fenics team mailing list archive

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

On 7 September 2010 19:23, Anders Logg <logg@xxxxxxxxx> wrote:
> On Tue, Sep 07, 2010 at 10:19:15AM -0700, Johan Hake wrote:
>> On Tuesday September 7 2010 10:08:34 Kristian Ølgaard wrote:
>> > On 7 September 2010 18:51, Johan Hake <johan.hake@xxxxxxxxx> wrote:
>> > > On Tuesday September 7 2010 09:24:40 Kristian Ølgaard wrote:
>> > >> On 7 September 2010 17:59, Johan Hake <johan.hake@xxxxxxxxx> wrote:
>> > >> > [snip]
>> > >> >
>> > >> >> > But how do we extract the different arguments? I suppose this is
>> > >> >> > collected by Doxygen, and we just need to parse these and output
>> > >> >> > them in a correct way?
>> > >> >>
>> > >> >> I don't think we need to parse the arguments and output them. We just
>> > >> >> get the function name and if we have more than one set of arguments
>> > >> >> i.e., a different signature we know that we have an overloaded method
>> > >> >> and how to handle it.
>> > >> >
>> > >> > And I guess the almighty generate_cpp_documentation.py script are able
>> > >> > to extract the argument information?
>> > >>
>> > >> No, but we should be able to figure this out from the signature (split
>> > >> ',' in '()').
>> > >
>> > > Ok! Anders mentioned this too.
>> > >
>> > >> >> The arguments should be described in the *Arguments* section of the
>> > >> >> individual docstring with links to classes formatted like
>> > >> >> _MeshEntity_, which we will substitute with :py:class:`MeshEntity` or
>> > >> >>
>> > >> >> :cpp:class:`MeshEntity` depending on which interface we document.
>> > >> >
>> > >> > Ok, but we only want that once for each method in python, even if it
>> > >> > is overloaded?
>> > >>
>> > >> No, I think we need to document the argument list for every overloaded
>> > >> version like it is done in docstrings.dolfin.cpp.Mesh.
>> > >
>> > > Agree, I think I misunderstood you.
>> > >
>> > >> >> Although I just realized that standard C++ stuff like double* which
>> > >> >> end up as numpy.array etc. should probably be handled.
>> > >> >
>> > >> > Yes this part I am a little worried about... But maybe a god
>> > >> > handwritten lookup table will do the trick? At least for 99% of the
>> > >> > cases ;)
>> > >>
>> > >> I share your concern, but if, as you suggest, we'll be able to get God
>> > >> to hand write our documentation I think we should be OK. :)
>> > >
>> > > Good to have God on our side!
>> > >
>> > >> (a lookup table would be my best bet at the moment)
>> > >
>> > > Ok!
>> > >
>> > >> >> On a related note:
>> > >> >> int some_func()
>> > >> >> and
>> > >> >> const int some_func() const
>> > >> >> are different in C++, but in Python we don't have const right?
>> > >> >> This will simplify the documentation a lot.
>> > >> >
>> > >> > Yes, we tend to %ignore all const versions of different methods.
>> > >> >
>> > >> > [snap]
>> > >> >
>> > >> >> >> >  * Extended methods needs to be handled in one of three ways:
>> > >> >> >> >    1) Write the docstring directly into the foo_post.i file
>> > >> >>
>> > >> >> I like this option, if this is where we have the code for a function,
>> > >> >> then this is where the docstring should be as it increases the
>> > >> >> probability of the docstring being up to date.
>> > >> >
>> > >> > Ok, lets settle on this one. We also need to make sure that all
>> > >> > %extended methods in the C++ layer gets a proper docstring. However I
>> > >> > am not really sure how this can be done :P
>> > >>
>> > >> I'm not sure I follow this, which %extended methods do you mean?
>> > >
>> > > There are two ways to extend a class.
>> > >
>> > >  1) The C++ layer
>> > >  2) The Python layer
>> > >
>> > > often we use 1) to create a protected helper method which is called using
>> > > an extended method in the Python layer, 2). The latter can be properly
>> > > documented directly.
>> > >
>> > > But some cases excists where we just extend the C++ layer, see for
>> > > example the IMPLEMENT_VARIABLE_INTERFACE macro in shared_ptr_classes.i.
>> > > These methods gets no docstrings and I am not sure it is possible to add
>> > > them later.
>> >
>> > OK, docstrings for 2) should go in the code as we agreed, and I guess
