GNOME Bugzilla – Bug 739054
Python xml not outputting info of functions inside __init__.py
Last modified: 2014-12-25 16:03:19 UTC
For example, project bleach in github: https://github.com/jsocol/bleach/tree/master/bleach The functions inside __init__.py are the main API of the project, and the xml output doesn't recognize any of them. ____init_____8py.xml output is: <?xml version='1.0' encoding='UTF-8' standalone='no'?> <doxygen xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="compound.xsd" version="1.8.8"> <compounddef id="____init_____8py" kind="file"> <compoundname>__init__.py</compoundname> <innernamespace refid="namespacebleach4">bleach4</innernamespace> <briefdescription> </briefdescription> <detaileddescription> </detaileddescription> <location file="/home/erez/project/temp/python/bleach4/__init__.py"/> </compounddef> </doxygen> There's also a report on __init__.py in stackoverflow: http://stackoverflow.com/questions/6654951/doxygen-chokes-on-init-py-files
The symbols can be found in xml/namespacebleach.xml. Doxygen did have a problem parsing the regular expression 'url_re', which should be corrected in the next Git update.
Thx Dimitri, Maybe there's something wrong with my setup, but Doxygen doesn't extract the xml/namespacebleach.xml for me. I can't find the functions inside __init__.py, for example "linkify" in "all.xml" as well. OPTIMIZE_OUTPUT_JAVA = YES, but even if = NO, the mentioned file isn't created in my setup. My setup is: # Doxyfile 1.8.8 #--------------------------------------------------------------------------- # Project related configuration options #--------------------------------------------------------------------------- DOXYFILE_ENCODING = UTF-8 PROJECT_NAME = "My Project" PROJECT_NUMBER = PROJECT_BRIEF = PROJECT_LOGO = OUTPUT_DIRECTORY = CREATE_SUBDIRS = NO ALLOW_UNICODE_NAMES = NO OUTPUT_LANGUAGE = English BRIEF_MEMBER_DESC = YES REPEAT_BRIEF = YES ABBREVIATE_BRIEF = ALWAYS_DETAILED_SEC = NO INLINE_INHERITED_MEMB = NO FULL_PATH_NAMES = YES STRIP_FROM_PATH = STRIP_FROM_INC_PATH = SHORT_NAMES = NO JAVADOC_AUTOBRIEF = NO QT_AUTOBRIEF = NO MULTILINE_CPP_IS_BRIEF = NO INHERIT_DOCS = YES SEPARATE_MEMBER_PAGES = NO TAB_SIZE = 4 ALIASES = TCL_SUBST = OPTIMIZE_OUTPUT_FOR_C = NO OPTIMIZE_OUTPUT_JAVA = YES OPTIMIZE_FOR_FORTRAN = NO OPTIMIZE_OUTPUT_VHDL = NO EXTENSION_MAPPING = MARKDOWN_SUPPORT = YES AUTOLINK_SUPPORT = YES BUILTIN_STL_SUPPORT = NO CPP_CLI_SUPPORT = NO SIP_SUPPORT = NO IDL_PROPERTY_SUPPORT = YES DISTRIBUTE_GROUP_DOC = NO SUBGROUPING = YES INLINE_GROUPED_CLASSES = NO INLINE_SIMPLE_STRUCTS = NO TYPEDEF_HIDES_STRUCT = NO LOOKUP_CACHE_SIZE = 0 #--------------------------------------------------------------------------- # Build related configuration options #--------------------------------------------------------------------------- EXTRACT_ALL = NO EXTRACT_PRIVATE = NO EXTRACT_PACKAGE = 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 = NO INTERNAL_DOCS = NO CASE_SENSE_NAMES = YES HIDE_SCOPE_NAMES = NO SHOW_INCLUDE_FILES = YES SHOW_GROUPED_MEMB_INC = NO FORCE_LOCAL_INCLUDES = NO INLINE_INFO = YES SORT_MEMBER_DOCS = YES SORT_BRIEF_DOCS = NO SORT_MEMBERS_CTORS_1ST = NO SORT_GROUP_NAMES = NO