[Biopython-dev] Releasing (a beta of) Biopython 1.62 this week?

Peter Cock p.j.a.cock at googlemail.com
Fri Aug 23 08:54:35 UTC 2013

On Fri, Aug 16, 2013 at 8:14 AM, Wibowo Arindrarto
<w.arindrarto at gmail.com> wrote:
> Hi Michiel, Peter,
> In preparation for the 1.62 release, I've made the following changes
> to Bio.NCBIStandalone and Bio.ParserSupport:
> * Migrated the two modules under Bio.SearchIO._legacy
> * Upgraded their PendingDeprecationWarning to BiopythonDeprecationWarning

So basically you're proposing formally deprecating parsing plain
text BLAST output (via NCBIStandalone and Bio.ParserSupport)
but continuing to support this format via SearchIO (using a copy
of the current parser as a private module)?

This then gives you the freedom to rewrite the old text parser
more simply (e.g. assuming only recent versions of the BLAST
suite), which might be nice.

> I've pushed the changes to this branch:
> https://github.com/bow/biopython/tree/bio_blast_migrate
> Tests seem to be running fine still, but now there is the awkward
> situation where if users import Bio.NCBIStandalone and/or
> Bio.ParserSupport directly they will be greeted with two warnings: the
> BiopythonWarning for the modules' deprecation and the
> BiopythonExperimentalWarning for SearchIO.
> We could suppress the SearchIO warning in Bio.NCBIStandalone and
> Bio.ParserSupport. But before this is done, I was wondering if we have
> a defined timeline for removing a BiopythonExperimentalWarning? (i.e.
> if it will be removed in this release, then we could do that instead).

It doesn't make sense to have a defined timetime for removing a
BiopythonExperimentalWarning - it will be on a case by case basis.

Do you think SearchIO is ready for that now (or in Biopython 1.63)?


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