Doxygen is a bit slow - it takes about a couple of minutes to process my whole project, so for small incremental changes this is longer than actually building the rest of my code. There are thousands of files without any documentation so I guess it is spending most of its time processing them. Is there any way to get it to skip files without any documentation?
What about getting it to only process changed files?
From Doxygen documentation:
How can I exclude all test directories from my directory tree?
Simply put an exclude pattern like this in the configuration file:
EXCLUDE_PATTERNS = /test/
So, you should be using patterns to exclude files. It's been a long time since I've used Doxygen, but i don't remember any option to process only changed files.
Doxygen is good at finding connections between files, either changed or not. But Doxygen does not remember informations about unchanged files, so it must process the whole codebase each time.
May be a solution would be to organize the project such that never changed files belong to one module which is excluded from Doxygen scope and whose documentation is already available. Then it would be possible to tell Doxygen to link newly built documentation to this existing module documentation.
Going further, it would also be possible to make Doxygen running module by module, processing only changed modules and a top level documentation which links to all module documentations.
I found that turning off the option SEARCH_INCLUDES made a big difference. It was looking through the whole platform SDK and include paths for the compiler which were not documented anyway and would not appear in the generated documentation.
There is a DOT_NUM_THREADS options which may increase the performance on multicore machines. Unfortunately doxygen itself is just single threaded.
Another approach would be to organize your code into modules run for each module a seperate doxygen instance and linkt the resulting tags together: http://www.stack.nl/~dimitri/doxygen/external.html