Add isort-related checks to ruff

[dalonsoa]

And re-run ruff in all files.

There are a lot of things changed that should have been changed when applying ruff the previous time. I'm not entirely sure if those changes were not implemented in full or if there have been additions afterwards modifying that or using a different set of rules (nor ruff). Is everyone using pre-commit hooks? I strongly recommend to do so, to ensure the repo code style is kept.

I've also updated the lint.yml action to be more thorough as I don't think it was running at all, otherwise these would have been catch.

Fixes ImperialCollegeLondon#9

[dalonsoa]

852c19c is actually running the tool - and all the resulting changes. The other 4 is about updating the configuration.

[plasorak]

What exactly is the pre-commit hook doing? Is this adding a commit after each PR to run isort?

[jamesturner246]

Hi @plasorak.

Devs set themselves up by running pre-commit install to install the hooks. From then on, pre-commit runs all installed hooks right when calling git commit. If hooks return failure, then the commit is rejected and the dev must fix the issue.

Some, like ruff, are smart enough to automatically make fixing changes. In which case you would just git add again the files auto-fixed by ruff, and then git commit again.

[dalonsoa]

@plasorak , as @jamesturner246 says, pre-commit does not change or add commits, but rather ensures that any commit follows whatever standards are defined, preventing the commit from being created until the issues are resolved.

drunc already contains a pre-commit-config.yaml indicating the checks to run on every commit only on the files modified by the commit. In this case, we only run ruff, but in other repositories (eg. in drunc_ui itself) we run lots of stuff, from formatting other file types to spell checking.

This is supported by a properly set CI workflow, which was not in this case. As mentioned in the PR description, this PR fixes that and ensures ruff is run correctly.