Begin work on super build. #83

slicer/collageradiomics/CMakeLists.txt → slicer/CMakeLists.txt

@@ -12,16 +12,47 @@ set(EXTENSION_ICONURL "https://github.com/radxtools/collageradiomics/raw/master/
 set(EXTENSION_SCREENSHOTURLS "https://github.com/radxtools/collageradiomics/raw/master/slicer/collageradiomics/CollageRadiomicsSlicer/Screenshot.jpg")
 set(EXTENSION_DEPENDS "NA") # Specified as a list or "NA" if no dependencies
 
+set(EXTENSION_BUILD_SUBDIRECTORY inner-build)
+
+set(SUPERBUILD_TOPLEVEL_PROJECT inner)
+
 #-----------------------------------------------------------------------------
 # Extension dependencies
 find_package(Slicer REQUIRED)
 include(${Slicer_USE_FILE})
+mark_as_superbuild(Slicer_DIR)
+
+find_package(Git REQUIRED)
+mark_as_superbuild(GIT_EXECUTABLE)
+
+#-----------------------------------------------------------------------------
+# SuperBuild setup
+option(${EXTENSION_NAME}_SUPERBUILD "Build ${EXTENSION_NAME} and the projects it depends on." ON)
+mark_as_advanced(${EXTENSION_NAME}_SUPERBUILD)
+if(${EXTENSION_NAME}_SUPERBUILD)
+  include("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake")
+  return()
+endif()
+
+#-----------------------------------------------------------------------------
+list(INSERT CMAKE_MODULE_PATH 0 ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
+include(SlicerRadiomicsAddCLI)
 
 #-----------------------------------------------------------------------------
 # Extension modules
-add_subdirectory(CollageRadiomicsSlicer)
+add_subdirectory(SlicerRadiomics)
+add_subdirectory(SlicerRadiomicsCLI)
 ## NEXT_MODULE
 
 #-----------------------------------------------------------------------------
-include(${Slicer_EXTENSION_GENERATE_CONFIG})
+# Install extension python packages
+install(CODE "message(\"CPack: - Install directory: ${python_packages_DIR}\")")
+install(
+    DIRECTORY "${python_packages_DIR}/"
+    DESTINATION ${Slicer_INSTALL_ROOT}${Slicer_BUNDLE_EXTENSIONS_LOCATION}
+    COMPONENT RuntimeLibraries
+    )
+
+#-----------------------------------------------------------------------------
+set(CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${CMAKE_BINARY_DIR};${EXTENSION_NAME};ALL;/")
 include(${Slicer_EXTENSION_CPACK})

slicer/SuperBuild.cmake

@@ -0,0 +1,68 @@
+#-----------------------------------------------------------------------------
+# Git protocol option
+#-----------------------------------------------------------------------------
+option(Slicer_USE_GIT_PROTOCOL "If behind a firewall turn this off to use http instead." ON)
+
+set(git_protocol "git")
+if(NOT Slicer_USE_GIT_PROTOCOL)
+  set(git_protocol "http")
+endif()
+
+#-----------------------------------------------------------------------------
+# Enable and setup External project global properties
+#-----------------------------------------------------------------------------
+set(ep_common_c_flags "${CMAKE_C_FLAGS_INIT} ${ADDITIONAL_C_FLAGS}")
+set(ep_common_cxx_flags "${CMAKE_CXX_FLAGS_INIT} ${ADDITIONAL_CXX_FLAGS}")
+
+#-----------------------------------------------------------------------------
+# Project dependencies
+#-----------------------------------------------------------------------------
+include(ExternalProject)
+
+foreach(dep ${EXTENSION_DEPENDS})
+  mark_as_superbuild(${dep}_DIR)
+endforeach()
+
+set(proj ${SUPERBUILD_TOPLEVEL_PROJECT})
+if(UNIX)
+  set(${proj}_DEPENDS python-collageradiomics)
+endif(UNIX)
+
+ExternalProject_Include_Dependencies(${proj}
+  PROJECT_VAR proj
+  SUPERBUILD_VAR ${EXTENSION_NAME}_SUPERBUILD
+  )
+
+ExternalProject_Add(${proj}
+  ${${proj}_EP_ARGS}
+  DOWNLOAD_COMMAND ""
+  INSTALL_COMMAND ""
+  SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}
+  BINARY_DIR ${EXTENSION_BUILD_SUBDIRECTORY}
+  BUILD_ALWAYS 1
+  CMAKE_CACHE_ARGS
+    -DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER}
+    -DCMAKE_CXX_FLAGS:STRING=${ep_common_cxx_flags}
+    -DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER}
+    -DCMAKE_C_FLAGS:STRING=${ep_common_c_flags}
+    -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=${CMAKE_OSX_DEPLOYMENT_TARGET}
+    -DCMAKE_OSX_SYSROOT:PATH=${CMAKE_OSX_SYSROOT}
+    -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
+    -DCMAKE_CXX_STANDARD:STRING=${CMAKE_CXX_STANDARD}
+    -DCMAKE_CXX_STANDARD_REQUIRED:BOOL=${CMAKE_CXX_STANDARD_REQUIRED}
+    -DCMAKE_CXX_EXTENSIONS:BOOL=${CMAKE_CXX_EXTENSIONS}
+    -DCMAKE_RUNTIME_OUTPUT_DIRECTORY:PATH=${CMAKE_RUNTIME_OUTPUT_DIRECTORY}
+    -DCMAKE_LIBRARY_OUTPUT_DIRECTORY:PATH=${CMAKE_LIBRARY_OUTPUT_DIRECTORY}
+    -DCMAKE_ARCHIVE_OUTPUT_DIRECTORY:PATH=${CMAKE_ARCHIVE_OUTPUT_DIRECTORY}
+    -DSlicer_DIR:PATH=${Slicer_DIR}
+    -DMIDAS_PACKAGE_EMAIL:STRING=${MIDAS_PACKAGE_EMAIL}
+    -DMIDAS_PACKAGE_API_KEY:STRING=${MIDAS_PACKAGE_API_KEY}
+    -D${EXTENSION_NAME}_SUPERBUILD:BOOL=OFF
+    -DEXTENSION_SUPERBUILD_BINARY_DIR:PATH=${${EXTENSION_NAME}_BINARY_DIR}
+    -DSubversion_SVN_EXECUTABLE:STRING=${Subversion_SVN_EXECUTABLE}
+    -DGIT_EXECUTABLE:STRING=${GIT_EXECUTABLE}
+  DEPENDS
+    ${${proj}_DEPENDS}
+  )
+
+ExternalProject_AlwaysConfigure(${proj})

