Small fixes

cmake_modules/ApiDoxygen.cmake

-find_package(Doxygen)
-
-set(OPENMM_GENERATE_API_DOCS OFF CACHE BOOL "Whether to create API documentation using Doxygen")
-IF(DOXYGEN_FOUND)
-    SET(DOXY_CONFIG "${CMAKE_CURRENT_BINARY_DIR}/Doxyfile")
-
-    CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/docs/Doxyfile.in 
-          ${DOXY_CONFIG}
-          @ONLY )
-
-    ADD_CUSTOM_COMMAND(
-        OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/html/index.html"
-        COMMAND ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG}
-        WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
-        COMMENT "Generating API documentation using Doxygen"
-        SOURCES "${CMAKE_CURRENT_SOURCE_DIR}/docs/Doxyfile.in") 
-    ADD_CUSTOM_TARGET(DoxygenApiDocs 
-        COMMAND ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG}
-        WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
-        COMMENT "Generating API documentation using Doxygen"
-        SOURCES "${CMAKE_CURRENT_SOURCE_DIR}/docs/Doxyfile.in") 
-    FILE(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/html/")
-
-    IF(OPENMM_GENERATE_API_DOCS)
-        INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/html/"
-                DESTINATION "docs/api/")
-    ENDIF(OPENMM_GENERATE_API_DOCS)
-ELSE(DOXYGEN_FOUND)
-ENDIF(DOXYGEN_FOUND)
-

docs-source/CMakeLists.txt

@@ -3,7 +3,8 @@
 #
 
 find_package(Doxygen QUIET)
-mark_as_advanced(CLEAR DOXYGEN_EXECUTABLE)
+set(OPENMM_GENERATE_API_DOCS OFF CACHE BOOL "Whether to create API documentation using Doxygen")
+
 IF(DOXYGEN_EXECUTABLE)
     # Generate C++ API documentation
     IF (OPENMM_GENERATE_API_DOCS)

docs-source/api-c++/CMakeLists.txt

@@ -38,6 +38,7 @@ add_custom_command(
             "${CMAKE_CURRENT_BINARY_DIR}/forces.rst.jinja2"
             "${CMAKE_CURRENT_BINARY_DIR}/extras.rst.jinja2"
             "${CMAKE_BINARY_DIR}/wrappers/python/src/swig_doxygen/doxygen/xml/index.xml"
+            RunSwig
 )
 
 add_custom_command(