Some assorted fixes

293f76e5 · Robert T. McGibbon · 60352b13 · 293f76e5 · 293f76e5 · 293f76e5
Commit 293f76e5 authored Dec 12, 2015 by Robert T. McGibbon
5 changed files
--- a/.travis.yml
+++ b/.travis.yml
@@ -142,8 +142,8 @@ script:
      ctest -I FailedTests.log;
    fi
  - if [[ ! -z "${DOCS_DEPLOY}" && "${DOCS_DEPLOY}" = "true" ]]; then
-      pip install sphinx numpydoc;
-      make DoxygenApiDocs PythonApiDocs;
+      pip install sphinx sphinxcontrib.lunrsearch sphinxcontrib.autodoc_doxygen;
+      make C++ApiDocs PythonApiDocs;
      mkdir -p api-docs;
      mv api-python api-docs;
      mv api-c++ api-docs;

--- a/docs-source/api-c++/CMakeLists.txt
+++ b/docs-source/api-c++/CMakeLists.txt
 set(STAGING_OUTPUT_FILES "") # Will contain all required package files
 file(GLOB STAGING_INPUT_FILES RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}"
-    "index.rst"
-    "core.rst.jinja2"
-    "integrators.rst.jinja2"
-    "forces.rst.jinja2"
-    "extras.rst.jinja2"
-    "render.py"
+    "*.rst"
+    "*.rst.jinja2"
+    "*.py"
    "_static/logo.png"
 )

+set(WRAPPER_DOXYGEN_DIR "${CMAKE_CURRENT_BINARY_DIR}/doxygen")
+file(MAKE_DIRECTORY "${WRAPPER_DOXYGEN_DIR}")
+
+configure_file(
+    ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in
+    ${WRAPPER_DOXYGEN_DIR}/Doxyfile
+    @ONLY
+)
+
+add_custom_command(
+    OUTPUT "${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..."
+)
+
 foreach(INIT_FILE ${STAGING_INPUT_FILES})
    set(infile "${CMAKE_CURRENT_SOURCE_DIR}/${INIT_FILE}")
    set(outfile "${CMAKE_CURRENT_BINARY_DIR}/${INIT_FILE}")
@@ -20,25 +34,19 @@ foreach(INIT_FILE ${STAGING_INPUT_FILES})
    set(STAGING_OUTPUT_FILES ${STAGING_OUTPUT_FILES} "${outfile}")
 endforeach(INIT_FILE ${STAGING_INPUT_FILES})

-
-set(DOXYGEN_XML_DIRECTORY "${CMAKE_BINARY_DIR}/wrappers/python/src/swig_doxygen/doxygen/xml/")
-configure_file("${CMAKE_CURRENT_SOURCE_DIR}/conf.py" "${CMAKE_CURRENT_BINARY_DIR}/conf.py")
-
-
 add_custom_command(
    OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/core.rst"
           "${CMAKE_CURRENT_BINARY_DIR}/integrators.rst"
           "${CMAKE_CURRENT_BINARY_DIR}/forces.rst"
           "${CMAKE_CURRENT_BINARY_DIR}/extras.rst"
    COMMAND "${PYTHON_EXECUTABLE}" "${CMAKE_CURRENT_BINARY_DIR}/render.py"
-            "${CMAKE_BINARY_DIR}/wrappers/python/src/swig_doxygen/doxygen/xml/"
+            "${WRAPPER_DOXYGEN_DIR}/xml/"
    DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/render.py"
            "${CMAKE_CURRENT_BINARY_DIR}/core.rst.jinja2"
            "${CMAKE_CURRENT_BINARY_DIR}/integrators.rst.jinja2"
            "${CMAKE_CURRENT_BINARY_DIR}/forces.rst.jinja2"
            "${CMAKE_CURRENT_BINARY_DIR}/extras.rst.jinja2"
-            "${CMAKE_BINARY_DIR}/wrappers/python/src/swig_doxygen/doxygen/xml/index.xml"
-            RunSwig
+            "${WRAPPER_DOXYGEN_DIR}/xml/index.xml"
 )

