[Biopython-dev] Bio.PopGen and SIMCOAL2 installation

[Peter]

On Mon, Nov 3, 2008 at 7:34 PM, Tiago Antão <tiagoantao at gmail.com> wrote:
> Hi,
>
> On Mon, Nov 3, 2008 at 12:43 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>> However, Bio.PopGen.SimCoal.Controller seems to assume the executable
>> will be called just simcoal2 (or simcoal2.exe on Windows), and thus
>> fails detect a binary called simcoal2_1_2.  The unit test however is
>> more flexible and looks for any binary on the path whose name starts
>> with simcoal2.  Ideally these two should be consistent.
>
> I am aware of this, in fact, this issue is documented in the tutorial
> (9.5.2.2). The idea is that the binary should be called simcoal2 as
> documented. This can be changed of course. My preference would be to
> change just the test code. Is this ok with you?
>
>> I can make test_PopGen_SimCoal.py pass by installing SIMCOAL2 as
>> simcoal2 rather than simcoal2_1_2, but is this a SIMCOAL2 installation
>> issue or a bug in Bio.PopGen.SimCoal.Controller?  In my experience it
>> is not normal for a Linux tool to include the full version in the
>> executable name - using just simcoal2 does make more sense.
>
> Agree. And, again, this is documented in the tutorial. I can go ahead
> and change the test code (please just confirm).

I had skimmed over the tutorial, but missed this bit - sorry.
Hopefully anyone interested in using SIMCOAL would have read this more
carefully, but perhaps it could be made more prominent? e.g. try to
include a few more keywords like install/installation and executable
as well as binary (which I did not think to search for at the time).

Let's just change test_PopGen_SimCoal.py to look for simcoal2 (or
simcoal2.exe on Windows) so it is consistent with
Bio.PopGen.SimCoal.Controller, and I would also mention what the
binary should be called in the SimCoalController __init__ docstring.

Peter