fenics team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Fri, Aug 27, 2010 at 01:30:56PM +0200, Kristian Ølgaard wrote:
> On 27 August 2010 13:17, Anders Logg <logg@xxxxxxxxx> wrote:
> > On Fri, Aug 27, 2010 at 12:11:10PM +0100, Garth N. Wells wrote:
> >>
> >>
> >> On 27/08/10 12:09, Anders Logg wrote:
> >> > On Fri, Aug 27, 2010 at 12:12:59PM +0200, Kristian Ølgaard wrote:
> >> >> On 27 August 2010 12:00, Garth N. Wells <gnw20@xxxxxxxxx> wrote:
> >> >>>
> >> >>>
> >> >>> On 27/08/10 10:51, Kristian Ølgaard wrote:
> >> >>>> On 27 August 2010 11:31, Garth N. Wells <gnw20@xxxxxxxxx> wrote:
> >> >>>>>
> >> >>>>>>>>>> The stuff that you have written for the Mesh class could easily go in
> >> >>>>>>>>>> to Mesh.h without causing too much clutter (reST looks nice), and I
> >> >>>>>>>>>> imagine it would be easy to add a folding mode to Emacs and other
> >> >>>>>>>>>> editors that will hide all lines starting with /// except for the
> >> >>>>>>>>>> first line.
> >> >>>>>>>>>>
> >> >>>>>>>>>> The simple script I wrote seems to work pretty well to extract the
> >> >>>>>>>>>> documentation. If it breaks somewhere, we could either improve the
> >> >>>>>>>>>> script or learn to write the code so the script does not break.
> >> >>>>>>>>>>
> >> >>>>>>>>>> The point here is that now the generated .rst files are in sync with
> >> >>>>>>>>>> the code, but in a day or two someone will edit one of the .h files in
> >> >>>>>>>>>> DOLFIN and the documentation and code will start to diverge.
> >> >>>>>>
> >> >>>>>> On second thought, what do you mean by diverge?
> >> >>>>>> I have test scripts in place the checks if a function in *.h is
> >> >>>>>> documented in *.rst, and if a function in *.rst is still present in
> >> >>>>>> *.h.
> >> >>>>>>
> >> >>>>>> If you mean the docstrings might change, we can perform the additional
> >> >>>>>> check where we test if the one liner docstring in *.h is present in
> >> >>>>>> the documentation in *.rst, then there can be no divergence and we can
> >> >>>>>> have short comments in the DOLFIN source code.
> >> >>>>>>
> >> >>>>>>>> Yes, but this problem is already there for the Python interface and it
> >> >>>>>>>> won't go away.
> >> >>>>>>>> I guess the key thing to this is that a new feature or a change in
> >> >>>>>>>> DOLFIN source code is not complete until the documentation has been
> >> >>>>>>>> updated.
> >> >>>>>>>>
> >> >>>>>>>
> >> >>>>>>> To save ourselves work for now, we could just let doxygen create the C++
> >> >>>>>>> programmers reference and provide a link to it. It doesn't seem very
> >> >>>>>>> sensible that we write our own parser to document the C++ code. With
> >> >>>>>>> doxygen, we also get class diagrams. We can then scan the doxygen
> >> >>>>>>> documentation for each class and improve it iteratively.
> >> >>>>>>
> >> >>>>>> Do you mean improve the Doxygen output, or the source  code (*.h
> >> >>>>>> files)? If we improve the output we can get diverging docs and code.
> >> >>>>>>
> >> >>>>>
> >> >>>>> I mean improve the strings following '///' in the .h files. In quite
> >> >>>>> some cases, just a few extra words would make a big difference.
> >> >>>>>
> >> >>>>> I'm coming around to putting all programming reference doc in the code.
> >> >>>>> I don't like lots of markup, but I don't see any other robust and easily
> >> >>>>> maintainable solution.
> >> >>>>
> >> >>>> As I wrote above, a test script is in place to pick up
> >> >>>> missing/obsolete docs, very little extra work is needed to also test
> >> >>>> if the short docstring in the source  code is correct. Then we run the
> >> >>>> tests as part of building the documentation.
> >> >>>>
> >> >>>
> >> >>> I just can't see myself hopping back and forth between the code and the
> >> >>> documentation when implementing and testing something new.
> >> >>
> >> >> I don't see why that would be necessary, the documentation can be
> >> >> updated and built later once the feature is in place and tested.
> >> >> But the feature can't be 'official' until it has been documented, it
> >> >> will require more self-discipline from the developers, which I don't
> >> >> think is necessarily a bad idea.
> >> >>
> >> >>>> I admit that the Doxygen output is much more detailed and the type
> >> >>>> information/links in argument lists is better compared to what is in
> >> >>>> Sphinx now, but that might change in the future (in Sphinx). On the
> >> >>>> downside, I personally find the Doxygen documentation overwhelming and
> >> >>>> I never use it for just that reason.
> >> >>>>
> >> >>>
> >> >>> Doxygen is an (imperfect) ready made solution for the programmers
> >> >>> reference - so one of my points is that we can forget about the C++
> >> >>> programmers reference for now and get on with the more importance task
> >> >>> of documenting demos. We can return to the C++ programmers reference
> >> >>> later (which, as you say, may improve in Sphinx in the future).
> >> >>
> >> >> I'm fine with using Doxygen and simply put a link to the index page, I
> >> >> just think it is worthwhile to carefully discuss the pros and cons.
> >> >>
> >> >> The Python interface still has to be documented manually since there
> >> >> is no way to extract docstrings from the source code since the
> >> >> intention is to add docstrings to the module.
> >> >>
> >> >>> We can some some very limited work to improve the doxygen output which
> >> >>> will make it easier to navigate.
> >> >>
> >> >> I just don't see how this can be integrated easily with the output from Doxygen.
> >> >> We don't want to manipulate the output files since they will be
> >> >> re-generated whenever we build the docs. It is possible though to link
> >> >> to the html pages of classes/functions, but it won't be naturally
> >> >> supported like it would be if everything is in Sphinx.
> >> >>
> >> >> Kristian
> >> >
> >> > I think that the simple script we have now does a fairly good job at
> >> > extracting the documentation. I like having it as part of the
> >> > reST-based documentation (so it looks like it's part of the
> >> > documentation), rather than as a separate set of pages generated by
> >> > Doxygen. But I wouldn't mind having Doxygen-generated pages in
> >> > addition.
> >> >
>
> I agree that having it in reST makes it look more like it is a part of
> the documentation.
>
> >> The doc generated by the script lacks links, which is a big drawback.
> >>
> >> Garth
> >
> > Links to other classes you mean?
> >
> > That would be easy to add to the script. We could just insert labels
> > and references into the generated code.
>
> What I have done with the links in the Mesh.rst so far is to put it in
> the *Arguments* section like:
> :cpp:class:`Point`, we can have still have this as part of the source
> code in the *.h files.
>
> Kristian

ok. Does everyone agree that as a first iteration, it would be good to
at least try to:

1. Move over the stuff from Mesh.rst (in the doc repo) to Mesh.h (in
DOLFIN)

2. Generate all .rst files in the doc repo from the C++ code

3. Evaluate if we can live with the more heavy commenting in the .h
files (or find a folding mode)

4. Evaluate if the simple extract script does its job well enough

?

--
Anders