[Biopython-dev] ApplicationResult and generic_run obsolete?

Peter biopython at maubp.freeserve.co.uk
Tue Jul 7 09:41:10 UTC 2009

On Tue, Jul 7, 2009 at 9:20 AM, Bartek
Wilczynski<bartek at rezolwenta.eu.org> wrote:
> On Tue, Jul 7, 2009 at 12:04 AM, Brad Chapman<chapmanb at 50mail.com> wrote:
>>> I'm fine with deprecating ApplicationReslut.
>> Bartek, you just won the typo of the month contest hands down.
> Well, It's always motivating to see that people actually read your
> posts carefully ;)

I read it, but just chuckled to myself ;)

Brad wrote:
>> My vote is to document using subprocess and avoid creating our own
>> wrapper. No one has to learn a Biopython specific API for running
>> programs, and subprocess provides plenty of flexibility to get stdout,
>> stderr and return codes. For places where we feel like using subprocess
>> is tricky, additional documentation within Biopython should help those
>> encountering it for the first time. This gives us more time to work
>> on biology problems, and leaves the running programs problems up to
>> the greater Python community.

Exactly. I'm sure there will still be questions on the mailing list from
people about using subprocess, but if our documentation is done
well enough this shouldn't be too much of a burden.

Bartek wrote:
>  well, having such a documentation would be a great thing. I've just gone
> through the docs for subprocess module and it seems to be the layer unifying
> all those crazy different ways of spawning processes. It's a shame  I somehow
> missed that it's there since python 2.4... So now, after doing my homework and
> checking what has been going on in python since 2004, I think that Brad's idea
> is better. We have dropped support for 2.3, so we can try to move from
> Application.generic_run to subprocess.Popen instead of trying to
> provide our own wrapper.  We just need good docs.

That seems unanimous so far: Deprecate Bio.Application.generic_run,
and document using subprocess instead. Good :)

Are you all happy with just marking Bio.Application.generic_run and
Bio.Application.ApplicationResult as obsolete for Biopython 1.51, with
the deprecation warning added in Biopython 1.52?

We'll need to update the Tutorial too - which reminds me, could someone
go over the "Alignment Tools" bit (currently section 6.3) to see if I've
pitched this at about the right level? On re-reading it just now I found an
fixed several typos.


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