Switching GitHub Actions to uv

[ebezzam]

As the title says, the GitHub Actions have been updated to use uv, according to their recommendations.

Other changes:

• the linting workflow wasn't actually outputting an error if files weren't properly linted. I've added the --check flag to do this, and used ruff to reformat files locally (hence the many files changes)
• a few notebooks needed manual changes due to an ambiguous variable name (i.e. l)
• updated installation docs on how to install with uv

[GJBoth]

This is wonderful, thank you very much! Everything looks good, except I don't see the uv version pinned in the action? That would be the only change I'd like to see.

[ebezzam]

@GJBoth I've set the uv version in both workflows

[ebezzam]

@GJBoth thanks for merging. I saw that ruff failed on the main branch 🤔 I'm looking into it

[ebezzam]

Looks ruff just released yesterday a new version (0.9.0) with a breaking change which is what the GitHub Action on the main branch installed: https://github.com/chromatix-team/chromatix/actions/runs/12711344838/job/35434459952#step:5:48

While the one in my fork used 0.8.6: https://github.com/ebezzam/chromatix/actions/runs/12688474060/job/35365083147#step:5:48

Should we do a new commit to reformat with 0.9.0 or limit the version of ruff?

[diptodip]

Thanks @ebezzam!

[GJBoth]

@ebezzam Well that's bad luck if I ever saw it...
Since we're changing to uv anyway, let's go for 0.9.0? What do you think?

[ebezzam]

I agree. I'll make a new PR for that, and add some info on setting up pre-commit hooks so that formatting is better integrated in the workflow.