[Biopython-dev] Developmental and experimental branches

Peter biopython at maubp.freeserve.co.uk
Sat Jan 10 14:46:13 UTC 2009

On Fri, Jan 9, 2009 at 10:51 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
> Hi all;
> In terms of the coding of experimental modules, Giovanni is taking
> an excellent approach. While they are under development, we can
> utilize one of the many free hosting platforms to develop it as a
> separate project in the Bio namespace. This allows interested users
> to get the code, contribute, and test. Once an interface and
> functionality is hammered out and they begin to stabilize, then it's
> a good time to package it up and roll it into Biopython provided the
> ol' mailing list consensus is happy.

This does describe recent large additions fairly well - such as
Bio.SeqIO, Bio.AlignIO, Bio.Entrez, Bio.PopGen and most recently
Bio.Graphics.GenomeDiagram (which is a little different in that it was
previously publicly available as a separate module).

Modifications to existing bits of code (for example I have some
proposals for Seq, SeqRecord and Alignment objects as enhancement
bugs) don't really work in the same way - but also by their nature
require more discussion because they can indirectly affect a lot of

> This is a nice development model as it leverages the community, but
> only rolls code into the main release when it stabilizes reasonable
> well. Peter has taken a really good development methodology --
> creating a rock solid stable core of modules, and actively deprecating
> or fixing those that fall out of line.

I really don't deserve all the credit here - Michiel has also been a
strong proponent for this "spring cleaning" as needed, for example how
our NCBI online bits have been rationalised, refocusing on Bio.Entrez
at the preferred module.

> My only suggestion would be to have a Biopython wiki page for the
> experimental modules as they are under development. Something simple
> with a description of the goals and a link to the source code would
> help the majority of people who don't follow the mailing list find
> and contribute to these.

Using the wiki in this way is a nice idea.  Tiago - do you fancy
adding a PopGen page describing the additions you're working on?  As a
bonus, once these do get into the main repository, you may find the
wiki text will be a useful basis for extending the documentation.


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