fenics team mailing list archive

[Kristian Ølgaard <k.b.oelgaard@xxxxxxxxx>]

On 7 September 2010 11:04, Anders Logg <logg@xxxxxxxxx> wrote:
> On Mon, Sep 06, 2010 at 05:56:13PM +0200, Kristian Ølgaard wrote:
>> On 6 September 2010 17:24, Johan Hake <johan.hake@xxxxxxxxx> wrote:
>> > 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.
>>
>> Yes, but we'll need some automated testing to make sure that the 1%
>> does not go out of sync with the code.
>> Most likely the 1% can't be handled because it is relatively important
>> (definitions in *.i files etc.).
>
> I imagine that "1%" will be the same as the "1%" that we have special
> treatment for in the SWIG files anyway, so it makes sense those need
> special treatment.

I think that we can automate that last 1% too.

> So the idea would be:
>
>  1. Document the C++ code in the C++ header files
>  2. Document the extra Python code in the Python files (?)
>  3. Document the extra SWIG stuff in a special file

All Python docstrings should be located where the code is.
In the Python layer (like dolfin/fem.py), or in the extended methods
in the *.i files for the dolfin/cpp.py module.

We then need to figure out how to change the syntax/name correctly
such that std::vector, double* etc. are mapped to the correct Python
arguments/return values, and how to handle the *example* code.

>> >> > > > 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.
>>
>> We don't. I wrote this script to be able to test the documentation in
>> *.rst files against dolfin.
>> Basically, I parse all files and keep track of the classes/functions
>> which are defined in dolfin and try to match those up against the
>> definitions in the documentation (and vise versa) to catch
>> missing/obsolete documentation.
>>
>> >> > 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?
>>
>> Definitely, and we don't have to maintain it.
>
> We would need to maintain the script that extracts data from the
> Doxygen-generated XML files.
>
>> >> 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.
>>
>> But some cases are not handled correctly already (nested classes etc.)
>> so I vote for Doxygen.
>
> Not that I'm insisting on not using Doxygen, but isn't it quite rare
> that we use nested classes? I think we decided at some point that we
> wanted to avoid it for some other reason. I don't remember which but
> it might have been a SWIG problem.

Look at http://www.fenics.org/newdoc/programmers-reference/cpp/function/Function.html
as a user I would be confused by LocalScratch and GatherScratch.

The documentation here is also rather confusing, yes we can fix it,
but similar cases will arise in the future.

http://www.fenics.org/newdoc/programmers-reference/cpp/mesh/MeshPrimitive.html

Kristian

> --
> Anders
>