Add CMake files

CMakeLists.txt

@@ -531,6 +531,8 @@ IF(OPENMM_BUILD_PYTHON_WRAPPERS)
 ENDIF(OPENMM_BUILD_PYTHON_WRAPPERS)
 
 
+
+
 #
 # Allow automated build and dashboard.
 #

docs-source/CMakeLists.txt

@@ -8,7 +8,7 @@ IF(DOXYGEN_EXECUTABLE)
     # Generate C++ API documentation
 
     SET(DOXY_CONFIG_C++ "${CMAKE_BINARY_DIR}/DoxyfileC++")
-    CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/DoxyfileC++.in 
+    CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/DoxyfileC++.in
           ${DOXY_CONFIG_C++}
           @ONLY )
     FILE(GLOB_RECURSE OPENMM_INCLUDES "openmm/include/*.h")
@@ -19,14 +19,14 @@ IF(DOXYGEN_EXECUTABLE)
         DEPENDS ${OPENMM_INCLUDES} ${OLLA_INCLUDES}
         WORKING_DIRECTORY "${CMAKE_BINARY_DIR}"
         COMMENT "Generating C++ API documentation using Doxygen")
-    ADD_CUSTOM_TARGET(C++ApiDocs 
+    ADD_CUSTOM_TARGET(C++ApiDocs
         DEPENDS "${CMAKE_BINARY_DIR}/api-c++/index.html"
         COMMENT "Generating C++ API documentation using Doxygen"
-        SOURCES 
+        SOURCES
             "${CMAKE_CURRENT_SOURCE_DIR}/DoxyfileC++.in"
             ${OPENMM_INCLUDES}
             ${OLLA_INCLUDES}
-    ) 
+    )
     FILE(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/api-c++/")
     INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/api-c++/"
             DESTINATION "docs/api-c++/")
@@ -35,9 +35,8 @@ IF(DOXYGEN_EXECUTABLE)
     ADD_CUSTOM_TARGET(DoxygenApiDocs
         DEPENDS "${CMAKE_BINARY_DIR}/api-c++/index.html"
         COMMENT "Generating C++ API documentation using Doxygen"
-        SOURCES 
+        SOURCES
         "${CMAKE_CURRENT_SOURCE_DIR}/DoxyfileC++.in"
-        "${CMAKE_CURRENT_SOURCE_DIR}/DoxyfilePython.in"
         ${OPENMM_INCLUDES}
         ${OLLA_INCLUDES}
     )
@@ -49,30 +48,7 @@ IF(DOXYGEN_EXECUTABLE)
     # 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)
+        ADD_SUBDIRECTORY(api-python)
     ENDIF (OPENMM_BUILD_PYTHON_WRAPPERS)
 ENDIF(DOXYGEN_EXECUTABLE)
 

