On Tue, Sep 07, 2010 at 02:56:47PM +0200, Kristian Ølgaard wrote: > On 7 September 2010 12:37, Anders Logg <[email protected]> wrote: > > On Tue, Sep 07, 2010 at 12:20:09PM +0200, Kristian Ølgaard wrote: > >> On 7 September 2010 11:04, Anders Logg <[email protected]> wrote: > >> > On Mon, Sep 06, 2010 at 05:56:13PM +0200, Kristian Ølgaard wrote: > >> >> On 6 September 2010 17:24, Johan Hake <[email protected]> wrote: > >> >> > On Monday September 6 2010 08:13:44 Anders Logg wrote: > >> >> >> On Mon, Sep 06, 2010 at 08:08:10AM -0700, Johan Hake wrote: > >> >> >> > On Monday September 6 2010 05:47:27 Anders Logg wrote: > >> >> >> > > On Mon, Sep 06, 2010 at 12:19:03PM +0200, Kristian Ølgaard wrote: > >> >> >> > > > > Do we have any functionality in place for handling > >> >> >> > > > > documentation > >> >> >> > > > > that should be automatically generated from the C++ > >> >> >> > > > > interface and > >> >> >> > > > > documentation that needs to be added later? > >> >> >> > > > > >> >> >> > > > No, not really. > >> >> >> > > > >> >> >> > > ok. > >> >> >> > > > >> >> >> > > > > I assume that the documentation we write in the C++ header > >> >> >> > > > > files > >> >> >> > > > > (like Mesh.h) will be the same that appears in Python using > >> >> >> > > > > help(Mesh)? > >> >> >> > > > > >> >> >> > > > Yes and no, the problem is that for instance overloaded > >> >> >> > > > methods will > >> >> >> > > > only show the last docstring. > >> >> >> > > > So, the Mesh.__init__.__doc__ will just contain the > >> >> >> > > > Mesh(std::str > >> >> >> > > > file_name) docstring. > >> >> >> > > > >> >> >> > > It would not be difficult to make the documentation extraction > >> >> >> > > script > >> >> >> > > we have (in fenics-doc) generate the docstrings module and just > >> >> >> > > concatenate all constructor documentation. We are already doing > >> >> >> > > the > >> >> >> > > parsing so spitting out class Foo: """ etc would be easy. > >> >> >> > > Perhaps that > >> >> >> > > is an option. > >> >> >> > > >> >> >> > There might be other overloaded methods too. We might try to setle > >> >> >> > on a > >> >> >> > format for these methods, or make this part of the 1% we need to > >> >> >> > handle > >> >> >> > our self. > >> >> >> > >> >> >> ok. Should also be fairly easy to handle. > >> >> > > >> >> > Ok. > >> >> > > >> >> >> > > > > But in some special cases, we may want to go in and handle > >> >> >> > > > > documentation for special cases where the Python > >> >> >> > > > > documentation > >> >> >> > > > > needs to be different from the C++ documentation. So there > >> >> >> > > > > should > >> >> >> > > > > be two different sources for the documentation: one that is > >> >> >> > > > > generated automatically from the C++ header files, and one > >> >> >> > > > > that > >> >> >> > > > > overwrites or adds documentation for special cases. Is that > >> >> >> > > > > the > >> >> >> > > > > plan? > >> >> >> > > > > >> >> >> > > > The plan is currently to write the docstrings by hand for the > >> >> >> > > > entire > >> >> >> > > > dolfin module. One of the reasons is that we rename/ignores > >> >> >> > > > functions/classes in the *.i files, and if we we try to > >> >> >> > > > automate the > >> >> >> > > > docstring generation I think we should make it fully automatic > >> >> >> > > > not > >> >> >> > > > just part of it. > >> >> >> > > > >> >> >> > > If we can make it 99% automatic and have an extra file with > >> >> >> > > special > >> >> >> > > cases I think that would be ok. > >> >> >> > > >> >> >> > Agree. > >> >> > >> >> Yes, but we'll need some automated testing to make sure that the 1% > >> >> does not go out of sync with the code. > >> >> Most likely the 1% can't be handled because it is relatively important > >> >> (definitions in *.i files etc.). > >> > > >> > I imagine that "1%" will be the same as the "1%" that we have special > >> > treatment for in the SWIG files anyway, so it makes sense those need > >> > special treatment. > >> > >> I think that we can automate that last 1% too. > >> > >> > So the idea would be: > >> > > >> > 1. Document the C++ code in the C++ header files > >> > 2. Document the extra Python code in the Python files (?) > >> > 3. Document the extra SWIG stuff in a special file > >> > >> All Python docstrings should be located where the code is. > >> In the Python layer (like dolfin/fem.py), or in the extended methods > >> in the *.i files for the dolfin/cpp.py module. > >> > >> We then need to figure out how to change the syntax/name correctly > >> such that std::vector, double* etc. are mapped to the correct Python > >> arguments/return values, and how to handle the *example* code. > >> > >> >> >> > > > Also, we will need to change the syntax in all *example* code > >> >> >> > > > of the > >> >> >> > > > docstrings. Maybe it can be done, but I'll need to give it > >> >> >> > > > some more > >> >> >> > > > careful thought. We've already changed the approach a few > >> >> >> > > > times now, > >> >> >> > > > so I really like the next try to close to our final > >> >> >> > > > implementation. > >> >> >> > > > >> >> >> > > I agree. :-) > >> >> >> > > > >> >> >> > > > > Another thing to discuss is the possibility of using Doxygen > >> >> >> > > > > to > >> >> >> > > > > extract the documentation. We currently have our own script > >> >> >> > > > > since > >> >> >> > > > > (I assume) Doxygen does not have a C++ --> reST converter. > >> >> >> > > > > Is that > >> >> >> > > > > correct? > >> >> >> > > > > >> >> >> > > > I don't think Doxygen has any such converter, but there exist a > >> >> >> > > > project http://github.com/michaeljones/breathe > >> >> >> > > > which makes it possible to use xml output from Doxygen in much > >> >> >> > > > the > >> >> >> > > > same way as we use autodoc for the Python module. I had a > >> >> >> > > > quick go at > >> >> >> > > > it but didn't like the result. No links on the index pages to > >> >> >> > > > function etc. So what we do now is better, but perhaps it > >> >> >> > > > would be a > >> >> >> > > > good idea to use Doxygen to extract the docstrings for all > >> >> >> > > > classes > >> >> >> > > > and functions, I tried parsing the xml output in the > >> >> >> > > > test/verify_cpp_ > >> >> >> > > > ocumentation.py script and it should be relatively > >> >> >> > > > simple to get the docstrings since these are stored as > >> >> >> > > > attributes of > >> >> >> > > > classes/functions. > >> >> >> > > > >> >> >> > > Perhaps an idea would be to use Doxygen for parsing and then > >> >> >> > > have our > >> >> >> > > own script that works with the XML output from Doxygen? > >> >> >> > > >> >> >> > I did not know we allready used Doxygen to extract information > >> >> >> > about > >> >> >> > class structure from the headers. > >> >> >> > >> >> >> I thought it was you who implemented the Doxygen documentation > >> >> >> extraction? > >> >> > > >> >> > Duh... I mean that I did not know we used it in fenics_doc, in > >> >> > verify_cpp_documentation.py. > >> >> > >> >> We don't. I wrote this script to be able to test the documentation in > >> >> *.rst files against dolfin. > >> >> Basically, I parse all files and keep track of the classes/functions > >> >> which are defined in dolfin and try to match those up against the > >> >> definitions in the documentation (and vise versa) to catch > >> >> missing/obsolete documentation. > >> >> > >> >> >> > What are the differences between using the XML from Doxygen to also > >> >> >> > extract the documentation, and the approach we use today? > >> >> >> > >> >> >> Pros (of using Doxygen): > >> >> >> > >> >> >> - Doxygen is developed by people that presumably are very good at > >> >> >> extracting docs from C++ code > >> >> >> > >> >> >> - Doxygen might handle some corner cases we can't handle? > >> >> > >> >> Definitely, and we don't have to maintain it. > >> > > >> > We would need to maintain the script that extracts data from the > >> > Doxygen-generated XML files. > >> > > >> >> >> Cons (of using Doxygen): > >> >> >> > >> >> >> - Another dependency > >> >> > > >> >> > Which we already have. > >> >> > > >> >> >> - We still need to write a script to parse the XML > >> >> > > >> >> > We should be able to ust the xml parser in docstringgenerator.py. > >> >> > > >> >> >> - The parsing of /// stuff from C++ code is very simple > >> >> > > >> >> > Yes, and this might be just fine. But if it grows we might consider > >> >> > using > >> >> > Doxygen. > >> >> > >> >> But some cases are not handled correctly already (nested classes etc.) > >> >> so I vote for Doxygen. > >> > > >> > Not that I'm insisting on not using Doxygen, but isn't it quite rare > >> > that we use nested classes? I think we decided at some point that we > >> > wanted to avoid it for some other reason. I don't remember which but > >> > it might have been a SWIG problem. > >> > >> Look at > >> http://www.fenics.org/newdoc/programmers-reference/cpp/function/Function.html > >> as a user I would be confused by LocalScratch and GatherScratch. > > > > Those can be easily fixed by letting the script stop parsing when it > > finds "private:". > > OK, and if we are sure that no other nested classes are present in > DOLFIN I guess things should be fine. > > >> The documentation here is also rather confusing, yes we can fix it, > >> but similar cases will arise in the future. > >> > >> http://www.fenics.org/newdoc/programmers-reference/cpp/mesh/MeshPrimitive.html > > > > That looks strange because Andre has used an arbitrary mix of "//" and > > "///" in his comments. Don't blame my script for that. :-) > > Alright alright, I'll never question the almighty > generate_cpp_documentation.py script again. :)
Sounds good. ;-) > In light of the above and the Doxygen line break issue, maybe it's > best to use your script as a first try? > We just need to break it up in parsing (intermediate representation), > modifying (C++ and Python syntax) and writing stages (dump in > respective folders in the documentation) and settle on the > intermediate representation such that we can easily switch to a > Doxygen parser in case we decide to. Sounds like a compiler to me. :-) And since I anticipated your comment, it is already broken up into two different stages: generate_documentation (should maybe be extract_documentation) write_documentation The intermediate representation is a simple Python list with class names, signatures, comments etc. I'm sure it can be improved and simplified. -- Anders _______________________________________________ Mailing list: https://launchpad.net/~fenics Post to : [email protected] Unsubscribe : https://launchpad.net/~fenics More help : https://help.launchpad.net/ListHelp
