[Biopython-dev] run_tests.py rewrite

Bruce Southey bsouthey at gmail.com
Tue Feb 3 15:15:37 UTC 2009

I do get your point and I do agree with it.

In part I see this as a necessary step to clean up the current tests 
that would permit a smoother change to a different testing framework if 
or when necessary. It is a different question whether or not to do such 
a change. Technically nose is required by Numpy 1.2+ (but only for 
testing) so it is not really an extra dependency on Biopython (unless 
Biopython is split into two components - with and without Numpy). But I 
do not see an real advantage for a new testing framework in the current 
code base without a major effect to change everything at once (I would 
at least act as a tester for any new framework). Perhaps it would make 
better sense to do that when porting Biopython to Python 3 because the 
tests will need to be examined and perhaps rewritten.


Peter wrote:
> On Tue, Feb 3, 2009 at 11:46 AM, Giovanni Marco Dall'Olio
> <dalloliogm at gmail.com> wrote:
>> ufff I am sorry but the more I think about it, the more it seems a
>> nonsense to me..
>> Why are you writing a new test-discovery framework for biopython, when
>> there are many already available that work fine and better?
>> Isn't it a waste of time, really? I am not criticizing you - but
>> speaking from a purely technical point of view, I really don't
>> understand.
> We're NOT writing a new test-discovery framework - in this recent
> change we're reusing part of the existing unittest framework included
> with python.
>> If you are worried that using nose will add a new prerequisite to
>> biopython (which is not true, by the way), you can easily include the
>> nose executable within the test dir, as I think many other projects
>> already do;
> Using nose would be another prerequisite for anyone running the tests
> (although as you point out, it may be possible to include it with
> Biopython).
>> Honestly, I have the feeling that you didn't even had a look at all
>> the links I posted in the old discussion on nose, neither you have
>> tried it, and that's so bad. You didn't discuss about the pros or cons
>> of nose, you just kept saying 'it would add a prerequisite to
>> biopython' (which is not true, again), and started writing your own
>> new test discovery framework.
> We didn't just start writing our own framework (which I agree would be
> a waste of time).  We already had a simple framework, and with
> Michiel's recent changes it make more use of the python unittest
> infrastructure.
> Peter
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