Merge setup.cfg into pyproject.toml and use dependency groups (#316)

[jaideepkathiresan]

This PR addresses Issue #316

Summary of Changes

1. Migrated all configuration from setup.cfg into pyproject.toml
2. Removed setup.cfg
3. Preserved all project metadata
4. Organized developer dependencies using PEP 735 dependency groups

[samcunliffe]

Thanks a lot for your first contribution, @jaideepkathiresan! 👋

I'm pretty confident we need to tweak the tox.ini to get tox to run the correct thing (dependency groups), then remove the old style [project.optional-dependencies].

Thanks for the work so far, sorry for the slight scope-drift. It's a bit of a bigger task than I first thought. Absolutely no worries if you don't have the capacity for this, just let us know and one of us will pick it up!

[jaideepkathiresan]

Hi @samcunliffe, thanks you so much for the feedback! Yeah, I guess for the current scope, you could assign someone else, I am also kind of occupied with something.
Thank-you so much @samcunliffe for reviewing, happy to have contributed the initial PR!

[samcunliffe]

@dstansby

As written, this solves the ticket. And I've pushed some commits to @jaideepkathiresan's branch so I probably shouldn't approve myself.

Follow up thoughts:

• We might want to merge tox.ini into pyproject.toml and also use tox-uv in the workflow (it's not too bad: rough proof of concept).
• We might want to drop tox entirely from our tools.
• We might want to switch to uv in the actions workflows and elsewhere.

Fixed, but not approving myself.