[Biopython-dev] Biopython 1.60 plans and beyond

[Peter Cock]

2012/2/18 Tiago Antão <tiagoantao at gmail.com>:
> 4. Code to do multi-tasking. Actually Bio.PopGen has a scheduler to do
> multiple (external) tasks at the same time, but I have written a new
> one. Maybe the code does not belong into biopython, but a discussion
> could be done around such a issue (I suppose people doing analysis of
> lots of data have been having that problem, not just me?).

I hear good things about Python's multiprocessing. I don't
really see that this is a Biopython issue per se, but a much
more general one for high performance computing in Python.
We should probably focus on providing some examples of
how to do this with the best standard/external libraries.

Right now I'm some simple job splitting/merging code in
Python for Galaxy jobs - we've got an in house server now
hooked up to our cluster, which will be the primary way for
non-programmers in the institute to run large jobs (e.g.
preprepared pipelines for protein annotation).

> 5. Some ensembl variation code: things like getting the ancestral
> SNP (versus the derived) or getting all the stuff (genes mostly) in
> a certain window position of the genome.

Sounds good - I've not had much cause to look at Ensembl
through work, but there would be interest in using this from
Python.

> On a side, I still have to do a 64 bit Windows port (remember?).

Oh yes - this issue is still in debate for NumPy/SciPy where
they have some quite complex build interdependencies to
sort out. Waiting for an official 64bit Windows NumPy was
one of our stumbling blocks.

> Another issue that has been crossing my mind regards the inclusion of
> new code: In my case I would really like to have something like a
> "beta" version of the API: ie releasing something that is deemed
> "unstable" API wise (to get comments from the community) and then
> stabilize it. Concretly: in the first/second version people should
> expect the API to not be stable and have changes.

We've sort of done that already in that we've said in the release
notes that whole modules are new and experimental (beta), and
subject to change. Are you thinking of more than that - e.g. an
import time warning?

Peter