ci: ruff format, isort, and lint

[kiyoon]

Instead of black/flake8/pylint, use ruff format, isort and lint as mentioned briefly in #406.

Changes:

1. precommit.sh to use ruff
2. github actions CI to check if ruff format and isort are applied. If not, show the diff in the summary.
3. ruff check --config ruff_essential.toml . to check essential syntax errors. (E9, F63, F7, F82)
4. Some settings in pyproject.toml, setup.cfg, ...
   a. move pytest config from pytest.ini to pyproject.toml
   b. move coverage config from setup.cfg to pyproject.toml
   c. use ruff format line-length of 79
   d. ruff lint rules
   e. pyright/basedpyright config (standard settings) to develop with a type checker

Build:

1. Correctly set python_requires (3.5 -> 3.8)
2. CI uses uv pip to install packages instead of pip for improved speed

Advantages:

• fast
• less dependencies (only one package compared to black, isort, flake8, pylint and extra dependencies they have)
• generally easier to config (sane defaults and good documentation in one place)

[kiyoon]

Applying ruff format and isort will change many files. Once you approve this PR, I will apply them all so it's easier to see what has actually changed!

So please don't merge just yet.

EDIT: The PR includes ruff format and isort now.

[kiyoon]

by the way, I plan to add more type information in the next PR.

If you mind having annotations import, we can remove the lint rule

[sobolevnrm]

by the way, I plan to add more type information in the next PR.

If you mind having annotations import, we can remove the lint rule

Yes, I do not want to import unused modules. Thank you!

[kiyoon]

I removed from __future__ import annotations and uv. Anything else?

[sobolevnrm]

Thank you for all of your work on this!

[kiyoon]

Thanks for reviewing! And I've rebased the #410 so it should be ready now as well :)