docs-source/DoxyfilePython.in

-# Doxyfile 1.5.3
-
-#---------------------------------------------------------------------------
-# Project related configuration options
-#---------------------------------------------------------------------------
-DOXYFILE_ENCODING      = UTF-8
-PROJECT_NAME           = @PROJECT_NAME@
-PROJECT_NUMBER         = 
-OUTPUT_DIRECTORY       = 
-CREATE_SUBDIRS         = NO
-OUTPUT_LANGUAGE        = English
-BRIEF_MEMBER_DESC      = YES
-REPEAT_BRIEF           = YES
-ABBREVIATE_BRIEF       = 
-ALWAYS_DETAILED_SEC    = NO
-INLINE_INHERITED_MEMB  = NO
-FULL_PATH_NAMES        = NO
-STRIP_FROM_PATH        = 
-STRIP_FROM_INC_PATH    = 
-SHORT_NAMES            = NO
-JAVADOC_AUTOBRIEF      = YES
-QT_AUTOBRIEF           = NO
-MULTILINE_CPP_IS_BRIEF = NO
-DETAILS_AT_TOP         = YES
-INHERIT_DOCS           = YES
-SEPARATE_MEMBER_PAGES  = NO
-TAB_SIZE               = 4
-ALIASES                = 
-OPTIMIZE_OUTPUT_FOR_C  = NO
-OPTIMIZE_OUTPUT_JAVA   = YES
-BUILTIN_STL_SUPPORT    = NO
-CPP_CLI_SUPPORT        = NO
-DISTRIBUTE_GROUP_DOC   = YES
-SUBGROUPING            = YES
-#---------------------------------------------------------------------------
-# Build related configuration options
-#---------------------------------------------------------------------------
-EXTRACT_ALL            = YES
-EXTRACT_PRIVATE        = NO
-EXTRACT_STATIC         = NO
-EXTRACT_LOCAL_CLASSES  = YES
-EXTRACT_LOCAL_METHODS  = NO
-EXTRACT_ANON_NSPACES   = NO
-HIDE_UNDOC_MEMBERS     = NO
-HIDE_UNDOC_CLASSES     = NO
-HIDE_FRIEND_COMPOUNDS  = NO
-HIDE_IN_BODY_DOCS      = YES
-INTERNAL_DOCS          = NO
-CASE_SENSE_NAMES       = YES
-HIDE_SCOPE_NAMES       = YES
-SHOW_INCLUDE_FILES     = YES
-INLINE_INFO            = YES
-SORT_MEMBER_DOCS       = YES
-SORT_BRIEF_DOCS        = NO
-SORT_BY_SCOPE_NAME     = NO
-GENERATE_TODOLIST      = YES
-GENERATE_TESTLIST      = YES
-GENERATE_BUGLIST       = YES
-GENERATE_DEPRECATEDLIST= YES
-ENABLED_SECTIONS       = 
-MAX_INITIALIZER_LINES  = 30
-SHOW_USED_FILES        = YES
-SHOW_DIRECTORIES       = YES
-FILE_VERSION_FILTER    =
-SHOW_NAMESPACES        = NO
-SHOW_FILES             = NO
-SHOW_DIRECTORIES       = NO
-#---------------------------------------------------------------------------
-# configuration options related to warning and progress messages
-#---------------------------------------------------------------------------
-QUIET                  = NO
-WARNINGS               = YES
-WARN_IF_UNDOCUMENTED   = YES
-WARN_IF_DOC_ERROR      = YES
-WARN_NO_PARAMDOC       = NO
-WARN_FORMAT            = "$file:$line: $text    "
-WARN_LOGFILE           = 
-#---------------------------------------------------------------------------
-# configuration options related to the input files
-#---------------------------------------------------------------------------
-INPUT                  = "@CMAKE_BINARY_DIR@/python/simtk/openmm" "@CMAKE_BINARY_DIR@/python/simtk/openmm/app"
-INPUT_ENCODING         = UTF-8
-FILE_PATTERNS          = 
-RECURSIVE              = NO
-EXCLUDE                = 
-EXCLUDE_SYMLINKS       = NO
-EXCLUDE_PATTERNS       = 
-EXCLUDE_SYMBOLS        = SerializationNode SerializationProxy SwigPyIterator
-EXAMPLE_PATH           = 
-EXAMPLE_PATTERNS       = 
-EXAMPLE_RECURSIVE      = NO
-IMAGE_PATH             = 
-INPUT_FILTER           = "@PYTHON_EXECUTABLE@ @CMAKE_BINARY_DIR@/python/filterPythonFiles.py"
-FILTER_PATTERNS        = 
-FILTER_SOURCE_FILES    = YES
-#---------------------------------------------------------------------------
-# configuration options related to source browsing
-#---------------------------------------------------------------------------
-SOURCE_BROWSER         = NO
-INLINE_SOURCES         = NO
-STRIP_CODE_COMMENTS    = YES
-REFERENCED_BY_RELATION = YES
-REFERENCES_RELATION    = YES
-REFERENCES_LINK_SOURCE = YES
-USE_HTAGS              = NO
-VERBATIM_HEADERS       = YES
-#---------------------------------------------------------------------------
-# configuration options related to the alphabetical class index
-#---------------------------------------------------------------------------
-ALPHABETICAL_INDEX     = NO
-COLS_IN_ALPHA_INDEX    = 5
-IGNORE_PREFIX          = 
-#---------------------------------------------------------------------------
-# configuration options related to the HTML output
-#---------------------------------------------------------------------------
-GENERATE_HTML          = YES
-HTML_OUTPUT            = api-python
-HTML_FILE_EXTENSION    = .html
-HTML_HEADER            = 
-HTML_FOOTER            = 
-HTML_STYLESHEET        = 
-HTML_ALIGN_MEMBERS     = YES
