Standardizing code formatting and linting; modernizing package installation

[lucaspar]

I'm opening this PR onto a refactoring branch as I'd like to add more tests to make sure the repo is in a better state before merging to main, but I'm open to your feedback, and we can discuss each of these changes.

Summary

• Standardized linting and code formatting;
• Fixed (most) linter warnings;
• Added type annotations;
• Modernized packaging by moving some attributes from setup.py to pyproject.toml (we can probably remove setup.py entirely if we switch from setuptools to hatch).
• Switched logging to loguru, which is more informative (file, method, line number), colorful, and requires no setup.
• Unified Shepherd terminology to match SADE configuration task(s) -> service(s).
  • I'm not sure about this one, and we can make "task" the preferred term if a "service" is a kind of "task". It's just something that was confusing when reading the code and config files, so I think we should settle on one preferred term to describe this unit.
  • ha, I just noticed your latest commit was renaming them to task; I can do the same here, then. Let's talk after the break.
• Added project instructions to run it with uv, which should be simpler and faster than pip or conda.
• Added --work-dir and --run-dir to make it explicit where Shepherd executes scripts from and where it creates output files. run here refers to a SADE Simulation Run, and it could be renamed before this is merged with main.
• Example #3 is working right now, but I'd like to formalize it as a test case to detect regressions.

Minimum Python version

Minimum Python version is 3.10 (type hints fail on 3.9, possibly other things do too). You can try it with this one-liner:

uv run --python=3.10 examples/example3/run_test.sh
# uv run also installs all dependencies and even the 3.10 interpreter if needed

And the most recent stable Python version:

uv run --python=3.13 examples/example3/run_test.sh