slicer/SuperBuild/External_python-collageradiomics.cmake

@@ -0,0 +1,92 @@
+set(proj python-collageradiomics)
+
+# Set dependency list
+set(${proj}_DEPENDENCIES "")
+
+# Include dependent projects if any
+ExternalProject_Include_Dependencies(${proj} PROJECT_VAR proj DEPENDS_VAR ${proj}_DEPENDENCIES)
+
+if(${CMAKE_PROJECT_NAME}_USE_SYSTEM_${proj})
+  ExternalProject_FindPythonPackage(
+    MODULE_NAME "collageradiomics"
+    REQUIRED
+    )
+endif()
+
+if(NOT DEFINED ${CMAKE_PROJECT_NAME}_USE_SYSTEM_${proj})
+  set(${CMAKE_PROJECT_NAME}_USE_SYSTEM_${proj} ${Slicer_USE_SYSTEM_python})
+endif()
+
+if(NOT ${CMAKE_PROJECT_NAME}_USE_SYSTEM_${proj})
+
+  if(NOT DEFINED git_protocol)
+    set(git_protocol "git")
+  endif()
+
+  ExternalProject_SetIfNotDefined(
+    ${CMAKE_PROJECT_NAME}_${proj}_GIT_REPOSITORY
+    "${git_protocol}://github.com/radxtools/collageradiomics"
+    QUIET
+    )
+
+  ExternalProject_SetIfNotDefined(
+    ${CMAKE_PROJECT_NAME}_${proj}_GIT_TAG
+    "origin/master"
+    QUIET
+    )
+
+  set(wrapper_script)
+  if(MSVC)
+    find_package(Vcvars REQUIRED)
+    set(wrapper_script ${Vcvars_WRAPPER_BATCH_FILE})
+  endif()
+
+  # Alternative python prefix for installing extension python packages
+  set(python_packages_DIR "${CMAKE_BINARY_DIR}/python-packages-install")
+  file(TO_NATIVE_PATH ${python_packages_DIR} python_packages_DIR_NATIVE_DIR)
+
+  set(_no_binary "")
+
+  # Install collageradiomics
+  set(_install_collageradiomics COMMAND ${CMAKE_COMMAND}
+      -E env
+        PYTHONNOUSERSITE=1
+        CC=${CMAKE_C_COMPILER}
+      ${wrapper_script} ${PYTHON_EXECUTABLE} -m pip install . ${_no_binary}
+        --prefix ${python_packages_DIR_NATIVE_DIR}
+    )
+
+  ExternalProject_Add(${proj}
+    ${${proj}_EP_ARGS}
+    GIT_REPOSITORY "${${CMAKE_PROJECT_NAME}_${proj}_GIT_REPOSITORY}"
+    GIT_TAG "${${CMAKE_PROJECT_NAME}_${proj}_GIT_TAG}"
+    SOURCE_DIR ${proj}
+    BUILD_IN_SOURCE 1
+    CONFIGURE_COMMAND ""
+    BUILD_COMMAND ""
+    INSTALL_COMMAND ${CMAKE_COMMAND} -E  echo_append ""
+    ${_install_pyyaml}
+    ${_install_collageradiomics}
+    DEPENDS
+      ${${proj}_DEPENDENCIES}
+    )
+
+  ExternalProject_GenerateProjectDescription_Step(${proj})
+
+  #-----------------------------------------------------------------------------
+  # Launcher setting specific to build tree
+  set(${proj}_PYTHONPATH_LAUNCHER_BUILD
+    ${python_packages_DIR}/${PYTHON_STDLIB_SUBDIR}
+    ${python_packages_DIR}/${PYTHON_STDLIB_SUBDIR}/lib-dynload
+    ${python_packages_DIR}/${PYTHON_SITE_PACKAGES_SUBDIR}
+    )
+  mark_as_superbuild(
+    VARS ${proj}_PYTHONPATH_LAUNCHER_BUILD
+    LABELS "PYTHONPATH_LAUNCHER_BUILD"
+    )
+
+  mark_as_superbuild(python_packages_DIR:PATH)
+
+else()
+  ExternalProject_Add_Empty(${proj} DEPENDS ${${proj}_DEPENDENCIES})
+endif()