[Biopython-dev] Deprecating simcoal and fdisk content in PopGen

Peter Cock p.j.a.cock at googlemail.com
Thu Jul 28 16:00:23 UTC 2016

Hi Tiago,

I have no objection to deprecating this, which will be a gradual


Tiago's PopGen code has plenty of unit tests but because
these tools are not open source friendly we never got them
integrated into the TravisCI setup - which is why it looks like
the PopGen code has a poor test coverage score:


The tests have been running via the buildbot system - these
are volunteer machines (currently looked after by me and
Tiago) where we had installed the dependencies manually:


We should also ask on the main Biopython mailing list.



On Thu, Jul 28, 2016 at 4:45 PM, Tiago Antao <tra at popgen.net> wrote:
> Dear all,
> I would like to deprecate a big part of PopGen, that is:
> - All the simcoal stuff
> - All the fdist stuff.
> Simcoal comes from the lack of source code and a free license.
> fdist from a lack of license.
> In simcoal case, I do not think we should support black box code (unless it
> is something very very popular which is definitely not the case).
> For the fdist case I suspect that 99%+ of the users are via my own
> applications, and I will take care of that myself. We would benefit my
> reducing Biopython's complexity a little bit.
> For simcoal, I understand that there might be a few (handful at most?)
> users, but I think the trade-off is well worth it.
> Any opinions?
> Regards,
> Tiago
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev

More information about the Biopython-dev mailing list