[Biopython-dev] Plans for Biopython 1.53

[Peter]

On Mon, Dec 7, 2009 at 4:33 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
>
> I'll chime in about the status of the Summer of Code stuff.

Thanks

> For Bio.TreeIO, I've borrowed the Newick tree parsing code from Nexus.Trees
> and changed it to construct Bio.Tree objects via Bio.TreeIO.NewickIO -- so
> the TreeIO API will work independently of file formats. For Bio.Tree, I'm
> about halfway done porting the Nexus tree methods, though it'll go faster
> now that the semester's over. (I'll post the details and ask for a code
> review soon.)
>
> My phyloxml branch won't be ready to land in time for a December release,
> but merging it into the trunk right after that is feasible. That would
> everyone time to try it out and suggest changes before Biopython 1.54
> cements the API.

That is what I was hoping for. Fingers crossed Tiago will be able to
spare some time to go over the basics of the phyloxml and TreeIO
work - more eyes on the code would be great.

> Separately: GitHub says Nick Matzke's BioGeography branch hasn't been
> touched since Aug. 19. It will need some love before it can be merged into
> the trunk. Is there a plan for this, Peter or Brad? If not, should I try to
> rescue it after TreeIO lands?

That sounds good as a tentative plan - Nick may want to be more
involved, but you would be the next logical choice to handle this.

Cheers,

Peter