[Biopython-dev] Doing the Biopython 1.61 release next week?

[Peter Cock]

On Fri, Feb 1, 2013 at 3:47 PM, Wibowo Arindrarto
<w.arindrarto at gmail.com> wrote:
> Hi Peter, Kai,
>
>
>>> There's still one bug for Bio.SearchIO that I would prefer to be
>>> fixed (https://redmine.open-bio.org/issues/3400). Is it possible to
>>> wait a few more days (no later than next week I hope) to sort this
>>> bug out?
>>
>> Sorry for letting this slip for so long, but I never got around to
>> write an actual test case.
>>
>> Bow, did we agree to use optionalcascade for now and then maybe
>> refactor? I'm pretty confident the code works as-is, all the BioPython
>> issues I've been running into with my production site have been in the
>> GenBank/EMBL parsers. :)
>
> Yes, we did :). I meant to do the optionalcascade refactor so the code
> is more maintainable (and to prevent a corner case bug). But in
> general, the optionalcascade fix looks to be fine. And for code marked
> with the BiopythonExperimentalWarning, having a fix without test cases
> seems better than no fix at all.

That sounds OK for now.

> Peter, if you're fine with Kai's fix, I think we can mark this bug
> solved and go on with the release. I'll add the test cases and
> refactor the code later on.

You mean this patch from https://redmine.open-bio.org/issues/3400 ?:
https://redmine.open-bio.org/attachments/1754/0001-SearchIO-Add-optionalcascade-getter-setter-to-allow-.patch

I can apply that if you want.

Peter