[Biopython-dev] Biopython 1.57 release plans

[Peter Cock]

2011/3/3 Eric Talevich <eric.talevich at gmail.com>:
> On Thu, Mar 3, 2011 at 6:41 AM, Peter Cock 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.

OK then.

> 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

Yeah, making sure nothing major is missing in the NEWS file is on
the TODO list for each release. I thought it was up to date...

>
>  - 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.
>

Looks about right - on the Python 2.4 side, I'm hoping other projects
like Galaxy will drop Python 2.4 ASAP, and that Biopython 1.57 really
will be the last release to work on Python 2.4 (all be it lacking some
features). In practice many of the things Python 2.4 lacks (e.g. SQLite)
also apply to Jython, but that is a different issue really.

>>
>> 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?
>

Probably best to discuss this on a new thread. Also consider "mean"
since there is more than one average ;)

Peter