-GENERATE_HTMLHELP      = NO
-HTML_DYNAMIC_SECTIONS  = YES
-CHM_FILE               = 
-HHC_LOCATION           = 
-GENERATE_CHI           = NO
-BINARY_TOC             = NO
-TOC_EXPAND             = NO
-DISABLE_INDEX          = NO
-ENUM_VALUES_PER_LINE   = 4
-GENERATE_TREEVIEW      = YES
-TREEVIEW_WIDTH         = 250
-#---------------------------------------------------------------------------
-# configuration options related to the LaTeX output
-#---------------------------------------------------------------------------
-GENERATE_LATEX         = NO
-LATEX_OUTPUT           = latex
-LATEX_CMD_NAME         = latex
-MAKEINDEX_CMD_NAME     = makeindex
-COMPACT_LATEX          = NO
-PAPER_TYPE             = a4wide
-EXTRA_PACKAGES         = 
-LATEX_HEADER           = 
-PDF_HYPERLINKS         = NO
-USE_PDFLATEX           = NO
-LATEX_BATCHMODE        = NO
-LATEX_HIDE_INDICES     = NO
-#---------------------------------------------------------------------------
-# configuration options related to the RTF output
-#---------------------------------------------------------------------------
-GENERATE_RTF           = NO
-RTF_OUTPUT             = rtf
-COMPACT_RTF            = NO
-RTF_HYPERLINKS         = NO
-RTF_STYLESHEET_FILE    = 
-RTF_EXTENSIONS_FILE    = 
-#---------------------------------------------------------------------------
-# configuration options related to the man page output
-#---------------------------------------------------------------------------
-GENERATE_MAN           = NO
-MAN_OUTPUT             = man
-MAN_EXTENSION          = .3
-MAN_LINKS              = NO
-#---------------------------------------------------------------------------
-# configuration options related to the XML output
-#---------------------------------------------------------------------------
-GENERATE_XML           = NO
-XML_OUTPUT             = xml
-XML_SCHEMA             = 
-XML_DTD                = 
-XML_PROGRAMLISTING     = YES
-#---------------------------------------------------------------------------
-# configuration options for the AutoGen Definitions output
-#---------------------------------------------------------------------------
-GENERATE_AUTOGEN_DEF   = NO
-#---------------------------------------------------------------------------
-# configuration options related to the Perl module output
-#---------------------------------------------------------------------------
-GENERATE_PERLMOD       = NO
-PERLMOD_LATEX          = NO
-PERLMOD_PRETTY         = YES
-PERLMOD_MAKEVAR_PREFIX = 
-#---------------------------------------------------------------------------
-# Configuration options related to the preprocessor   
-#---------------------------------------------------------------------------
-ENABLE_PREPROCESSING   = YES
-MACRO_EXPANSION        = YES
-EXPAND_ONLY_PREDEF     = YES
-SEARCH_INCLUDES        = YES
-INCLUDE_PATH           = 
-INCLUDE_FILE_PATTERNS  = 
-PREDEFINED             = 
-EXPAND_AS_DEFINED      = 
-SKIP_FUNCTION_MACROS   = YES
-#---------------------------------------------------------------------------
-# Configuration::additions related to external references   
-#---------------------------------------------------------------------------
-TAGFILES               = 
-GENERATE_TAGFILE       = "api-python/@PROJECT_NAME@DoxygenTagfile"
-ALLEXTERNALS           = NO
-EXTERNAL_GROUPS        = YES
-PERL_PATH              = /usr/bin/perl
-#---------------------------------------------------------------------------
-# Configuration options related to the dot tool   
-#---------------------------------------------------------------------------
-CLASS_DIAGRAMS         = YES
-MSCGEN_PATH            = /Applications/Doxygen.app/Contents/Resources/
-HIDE_UNDOC_RELATIONS   = YES
-HAVE_DOT               = NO
-CLASS_GRAPH            = YES
-COLLABORATION_GRAPH    = YES
-GROUP_GRAPHS           = YES
-UML_LOOK               = NO
-TEMPLATE_RELATIONS     = YES
-INCLUDE_GRAPH          = YES
-INCLUDED_BY_GRAPH      = YES
-CALL_GRAPH             = NO
-CALLER_GRAPH           = NO
-GRAPHICAL_HIERARCHY    = YES
-DIRECTORY_GRAPH        = YES
-DOT_IMAGE_FORMAT       = png
-DOT_PATH               = 
-DOTFILE_DIRS           = 
-DOT_GRAPH_MAX_NODES    = 50
-MAX_DOT_GRAPH_DEPTH    = 0
-DOT_TRANSPARENT        = NO
-DOT_MULTI_TARGETS      = NO
-GENERATE_LEGEND        = YES
-DOT_CLEANUP            = YES
-#---------------------------------------------------------------------------
-# Configuration::additions related to the search engine   
-#---------------------------------------------------------------------------
-SEARCHENGINE           = YES

