[Biopython-dev] Plans for Biopython 1.53

[Peter]

On Wed, Dec 9, 2009 at 3:57 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> Good news:
>
> I've tweaked the RestrictionCompiler.py code to modify how it generates
> Bio/Restriction/Restriction_Dictionary.py in order to build the dictionaries
> incrementally. Together with the removal of the C code DNAUtils, this
> means (after a clean install) that Jython likes Bio.Restriction and that
> test_Restiction.py passes on Jython 2.5.1 (and C Python too).
>
> Bad news:
>
> I think I have broken test_CAPS.py (under both Jython and Python).
> It looks like it hits some bits of Bio.Restriction are not covered by
> test_Restiction.py
>
> I'm working on it still ...

Solved: the check_bases function in Bio.Restriction also used to
make things uppercase (but the docstring didn't make this clear
and the C code was non-obvious).

I think this means the whole test suite passes on Jython 2.5.1
(barring those bits with C code dependencies, BioSQL, or the
known Jython issues with DTD passing or the missing buffer
function).

Kyle - could you confirm this on your machine please?

Thanks,

Peter