 add_custom_command(
@@ -46,12 +54,12 @@ add_custom_command(
    COMMAND "${PYTHON_EXECUTABLE}" -m sphinx . "${CMAKE_BINARY_DIR}/api-c++"
    WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
    DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/conf.py"
-            "${CMAKE_CURRENT_BINARY_DIR}/core.rst"
-            "${CMAKE_CURRENT_BINARY_DIR}/forces.rst"
-            "${CMAKE_CURRENT_BINARY_DIR}/extras.rst"
-            "${CMAKE_CURRENT_BINARY_DIR}/integrators.rst"
-            "${CMAKE_CURRENT_BINARY_DIR}/index.rst"
-            "${CMAKE_CURRENT_BINARY_DIR}/_static/logo.png"
+                "${CMAKE_CURRENT_BINARY_DIR}/core.rst"
+                "${CMAKE_CURRENT_BINARY_DIR}/forces.rst"
+                "${CMAKE_CURRENT_BINARY_DIR}/extras.rst"
+                "${CMAKE_CURRENT_BINARY_DIR}/integrators.rst"
+                "${CMAKE_CURRENT_BINARY_DIR}/index.rst"
+                "${CMAKE_CURRENT_BINARY_DIR}/_static/logo.png"
 )

 file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/api-c++/)

--- a/docs-source/api-c++/Doxyfile.in
+++ b/docs-source/api-c++/Doxyfile.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   = NO
+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_SOURCE_DIR@/openmmapi" \
+                         "@CMAKE_SOURCE_DIR@/olla" \
+                         "@CMAKE_SOURCE_DIR@/serialization/include/openmm/serialization/XmlSerializer.h" \
+                         "@CMAKE_SOURCE_DIR@/plugins/drude/openmmapi/include" \
+                         "@CMAKE_SOURCE_DIR@/plugins/rpmd/openmmapi/include" \
+                         "@CMAKE_SOURCE_DIR@/plugins/amoeba/openmmapi/include"
+INPUT_ENCODING         = UTF-8
+FILE_PATTERNS          =
+RECURSIVE              = YES
+EXCLUDE                =
+EXCLUDE_SYMLINKS       = NO
+EXCLUDE_PATTERNS       = */tests/* \
+                         */openmmapi/src/* \
+                         */.svn/* \
+                         */internal/* \
+                         */olla/include/openmm/kernels.h \
+                         */DrudeKernels.h \
+                         */RpmdKernels.h \
+                         */amoebaKernels.h \
+EXCLUDE_SYMBOLS        =
+EXAMPLE_PATH           =
+EXAMPLE_PATTERNS       =
+EXAMPLE_RECURSIVE      = NO
+IMAGE_PATH             =
+INPUT_FILTER           =
+FILTER_PATTERNS        =
+FILTER_SOURCE_FILES    = NO
+#---------------------------------------------------------------------------
+# 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          = NO
+HTML_OUTPUT            = api-c++
+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           = YES
+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-c++/@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
--- a/docs-source/api-c++/conf.py
+++ b/docs-source/api-c++/conf.py
@@ -40,4 +40,4 @@ html_sidebars = {
    ]
 }

-doxygen_xml = "@DOXYGEN_XML_DIRECTORY@"
+doxygen_xml = "doxygen/xml"
--- a/docs-source/api-c++/render.py
+++ b/docs-source/api-c++/render.py
@@ -24,8 +24,14 @@ def load_doxygen_xml(doxygen_xml):


 def subclasses(root, parent):
-    xp_query = ('.//compounddef/basecompoundref[text()="%s"]'
-                '/../compoundname') % parent
+    parent_el = root.xpath('.//compounddef/compoundname[text()="%s"]/..' % parent)
+    if len(parent_el) == 1:
+        parent_id = parent_el[0].get('id')
+    else:
+        raise ValueError("Can't find %s" % parent)
+
+    xp_query = ('.//compounddef/basecompoundref[@refid="%s"]'
+                '/../compoundname') % parent_id
    return [parent] + [n.text.strip() for n in root.xpath(xp_query)]