[Biopython-dev] Deprecating Bio.ParserSupport, Bio.Blast.NCBIStandalone

[Michiel de Hoon]

Hi Bow,

Yes, that is correct.
Responding to Peter's email: Peter, do you agree with this approach?

Best,
-Michiel.

--- On Fri, 2/1/13, Wibowo Arindrarto <w.arindrarto at gmail.com> wrote:

> From: Wibowo Arindrarto <w.arindrarto at gmail.com>
> Subject: Re: [Biopython-dev] Deprecating Bio.ParserSupport, Bio.Blast.NCBIStandalone
> To: "Michiel de Hoon" <mjldehoon at yahoo.com>
> Cc: "Peter Cock" <p.j.a.cock at googlemail.com>, "BioPython-Dev Mailing List" <biopython-dev at biopython.org>
> Date: Friday, February 1, 2013, 5:29 AM
> Hi Michiel, Peter, everyone,
> 
> >> > I'm OK with using the setUp and tearDown
> arguments to
> >> > doctest.DocTestSuite to do the directory
> magic, but
> >> keeping the test files
> >> > under Tests/.
> >>
> >> As a more elegant version of the
> Bio._utils.run_doctest()
> >> function?
> >
> > Exactly. Bow, do you want to give this approach a try?
> (Assuming that there are no further objections from the
> other developers).
> 
> Just to be clear, we are:
> 
> * changing all module's doctest file path to use relative
> paths (with
> respect to the module's location),
> * replacing the run_doctest() import with a simpler doctest
> import and
> `doctest.testmod()` in each module having this doctest
> * resorting to setUp and tearDown in the DocTestSuite in
> `run_tests.py` so that each module / submodule can find
> their test
> files
> * and refactoring all string functions in Bio._utils to
> Bio.Phylo and
> Bio.SearchIO, so that we can remove Bio._utils,
> 
> right?
> 
> I'd be happy to give this a shot if everyone feels the same
> :).
> 
> Regards,
> Bow
>