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

[Eric Talevich]

On Mon, Jun 22, 2009 at 12:44 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Mon, Jun 22, 2009 at 5:14 PM, Eric Talevich<eric.talevich at gmail.com>
> wrote:
> > Biopython has a couple of core objects that I'm reusing in my project.
> There
> > was a quirk in these libraries (related to this:
> >
> http://effbot.org/pyfaq/why-are-default-values-shared-between-objects.htm)
> > that made the objects slightly more awkward to instantiate, but the
> issues
> > were recently fixed. I'd like to merge these fixes soon.
>
> Brad just committed a fix for Bug 2841 - is there anything else you still
> think needs fixing in the latest trunk code in this area? I'm not sure what
> you meant my "merge" in this context.
>

I meant pull -- merging from biopython/master into my etal/phyloxml branch.


> > So, GSoC requires a tarball of the code we write at the end of the
> summer.
> > Merging from upstream would bring code that I didn't write into my
> > development tree -- which I could probably filter out with the right
> > arguments to git-diff, but nonetheless, my project history would no
> longer
> > be entirely clean. Does Google care about this? Or is it safe to go ahead
> > and pull from the next stable release of Biopython (coming soon)?
>
> This probably depends on the GSoC rules - from the Biopython license
> point of view I don't see a problem with you providing a complete tarball
> (i.e. all of Biopython plus your code). Ideally use the latested current
> stable
> release for this (and for your timetable that will probably be Biopython
> 1.51 or 1.52 depending on how things go).
>

OK, good. The GSoC guidelines from previous years look like they're
reasonably flexible, I just want to be sure. Also, here's a rant from Linux
Torvalds about how to merge from upstream in Git:

http://www.mail-archive.com/dri-devel@lists.sourceforge.net/msg39091.html

According to that, I should pull from the Biopython master branch at the
1.51 tag when that happens (no rebasing, since I've pushed my stuff to
github already), and if I want to land in time for 1.52, then pull from
biopython/master then, fix any merging issues, and immeditely submit a pull
request on GitHub. Otherwise, pull from the 1.52 tag, rinse, repeat.

(By the way, do you think
GitMigration<http://www.biopython.org/wiki/GitMigration>will be
complete before or after GSoC ends? If we're still rocking CVS then
it's less important to keep a clean branch history.)

Best,
Eric