[Biopython-dev] biopython on github

[Peter]

On Fri, Mar 20, 2009 at 12:55 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
>
> Peter, the repository deletion was very quick for me, so it looks like it
> got stuck somewhere with the GitHub downtime.

They've fixed it - I picked a bad day to delete a "fork".

Giovanni wrote:
>> > I see that you have renamed your fork as seqio-quality. Ok, but I
>> > think it is better to keep the fork's name as 'biopython', and then
>> > create many branches inside it.

Agreed - when I did that, I hadn't appreciated github's distinction between
branches and forks.

Peter wrote:
>> I don't think I had entirely understood github's use of fork versus branch.
>> I'll have so do some more reading and try again once my account has
>> settled down.  Thanks for the details in your email.

Brad wrote:
> Wow, now I am mad confused. I thought forks and branches were
> conceptually the same. Giovanni, it seems like you are suggesting one
> branch (the GitHub fork) and then a second branch (the git branch
> command). We were thinking of a standard case as:
>
> 1. Fork the Biopython trunk at GitHub. Name this something so it
> makes sense what the fork/branch is for.
> 2. Work on the fork/branch. If you want, invite others to work on it
> with you.
> 3. When finished, be sure you are up to date with the master
> Biopython trunk.
> 4. Submit the fork/branch for inclusion in Biopython.
> 5. Once included, delete the fork/branch.

If I understand correctly, a potential contributor does this:
1. Fork Biopython trunk at GitHub, which will give you your own
public repository (aka a "fork" in github's terminology), called
by default contributorname/biopython, containing initially a
single master branch, e.g.
http://github.com/peterjc/biopython/tree/master
2. Using the git command line tool, create a branch within your
repository to work on a problem, say bug2551, and upload this
branch to your github account. e.g.
http://github.com/peterjc/biopython/tree/bug2551 (I presume)
3. Work on your code, and commit changes to your bug2551 branch
and push these up to your github account.
4. Once you are happy, submit this bug2551 branch for inclusion in
Biopython (in the short term via Bugzilla, but if/when we have moved
to github fully, as a pull request to the main biopython master,
or if appropriate the master of the mainterainer of that module).
5. Once the changes are in the main Biopython, you can delete
the bug2551 branch (but not the whole "fork" which may contain
other branches).

Almost the same... I'll try this shortly (maybe Monday).

Peter