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

[Brad Chapman]

Peter;

[Internal Application API]

> As you just suggested ("just dump that..."), I did (earlier today)
> remove the "input" and "output" labels given to the parameters
> via the types argument. These were only used in the old
> ApplicationResult object (deprecated and just removed after
> the release of Biopython 1.56). In addition to these two now
> useless tags (input and output), there was one other tag "file",
> and that is still present and used in most if not all the wrappers.
> 
> It is being used for some important functionality - supporting
> nasty filenames, in particular those with spaces in them. 

Cool, sorry I totally missed this use of the types argument. Glad 
it's actually being useful for something.

> I want to keep this functionality, but change the current
> interface - which is to use types=["file"] or the default of
> types=[]. The simplest option is to replace it with a
> boolean (e.g. filename=True, or auto_quote=True).

Definitely a good idea +1 for the filename=True argument to turn on
quoting. This makes it more clear what is happening, and does give
you room in case we need other adjustments in the future. I like
this better than subclassing, since hopefully it's a limited case
and we won't have to do too much manual adjustment of input
parameters.

Thanks again for tackling this,
Brad