[Biopython-dev] Plans for Biopython 1.53

[Brad Chapman]

Hi Eric;

> I'll chime in about the status of the Summer of Code stuff.
> 
> 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.

This sounds awesome. Thanks for keeping up with the code; looking
forward to seeing it get in to the main branch.

> 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?

No plan from my end; hopefully Nick will chime in. If Nick doesn't
have time, it would be beyond great if you could finalize and merge the
most useful parts. Thanks for volunteering on this.

Brad