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. 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 Kristian > -- > Anders > _______________________________________________ Mailing list: https://launchpad.net/~fenics Post to : [email protected] Unsubscribe : https://launchpad.net/~fenics More help : https://help.launchpad.net/ListHelp
