Created CMake targets for building Sphinx documentation

CMakeLists.txt

@@ -496,89 +496,7 @@ ELSE (EXECUTABLE_OUTPUT_PATH)
   SET (TEST_PATH .)
 ENDIF (EXECUTABLE_OUTPUT_PATH)
 
-# Build and install documentation
-
-find_package(Doxygen QUIET)
-mark_as_advanced(CLEAR DOXYGEN_EXECUTABLE)
-IF(DOXYGEN_EXECUTABLE)
-    # Generate C++ API documentation
-
-    SET(DOXY_CONFIG_C++ "${CMAKE_CURRENT_BINARY_DIR}/DoxyfileC++")
-    CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/docs/DoxyfileC++.in 
-          ${DOXY_CONFIG_C++}
-          @ONLY )
-    FILE(GLOB_RECURSE OPENMM_INCLUDES "openmm/include/*.h")
-    FILE(GLOB_RECURSE OLLA_INCLUDES "olla/include/*.h")
-    ADD_CUSTOM_COMMAND(
-        OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/api-c++/index.html"
-        COMMAND ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG_C++}
-        DEPENDS ${OPENMM_INCLUDES} ${OLLA_INCLUDES}
-        WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
-        COMMENT "Generating C++ API documentation using Doxygen")
-    ADD_CUSTOM_TARGET(C++ApiDocs 
-        DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/api-c++/index.html"
-        COMMENT "Generating C++ API documentation using Doxygen"
-        SOURCES 
-            "${CMAKE_CURRENT_SOURCE_DIR}/docs/DoxyfileC++.in"
-            ${OPENMM_INCLUDES}
-            ${OLLA_INCLUDES}
-    ) 
-    FILE(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/api-c++/")
-    INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/api-c++/"
-            DESTINATION "docs/api-c++/")
-    INSTALL(FILES "docs/C++ API Reference.html"
-            DESTINATION "docs/")
-    ADD_CUSTOM_TARGET(DoxygenApiDocs
-        DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/api-c++/index.html"
-        COMMENT "Generating C++ API documentation using Doxygen"
-        SOURCES 
-        "${CMAKE_CURRENT_SOURCE_DIR}/docs/DoxyfileC++.in"
-        "${CMAKE_CURRENT_SOURCE_DIR}/docs/DoxyfilePython.in"
-        ${OPENMM_INCLUDES}
-        ${OLLA_INCLUDES}
-    )
-    set(OPENMM_GENERATE_API_DOCS OFF CACHE BOOL "Whether to create API documentation using Doxygen")
-    IF (OPENMM_GENERATE_API_DOCS)
-        SET_TARGET_PROPERTIES(DoxygenApiDocs PROPERTIES EXCLUDE_FROM_ALL FALSE)
-    ENDIF (OPENMM_GENERATE_API_DOCS)
-
-    # Generate Python API documentation
-
-    IF (OPENMM_BUILD_PYTHON_WRAPPERS)
-        SET(DOXY_CONFIG_PYTHON "${CMAKE_CURRENT_BINARY_DIR}/DoxyfilePython")
-        CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/docs/DoxyfilePython.in 
-            ${DOXY_CONFIG_PYTHON}
-            @ONLY )
-        ADD_CUSTOM_COMMAND(
-            OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/api-python/index.html"
-            COMMAND ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG_PYTHON}
-            DEPENDS RunSwig
-            WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
-            COMMENT "Generating Python API documentation using Doxygen")
-        ADD_CUSTOM_TARGET(PythonApiDocs 
-            DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/api-python/index.html"
-            COMMENT "Generating Python API documentation using Doxygen"
-            SOURCES 
-                "${CMAKE_CURRENT_SOURCE_DIR}/docs/DoxyfilePython.in"
-                ${OPENMM_INCLUDES}
-                ${OLLA_INCLUDES}
-        ) 
-        FILE(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/api-python/")
-        INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/api-python/"
-                DESTINATION "docs/api-python/")
-        INSTALL(FILES "docs/Python API Reference.html"
-                DESTINATION "docs/")
-        ADD_DEPENDENCIES(DoxygenApiDocs PythonApiDocs)
-    ENDIF (OPENMM_BUILD_PYTHON_WRAPPERS)
-ENDIF(DOXYGEN_EXECUTABLE)
-
-install(FILES docs/OpenMMUsersGuide.pdf docs/OpenMMDeveloperGuide.pdf
-    DESTINATION docs/)
-
-FILE(GLOB LICENSE_FILES "docs/licenses/*.txt")
-install(FILES ${LICENSE_FILES}
-    DESTINATION licenses/)
-
+ADD_SUBDIRECTORY(docs)
 ADD_SUBDIRECTORY(tests)
 ADD_SUBDIRECTORY(examples)
 

