Update CI

[molpopgen]

• bump ubuntu image and python
• Remove version pins from requirements files
• Add requirements_CI.txt
• update remaining work flow files
• remove global locked file
• Add pinned requirements files
• use pinned requirements files in CI

[molpopgen]

@grahamgower -- This is all working other than codecov. The one test that needed updating was pretty straightforward as there was already a pytest warning filter in place. I just made the filter much stricter.

I think I should also squash this down to 1 commit before merging?

[grahamgower]

LGTM. It would be good to squash this at least a little, yeah. Feel free to merge when you're satisfied.

[grahamgower]

@molpopgen, If you rebase, then the codecov upload should now work.

Do we also need to bump the .github/mergify.yml file for dependabot to work again? Do you know if/how dependabot integrates with the uv method of managing requirements?

[molpopgen]

Do we also need to bump the .github/mergify.yml file for dependabot to work again? Do you know if/how dependabot integrates with the uv method of managing requirements?

I'll look into this. I seem to recall that github has opened an issue on this repo for one or more of our automated things.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.81%. Comparing base (a296850) to head (109392f).
Report is 3 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #583   +/-   ##
=======================================
  Coverage   99.81%   99.81%           
=======================================
  Files           5        5           
  Lines        1600     1600           
=======================================
  Hits         1597     1597           
  Misses          3        3           

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[molpopgen]

@grahamgower -- I squashed all previous commits and separately updated mergify.

As for uv, it only handles stuff in the Python ecosystem. AFAICT, it has no understanding of github work flows, etc..

[molpopgen]

@grahamgower -- I was hoping to have some way to actually test mergify but I have no idea how it works. I'm trying to find some kind of @mergify squash and rebase command but not having any luck with their docs.

[grahamgower]

I think it's one of those things that is only acted upon after it's committed in the repository.