[Biopython-dev] jython/testing

[Peter Cock]

On Wed, Aug 15, 2012 at 12:18 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Tue, Aug 14, 2012 at 9:39 PM, Tiago Antão <tiagoantao at gmail.com> wrote:
>> Hi,
>>
>> I have been trying to use biopython with jython 2.7 alpha 2. Here
>> follows a report.
>>
>>
>> There are still a few problems (with SeqIO only):
>> test_SeqIO ... ERROR
>> test_SeqIO_QualityIO ... FAIL
>> test_SeqIO_index ... FAIL
>>
>> The errors are something like (all the same kind of stuff really):
>>
>> ...
>
> I see that on my machine too. From looking at the tracebacks and
> the associated code, the failures all involve BytesIO (or StringIO
> depending on the Python version). Note that BytesIO is new in
> Python 2.6, and thus also new in Jython 2.7 compared to Jython 2.5.
>
> This is enough to demonstrate a bug in Jython 2.7a2, which explains
> some if not all of our unit test failures:
>
> ...
>
> I will report this.

Filed as http://bugs.jython.org/issue1959 with a shorter test case.

Peter