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This page explains how to write the documentation for your code.
Here is a template of a documented .h file, and of a .cc file. The resulting doxygen page is here.
This documentation should be written in a file [Package]/doc/[Package].doc, according to the template Documentation/ReferenceManualPages/template/Package.doc. The simplest way of doing this is to go to the doc/ directory in your package and then run the script makePackageDoc, which is available in your PATH, once you have done eval `scramv1 runtime -csh`. This script creates the file [Package].doc according to the above template, and automatically includes inside it a list of the classes and modules to be documented.
Documentation on modules can include .cfi files as follows:
\htmlinclude myfile.cfi
> cmsrel CMSSW_4_3_0 > cd CMSSW_4_3_0/src/ > cmsenv > cvs co Documentation/ReferenceManualScripts/doxygen > cvs co YOUR_PACKAGE(s) > cd .. > scram b doxygen wait... > firefox doc/html/index.html