fenics team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

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....

It's working alright now. It's looking pretty good. I'll be pushing
soon so you can check.

--
Anders