fenics team mailing list archive

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

On 26 August 2010 22:13, Anders Logg <logg@xxxxxxxxx> wrote:
> On Thu, Aug 26, 2010 at 10:09:16PM +0200, Kristian Ølgaard wrote:
>> On 26 August 2010 22:04, Anders Logg <logg@xxxxxxxxx> wrote:
>> > On Thu, Aug 26, 2010 at 09:34:01PM +0200, Kristian Ølgaard wrote:
>> >> On 26 August 2010 20:35, Anders Logg <logg@xxxxxxxxx> wrote:
>> >> > On Thu, Aug 26, 2010 at 08:16:41PM +0200, Anders Logg wrote:
>> >> >> On Thu, Aug 26, 2010 at 08:09:56PM +0200, Kristian Ølgaard wrote:
>> >> >> > On 26 August 2010 19:51, Anders Logg <logg@xxxxxxxxx> wrote:
>> >> >> > > On Thu, Aug 26, 2010 at 07:42:35PM +0200, Kristian Ølgaard wrote:
>> >> >> > >> On 26 August 2010 18:22, Anders Logg <logg@xxxxxxxxx> wrote:
>> >> >> > >> > I've thought some more on how to organize/synchronize the FEniCS
>> >> >> > >> > documentation (in fenics-doc) with the documentation we have in the
>> >> >> > >> > code.
>> >> >> > >> >
>> >> >> > >> > I think it is important that
>> >> >> > >> >
>> >> >> > >> > (1) the strings we have in the code are the same as those that appear
>> >> >> > >> > on in the HTML documentation (which we write in Sphinx).
>> >> >> > >> >
>> >> >> > >> > (2) the strings we have in the code are short (so they don't clutter
>> >> >> > >> > up the code)
>> >> >> > >>
>> >> >> > >> I disagree. The whole idea of the documentation effort was to document
>> >> >> > >> in one place
>> >> >> > >> (using carefully handwritten and elaborate explanations including
>> >> >> > >> examples and links to demos etc.) and code in another.
>> >> >> > >> The comments in the code should be very short and precise such that
>> >> >> > >> together with the class/function definition and type info the
>> >> >> > >> developer can complete the task without looking elsewhere. These kind
>> >> >> > >> of comments, I expect, will look weird when put next to an elaborate
>> >> >> > >> explanation on how the class/function works including all the bells
>> >> >> > >> and whistles.
>> >> >> > >>
>> >> >> > >> > If we look at these two, it seems that (1) implies that we should
>> >> >> > >> > write the documentation as part of the code and then extract it using
>> >> >> > >> > some tool.
>> >> >> > >> >
>> >> >> > >> > But (2) prevents that since we don't want to constrain the
>> >> >> > >> > documentation for all functions to be very short.
>> >> >> > >> >
>> >> >> > >> > How about the following solution.
>> >> >> > >> >
>> >> >> > >> > * Write short docstrings in the code
>> >> >> > >> >
>> >> >> > >> > * Auto-generate all the .rst input files for the Programmer's
>> >> >> > >> >  Reference using a simple Python script that looks for '///'
>> >> >> > >> >
>> >> >> > >> > * The script looks at the code to generate the signature of the
>> >> >> > >> >  function and the text that comes immediately after.
>> >> >> > >>
>> >> >> > >> This might be possible for a simple
>> >> >> > >> 'change-order-of-comment-and-function' script where you manipulate the
>> >> >> > >> output manually afterwards, but if you want to run this more than once
>> >> >> > >> you will have to pick up nested class/struct definitions templates and
>> >> >> > >> all kinds of crap.
>> >> >> > >> I tried to write a parser like this to check if all classes and
>> >> >> > >> functions were documented, but gave up and let Doxygen do the dirty
>> >> >> > >> work. (But do we want to do this just to generate 20 characters of
>> >> >> > >> docstring automatically?)
>> >> >> > >>
>> >> >> > >> >  But it also looks in a hand-written .rst file that contains any
>> >> >> > >> >  additional stuff we want to put below.
>> >> >> > >> >
>> >> >> > >> > So for the code example in the style manual, the things that get
>> >> >> > >> > picked up from the code are
>> >> >> > >> >
>> >> >> > >> >  // Return the cell which is closest to the given point
>> >> >> > >> >  uint closest_cell(const Point & point) const
>> >> >> > >> >
>> >> >> > >> > which gets converted to
>> >> >> > >> >
>> >> >> > >> > .. cpp:function:: uint closest_cell(const Point & point) const
>> >> >> > >> >
>> >> >> > >> >    Return the cell which is closest to the given point
>> >> >> > >> >
>> >> >> > >> > The script also looks in a file for "closest_cell" below which we have
>> >> >> > >> > written all the *Arguments* stuff that will be thrown in below.
>> >> >> > >> >
>> >> >> > >> > Will that work?
>> >> >> > >>
