@ruebot I wonder if you are willing to give this a test run on Ubuntu given the instructions we have in the README? No rush.

Sure!

Feel free to try out some different collections as well. It should just be a matter of adding the files to the data folder and changing coll_id to whatever. (When we I create the view in AUK, I'm going to change the default folder to ./)

No dice getting past the "Setup" cell. Biggest difference in the versions of the required libraries is matplotlib at 3.0.3. Can you verify what you have on your end with pip show matplotlib?

Local desktop, Ubuntu 18:04

• Python 3.6.7
• jupyter 1.0.0
• ggplot 0.11.5
• matplotlib 3.0.3
• numpy 1.16.0
• pandas 0.24.1
• networkx 2.2
• nltk 3.4

Clean Ubuntu 18.04 VM:

• Python 3.7.2
• jupyter 1.0.0
• ggplot 0.11.5
• matplotlib 3.0.3
• numpy 1.16.2
• pandas 0.24.1
• networkx 2.2
• nltk 3.4

We also might want to consider creating a Dockerflle for this since we're going to have these problems all over the place. I'm happy to do this if y'all want.

Forgot to add this:

$ pip install matplotlib==1.15.1
Collecting matplotlib==1.15.1
  Could not find a version that satisfies the requirement matplotlib==1.15.1 (from versions: 0.86, 0.86.1, 0.86.2, 0.91.0, 0.91.1, 1.0.1, 1.1.0, 1.1.1, 1.2.0, 1.2.1, 1.3.0, 1.3.1, 1.4.0, 1.4.1rc1, 1.4.1, 1.4.2, 1.4.3, 1.5.0, 1.5.1, 1.5.2, 1.5.3, 2.0.0b1, 2.0.0b2, 2.0.0b3, 2.0.0b4, 2.0.0rc1, 2.0.0rc2, 2.0.0, 2.0.1, 2.0.2, 2.1.0rc1, 2.1.0, 2.1.1, 2.1.2, 2.2.0rc1, 2.2.0, 2.2.2, 2.2.3, 2.2.4, 3.0.0rc2, 3.0.0, 3.0.1, 3.0.2, 3.0.3)
No matching distribution found for matplotlib==1.15.1

Hi Nick: Here's what I have for "pip show matplotlib"

Name: matplotlib
Version: 3.0.2
Summary: Python plotting package
Home-page: http://matplotlib.org
Author: John D. Hunter, Michael Droettboom
Author-email: matplotlib-users@python.org
License: BSD
Location: /usr/local/lib/python3.7/site-packages
Requires: python-dateutil, cycler, kiwisolver, numpy, pyparsing
Required-by: ggplot

Also - I think Dockerfile is a great idea once we get everything figured out. If you could take that on, it would be great, since I'd have to read a lot of Dockermentation to do same.

Ok. So the matplotlib version is off in the README. Can you verify the other version numbers here, and then I'll start on a Docker image.

Will do. Just a note: Ian did the README, so Matplotlib 1.15.1 may have worked for him. Probably worth moving to 3 anyway though.

Only differences I have are:
numpy 1.15.1
pandas 0.23.4

Dockerfile and instructions added in docker branch.

We need to sort out some issues still, this will be the best place to do it so it just works... or well, works in a controlled Docker environment for everybody that can use it.

Locally, I hacked ggplot to fix the issue. I think we should just drop ggplot, as it will always be behind the scipy libraries. The notebook is not using it now.

Let’s drop ggplot then if nothing is using it?

ggplot removed in #12

Resolved with e880b87