SORT_BY_SCOPE_NAME = NO STRICT_PROTO_MATCHING = NO GENERATE_TODOLIST = YES GENERATE_TESTLIST = YES GENERATE_BUGLIST = YES GENERATE_DEPRECATEDLIST= YES ENABLED_SECTIONS = MAX_INITIALIZER_LINES = 30 SHOW_USED_FILES = YES SHOW_FILES = YES FILE_VERSION_FILTER = LAYOUT_FILE = CITE_BIB_FILES = #--------------------------------------------------------------------------- # 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 = INPUT_ENCODING = UTF-8 FILE_PATTERNS = RECURSIVE = YES EXCLUDE = EXCLUDE_SYMLINKS = NO EXCLUDE_PATTERNS = */tests/* */test/* EXCLUDE_SYMBOLS = EXAMPLE_PATH = EXAMPLE_PATTERNS = EXAMPLE_RECURSIVE = NO IMAGE_PATH = INPUT_FILTER = FILTER_PATTERNS = FILTER_SOURCE_FILES = NO FILTER_SOURCE_PATTERNS = USE_MDFILE_AS_MAINPAGE = #--------------------------------------------------------------------------- # Configuration options related to source browsing #--------------------------------------------------------------------------- SOURCE_BROWSER = NO INLINE_SOURCES = NO STRIP_CODE_COMMENTS = YES REFERENCED_BY_RELATION = NO REFERENCES_RELATION = NO REFERENCES_LINK_SOURCE = YES SOURCE_TOOLTIPS = YES USE_HTAGS = NO VERBATIM_HEADERS = YES #--------------------------------------------------------------------------- # Configuration options related to the alphabetical class index #--------------------------------------------------------------------------- ALPHABETICAL_INDEX = YES COLS_IN_ALPHA_INDEX = 5 IGNORE_PREFIX = #--------------------------------------------------------------------------- # Configuration options related to the HTML output #--------------------------------------------------------------------------- GENERATE_HTML = NO HTML_OUTPUT = html HTML_FILE_EXTENSION = .html HTML_HEADER = HTML_FOOTER = HTML_STYLESHEET = HTML_EXTRA_STYLESHEET = HTML_EXTRA_FILES = HTML_COLORSTYLE_HUE = 220 HTML_COLORSTYLE_SAT = 100 HTML_COLORSTYLE_GAMMA = 80 HTML_TIMESTAMP = YES HTML_DYNAMIC_SECTIONS = NO HTML_INDEX_NUM_ENTRIES = 100 GENERATE_DOCSET = NO DOCSET_FEEDNAME = "Doxygen generated docs" DOCSET_BUNDLE_ID = org.doxygen.Project DOCSET_PUBLISHER_ID = org.doxygen.Publisher DOCSET_PUBLISHER_NAME = Publisher GENERATE_HTMLHELP = NO CHM_FILE = HHC_LOCATION = GENERATE_CHI = NO CHM_INDEX_ENCODING = BINARY_TOC = NO TOC_EXPAND = NO GENERATE_QHP = NO QCH_FILE = QHP_NAMESPACE = org.doxygen.Project QHP_VIRTUAL_FOLDER = doc QHP_CUST_FILTER_NAME = QHP_CUST_FILTER_ATTRS = QHP_SECT_FILTER_ATTRS = QHG_LOCATION = GENERATE_ECLIPSEHELP = NO ECLIPSE_DOC_ID = org.doxygen.Project DISABLE_INDEX = NO GENERATE_TREEVIEW = NO ENUM_VALUES_PER_LINE = 4 TREEVIEW_WIDTH = 250 EXT_LINKS_IN_WINDOW = NO FORMULA_FONTSIZE = 10 FORMULA_TRANSPARENT = YES USE_MATHJAX = NO MATHJAX_FORMAT = HTML-CSS MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest MATHJAX_EXTENSIONS = MATHJAX_CODEFILE = SEARCHENGINE = YES SERVER_BASED_SEARCH = NO EXTERNAL_SEARCH = NO SEARCHENGINE_URL = SEARCHDATA_FILE = searchdata.xml EXTERNAL_SEARCH_ID = EXTRA_SEARCH_MAPPINGS = #--------------------------------------------------------------------------- # 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 = a4 EXTRA_PACKAGES = LATEX_HEADER = LATEX_FOOTER = LATEX_EXTRA_FILES = PDF_HYPERLINKS = YES USE_PDFLATEX = YES LATEX_BATCHMODE = NO LATEX_HIDE_INDICES = NO LATEX_SOURCE_CODE = NO LATEX_BIB_STYLE = plain #--------------------------------------------------------------------------- # 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_SUBDIR = MAN_LINKS = NO #--------------------------------------------------------------------------- # Configuration options related to the XML output #--------------------------------------------------------------------------- GENERATE_XML = YES XML_OUTPUT = xml XML_PROGRAMLISTING = NO #--------------------------------------------------------------------------- # Configuration options related to the DOCBOOK output #--------------------------------------------------------------------------- GENERATE_DOCBOOK = NO DOCBOOK_OUTPUT = docbook DOCBOOK_PROGRAMLISTING = NO #--------------------------------------------------------------------------- # 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 = NO EXPAND_ONLY_PREDEF = NO SEARCH_INCLUDES = YES INCLUDE_PATH = INCLUDE_FILE_PATTERNS = PREDEFINED = EXPAND_AS_DEFINED = SKIP_FUNCTION_MACROS = YES #--------------------------------------------------------------------------- # Configuration options related to external references #--------------------------------------------------------------------------- TAGFILES = GENERATE_TAGFILE = ALLEXTERNALS = NO EXTERNAL_GROUPS = YES EXTERNAL_PAGES = YES PERL_PATH = /usr/bin/perl #--------------------------------------------------------------------------- # Configuration options related to the dot tool #--------------------------------------------------------------------------- CLASS_DIAGRAMS = YES MSCGEN_PATH = DIA_PATH = HIDE_UNDOC_RELATIONS = YES HAVE_DOT = NO DOT_NUM_THREADS = 0 DOT_FONTNAME = Helvetica DOT_FONTSIZE = 10 DOT_FONTPATH = CLASS_GRAPH = YES COLLABORATION_GRAPH = YES GROUP_GRAPHS = YES UML_LOOK = NO UML_LIMIT_NUM_FIELDS = 10 TEMPLATE_RELATIONS = NO INCLUDE_GRAPH = YES INCLUDED_BY_GRAPH = YES CALL_GRAPH = NO CALLER_GRAPH = NO GRAPHICAL_HIERARCHY = YES DIRECTORY_GRAPH = YES DOT_IMAGE_FORMAT = png INTERACTIVE_SVG = NO DOT_PATH = DOTFILE_DIRS = MSCFILE_DIRS = DIAFILE_DIRS = PLANTUML_JAR_PATH = DOT_GRAPH_MAX_NODES = 50 MAX_DOT_GRAPH_DEPTH = 0 DOT_TRANSPARENT = NO DOT_MULTI_TARGETS = NO GENERATE_LEGEND = YES DOT_CLEANUP = YES Thx again
Since the Python code isn't documented you need to set at least EXTRACT_ALL to YES. I also enabled EXTRACT_PRIVATE = YES EXTRACT_PACKAGE = YES EXTRACT_STATIC = YES in my config file.
Thx Dimitri, The config wasn't the problem it still outputs correctly to the xml even with EXTRACT_ALL = NO, regardless if it's documented or not. The reason some key functions in __init__.py (like "linkify")were missing, is that they appeared after the regular expression 'url_re' that caused the bug in the first place. Once I deleted these lines from __init__.py, everything works smoothly. Thx again
This bug was previously marked ASSIGNED, which means it should be fixed in doxygen version 1.8.9. Please verify if this is indeed the case. Reopen the bug if you think it is not fixed and please include any additional information that you think can be relevant (preferrably in the form of a self-contained example).