[Biopython-dev] Jupyter notebook tutorial tests

Vincent Davis vincent at vincentdavis.net
Tue Dec 8 14:56:43 UTC 2015

Doing a little research on testing notebooks:

is not up-to-date, i.e. will not run with jupyter and maybe not with

I tested pytest-ipynb, it works but has 2 issues, 1, looks for files
starting with test_ 2, uses py.test.

Both of the above projects could possibly be modified to work.

A very simple option to verify the notebooks run (without error) is to just
run this command (you can provide a list of notebooks)

$ jupyter nbconvert --to notebook --execute "02 - Quick Start.ipynb"

If there is an error it will stop and report the error.

I am also trying to extract the source and result from a notebook (this is
easy) and insert them into a doctest. I have parts of this working thanks
to the python mailing list.

Vincent Davis
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython-dev/attachments/20151208/cd6b1b15/attachment.html>

More information about the Biopython-dev mailing list