library, docs & test updates

[chrstnbwnkl]

• Updates Python (at least 3.9 required now, 3.8 support was dropped)
• Dependency updates:
  • FastAPI
  • SQLModel
  • Pydantic (major version update, cause of a lot of the changes proposed by the PR)
• linting/formatting
  • ruff to replace flake8 (flake8 seems to be behind on some dependency updates anyway)
• Doc updates
• YAML/MD formatting was off
• Valhalla was complaining about GDAL not being found (I guess the base image has it so I just installed it)
• Test updates
  • dependency updates broke some of the tests because the error responses changed