Update supported Python versions to drop 3.6, include 3.9 and 3.10

[victorlin]

Description of proposed changes

This PR updates supported Python versions based on current EOL status.

• Add variable for Augur version associated with min Python version: 3f09747
• Update CI matrix and minimum version references: 65c736f
• Bump Augur version associated with min Python version to 14: 6451394

Note: I didn't update minimum version for biopython, since I'm not sure what we want to support. I'm thinking we bump from 1.67 to 1.73 like 3dd5160 (not in PR), would that be reasonable? We could also try a matrix based on this discussion.

Related issue(s)

• Bump minimum Python dependency to 3.7 #793

[codecov]

Codecov Report

Merging #822 (fc5b396) into master (058372d) will increase coverage by 0.01%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master     #822      +/-   ##
==========================================
+ Coverage   33.81%   33.83%   +0.01%     
==========================================
  Files          41       41              
  Lines        5905     5905              
  Branches     1466     1507      +41     
==========================================
+ Hits         1997     1998       +1     
+ Misses       3825     3824       -1     
  Partials       83       83              

Impacted Files	Coverage Δ
augur/import_beast.py	7.14% <0.00%> (+0.02%)	⬆️
augur/export_v2.py	11.00% <0.00%> (+0.14%)	⬆️

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[huddlej]

Looks good! We will also need to make a separate PR for the Bioconda recipe to update the minimum Python versions for host and run.

I like the idea of using a BioPython matrix (in a separate PR) instead of hardcoding a specific, for the reasons @tsibley lists in the discussion you linked to. The main issue being that we could have passing tests for the old version of BioPython but failing tests for newer versions.

As noted in the since_augur_version variable in setup.py, we will need a major release for this PR. Since #839 may also introduce a breaking change to the UI for augur tree, we might release these both at the same time in 14.0.0.

[victorlin]

@huddlej

We will also need to make a separate PR for the Bioconda recipe to update the minimum Python versions

At what stage in the release process should this happen? I assume it would be best to somehow link this to the auto-bump PR once we push the new version to pip, but we would have to be diligent to catch it before a maintainer merges. Or do they have a more manual process for major version changes?

[victorlin]

Nevermind, I see you answered my question a couple months ago in #793. I'll plan to open a draft PR in bioconda, then link it to the auto-bump PR once that happens. Shouldn't be difficult to catch it before they merge.