About Using CVS:
this page seems to be mostly directed to developers that have commit privileges to the repository.
Instructions for users of bioperl that don't have this privilege are lacking.
How do you go about checking out code, modifying it (minor edits, major additions (e.g. add a new method, for example to support a new file format) and submitting it back? What is the recommended format of submission? Patches? What kind of diff format is the preferred one? Unified diff? Context diff? If several files are affected, should we submit a recursive diff from the top of the checked out code hierarchy?
- First thing: for any questions you should always read the FAQ first (most of yours are answered there). The first section here details how to check out code anonymously and, IMHO, pretty clearly explains that procedure. If one wants really detailed instructions on using CVS, they can refer to the cvs manual. If you use a GUI to CVS (like TortoiseCVS) then it requires a little more setup. We haven't had a lot of requests for that, but the procedure is pretty simple. As for submitting modified code (additions, edits, etc), the FAQ and Advanced BioPerl pages answer the rest of your questions. In short, the best place to submit or request changes, add modules, ask questions, etc. is to is the main bioperl-l mailing list; an alternate route is by submitting a request via Bugzilla (add your change/patch/whatever as an enhancement to bioperl). The mailing list is always a good place to start since you'll get feedback there fairly quickly. If you plan on making radical changes, the mail list is definitely the place to go as many people out there use the CVS code in production environments. As for using a specific version of diff, we're pretty free thinkers around here. I don't believe there is a specific diff format that is universally used here, though I'm a relatively new bioperl developer, so I may be wrong (and if so, will add any pertinent info where needed). --Chris Fields 15:16, 3 April 2006 (EDT)