docs-source/api-python/CMakeLists.txt

+set(STAGING_OUTPUT_FILES "") # Will contain all required package files
+file(GLOB STAGING_INPUT_FILES RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}"
+    "app.rst.jinja2"
+    "library.rst.jinja2"
+    "index.rst"
+    "render.py"
+    "conf.py"
+    "_static/logo.png"
+    "_templates/class.rst"
+)
+
+foreach(INIT_FILE ${STAGING_INPUT_FILES})
+    set(infile "${CMAKE_CURRENT_SOURCE_DIR}/${INIT_FILE}")
+    set(outfile "${CMAKE_CURRENT_BINARY_DIR}/${INIT_FILE}")
+    add_custom_command(
+        OUTPUT "${outfile}"
+        COMMAND "${CMAKE_COMMAND}" -E copy_if_different "${infile}" "${outfile}"
+        DEPENDS "${infile}"
+        COMMENT "CMake-copying file ${infile} to ${outfile}")
+    set(STAGING_OUTPUT_FILES ${STAGING_OUTPUT_FILES} "${outfile}")
+endforeach(INIT_FILE ${STAGING_INPUT_FILES})
+
+
+add_custom_command(
+    OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/app.rst"
+           "${CMAKE_CURRENT_BINARY_DIR}/library.rst"
+    COMMAND "${PYTHON_EXECUTABLE}" "${CMAKE_CURRENT_BINARY_DIR}/render.py"
+    DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/app.rst.jinja2"
+            "${CMAKE_CURRENT_BINARY_DIR}/library.rst.jinja2"
+            "${CMAKE_CURRENT_BINARY_DIR}/render.py"
+)
+
+add_custom_command(
+    OUTPUT "${CMAKE_BINARY_DIR}/api-python/index.html"
+    COMMAND "${PYTHON_EXECUTABLE}" -m sphinx . "${CMAKE_BINARY_DIR}/api-python"
+    WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
+    DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/conf.py"
+            "${CMAKE_CURRENT_BINARY_DIR}/app.rst"
+            "${CMAKE_CURRENT_BINARY_DIR}/library.rst"
+            "${CMAKE_CURRENT_BINARY_DIR}/index.rst"
+            "${CMAKE_CURRENT_BINARY_DIR}/_static/logo.png"
+            "${CMAKE_CURRENT_BINARY_DIR}/_templates/class.rst"
+            # PythonInstall
+)
+
+add_custom_target(PythonApiDocs DEPENDS ${CMAKE_BINARY_DIR}/api-python/index.html)
+INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/api-python/"
+        DESTINATION "docs/api-python/")
+INSTALL(FILES "Python API Reference.html"
+        DESTINATION "docs/")

docs-source/python-api/render.py → docs-source/api-python/render.py

@@ -3,7 +3,7 @@ The function of this script is to render the Jinja2 templates in the current
 directory into input files for sphinx. It introspects the OpenMM Python module
 to find all of the classes and formats them for inclusion into the templates.
 """
-from os.path import dirname, join, splitext
+from os.path import dirname, join, splitext, basename
 from glob import glob
 import inspect
 
@@ -119,7 +119,7 @@ def main():
     data = library_template_variables()
     data.update(app_template_variables())
 
-    for template_fn in glob(join(here, '*.jinja2')):
+    for template_fn in map(basename, glob(join(here, '*.jinja2'))):
         output_fn = splitext(template_fn)[0]
         print('Rendering %s to %s...' % (template_fn, output_fn))
 

docs-source/python-api/Makefile

-# Makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-PAPER         =
-BUILDDIR      = _build
-
-# Internal variables.
-PAPEROPT_a4     = -D latex_paper_size=a4
-PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-# the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-
-all: html
-
-html:	builddir render
-	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)
-	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)"
-
-builddir:
-	mkdir -p $(BUILDDIR)
-
-clean:
-	rm -rf $(BUILDDIR)/*
-	rm -rf generated/*.rst
-
-render:
-	python render.py