[Biopython-dev] Namespace for online resources?

[Peter Cock]

On Fri, Feb 1, 2013 at 7:05 PM, Lenna Peterson <arklenna at gmail.com> wrote:
> On Fri, Feb 1, 2013 at 9:14 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>>
>>
>> People leaning for a Bio.WWW grouping: Bow, Lenna, Kevin
>> (which could be a big disruption with lots of code relocation)
>>
>> People leaning against a Bio.WWW grouping: Michiel, Peter (me)
>> (which would also be the status quo, so no disruption).
>>
>
> I concede that the potential benefit of refactoring to separate WWW is
> outweighed both by potential downsides and the disruption and effort
> involved.
>
>> In the specific case of Kevin's TAIR code for fetch Arabidopsis sequences,
>> Bio.TAIR (lower case?) is consistent with current usage. Somewhere under
>> Bio.Seq* also seems sensible to me, as I wrote at the start of this
>> thread.
>>
>
> Populating the top level namespace with a submodule for each web-only
> service has the risk of creating too many submodules. Bio.Seq* makes sense,
> because the TAIR code pulls data into a Seq. Web services that connect to a
> single biopython representation can be organized under that submodule. Web
> services that return multiple types of information (e.g. Entrez) are big
> enough to logically comprise their own submodule.
>
> Is my interpretation of the biopython classification scheme more or less
> correct?

Yes that sounds about right :)

Of course, the historical muddle of Bio.Seq* is something we've talked
about addressing recently - see this thread from October,
http://lists.open-bio.org/pipermail/biopython-dev/2012-October/009999.html

Peter