fenics team mailing list archive

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

On 25 July 2010 20:29, Johan Hake <johan.hake@xxxxxxxxx> wrote:
> On Saturday July 24 2010 09:48:44 Kristian Ølgaard wrote:
>> On 22 July 2010 20:10, Johan Hake <johan.hake@xxxxxxxxx> wrote:
>> > On Monday July 19 2010 12:54:44 Kristian Oelgaard wrote:
>> >> On 23 June 2010 15:35, Kristian Oelgaard <k.b.oelgaard@xxxxxxxxx> wrote:
>> >> > On 23 June 2010 10:55, Kristian Oelgaard <k.b.oelgaard@xxxxxxxxx>
> wrote:
>> >> >> On 22 June 2010 19:03, Johan Hake <johan.hake@xxxxxxxxx> wrote:
>> >> >>> On Tuesday June 22 2010 08:28:37 Kristian Oelgaard wrote:
>> >> >>>> I've started writing the programmer's reference for FEniCS.
>> >> >>>> One of the features that we decided on was that doc-strings for
>> >> >>>> PyDOLFIN should be written and maintained as part of the
>> >> >>>> documentation project and then added to the dolfin module on
>> >> >>>> import.
>> >> >>>>
>> >> >>>> I thought about doing this in the following way:
>> >> >>>>
>> >> >>>> 1) Create a pseudo module 'dolfin-doc' which is a copy of the
>> >> >>>> classes and functions in the 'real' dolfin module only it contains
>> >> >>>> no code at all, just doc-strings. (This approach will also make it
>> >> >>>> easy to create a script to check if all functions are documented
>> >> >>>> or if any docs are obsolete).
>> >> >>>
>> >> >>> Sounds good. I first thought of a structure (other than a dummy
>> >> >>> class) that just mimics the class hierarchy, but in some way that
>> >> >>> is what you actually suggests and it is probably as easy as
>> >> >>> anything else.
>> >> >>>
>> >> >>>> 2) Use the autodoc functionality of Sphinx to create parts of the
>> >> >>>> documentation for functions and classes
>> >> >>>>
>> >> >>>> 3) Manually add additional information (in the reST file) and links
>> >> >>>> to other parts of the documentation like demos etc. This will not
>> >> >>>> be available using help() in the Python interpreter.
>> >> >>>>
>> >> >>>> 4) In the dolfin.__init__.py function import the 'dolfin-doc'
>> >> >>>> module and copy the doc-strings from all classes and functions to
>> >> >>>> the classes and functions in the real dolfin module as was
>> >> >>>> suggested by Johan Hake.
>> >> >>>>
>> >> >>>> The problem with this approach is that assigning to __doc__ is not
>> >> >>>> permitted for objects of 'type' type.
>> >> >>>>
>> >> >>> :(
>> >> >>>
>> >> >>> I did not anticipate this. Not sure why this is. I have got the
>> >> >>> impression that numpy get around this. They use numpydoc to
>> >> >>> dynamically add their documentation. It makes heavy use of sphinx,
>> >> >>> but I couldn't figure how they get around that __doc__ is
>> >> >>> read-only.
>> >> >>
>> >> >> To me it looks like numpydoc is a Sphinx extension that translates
>> >> >> the Numpy docstrings into something that Sphinx can understand, not
>> >> >> the other way around which is what we want.
>> >> >>
>> >> >> http://projects.scipy.org/numpy/browser/trunk/doc/sphinxext/README.tx
>> >> >> t
>> >> >>
>> >> >> So I think our best bet is to proceed with your suggestions below.
>> >> >>
>> >> >> Kristian
>> >> >>
>> >> >>> While it might be cool to look into what NumPy have done, (they also
>> >> >>> define a pseudo classes, which they populate with docstrings, (look
>> >> >>> into phantom_import.py), and they also define some nice format for
>> >> >>> the reST used in the docstrings), I suggest two things we can do:
>> >> >>>
>> >> >>> 1) SWIG can generate docstrings. We do that allready using parsed
