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

[Peter Cock]

On Mon, Nov 26, 2012 at 1:38 PM, Wibowo Arindrarto
<w.arindrarto at gmail.com> wrote:
> 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 :).
>
> cheers,
> Bow

That's fine - I found both branches :)

I've actually done a trial merge on the non-rebased one and
then cherry-picked the experimental warning - looks good.

Once that's done there is some housekeeping to do, like
the indexing code duplication with Bio.SeqIO, and tackling
indexing BGZF compressed files with Bio.SearchIO which
I will have a go at.

Peter

P.S. I had intended to do this earlier this month, but we
had the OBF server issues to deal with.