docs/CMakeLists.txt

+#
+# Build and install API documentation
+#
+
+find_package(Doxygen QUIET)
+mark_as_advanced(CLEAR DOXYGEN_EXECUTABLE)
+IF(DOXYGEN_EXECUTABLE)
+    # Generate C++ API documentation
+
+    SET(DOXY_CONFIG_C++ "${CMAKE_BINARY_DIR}/DoxyfileC++")
+    CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/DoxyfileC++.in 
+          ${DOXY_CONFIG_C++}
+          @ONLY )
+    FILE(GLOB_RECURSE OPENMM_INCLUDES "openmm/include/*.h")
+    FILE(GLOB_RECURSE OLLA_INCLUDES "olla/include/*.h")
+    ADD_CUSTOM_COMMAND(
+        OUTPUT "${CMAKE_BINARY_DIR}/api-c++/index.html"
+        COMMAND ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG_C++}
+        DEPENDS ${OPENMM_INCLUDES} ${OLLA_INCLUDES}
+        WORKING_DIRECTORY "${CMAKE_BINARY_DIR}"
+        COMMENT "Generating C++ API documentation using Doxygen")
+    ADD_CUSTOM_TARGET(C++ApiDocs 
+        DEPENDS "${CMAKE_BINARY_DIR}/api-c++/index.html"
+        COMMENT "Generating C++ API documentation using Doxygen"
+        SOURCES 
+            "${CMAKE_CURRENT_SOURCE_DIR}/DoxyfileC++.in"
+            ${OPENMM_INCLUDES}
+            ${OLLA_INCLUDES}
+    ) 
+    FILE(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/api-c++/")
+    INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/api-c++/"
+            DESTINATION "docs/api-c++/")
+    INSTALL(FILES "C++ API Reference.html"
+            DESTINATION "docs/")
+    ADD_CUSTOM_TARGET(DoxygenApiDocs
+        DEPENDS "${CMAKE_BINARY_DIR}/api-c++/index.html"
+        COMMENT "Generating C++ API documentation using Doxygen"
+        SOURCES 
+        "${CMAKE_CURRENT_SOURCE_DIR}/DoxyfileC++.in"
+        "${CMAKE_CURRENT_SOURCE_DIR}/DoxyfilePython.in"
+        ${OPENMM_INCLUDES}
+        ${OLLA_INCLUDES}
+    )
+    set(OPENMM_GENERATE_API_DOCS OFF CACHE BOOL "Whether to create API documentation using Doxygen")
+    IF (OPENMM_GENERATE_API_DOCS)
+        SET_TARGET_PROPERTIES(DoxygenApiDocs PROPERTIES EXCLUDE_FROM_ALL FALSE)
+    ENDIF (OPENMM_GENERATE_API_DOCS)
+
+    # Generate Python API documentation
+
+    IF (OPENMM_BUILD_PYTHON_WRAPPERS)
+        SET(DOXY_CONFIG_PYTHON "${CMAKE_BINARY_DIR}/DoxyfilePython")
+        CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/DoxyfilePython.in 
+            ${DOXY_CONFIG_PYTHON}
+            @ONLY )
+        ADD_CUSTOM_COMMAND(
+            OUTPUT "${CMAKE_BINARY_DIR}/api-python/index.html"
+            COMMAND ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG_PYTHON}
+            DEPENDS RunSwig
+            WORKING_DIRECTORY "${CMAKE_BINARY_DIR}"
+            COMMENT "Generating Python API documentation using Doxygen")
+        ADD_CUSTOM_TARGET(PythonApiDocs 
+            DEPENDS "${CMAKE_BINARY_DIR}/api-python/index.html"
+            COMMENT "Generating Python API documentation using Doxygen"
+            SOURCES 
+                "${CMAKE_CURRENT_SOURCE_DIR}/DoxyfilePython.in"
+                ${OPENMM_INCLUDES}
+                ${OLLA_INCLUDES}
+        ) 
+        FILE(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/api-python/")
+        INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/api-python/"
+                DESTINATION "docs/api-python/")
+        INSTALL(FILES "Python API Reference.html"
+                DESTINATION "docs/")
+        ADD_DEPENDENCIES(DoxygenApiDocs PythonApiDocs)