>> >> >>> doxygen documentation. All of this is gathered in docstrings.i. I
>> >> >>> suggest generating such a file from our documentation. We need to
>> >> >>> turn of %feature("autodoc","1") in dolfin.i to get rid of the long
>> >> >>> and sometimes faulty generated signatures.
>> >> >
>> >> > I turns out that it's only the __doc__ of the class I can't assign to,
>> >> > not the __doc__ of member functions (and regular functions).
>> >> > A simpler solution (at least for me) is to parse the cpp.py module
>> >> > once generated and substitute all docstrings of classes with the
>> >> > docstrings from the dolfindoc module rather than creating the
>> >> > docstrings.i file.
>> >> >
>> >> > Then for the classes that we manually add we use the method you
>> >> > described below, but only for class.__doc__ .
>> >> >
>> >> > class Foo(object):
>> >> >    __doc__ = dolfindoc.Foo.__doc__
>> >> >    def bar(self):
>> >> >        "this doc string will be substituted with the
>> >> > dolfindoc.Foo.__dict__["bar"].__doc__."
>> >> >        pass
>> >>
>> >> Unfortunately it turned out I was too quick to make this conclusion.
>> >> For instance,
>> >> for the Swig generated class Mesh in the module cpp I can't assign to
>> >>
>> >> Mesh.__doc__
>> >>
>> >> because it is a 'type' object as pointed our earlier, I can assign to:
>> >>
>> >> Mesh.__dict__["__init__"].__doc__
>> >>
>> >> but not
>> >>
>> >> Mesh.__dict__["size"].__doc__
>> >>
>> >> along with practically all other member functions.
>> >>
>> >> The reason is that Swig, after the class definitions does this:
>> >>
>> >> Mesh.size = new_instancemethod(_cpp.Mesh_size,None,Mesh)
>> >>
>> >> to which no assignment is possible.
>> >> 'AttributeError: attribute '__doc__' of 'instancemethod' objects is
>> >> not writable'
>> >> The code in Mesh.size is already
>> >>
>> >>     def size(self, *args):
>> >>         return _cpp.Mesh_size(self, *args)
>> >>
>> >> so why Swig overrides the method I don't know. If it didn't I could
>> >> assign to the docstring.
>> >>
>> >> Recall that my initial plan was to simply parse the cpp.py file and
>> >> substitute the docstrings of all classes with what the pseudo module
>> >> dolfindoc would define. However, that doesn't seem so practical
>> >> anymore since I would need to also comment out all lines where
>> >> instancemethods are being assigned to class members such that on
>> >> import (in dolfin/__init__.py) I can loop classes and assign to
>> >> function docstrings. This is of course possible but seems a bit
>> >> awkward and I don't know what implications the commenting out of
>> >> instancemethod assignment will have.
>> >> As I see it, two solutions remain.
>> >>
>> >> 1) Take the pseudo module dolfindoc from the FEniCS documentation and
>> >> create a docstring.i generator. The script
>> >> dolfin/dolfin/swig/generator.py should then try to import the
>> >> dolfindoc module, if successful use that to create docstring.i,
>> >> otherwise use the Doxy2SWIG generator.
>> >
>> > I thought that you landed on this alternative. The point is to generate a
>> > dosctrings.i file from the FEniCS documentation. Then for the extended
>> > Python layer we can use a generated Python module to assign the
>> > docstrings:
>> >
>> >  class VariationalProblem(...):
>> >     ...
>> >     __doc__ generated_docstring_module.VariationalProblem.__doc__
>>
>> This approach is getting more and more complicated; it turns out we
>> also need to generate all the
>> _post.i files to get the docstrings correct.
>
> Do yo meen the extended python functions that resides in these files?

