[Biopython-dev] Biopython 1.57 release plans

[Eric Talevich]

On Thu, Mar 3, 2011 at 6:41 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Thu, Mar 3, 2011 at 11:35 AM, João Rodrigues <anaryin at gmail.com> wrote:
> > Hey Peter, should we include the Bio.PDB things we've been discussing for
> a
> > while now? That has been a bit quiet lately so I dunno how it stands with
> > you guys.
>
> I'm tempted to say no, try and get the release out within a week, and
> then work with you and Eric to merge the code. I'm worried the merge
> might push the release back, and I would like to get it out this month.
> What's your impression Eric?
>

João, I'm sorry to put this off again -- but I think we should do that merge
after the 1.57 release. The API for the functions renumber_residues and
remove_disordered_atoms is tricky to get right, because they have to support
so many variations on the same concept. I'd like to give dev-version testers
some time with it before locking down the API with a stable release.

I'm looking at the NEWS file and I don't see any mention of the GSoC work
that we already merged -- was that in time for the 1.56 release, or just
after?

Here's what's already in 1.57 (pre-release):

 - index_db(), which I think people will really like
 - Blast+ support: blast_formatter
 - Some improvements to SeqiO and SeqRecord
 - Last release to support Python 2.4, for real this time


Dropping 2.4 support might also let us tighten up the Bio.PDB code a bit.


> Also which github branch are you considering merging? I can do a trial
> merge (offline) and run some tests here (I have access to all the main
> platforms).
>

It's here:
https://github.com/JoaoRodrigues/biopython/commits/pdb_enhancements

Comment on remove_disordered_atoms: I'm trying to think of a more obvious
way to make the "Average" option work. It's the default, so users won't
normally have to type it, but having "A" and "Average" seems prone to
autocomplete issues (mentally or in the IDE). How about making "average"
lowercase?

Best,
Eric