Python xml not outputting info of functions inside __init__.py (Origin: bugzilla #739054)

[doxygen]

status RESOLVED severity critical in component general for ---
Reported in version 1.8.8 on platform Other
Assigned to: Dimitri van Heesch

On 2014-10-23 07:35:00 +0000, erez.oxman@gmail.com wrote:

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:

__init__.py bleach4

There's also a report on init.py in stackoverflow:
http://stackoverflow.com/questions/6654951/doxygen-chokes-on-init-py-files

On 2014-11-16 12:52:51 +0000, Dimitri van Heesch wrote:

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.

On 2014-11-16 13:53:53 +0000, erez.oxman@gmail.com wrote:

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

On 2014-11-16 14:00:30 +0000, Dimitri van Heesch wrote:

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.

On 2014-11-16 16:50:07 +0000, erez.oxman@gmail.com wrote:

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

On 2014-12-25 16:03:19 +0000, Dimitri van Heesch wrote:

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).