[Biopython-dev] Biopython under PyPy

[Peter Cock]

On Sun, Sep 25, 2011 at 2:56 AM, Eric Talevich <eric.talevich at gmail.com> wrote:
>>
>> I could take a look at test_Restriction.py this weekend, I think.
>>
>
> I think it could be a bug in PyPy, but I'm not sure.
>
> The underlying error in test_Restriction and test_CAPS is triggered by
> "import Bio.Restriction.Restriction":
>
> Traceback:
> [...]
>     super(RestrictionType, cls).__init__(cls, name, bases, dct)
> TypeError: unbound method __init__() must be called with BssMI instance as
> first argument (got RestrictionType instance instead)
>
>
> Adding a print statement before the failing line:
>
>         print cls, name, isinstance(cls, RestrictionType)
>         super(RestrictionType, cls).__init__(cls, name, bases, dct)
>
> Gives:
>
> BssMI BssMI True
> [the same error...]
>
> I'm not even sure how to turn this into a simple test case for the PyPy
> folks to look at. Anyone else want to take a crack at it? The fun starts
> near the bottom of Bio/Restriction/Restriction.py -- search for the word
> "magic".
>

That doesn't surprise me, we had trouble with that bit before going to
Python 2.6:
http://bugzilla.open-bio.org/show_bug.cgi?id=2604

Peter