[Biopython-dev] Bio.PopGen status

[Tiago Antão]

Hi,

This is a short email regarding Bio.PopGen status.

1. All the code on the repository should be stable.
2. The Biopython version that is schedule for release soon will have
support for coalescent population genetics' simulations
3. A short number of test code cases are included.
4. Documentation was produced and is available on the Tutorial. I
believe that it is satisfactory (tell me if you disagree).
5. Bio.PopGen is still not "version 1" in the sense that the
fundamental statistics code is missing. This was a conscious strategy
to start with selection detection and coalescent simulation in order
to begin with arguably less important stuff so that newbie errors (in
the sense that I was a newbie developer to biopython) would have less
impact.
6. Statistics is my next task and hopefully will coincide with the
biopython release after this one. This will be, at least, for me,
"version 1" of Bio.PopGen
7. In the code, there is, since the original Bio.PopGen, code that is
able to execute external simulators in parallel (thus taking advantage
of multi core architectures for computationally intensive
simulations). This is, unfortunately, not documented. I will document
this (maybe in a separate document from the tutorial) in the future. I
don't think this is priority 1. But others might be interested in
using this code for computationally intensive tasks using external
programs. In case you want to know more details about this, please say
so.

>From a biopython release perspective, Bio.PopGen with new coalescent
simulation features is fully ready. Please go ahead and release
whenever is more convenient.

-- 
http://www.tiago.org/ps