[Biopython-dev] Tutorial

Peter Cock p.j.a.cock at googlemail.com
Sun Dec 13 13:03:02 UTC 2015

On Sat, Dec 12, 2015 at 9:40 PM, Tiago Antao <tra at popgen.net> wrote:
> Hi,
> Vincent Davis and me have been trying to convert the tutorial to
> notebook format.
> Currently I adapted a test script from Vincent and generated a
> travis.yml file
> https://travis-ci.org/tiagoantao/biopython-notebook
> We now have a framework to automatically test tutorial code as soon as
> it is translated to notebooks.


> There are a couple of things that I have noticed:
> 1. Some code is not being tested in the current tutorial framework (if
> that was the case then errors should have been raised - ex files that
> cannot be downloaded anymore)

Yes, none of the online tests are currently enabled. This would
be worth adding to the test_Tutorial.py framework. Also things
with command line dependencies.

If you spotted any untested example without dependencies,
please try adding the doctest comment markup to see if we
can expand the test_Tutorial.py coverage.

> 2. Some downloads are quite big and I suspect that we should try to
> make them smaller as they can be a big burden on users.

Some of these like the SeqIO indexing chapter uses the full
SwissProt file, or a one of the smaller GenBank divisions like
viruses (still multiple files). These are real world examples
of how you can use the indexing capabilities on large files -
and I had already tried to pick smaller datasets where possible.
If you can think of suitable alternatives here, that would be good.

What other big datasets are you thinking of here? That was
all that came to mind, but the Tutorial has a lot in it.


More information about the Biopython-dev mailing list