[Biopython-dev] Changing the details of the app wrapper private API

[Brad Chapman]

Peter;

[New application wrapper internals]

> Thanks for looking it over - I've take that as an approval and committed it:
> https://github.com/biopython/biopython/commit/6957dd51be97e3cc258a36ca0904d5cbfd0de328

Great. Thanks again for taking this on.

> What are your thoughts regarding the types=["file"] stuff? Should we
> leave it, replace it with a boolean, or look at the subclass route?
> Other useful subclasses as well as a _FileOption include things like
> _IntegerOption and _FloatOption (although the later is interesting
> with things like "1e-10" which BLAST accepts for example, but not
> all tools taking float arguments would like that).

It might be easiest just to dump that. My initial idea behind this
was that if you label things with their output type, they could be
processed specifically downstream in a pipeline. This was probably
way too ambitious, and it might be simpler to keep it lightweight.
The application wrappers are working better as a simple way to
specify a command line.

Brad