[gmx-developers] Using doxygen in gmx

David van der Spoel spoel at xray.bmc.uu.se
Tue Mar 5 22:11:47 CET 2013

On 2013-03-05 20:01, Teemu Murtola wrote:
> Hi,
> On Tue, Mar 5, 2013 at 5:23 PM, David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>     how can I get doxygen to pick up comments on methods, classes,
>     namespaces etc.? Is it sufficient to have the proper comments in
>     random files for doxygen to pick it up? Or do I need to add
>     filenames/directory names to some input script?
> Assuming you are on the master branch (or somewhere derived from it),
> you don't need to do anything special for Doxygen to consider your file.
> Everything under src/ is recursively included. Some files/directories
> are excluded (the list is in doxygen/Doxyfile-common.cmakein), but that
> should not normally affect you. If your comments don't seem to appear in
> the output, then there may be issues with the enclosing scope
> (file/namespace/class) not being properly documented. This is mentioned
> at http://www.gromacs.org/Developer_Zone/Programming_Guide/Doxygen,
> along with a lot of other stuff related to Doxygen, but I don't know all
> the rules without more thorough testing.
> Teemu
Thanks! Indeed that works, just had to add more comments to the files.

I can highly recommend adding those doxygen comments, the reward in 
terms of the documentation is amazing. All of a sudden I understand my 
own code!

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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