refactor: supply pre-commit-hooks and replace flake8+isort+black with ruff

[tedil]

A bit of a spring-cleaning PR:

1. provides a pre-commit hook configuration file which runs linting and formatting on git commit.
2. replaces the trinity of flake8, isort and black with ruff
3. fixed lints and re-formatted with ruff, which is why so many files are modified.

I initially only wanted to add the pre-commit hooks, but ... well, here we are, with 263 files modified due to formatting/lint fixes.

[github-actions]

• Please format your Python code with black: make black
• Please format your Snakemake code with snakefmt: make snakefmt
• Please organize your imports isorts: make isort
• Please ensure that your code passes flake8: make flake8

You can trigger all lints locally by running make lint

[coveralls]

coverage: 85.775% (+0.03%) from 85.742%
when pulling becdbba on pre-commit-hooks-and-ruff
into af961cc on main.

[tedil]

superseded by #496