[Biopython-dev] SearchIO, was: PEP8 lower case module names?

[Peter Cock]

On Thu, Nov 1, 2012 at 6:10 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
> On Tue, Oct 30, 2012 at 7:03 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>>
>> On Mon, Oct 29, 2012 at 5:54 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
>> >
>> > Peter;
>> >
>> >> In the case of Bow's SearchIO code, what would you prefer?
>> >> e.g. Bio.SearchIO as it is now on his branch?
>> >
>> > I like plain ol' Search the best but don't have a strong preference. I'm
>> > terrible at naming things so trust everyone's judgment on this.
>> >
>> > Brad
>>
>> Since we have no clear consensus, I propose we add Bow's code
>> as Bio.SearchIO (which is how it is written right now), with the new
>> BiopythonExperimentalWarning in place (to alert people that it may
>> change in the next release). We can then rename or move it at a
>> later date. This will make it easier for people to test the code, and
>> also suggest further changes or additions (e.g. Kai's HMMER work).
>>
>> If we and when we agree a consolidation of the Bio.SeqXXX
>> modules, then Bio.SearchIO could move too. If this happens
>> before any public release as Bio.SearchIO so much the better.
>>
>> Adopting lower case module names under Python 3 is also a
>> separate issue.
>>
>> Peter
>>
>
> +1
>
> Regarding ...

I plan to do the commit today, barring any last minute objections.

I am leaning towards a merge from Bow's original (un-rebased) branch,
which had only three trivial conflicts to handle.

Peter