>> >> >> > >> Yes, but the work flow is getting complex, and you'll need to know
>> >> >> > >> what you get from the source code so you don't repeat yourself.
>> >> >> > >> It is much easier to have the documentation in one place.
>> >> >> > >>
>> >> >> > >> > Another solution would be to just write everything as part of the
>> >> >> > >> > code, and just add some settings to our editors that will fold the
>> >> >> > >> > extra stuff away so we don't need to see it. Maybe that is the most
>> >> >> > >> > robust solution?
>> >> >> > >>
>> >> >> > >> The general consensus the last time this issue came up was not to
>> >> >> > >> clutter the code with documentation markup.
>> >> >> > >>
>> >> >> > >> Kristian
>> >> >> > >
>> >> >> > > I agree it's good to have the documentation in one place, but it would
>> >> >> > > be good if we found a way to keep it in sync. Helper scripts can do
>> >> >> > > some of that work, but we probably won't be able to pick up things
>> >> >> > > like having
>> >> >> > >
>> >> >> > >  "Compute the number of neighbors"
>> >> >> > >
>> >> >> > > in one place and
>> >> >> > >
>> >> >> > >  "Return the number of neighbors"
>> >> >> > >
>> >> >> > > in other places. Things like this will creep in over time. It might
>> >> >> > > not be a big issue but I find it a bit annoying.
>> >> >> >
>> >> >> > I see. A simpler approach, rather than generating docstrings would be
>> >> >> > to have a script that
>> >> >> > simply looks for '///' comments in dolfin/mesh/Mesh.h and check if the
>> >> >> > EXACT same strings are present in
>> >> >> > programmers-reference/cpp/mesh/Mesh.rst, if not crash test and let
>> >> >> > user figure out manually why it failed and which comment/docstring
>> >> >> > should be changed.
>> >> >> > This won't be completely bulletproof, but much much simpler than
>> >> >> > parsing a C++ library.
>> >> >>
>> >> >> Yes, that might be a good solution.
>> >> >>
>> >> >> > I currently check if the docstrings of the documentation for the
>> >> >> > Python interface is equal to the docstrings of the DOLFIN module after
>> >> >> > import so that sort of works in the same way, only in this case I know
>> >> >> > that the docstring I check belongs to function 'bar' of class 'foo'.
>> >> >> >
>> >> >> > Then we use the stub-generator that you have know to give us the first
>> >> >> > set of *.rst files and then add the '///' comments check to the
>> >> >> > verify_cpp_documentation.py script.
>> >> >>
>> >> >> It's almost there now, I just need to do some polishing.
>> >> >>
>> >> >> Sphinx is currently crashing when it generates the documentation from
>> >> >> the .rst files I generate.
>> >> >>
>> >> >> Exception occurred:
>> >> >>   File "/usr/lib/pymodules/python2.6/docutils/nodes.py", line 1898, in
>> >> >>   dupname
>> >> >>     node['names'].remove(name)
>> >> >> ValueError: list.remove(x): x not in list
>> >> >>
>> >> >> Any ideas what this might be?
>> >> >
>> >> > Looks like this happens when there are multiple functions with the
>> >> > same signature.
>> >>
>> >> Very likely,  and that's probably because you need to extract 'const'
>> >> information too, and that's just the tip of the iceberg if we proceed
>> >> down this road....
>> >
>> > Try now.
>> >
>> > You need to set DOLFIN_DIR to the DOLFIN source tree.
>> >
>> > Then run
>> >
>> >  python utils/generate_cpp_doc.py
>> >  make html
>> >
>> > The generated stuff is in {source/build}/programmers-reference/test/cpp
>>
>> OK, I'm just finishing a DOLFIN build to test the docstrings in the
>> Python interface. Will test soon.
>>
>> > I'll be moving it to {source/build}/programmers-reference/cpp and make
>> > sure not to overwrite the Mesh and Point class documentation that you
>> > have written.
>>
>> There is no C++ documentation for Point, only for the Python interface
>> and that was just to see how some of the autodoc functions worked.
>> Anyway, we can always dig it up by reverting the repo to hack away.
>
> I noticed that. I just remember seeing something about the Point
> class.
>
> Anyway, it seems to work now. What is missing is to generate the
> index.rst files for each module.

Looks pretty good to me. Do you need to generate the index.rst files?
Can't you just add the output from 'ls *.h' in the modules to the
index.rst files?
Once we're finished editing the *.rst files you have generated we
should be able to run the script verify_cpp_documentation.py which
should tell us if we missed any.
BTW, I'm done for today.

Kristian

> --
> Anders
>