[Biopython-dev] Plans for Biopython 1.53

[Eric Talevich]

On Mon, Dec 7, 2009 at 8:28 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> Hi all,
>
> I would like us to do the Biopython 1.53 release this month.
>
> We still have lots of new stuff that hasn't yet landed on the
> trunk, but despite that, looking at the NEWS file we have
> had plenty of improvements in the two months and a bit
> since Biopython 1.52 was released:
>
> http://biopython.open-bio.org/SRC/biopython/NEWS
> http://github.com/biopython/biopython/blob/master/NEWS
>
> One good reason for doing Biopython 1.53 soon is the
> NCBI said they plan to start using the new Jan 2010 DTD
> files for MedLine/PubMed as early as mid December:
> http://lists.open-bio.org/pipermail/biopython-dev/2009-November/007020.html
>
> Any comments on how things stand on the trunk - is there
> anything people think needs to be fixed before the release?
>
>
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.

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?

Cheers,
Eric