[Biopython-dev] Tutorial problems

Tiago Rodrigues Antao tra at popgen.net
Sat Dec 5 02:54:21 UTC 2015


I am converting the tutorial to jupyter notebooks and I have found a
few problems. I am too tired to put here an exhaustive list, but they
are of the following types:

1. Data download: data moved places or has a different content (seqio)
2. Visualization: Mostly affecting Bio.Phylo. With Python 3 I have to
monkey patch networkx, also networkx is suggesting that they might
discontinue in the future drawing functions

GenomeDiagram is also affected, but because of data download issues (I
do not think they are visualization/librariy problems)

I think we need to test data download on the tutorial from time to
time, and see if the results are still OK.


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