On Tue, Sep 07, 2010 at 04:46:53PM +0200, Kristian Ølgaard wrote: > On 7 September 2010 16:13, Anders Logg <[email protected]> wrote: > > On Tue, Sep 07, 2010 at 03:50:11PM +0200, Kristian Ølgaard wrote: > >> On 7 September 2010 15:02, Anders Logg <[email protected]> wrote: > >> > 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. :-) > >> > >> Yup. > >> > >> > And since I anticipated your comment, it is already broken up into two > >> > different stages: > >> > > >> > generate_documentation (should maybe be extract_documentation) > >> > write_documentation > >> > >> Nice. > >> > >> > The intermediate representation is a simple Python list with class > >> > names, signatures, comments etc. I'm sure it can be improved and > >> > simplified. > >> > >> We will most likely need to refine it w.r.t. information, but I don't > >> think that we can simplify it, most likely it will become a little > >> more complex. > >> > >> BTW, shouldn't the extract_documentation() part be in DOLFIN since we > >> intend to use to generate the docstrings.i file? > >> > >> Then write_cpp_documentation() and write_python_documentation() is > >> part of fenics-doc, but they'll import extract_documentation() from > >> DOLFIN. Otherwise we'll end up with redundant code. > > > > Yes, that sounds like a good idea. > > > > Perhaps we should have a module 'documentation' as part of DOLFIN: > > > > from dolfin import documentation > > > > doc = documentation.extract_documentation(DOLFIN_DIR=...) > > > > The extract_documentation function would look for the DOLFIN_DIR > > environment variable and if it is not set, it would need the argument > > to be supplied. > > Sounds OK to me, but can't we just use os.path.abspath(__file__) to > get the file name, and then use our knowledge of the relative > location. We still need the DOLFIN_DIR for the writee_*_documentation > scripts to work though.
Yes, that sounds better. -- Anders > > If we make it a part of DOLFIN, I have a feeling it will be more > > robust since it just needs to extract the documentation, while other > > scripts are responsible for generating various kinds of output. > > I agree. > > Kristian > > > -- Anders _______________________________________________ Mailing list: https://launchpad.net/~fenics Post to : [email protected] Unsubscribe : https://launchpad.net/~fenics More help : https://help.launchpad.net/ListHelp