+    ENDIF (OPENMM_BUILD_PYTHON_WRAPPERS)
+ENDIF(DOXYGEN_EXECUTABLE)
+
+
+#
+# Build and install the User Guide and Developer Guide
+#
+
+SET(SPHINX_BUILD_DIR "${CMAKE_BINARY_DIR}/sphinx-docs/")
+FILE(MAKE_DIRECTORY "${SPHINX_BUILD_DIR}")
+
+ADD_CUSTOM_COMMAND(
+    OUTPUT "${SPHINX_BUILD_DIR}/userguide/latex/OpenMMUsersGuide.pdf"
+    COMMAND "${CMAKE_MAKE_PROGRAM}" BUILDDIR="${SPHINX_BUILD_DIR}/userguide" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" latexpdf
+    WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/usersguide"
+    COMMENT "Generating PDF user guide"
+)
+ADD_CUSTOM_COMMAND(
+    OUTPUT "${SPHINX_BUILD_DIR}/developerguide/latex/OpenMMDeveloperGuide.pdf"
+    COMMAND "${CMAKE_MAKE_PROGRAM}" BUILDDIR="${SPHINX_BUILD_DIR}/developerguide" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" latexpdf
+    WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/developerguide"
+    COMMENT "Generating PDF developer guide"
+)
+ADD_CUSTOM_TARGET(sphinxpdf
+    DEPENDS "${SPHINX_BUILD_DIR}/userguide/latex/OpenMMUsersGuide.pdf" "${SPHINX_BUILD_DIR}/developerguide/latex/OpenMMDeveloperGuide.pdf"
+)
+
+ADD_CUSTOM_COMMAND(
+    OUTPUT "${SPHINX_BUILD_DIR}/userguide/html/index.html"
+    COMMAND "${CMAKE_MAKE_PROGRAM}" BUILDDIR="${SPHINX_BUILD_DIR}/userguide" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" html
+    WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/usersguide"
+    COMMENT "Generating PDF user guide"
+)
+ADD_CUSTOM_COMMAND(
+    OUTPUT "${SPHINX_BUILD_DIR}/developerguide/html/index.html"
+    COMMAND "${CMAKE_MAKE_PROGRAM}" BUILDDIR="${SPHINX_BUILD_DIR}/developerguide" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" html
+    WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/developerguide"
+    COMMENT "Generating PDF developer guide"
+)
+ADD_CUSTOM_TARGET(sphinxhtml
+    DEPENDS "${SPHINX_BUILD_DIR}/userguide/html/index.html" "${SPHINX_BUILD_DIR}/developerguide/html/index.html"
+)
+
+install(FILES "${SPHINX_BUILD_DIR}/userguide/latex/OpenMMUsersGuide.pdf" "${SPHINX_BUILD_DIR}developerguide/latex/OpenMMDeveloperGuide.pdf"
+    DESTINATION docs/)
+
+FILE(GLOB LICENSE_FILES "licenses/*.txt")
+install(FILES ${LICENSE_FILES}
+    DESTINATION licenses/)

docs/developerguide/conf.py

@@ -49,9 +49,9 @@ copyright = u'2011-2014, Stanford University'
 # built documents.
 #
 # The short X.Y version.
-version = '6.0'
+version = os.getenv('OPENMM_VERSION')
 # The full version, including alpha/beta/rc tags.
-release = '6.0'
+release = os.getenv('OPENMM_VERSION')
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/usersguide/application.rst

@@ -2188,7 +2188,7 @@ second atom has class OS and the third has class P:
     <Proper class1="" class2="OS" class3="P" class4="" per="3" phase="0.0" k="0.66944"/>
 
 <CustomNonbondedForce>
-===============
+======================
 
 To add a CustomNonbondedForce to the System, include a tag that looks like this:
 

docs/usersguide/conf.py

@@ -49,9 +49,9 @@ copyright = u'2008-2014, Stanford University'
 # built documents.
 #
 # The short X.Y version.
-version = '6.0'
+version = os.getenv('OPENMM_VERSION')
 # The full version, including alpha/beta/rc tags.
-release = '6.0'
+release = os.getenv('OPENMM_VERSION')
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.