The number of warnings produced when running doxygen had gotten kind of out of control, making it quite hard to work on the documentation. To address this, various people have been assigned issues to fix their documentation bugs. To make this easier, I've refactored the documentation generation code to make it faster to check on warnings in a particular module. You can now do: - IMP-doc to build the documentation for all of IMP - IMP.core-doc to (re-)build the documentation for just IMP.core (remove doc/html/core/index.html if it has already been generated)
This means, that once you make some changes to the documentation of your code, you can run a relatively quick build to make sure nothing broke/look at the result. See the change log (or run "git imp update" for more info).
As a side note, if you are in the habit of documenting parameters in doxygen using the \param (or @param) commands, please be very careful. Getting a parameter name wrong, or leaving out a parameter results in a warning, and there are tons of these. This both makes the resulting documentation not very useful and makes it hard for anyone to work on the documentation.
And one last note, you are, in general, best off using the latest version of doxygen as important bugs are fixed useful capabilities are added at a pretty rapid clip. It is quite easy to install by downloading from http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.4.linux.bin.tar.gz (on linux) or via homebrew on a mac.
I would like to move towards treating doxygen warnings as errors so as to try to keep it warning free, but we are a ways from that.
Thanks.