDE_DIRS}")
+include_directories("${Python3_INCLUDE_DIRS}")
 
 include_directories("${CMAKE_CURRENT_SOURCE_DIR}")
 
@@ -36,15 +21,15 @@ file(MAKE_DIRECTORY ${WRAPPER_MASTER_INDEX_OUTPUT_DIR}/python)
 
 ###############################################################################
 # Configure Python wrapping installation
-if(PYTHON_EXECUTABLE AND NOT PY_SITE_PACKAGES_PATH)
+if(Python3_EXECUTABLE AND NOT PY_SITE_PACKAGES_PATH)
   set(python_check "from __future__ import print_function\ntry:\n    import distutils.sysconfig\n    print(distutils.sysconfig.get_python_lib(plat_specific=1, prefix=''))\nexcept:\n    pass")
   file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/detect_site_package_path.py ${python_check})
-  execute_process(COMMAND "${PYTHON_EXECUTABLE}" "${CMAKE_CURRENT_BINARY_DIR}/detect_site_package_path.py"
+  execute_process(COMMAND "${Python3_EXECUTABLE}" "${CMAKE_CURRENT_BINARY_DIR}/detect_site_package_path.py"
     OUTPUT_VARIABLE py_spp
     ERROR_VARIABLE py_spp
   )
 
-  execute_process(COMMAND "${PYTHON_EXECUTABLE}" -c "from __future__ import print_function\nimport sys\nprint(sys.prefix)"
+  execute_process(COMMAND "${Python3_EXECUTABLE}" -c "from __future__ import print_function\nimport sys\nprint(sys.prefix)"
     OUTPUT_VARIABLE py_prefix
     ERROR_VARIABLE py_prefix
     OUTPUT_STRIP_TRAILING_WHITESPACE

diff --git a/Wrapping/Generators/Python/Tests/pythonTestDriver.py.in b/Wrapping/Generators/Python/Tests/pythonTestDriver.py.in
@@ -1,4 +1,4 @@
-#!@PYTHON_EXECUTABLE@
+#!@Python3_EXECUTABLE@
 
 # set environment variables
 
@@ -57,7 +57,7 @@ if len(args) < 1:
 
 # call the program, and exit if it fail
 
-command = ["@PYTHON_EXECUTABLE@"] + args
+command = ["@Python3_EXECUTABLE@"] + args
 if options.verbose:
   print(sys.stderr, "+", " ".join(command))
 returnValue = subprocess.call( command )

diff --git a/Wrapping/Generators/SwigInterface/CMakeLists.txt b/Wrapping/Generators/SwigInterface/CMakeLists.txt
@@ -6,9 +6,23 @@ if("${CMAKE_BINARY_DIR}" MATCHES "^.* .*$")
   message(FATAL_ERROR "Swig and PCRE do not support paths with space characters. Please change build directory name.")
 endif()
 
-###############################################################################
-# Find python
-find_package(PythonInterp REQUIRED)
+# Prefer to use more robust FindPython3 module if greater than cmake 3.12.0
+if("${CMAKE_VERSION}" VERSION_LESS_EQUAL "3.12.0")
+  # Use of PythonInterp and PythonLibs is dprecated since cmake version 3.12.0
+
+  # configure python (find PythonInterp first, as of cmake 3.1)
+  find_package(PythonInterp)
+  # Check for supported python versions
+  if(PYTHON_VERSION_STRING VERSION_LESS 3.5)
+    message(FATAL_ERROR "Python versions less than 3.5 are not supported. Python version: \"${PYTHON_VERSION_STRING}\".")
+  endif()
+
+  ## For forward compatibility with cmake 3.12.0 or greater
+  set(Python3_EXECUTABLE ${PYTHON_EXECUTABLE})
+else()
+  find_package(Python3 COMPONENTS Interpreter REQUIRED)
+endif()
+
 
 ###############################################################################
 # Build swig
@@ -354,7 +368,7 @@ macro(itk_end_wrap_module_swig_interface)
   if(number_interface_files GREATER 0)
     add_custom_command(
       OUTPUT ${i_files} ${typedef_files} ${idx_files}
-      COMMAND ${PYTHON_EXECUTABLE} ${IGENERATOR}
+      COMMAND ${Python3_EXECUTABLE} ${IGENERATOR}
         ${mdx_opts}
         ${swig_libs}
         -w1 -w3 -w51 -w52 -w53 -w54