>> > 1) will fall under the 1% category which we may/may not be able to
>> > handle in a clever way later.
>>
>> Ok.
>>
>> > >> > [snup]
>> > >> >
>> > >> >> > Why do we need to assign to these methods? They already get their
>> > >> >> > docstrings from the docstrings.i file. However if we want to get
>> > >> >> > rid of the new_instancemethod assignment above, we can just remove
>> > >> >> > the
>> > >> >>
>> > >> >> Some history.
>> > >> >> Initially, we wanted to have all docstrings separated from the DOLFIN
>> > >> >> code and collected in the fenics-doc module. The easiest way to get
>> > >> >> the >>> help(dolfin) docstring correct is to assign to __doc__
>> > >> >> dynamically.
>> > >> >> If we could do this we wouldn't even need the docstrings.i file and
>> > >> >> things would be simple.
>> > >> >> However, we discovered that this was not possible, and because of
>> > >> >> that we still need to generate the docstrings.i file.
>> > >> >> Then, still assuming we wanted to separate docs from code and keeping
>> > >> >> docstrings in fenics-doc, I thought it would be easier to generate
>> > >> >> the docstrings.i file from the handwritten docstrings module in
>> > >> >> fenics-doc.
>> > >> >> Some methods don't get their docstrings from the docstrings.i file
>> > >> >> though, so we still need to assign to __doc__ which is the easiest
>> > >> >> thing to do.
>> > >> >> Just recently we decided to extract the docstrings from the C++
>> > >> >> implementation thus moving the docs back into DOLFIN. This makes the
>> > >> >> docstrings module almost superfluous with the only practical usage is
>> > >> >> to have documentation for the extended methods defined in the _post.i
>> > >> >> files but if we put the docstrings directly in the _post.i files we
>> > >> >> no longer need it.
>> > >> >
>> > >> > Ok, then I do not see any reason for a separate docstring module,
>> > >> > makes life a lite bit easier...
>> > >>
>> > >> Agree.
>> > >
>> > > Ok.
>> > >
>> > >> > [snep]
>> > >> >
>> > >> >> > I am confused. Do you suggest that we just document the extended
>> > >> >> > Python layer directly in the python module as it is today? Why
>> > >> >> > should we then dumpt the docstrings in a separate docstring
>> > >> >> > module? So autodoc can have something to shew on? Couldn't autodoc
>> > >> >> > just shew on the dolfin module directly?
>> > >> >>
>> > >> >> I'm confused too. :) I guess my head has not been properly reset
>> > >> >> between the changes in documentation strategies.
>> > >> >> The Sphinx autodoc can only handle one dolfin module, so we need to
>> > >> >> either import the 'real' one or the docstrings dolfin module.
>> > >> >> If we can completely remove the need for the docstrings module, then
>> > >> >> we should of course include the 'real' one.
>> > >> >
>> > >> > Ok!
>> > >> >
>> > >> >> >> Then programmer's writing the Python
>> > >> >> >> layer just need to document while they're coding, where they are
>> > >> >> >> coding just like they do (or should anyways) for the C++ part.
>> > >> >> >
>> > >> >> > Still confused why we need a certain docstring module.
>> > >> >>
>> > >> >> Maybe we don't.
>> > >> >>
>> > >> >> >> >  2) for the extended Python layer in the cpp.py
>> > >> >> >> >
>> > >> >> >> > For the rest, and this will be the main part, we rely on parsed
>> > >> >> >> > docstrings from the headers.
>> > >> >> >> >
>> > >> >> >> > The python programmers reference will then be generated based on
>> > >> >> >> > the actual dolfin module using sphinx and autodoc.
>> > >> >> >>
>> > >> >> >> We could/should probably use either the dolfin module or the
>> > >> >> >> generated docstring module to generate the relevant reST files.
>> > >> >> >> Although we might need to run some cross-checks with the Doxygen
>> > >> >> >> xml to get the correct file names where the classes are defined
>> > >> >> >> in DOLFIN such that we retain the original DOLFIN source tree
>> > >> >> >> structure. Otherwise all our documentation will end up in cpp.rst
>> > >> >> >> which I would hate to navigate through as a user.
>> > >> >> >
>> > >> >> > This one got to technical for me. Do you say that there is no way
>> > >> >> > to split the documentation into smaller parts without relying on
