fenics team mailing list archive

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

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

> Perhaps we'll find that we should use a fancy tool like Doxygen, but
> it seems it's not that complicated and it took a very short time to
> write our own script.
>
> --
> Anders
>