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 <[email protected]> wrote: > > > On Tuesday September 7 2010 09:24:40 Kristian Ølgaard wrote: > > >> On 7 September 2010 17:59, Johan Hake <[email protected]> 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. :-) -- Anders _______________________________________________ Mailing list: https://launchpad.net/~fenics Post to : [email protected] Unsubscribe : https://launchpad.net/~fenics More help : https://help.launchpad.net/ListHelp
