Problems with Doxygen and doxypi documenting Python code - python-2.7

Question

I'm using Doxygen 1.8.11 to document a large base of Python code. I'm using it because I wanted the LaTeX documentation support (in addition to .html).
Originally, I documented my code following the Doxygen recommendations, meaning without docstrings. This means something like:
""" description at beginning of file """
##
# description of a class
#
class Class(object):
##
# Constructor
# #param a a variable
# #param b another variable
def __init__(a,b):
......etc.
I didn't like this and I found doxypy 0.4.1 and use this as an input filter to my code. Now, I write:
""" description at beginning of file """
class Class(object):
"""description of class
def __init__(a,b):
"""Constructor
#param a a variable
#param b another variable
"""
......etc.
Although I don't really care whether the Python gods are angered by not using docsstrings, I wanted to try to be conformant and anyway, this works better with other tools I'm using.
The problem I found (that I worked around in a very nasty way - with a not good side-effect also) is that when I use the docstring documented code, with doxypy, it converts the above to:
## description at beginning of file
#
##
# description of a class
#
class Class(object):
##
# Constructor
# #param a a variable
# #param b another variable
def __init__(a,b):
......etc.
Now, here's the problem. The first line in my file used to have a docstring, even in the Doxygen suggested format. I found that if I did not have this docstring, Doxygen would act as if the code is not documented and would not include it in my documentation (I need to be clear here and say that this problem was only for things that were def'd - not classes - i.e. functions
in my software declared like:
def func(a,b)
...
It simply would not put these in the documentation unless I set the EXTRACT_ALL parameter in the Doxygen configuration file. Obviously, I don't want to extract everything and wanted some control - but unsetting this made these defs disappear.
So, I circumvented some kind of doxygen problem by putting that docstring at the top of my code. Now, when I switched to doxypy as my input filter, this
docstring is gone. And I can find no way to make doxypy ignore this string. So I hacked doxypy to shove a docstring at the front of the emitted lines and now it works - but code listing references are off by a line (Doxygen warned me about this in the manual). (I could still fix this by including a dummy line at the top of the file and instead of doxygen appending a docstring, it could simply replace the dummy line).
So, my questions are:
is there any way to get def'd functions included in my documentation without a docstring at the top of the file and without using the EXTRACT_ALL setting? Is this a known issue or am I doing something wrong?
is there any way to get doxypy to not convert a docstring to the doxygen format? i.e. some specially tagged docstring not to convert.
Thanks for any help.
here's my doxygen config file (with comments stripped):
DOXYFILE_ENCODING = UTF-8
PROJECT_NAME = SignalIntegrity
PROJECT_NUMBER = 1.0
PROJECT_BRIEF = "Signal Integrity Tools in Python"
