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

[Peter Cock]

On Tue, Jan 29, 2013 at 9:54 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>
>> As for the doctest-related functions, do you propose to move
>> them to a specific doctest-related module as well?
>
> For the doctest-related functions, we first need to understand
> what the purpose is, before deciding how to implement it (and
> in what module the code should be).

When editing doctests, it is convenient to be able to run them on
the current file, e.g.

~/biopython $ emacs Bio/SeqRecord.py
~/biopython $ python Bio/SeqRecord.py

Or,

~/biopython/Bio $ emacs SeqRecord.py
~/biopython/Bio $ python SeqRecord.py

To do that, many of our modules had a repeated bit of code at
the bottom, now moved to a shared function in Bio/_utils.py
resulting in a lot less boiler plate code, e.g.

https://github.com/biopython/biopython/commit/8b59d89bb4e282192ddee751e24ceef4afa63528

Bow had initially done this for the doctests in Bio.SearchIO,
but I agreed it make sense to do this elsewhere.

Peter