[Biopython-dev] run_tests.py rewrite

[Giovanni Marco Dall'Olio]

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.

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;

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.
With nose, you could have a good testing infrastructure and take
advantage of things like global fixtures, automatic formatting of the
output, integration with profilers, and a lot of things more.

It seems a nonsense to me, because with biopython you provide source
code that you make available to all the bioinformaticians, with the
idea that reuse of the code is good; but then, you don't want to use
the code written by someone else.
I have seen many bioinformatician telling me that they don't use
biopython because they don't have the time to study it and they don't
know how it works. I really believe that this is terrible, making the
whole bioinformatics field a mess.

Cheers :)

On Tue, Feb 3, 2009 at 11:35 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>>> I think Michiel has only switched over test_Cluster.py thus far.  The
>>> doctests are currently run via test_docstrings.py which is still a
>>> print-and-compare test for now.
>>
>> ah! I see.
>
> I was wrong - as Michiel clarified in a later comment, run_tests.py
> should have been finding all the unittest based tests (but right now
> it isn't).  As in my earlier email, some of our unittest cases use a
> prefix of "t" and others use "test" meaning only some of the unittest
> test cases are currently being detected.  One this is fixed, then
> test_docstring should work too.
>
>>> Could you show us the error with test_CAPS.py please, with details of
>>> your setup.  This test is working for me.
>>
>> sorry.. it works fine if I run it from within the Tests dir.
>
> Good.  Thanks.
>
> Peter
>



-- 

My blog on bioinformatics (now in English): http://bioinfoblog.it