[Biopython-dev] Statistics in population genetics module - Part I

[Tiago Antão]

Hi,

On Mon, Nov 3, 2008 at 3:36 PM, Giovanni Marco Dall'Olio
<dalloliogm at gmail.com> wrote:
> For how much time do you think a biopython module should be kept compatible
> with older versions, more or less?

That is an interesting discussion. My view is that biopython is fairly
conservative in that regard. I am not saying that I agree/disagree.
There seems to be a certain policy in place, and I respect it. But the
point is: Bio.PopGen has to have the same policy has the rest.

> It will take a long time to develop the module, and it is sure that we will
> make some mistakes. So, what is the best way to proceed? What if we create a

I will try to offer my view about this as soon as possible (in the next days).

> At the moment I am working with a separated git repository for all the
> popgen modules. The problem is that I didn't include all biopython modules
> in the repository, so, if any of my changes breaks something in biopython, I
> won't know it until I'll merge everything with biopython code.

It won't probably break anything as long as you don't change existing
code. If you are only doing your parser I suppose it will be very
easily accepted in (dont forget test cases and documentation).
Regarding Statistics we need to discuss it.

> p.s. When python3000 will be released, it will be probably necessary to
> rewrite large portions of biopython, if not creating a 'biopython 2' version
> (I think they were discussing something like this in bioperl's list).

Peter and Michiel opinions on this topic are be fundamental (they do
most of the work maintaining biopython). But I suppose retro
compatibility is a must.

> I thought that maybe, even if we make some 'mistakes' in this version of
> biopython, we will be able to fix them in a later version.

Mistakes should not break existing code. That is really something we
should try to avoid.

> I think that a good idea would be starting collecting use cases to have an
> idea how many things we'll have to implement in this module.

This might sound elitist, but most people doing population genetics
don't really have any idea of what they should expect from software.
While for the "business of sequences and alignment" there is a large,
mature software community, the same doesn't happen in population
genetics. Or to put it in another way: you don't want to imagine the
type of questions that arrive to my private mailbox ;) .

> I sent that mail to the Open::Bio::I last week, but still haven't received
> many replies... I will send a message to the various Bio.* mailing list in
> the next days.

OBF, in my view, is a bit slow and bureaucratic.
Anyway, i think that anybody's views will get more importance in
proportion of the quantity of code submitted and time devoted to
maintenance of the whole thing.


Tiago