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

[Peter Cock]

Hi Tiago,

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

http://biopython.org/wiki/Deprecation_policy

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:

https://codecov.io/gh/biopython/biopython

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:

http://testing.open-bio.org/biopython/tgrid

We should also ask on the main Biopython mailing list.

Thanks,

Peter


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
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