fenics team mailing list archive

[Johan Hake <johan.hake@xxxxxxxxx>]

On Monday September 6 2010 08:13:44 Anders Logg wrote:
> On Mon, Sep 06, 2010 at 08:08:10AM -0700, Johan Hake wrote:
> > On Monday September 6 2010 05:47:27 Anders Logg wrote:
> > > On Mon, Sep 06, 2010 at 12:19:03PM +0200, Kristian Ølgaard wrote:
> > > > > Do we have any functionality in place for handling documentation
> > > > > that should be automatically generated from the C++ interface and
> > > > > documentation that needs to be added later?
> > > > 
> > > > No, not really.
> > > 
> > > ok.
> > > 
> > > > > I assume that the documentation we write in the C++ header files
> > > > > (like Mesh.h) will be the same that appears in Python using
> > > > > help(Mesh)?
> > > > 
> > > > Yes and no, the problem is that for instance overloaded methods will
> > > > only show the last docstring.
> > > > So, the Mesh.__init__.__doc__ will just contain the Mesh(std::str
> > > > file_name) docstring.
> > > 
> > > It would not be difficult to make the documentation extraction script
> > > we have (in fenics-doc) generate the docstrings module and just
> > > concatenate all constructor documentation. We are already doing the
> > > parsing so spitting out class Foo: """ etc would be easy. Perhaps that
> > > is an option.
> > 
> > There might be other overloaded methods too. We might try to setle on a
> > format for these methods, or make this part of the 1% we need to handle
> > our self.
> 
> ok. Should also be fairly easy to handle.

Ok.

> > > > > But in some special cases, we may want to go in and handle
> > > > > documentation for special cases where the Python documentation
> > > > > needs to be different from the C++ documentation. So there should
> > > > > be two different sources for the documentation: one that is
> > > > > generated automatically from the C++ header files, and one that
> > > > > overwrites or adds documentation for special cases. Is that the
> > > > > plan?
> > > > 
> > > > The plan is currently to write the docstrings by hand for the entire
> > > > dolfin module. One of the reasons is that we rename/ignores
> > > > functions/classes in the *.i files, and if we we try to automate the
> > > > docstring generation I think we should make it fully automatic not
> > > > just part of it.
> > > 
> > > If we can make it 99% automatic and have an extra file with special
> > > cases I think that would be ok.
> > 
> > Agree.
> > 
> > > > Also, we will need to change the syntax in all *example* code of the
> > > > docstrings. Maybe it can be done, but I'll need to give it some more
> > > > careful thought. We've already changed the approach a few times now,
> > > > so I really like the next try to close to our final implementation.
> > > 
> > > I agree. :-)
> > > 
> > > > > Another thing to discuss is the possibility of using Doxygen to
> > > > > extract the documentation. We currently have our own script since
> > > > > (I assume) Doxygen does not have a C++ --> reST converter. Is that
> > > > > correct?
> > > > 
> > > > I don't think Doxygen has any such converter, but there exist a
> > > > project http://github.com/michaeljones/breathe
> > > > which makes it possible to use xml output from Doxygen in much the
> > > > same way as we use autodoc for the Python module. I had a quick go at
> > > > it but didn't like the result. No links on the index pages to
> > > > function etc. So what we do now is better, but perhaps it would be a
> > > > good idea to use Doxygen to extract the docstrings for all classes
> > > > and functions, I tried parsing the xml output in the
> > > > test/verify_cpp_
> > > > ocumentation.py script and it should be relatively
> > > > simple to get the docstrings since these are stored as attributes of
> > > > classes/functions.
> > > 
> > > Perhaps an idea would be to use Doxygen for parsing and then have our
> > > own script that works with the XML output from Doxygen?
> > 
> > I did not know we allready used Doxygen to extract information about
> > class structure from the headers.
> 
> I thought it was you who implemented the Doxygen documentation extraction?

Duh... I mean that I did not know we used it in fenics_doc, in 
verify_cpp_documentation.py.

> > What are the differences between using the XML from Doxygen to also
> > extract the documentation, and the approach we use today?
> 
> Pros (of using Doxygen):
> 
>   - Doxygen is developed by people that presumably are very good at
>     extracting docs from C++ code
> 
>   - Doxygen might handle some corner cases we can't handle?
> 
> Cons (of using Doxygen):
> 
>   - Another dependency

Which we already have.

>   - We still need to write a script to parse the XML

We should be able to ust the xml parser in docstringgenerator.py.

>   - The parsing of /// stuff from C++ code is very simple

Yes, and this might be just fine. But if it grows we might consider using 
Doxygen. 

Would it be possible to setle on a format of the extracted documentation which 
we use as input to generate reST documentation. It would make it easier to do 
a switch to Doxygen XML whenever we figure this is needed, ie we just switch 
the backend of the documentation parser.

Johan

> --
> Anders