pyproject: sync with mesa/mesa and ensure tests run against GitHub repo

[annapurna-gupta]

Closes mesa/mesa#2782 (pyproject sync checklist item)

Changes:

• Add allow-direct-references = true for hatchling
• Sync ruff target-version to py312
• Add codespell section
• Add extend-exclude = ["build"] to ruff
• Install mesa from GitHub main in all test dependency groups

[EwoutH]

Thanks for the PR. Could you explain all changes in the PR description?

I think most of this makes sense. @quaquel, do you see anything weird?

[annapurna-gupta]

Thanks for the PR. Could you explain all changes in the PR description?

I think most of this makes sense. @quaquel, do you see anything weird?

Thanks for the review!

1. Added allow-direct-references = true so that dependencies specified via Git URLs can be used.
2. Sync Ruff target-version to py312 — synced from mesa/mesa main so that linting rules stay consistent.
3. Add ignore-words-list for codespell — synced from mesa/mesa main to ensure consistent spell-check behavior.
4. Add extend-exclude = ["build"] — tells Ruff to skip the auto-generated build/ folder so it only checks actual source code.
5. Install Mesa from GitHub main in all test dependency groups — this ensures tests run against the latest Mesa development version rather than a potentially outdated PyPI release.