Yes, they will need a docstring too. But since Swig doesn't mess with
these particular (member-) functions, it is actually possible to
assign to __doc__ dynamically (on import) so maybe that would be an
easier option.

>> At this point it seems a
>> lot easier to me to simply extend the Python layer with everything we
>> want to have detailed documentation for and distribute the
>> dolfindocstrings module with DOLFIN so we can do:
>>
>> class VariationalProblem(...):
>>      ...
>>    __doc__ generated_docstring_module.VariationalProblem.__doc__
>>
>> this way we handle the docstrings in a uniform way, else we need to
>> generate docstrings.i for some functions, *_post.i files for other
>> functions and STILL do the assign to __doc__ trick.
>>
>> For functions that we don't extend in the Python layer we still have
>> the oneliner docs from the header files extended with some random
>> output from Swig.
>
> How do we handle the documentation of the pure cpp classes, for example
> cpp.Mesh?

For all functions/classes we put a docstring in the docstringsmodule
and distribute this module with DOLFIN.

The current approach that we're pursuing is:
For the classes in cpp, we generate the docstrings.i,
For add on functions in *_post.i we need to either generate *_post.i
or assign to __doc__ of those particular functions on import.
For classes functions in the Python layer we just assign to __doc__ in
the definition of classes/functions.

or as I suggested:

Extend the Python layer with whatever classes/functions that we want
to have documented in detail and assign to __doc__ in the definitions.

Kristian

> Johan
>
>> Kristian
>>
>> >> One question w.r.t this approach, when is docstrings.i being
>> >> generated? I see it is distributed with DOLFIN but shouldn't it be
>> >> generated everytime DOLFIN is rebuild with enablePython, or does
>> >> enableDocs have to be switched on as well?
>> >
>> > It is generated by running dolfin/swig/generate.py. It takes quite a long
>> > time so I think it is good to pre-generate this in the distribution.
>> >
>> >> 2) Extend our Python layer with all functions and classes that we want
>> >> to use the dolfindoc docstrings for.
>> >> These should just be empty and redirect calls to classes and functions
>> >> of the cpp. In dolfin/mesh/mesh.py:
>> >>
>> >> class Mesh(cpp.Mesh):
>> >>     def size(self):
>> >>         try:
>> >>             import dolfindoc.mesh.mesh
>> >>             __doc__ = dolfindoc.mesh.mesh.Mesh.__doc__
>> >>         except:
>> >>             __doc__ = cpp.Mesh.__doc__
>> >>         return cpp.Mesh.size()
>> >>
>> >> An additional benefit of this approach is that the module structure
>> >> can be identical to what we have in the _real_ DOLFIN, not as it is
>> >> now where everything is dumped in the dolfin.cpp module.
>> >> I don't know how much overhead this will create, alternatively we can
>> >> skip the try/except clause and simply have the documentation as a
>> >> dependency, or not add the docstrings for memberfunctions and add them
>> >> later on import as was the original idea.
>> >
>> > This sounds cumbersome and in the example above will the try: except
>> > clause be called everytime size is called.
>> >
>> > Johan
>> >
>> >> Suggestions and comments are more than welcome!
>> >>
>> >> Kristian
>> >>
>> >> > then in dolfin/__init__.py we load the classes as we do now from the
>> >> > dolfin module, and then iterate over all functions and member
>> >> > functions and substitute docstrings from the dolfindoc module.
>> >> >
>> >> > Kristian
>> >> >
>> >> >>> 2) The added python classes and methods can be documented using your
>> >> >>> suggested approach, but instead of adding the docstring after class
>> >> >>> creation, do it during class (method or function) creation, a la:
>> >> >>>
>> >> >>>  class Foo(object):
>> >> >>>      __doc__ = docstrings.Foo.__doc__
>> >> >>>      ...
>> >> >>>
>> >> >>> where docstrings is the generated module containing the docstrings.
>> >> >>>
>> >> >>> Johan
>> >> >>>
>> >> >>>> In other words we can't assign to the __doc__ of
>> >> >>>>
>> >> >>>> class Foo(object):
>> >> >>>>     "Foo doc"
>> >> >>>>     pass
>> >> >>>>
>> >> >>>> Which is a new-style class and found in UFL and the SWIG code in
>> >> >>>> DOLFIN.
>> >> >>>>
>> >> >>>> It works fine for
>> >> >>>>
>> >> >>>> def some_function(v):
>> >> >>>>     "function doc"
>> >> >>>>     return 2*v
>> >> >>>>
>> >> >>>> and
>> >> >>>>
>> >> >>>> class Bar:
>> >> >>>>     "Bar doc"
>> >> >>>>     pass
>> >> >>>>
>> >> >>>> which is the old-style class often found in FFC.
>> >> >>>>
>> >> >>>> Does anyone have a solution or comments to the above approach, or
>> >> >>>> maybe we can do it in a completely different way.
>> >> >>>>
>> >> >>>> I read about some workaround for the 'assign to __doc__' problem,
>> >> >>>> but it doesn't seem that nice and it might be a problem to
>> >> >>>> incorporate in the SWIG generated code?
>> >> >>>>
>> >> >>>> http://stackoverflow.com/questions/71817/using-the-docstring-from-o
>> >> >>>> ne- metho d-to-automatically-overwrite-that-of-another-me
>> >> >>>>
>> >> >>>>
>> >> >>>> Kristian
>> >> >>>>
>> >> >>>> _______________________________________________
>> >> >>>> Mailing list: https://launchpad.net/~fenics
>> >> >>>> Post to     : fenics@xxxxxxxxxxxxxxxxxxx
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>> >>
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>