PROJECT_LOGO = ../AppIcon2.ico
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
GROUP_NESTED_COMPOUNDS = NO
SUBGROUPING = YES
INLINE_GROUPED_CLASSES = NO
INLINE_SIMPLE_STRUCTS = NO
TYPEDEF_HIDES_STRUCT = NO
LOOKUP_CACHE_SIZE = 0
EXTRACT_ALL = NO
EXTRACT_PRIVATE = NO
EXTRACT_PACKAGE = YES
EXTRACT_STATIC = YES
EXTRACT_LOCAL_CLASSES = YES
EXTRACT_LOCAL_METHODS = NO
EXTRACT_ANON_NSPACES = YES
HIDE_UNDOC_MEMBERS = YES
HIDE_UNDOC_CLASSES = YES
HIDE_FRIEND_COMPOUNDS = NO
HIDE_IN_BODY_DOCS = NO
INTERNAL_DOCS = NO
CASE_SENSE_NAMES = YES
HIDE_SCOPE_NAMES = YES
HIDE_COMPOUND_REFERENCE= 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
SHOW_NAMESPACES = YES
FILE_VERSION_FILTER =
LAYOUT_FILE =
CITE_BIB_FILES =
QUIET = NO
WARNINGS = YES
WARN_IF_UNDOCUMENTED = YES
WARN_IF_DOC_ERROR = YES
WARN_NO_PARAMDOC = NO
WARN_AS_ERROR = NO
WARN_FORMAT = "$file:$line: $text"
WARN_LOGFILE =
INPUT = "../SignalIntegrity/"
INPUT_ENCODING = UTF-8
FILE_PATTERNS =
RECURSIVE = YES
EXCLUDE =
EXCLUDE_SYMLINKS = NO
EXCLUDE_PATTERNS =
EXCLUDE_SYMBOLS =
EXAMPLE_PATH =
EXAMPLE_PATTERNS =
EXAMPLE_RECURSIVE = NO
IMAGE_PATH =
INPUT_FILTER = ~/Work/PySI/Doc/doxypy.py
FILTER_PATTERNS =
FILTER_SOURCE_FILES = NO
FILTER_SOURCE_PATTERNS =
USE_MDFILE_AS_MAINPAGE =
SOURCE_BROWSER = YES
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
CLANG_ASSISTED_PARSING = NO
CLANG_OPTIONS =
ALPHABETICAL_INDEX = YES
COLS_IN_ALPHA_INDEX = 5
IGNORE_PREFIX =
GENERATE_HTML = YES
HTML_OUTPUT = xhtml
HTML_FILE_EXTENSION = .xhtml
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 = NO
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 =
GENERATE_LATEX = YES
LATEX_OUTPUT = latex
LATEX_CMD_NAME = latex
MAKEINDEX_CMD_NAME = makeindex
COMPACT_LATEX = NO
PAPER_TYPE = letter
EXTRA_PACKAGES =
LATEX_HEADER =
LATEX_FOOTER =
LATEX_EXTRA_STYLESHEET =
LATEX_EXTRA_FILES =
PDF_HYPERLINKS = YES
USE_PDFLATEX = YES
LATEX_BATCHMODE = NO
LATEX_HIDE_INDICES = NO
LATEX_SOURCE_CODE = NO
LATEX_BIB_STYLE = plain
LATEX_TIMESTAMP = NO
GENERATE_RTF = NO
RTF_OUTPUT = rtf
COMPACT_RTF = NO
RTF_HYPERLINKS = NO
RTF_STYLESHEET_FILE =
RTF_EXTENSIONS_FILE =
RTF_SOURCE_CODE = NO
GENERATE_MAN = NO
MAN_OUTPUT = man
MAN_EXTENSION = .3
MAN_SUBDIR =
MAN_LINKS = NO
GENERATE_XML = NO
XML_OUTPUT = xml
XML_PROGRAMLISTING = YES
GENERATE_DOCBOOK = NO
DOCBOOK_OUTPUT = docbook
DOCBOOK_PROGRAMLISTING = NO
GENERATE_AUTOGEN_DEF = NO
GENERATE_PERLMOD = NO
PERLMOD_LATEX = NO
PERLMOD_PRETTY = YES
PERLMOD_MAKEVAR_PREFIX =
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
TAGFILES =
GENERATE_TAGFILE =
ALLEXTERNALS = NO
EXTERNAL_GROUPS = YES
EXTERNAL_PAGES = YES
PERL_PATH = /usr/bin/perl
CLASS_DIAGRAMS = YES
MSCGEN_PATH =
DIA_PATH =
HIDE_UNDOC_RELATIONS = NO
HAVE_DOT = YES
DOT_NUM_THREADS = 0
DOT_FONTNAME = Helvetica
DOT_FONTSIZE = 10
DOT_FONTPATH =
CLASS_GRAPH = YES
COLLABORATION_GRAPH = YES
GROUP_GRAPHS = YES
UML_LOOK = YES
UML_LIMIT_NUM_FIELDS = 10
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 = svg
INTERACTIVE_SVG = NO
DOT_PATH =
DOTFILE_DIRS =
MSCFILE_DIRS =
DIAFILE_DIRS =
PLANTUML_JAR_PATH =
PLANTUML_INCLUDE_PATH =
DOT_GRAPH_MAX_NODES = 50
MAX_DOT_GRAPH_DEPTH = 0
DOT_TRANSPARENT = NO
DOT_MULTI_TARGETS = NO
GENERATE_LEGEND = YES
DOT_CLEANUP = YES