[Biopython-dev] GSoC Weekly Update 12: PhyloXML for Biopython

[Eric Talevich]

On Tue, Aug 11, 2009 at 9:20 AM, Brad Chapman <chapmanb at 50mail.com> wrote:

>
> How did you like the Git/GitHub experience? One thing we should push
> after this release is moving over to that as the official
> repository. Since you have been doing full time Git work this
> summer, your experience will be really helpful. I still rely on CVS
> as a bit of a crutch, but should learn to do things fully in Git.
>
>
I liked it a lot! I've spent some time with Subversion, Bazaar, Mercurial
and Git now, and I'm confident that Git was the right choice for Biopython.
My commit history shows a quick flurry of activity on each of the past few
Fridays -- that's from a couple days of exploration toward the end of the
week, then repeated calls to "git add -i" to pick out the parts that are
worth keeping. I'm careful with git-rebase, but "git commit --amend" gets a
fair amount of use. I could add a section on the Biopython wiki's GitUsage
page, called something like "Managing Commits", giving some examples of
this.

GitHub has been down briefly a few times. It was only a problem because it
happened on Monday mornings, when I wanted to push an updated README to my
public fork at the same time as my weekly update e-mail to this list. Having
a mirror on GitHub is great for getting started with Biopython development,
but I'm still unclear on how changes should propagate back upstream after
Biopython switches from CVS to Git. Pull requests? Core devs pushing to a
central Git repository on OBF servers? Maybe the BioRuby folks have advice;
if this has been settled on biopython-dev, I've missed it.

Anyway.

To create the final patch tarball next Monday for GSoC, I believe the right
incantation looks like this:

git format-patch -o gsoc-phyloxml master...phyloxml
tar czf gsoc-phyloxml.tgz gsoc-phyloxml

That's cleaner than I expected it to be. Neat.

Cheers,
Eric