>> > >> >> > the c++ module/file structure?
>> > >> >>
>> > >> >> But how would you split it?
>> > >> >
>> > >> > I do not know. But then I do not know what the generation step can
>> > >> > take as different inputs.
>> > >>
>> > >> The write_python_documentation step should probably take the dolfin
>> > >> module and the intermediate representation.
>> > >
>> > > What is the intermediate representation?
>> >
>> > It is whatever output we get from the extract_documentation script
>> > which we'll add to the dolfin module. How it will look depends a bit
>> > on what we need in the write_cpp_documentation and
>> > write_python_documentation functions in fenics-doc.
>>
>> Ok.
>>
>> > >> >> It makes sense to keep the classes Mesh
>> > >> >> and MeshEntity in the mesh/ part of the documentation. Unfortunately,
>> > >> >> Swig doesn't add info to the classes in the cpp.py module about where
>> > >> >> they were originally defined. This is why we need to pair it with
>> > >> >> info from the xml output.
>> > >> >
>> > >> > Ok, but say we keep all documentation in one module. If you are able
>> > >> > to pair the different classes or functions with a module name, or
>> > >> > file name you are able to create documentation which is structured
>> > >> > after this hierarchy?
>> > >>
>> > >> We need to figure out something, having everything in the cpp.py
>> > >> module would create one big mess and it makes sense to follow the
>> > >> DOLFIN C++ structure even for the Python interface.
>> > >
>> > > Ok, but we do not have everything in a big cpp file. Types get imported
>> > > into the Dolfin namespace in __init__ mostly from cpp.py.
>> >
>> > My point is, there's no telling where the cpp.Mesh class was
>> > originally defined. Everything from la to mesh to fem is dumped in the
>> > cpp.py module.
>>
>> Ok, but don't you just need a way to associate the classes to different
>> modules? I thought this was what you used the doxygen output to. If we instead
>> use the module representation we should be able to do this association
>> directly with just the dolfin tree as the assosiated types should reside in:
>>
>>   dolfin.submodule.__dict__
>>
>> > > Would it help to add the cpp imports to submodules instead of the main
>> > > __init__ file? We already have the submodules:
>> > >
>> > >  mesh, common, compilemodules, fem, adaptivity and function
>> > >
>> > > We could add:
>> > >
>> > >  io, log, nls, ode, parameter, ale
>> > >
>> > > and drag in stuff from cpp.py in these modules instead. In this way we
>> > > structure the main __init__ file better, and you might be able to
>> > > structure the pythons reference manual better?
>> >
>> > I'm quite sure I tried something like this, and the problem was that
>> > even if you do:
>> >
>> > from dolfin.cpp import Mesh
>> >
>> > in dolfin/mesh/__init__.py
>> >
>> > the Mesh class will still point to dolfin.cpp when you inspect it -->
>> > difficult to create the proper structure for the *.rst files.
>>
>> Would something that I sceted above work?
>>
>> > I'll need to double check though that this is really the case.
>> > And even if we can use the approach you outline above it means that we
>> > have more stuff we need to manually maintain.
>>
>> Sure, but now everything is throwed into dolfin/__init__.py which is really a
>> mess now.
>>
>> Johan
>
> This discussion is getting long and complex. I'm tempted to just let
> the two of you sort it out between you and then ask for a 10-line
> summary.
>
> And then, of course, suggest a completely different solution. :-)

That's what we're afraid of. In fact this is the reason we're still
discussing, to avoid implementing something which you'll tell us to
redo :)

I think we're quite close to a converged solution were the last
details concerns the structure of the Python documentation i.e., how
to retrieve the original DOLFIN library structure from the cpp.py
module.

Just a crazy thought, is it possible to tell Swig to split the modules
for us? Such that we get
dolfin/mesh --> site-packages/dolfin/mesh.
This will also speed up the compilation of the Python module if more
than one process is used.

Kristian

> --
> Anders
>
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