Finished wrappers for main library

wrappers/CMakeLists.txt

-# INCLUDE(FindJava)
+find_package(Doxygen REQUIRED)
+mark_as_advanced(CLEAR DOXYGEN_EXECUTABLE)
 
-set(GCCXML_EXTRA_ARGS "" CACHE STRING "Additional arguments to gccxml, such as '--gccxml-compiler;msvc8'")
-SET(GCCXML_ARGS) # start empty
-FOREACH(subdir ${API_INCLUDE_DIRS})
-    SET(GCCXML_ARGS ${GCCXML_ARGS} -I${subdir})
-ENDFOREACH(subdir)
-SET(GCCXML_ARGS ${GCCXML_ARGS} ${GCCXML_EXTRA_ARGS})
-SET(SAXON_CMD ${JAVA_RUNTIME} -jar ${CMAKE_SOURCE_DIR}/wrappers/saxonb9-1-0-7j/saxon9.jar)
+# WRAPPER_DOXYGEN_DIR is a workspace directory where wrapper files will be created
+set(WRAPPER_DOXYGEN_DIR "${CMAKE_CURRENT_BINARY_DIR}/doxygen")
+file(MAKE_DIRECTORY "${WRAPPER_DOXYGEN_DIR}")
 
-# find_program(GCCXML_PATH gccxml PATH
-#     /usr/local/bin
-#     "C:/Program Files/gccxml 0.9/bin"
-# )
+# Step 1 - Create Doxyfile to point to OpenMM headers
+configure_file(
+    ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in
+    ${WRAPPER_DOXYGEN_DIR}/Doxyfile
+    @ONLY
+)
 
-ADD_CUSTOM_COMMAND(OUTPUT OpenMMApi.xml
-     COMMAND ${GCCXML_PATH} ${GCCXML_ARGS} ${CMAKE_SOURCE_DIR}/openmmapi/include/OpenMM.h -fxml=OpenMMApi.xml
-     DEPENDS ${CMAKE_SOURCE_DIR}/openmmapi/include/OpenMM.h)
-ADD_CUSTOM_COMMAND(OUTPUT OpenMMCWrapper.h
-     COMMAND ${SAXON_CMD} -t -s:OpenMMApi.xml -xsl:${CMAKE_CURRENT_SOURCE_DIR}/CWrapper_Header.xslt -o:OpenMMCWrapper.h
-     DEPENDS OpenMMApi.xml ${CMAKE_CURRENT_SOURCE_DIR}/CWrapper_Header.xslt)
-ADD_CUSTOM_COMMAND(OUTPUT OpenMMCWrapper.cpp
-     COMMAND ${SAXON_CMD} -t -s:OpenMMApi.xml -xsl:${CMAKE_CURRENT_SOURCE_DIR}/CWrapper_Source.xslt -o:OpenMMCWrapper.cpp
-     DEPENDS OpenMMApi.xml ${CMAKE_CURRENT_SOURCE_DIR}/CWrapper_Source.xslt)
-ADD_CUSTOM_COMMAND(OUTPUT OpenMMFortranModule.f90
-     COMMAND ${SAXON_CMD} -t -s:OpenMMApi.xml -xsl:${CMAKE_CURRENT_SOURCE_DIR}/FortranWrapper_Header.xslt -o:OpenMMFortranModule.f90
-     DEPENDS OpenMMApi.xml ${CMAKE_CURRENT_SOURCE_DIR}/FortranWrapper_Header.xslt)
-ADD_CUSTOM_COMMAND(OUTPUT OpenMMFortranWrapper.cpp
-     COMMAND ${SAXON_CMD} -t -s:OpenMMApi.xml -xsl:${CMAKE_CURRENT_SOURCE_DIR}/FortranWrapper_Source.xslt -o:OpenMMFortranWrapper.cpp
-     DEPENDS OpenMMApi.xml ${CMAKE_CURRENT_SOURCE_DIR}/FortranWrapper_Source.xslt)
+# Step 2 - Run doxygen to analyze the headers
+add_custom_command(
+    OUTPUT "${WRAPPER_DOXYGEN_DIR}/xml/index.xml"
+    COMMAND "${DOXYGEN_EXECUTABLE}"
+    DEPENDS "${WRAPPER_DOXYGEN_DIR}/Doxyfile"
+    WORKING_DIRECTORY "${WRAPPER_DOXYGEN_DIR}"
+    COMMENT "Parsing OpenMM header files with Doxygen..."
+)
 
-ADD_CUSTOM_TARGET(ApiWrappers DEPENDS OpenMMCWrapper.h OpenMMCWrapper.cpp OpenMMFortranModule.f90 OpenMMFortranWrapper.cpp)
+# Step 3 - Generate the wrappers
+ADD_CUSTOM_COMMAND(OUTPUT OpenMMCWrapper.h OpenMMCWrapper.cpp OpenMMFortranModule.f90 OpenMMFortranWrapper.cpp
+     COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/generateWrappers.py" "${WRAPPER_DOXYGEN_DIR}/xml" "${CMAKE_CURRENT_BINARY_DIR}"
+     DEPENDS "${WRAPPER_DOXYGEN_DIR}/xml/index.xml" "${CMAKE_CURRENT_SOURCE_DIR}/generateWrappers.py")
 
+ADD_CUSTOM_TARGET(ApiWrappers DEPENDS OpenMMCWrapper.h OpenMMCWrapper.cpp OpenMMFortranModule.f90 OpenMMFortranWrapper.cpp)
 
 INSTALL_FILES(/include FILES OpenMMCWrapper.h OpenMMFortranModule.f90)