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

[Wibowo Arindrarto]

Hi Michiel, everyone,

>>> I'd prefer if developers first write to the dev mailing list if they want to make any major changes, or changes that affect Biopython overall. It can be hard to understand the implications just from looking at a pull request, and there may be so many pull requests that the important ones may be missed anyway.

>>> I think it's OK to have a _utils submodule inside Bio.SearchIO. Since you are developing and maintaining that module, to a large degree it's up to you how you want to organize your code. For the same reason, for Bio.Phylo it's better to discuss with Eric Talevich first to see what he thinks.

Noted. I'm sorry that this is causing more headaches than it solves.
I'll be sure to notify the dev-mailing list for other similar changes.

>>> 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.

Indeed, the doctests functions are two simple small functions to make
it easier to run doctests. The first one looks up the test directory
(our Tests directory) and the second one simply executes the doctest.

Best,
Bow