[Biopython-dev] [GSoC] Project Proposal for Google Summer of Code

[Peter Cock]

On Wed, Mar 4, 2015 at 3:57 AM, Joshua Klein <mobiusklein at gmail.com> wrote:
> The codebase can be found at https://github.com/mobiusklein/pygly2 where I
> am actively committing new code. I had borrowed a large portion of an
> implementation of one facet of the library from another project released
> under the Apache 2.0 license, which is more restrictive than the BSD
> license. I've contacted the author with regard to how he would like us to
> treat that component.

OK.

> Assuming all these things pass smoothly, namespaces may be a complicated
> matter now that I have read through more of the Bio codebase. At the risk of
> sounding too general, the vast majority of the common namespaces in Bio are
> related to operations on many different data formats that happen to result
> in Seq or SeqRecord objects. This leads to lots of infrastructure and class
> design being built up around ways of converting many different resources
> into those types of objects. It would be sensible to keep the structures I'm
> building in a separate namespace as they talk about distinctly different
> data structures that don't share any class hierarchy.

Certainly, e.g. Bio.Cluster is self contained and has nothing to do with
Seq/SeqRecord.

> I should post to the general user mailing list to find out about general
> interest before trying to make the value judgement on whether integration is
> a worthwhile investment. That's biopython at mailman.open-bio.org, correct?

Yes, although there are aliases that work too. See:
http://mailman.open-bio.org/mailman/listinfo/biopython

Thanks,

Peter