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

Wibowo Arindrarto w.arindrarto at gmail.com
Mon Nov 26 13:38:23 UTC 2012

Hi Peter and everyone,

If it helps, I've done the rebase (also resolving the three conflicts)
with the latest master branch. On top of it, I've also added the new
BiopythonExperimentalWarning in Bio.SearchIO.__init__.py. It's
available here: https://github.com/bow/biopython/tree/searchio.

However if you're interested in inspecting the non-rebased branch,
I've also kept it here:
https://github.com/bow/biopython/tree/searchio-nonrebased. Note that
this one doesn't have the new experimental warning since it's a
feature added more recently.

Also, in both branches, the tutorial has been changed with the
addition of the (draft) Bio.SearchIO tutorial.

Let me know which one you prefer and I'll submit a pull request :).


On Mon, Nov 26, 2012 at 2:29 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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
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