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

[Peter]

On Tue, Dec 7, 2010 at 1:29 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
> 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.

Easily done if you haven't been looking at this code for a while ;)

>> 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.

OK, filename=True it is (default False).

https://github.com/biopython/biopython/commit/fd99b976d5775e35cd251a781fb601ffb6906014

Peter

P.S. As part of this work I've also started adding a minimal doctest
to each app wrapper to construct a command line but not actually
call it. These will then be run regardless of the dependency, and
check there are no stupid problems with the wrapper. e.g.
https://github.com/biopython/biopython/commit/6a93cb64e0211a9e061019220f96030871832f9e

The EMBOSS wrappers still need doctests. In hindsight the test
coverage here was a bit lacking.... test_Emboss.py covers a lot
but not all the wrappers.

Note I'm trying to make each example doctest moderately useful to
anyone trying to use the tool for the first time.