Update to python 3.9

[MrCreosote]

Needed to update a few libraries for compatibility

Also minor simplifications to a test fixture

[lgtm-com[bot]]

This pull request introduces 2 alerts when merging 1b1560b3e951316f4e971e0339d187275c3fa611 into 19abc6b84df9a8b796ca17fa2bfafcbe39fdfe77 - view on LGTM.com

new alerts:

• 2 for Module is imported with 'import' and 'import from'

[MrCreosote]

LGTM is complaining about files this PR doesn't touch

[bio-boris]

Might as well upgrade it to 3.9, it works for me for FROM python:3.9

[MrCreosote]

I did 3.8 because 3.9 isn't in apt for my distribution yet, and the features I want are in 3.7. If I need 3.9 I'll go through the hassle of installing a ppa then

[bio-boris]

I'm in favor of taking it all the way to 3.9 if we are upgrading python. It shouldn't take more than a few minutes to install miniconda for 3.9, setup a virtualenv and install requirements.txt, or to just use the python in the docker container. I don't think we have any policy on upgrading services based on using python versions with the latest EOL vs developer convenience, but otherwise the PR looks fine and deployed to CI

[MrCreosote]

I wouldn't touch *conda if you served it to me on a skewer with hollandaise sauce. Several times bitten, several times shy

[sonarcloud[bot]]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[MrCreosote]

Turns out I need features in 3.9 as well, so you get your wish

[lgtm-com[bot]]

This pull request introduces 2 alerts when merging 9774dd2e265ce12e6d6eb83d4b000b3e338bc2a7 into 19bdd194e8e3eeaccc478423d3354661256c342e - view on LGTM.com

new alerts:

• 2 for Module is imported with 'import' and 'import from'