[Biopython-dev] plink phasing and others

Peter Cock p.j.a.cock at googlemail.com
Mon Apr 16 15:18:10 UTC 2012

2012/4/16 Tiago Antão <tiagoantao at gmail.com>:
> Just a few practical things:
> 1. we still do not allow matplotlib dependencies, correct?

They would be run time dependencies, right? Not compile/build time?
We already have things like 'soft' dependencies on ReportLab and
NetworkX, and even matplotlib. It does complicate the unit tests a
bit to skip anything gracefully.

> 2. to what part of the name space should plink and phasing be added?

Unclear to me right now.

> 3. Are we on epidoc or sphinx? Or moving from one to the other?
> doctest is acceptable right?

We're still using LaTeX for the tutorial, and epydoc for the API docs.

Using doctest is acceptable and encouraged for documentation,
but be wary of cross platform differences. If you have a doctest
which has dependencies see test_wise.py rather than adding it
to run_tests.py

> 4. What is the current best way to run external applications? There
> was an application wrapper class in the past...

For simple Unix style applications controlled via the command line,
use the Bio.Application framework as in Bio.Align.Applications or
Bio.Sequencing.Applications, Bio.Phylo.Applications, or
Bio.Emboss.Applications (etc?).


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