[JOSS REVIEW] Specify linting rules in a config file

[Zeitsperre]

In the workflows, there are linting calls that have flagged values (for flake8):

- name: Lint with flake8
  run: |
    # stop the build if there are Python syntax errors or undefined names
    flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
    # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
    flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics

It would be better to have these flake8 (or ruff) rules specified in a configuration file (flake8: .flake8/setup.cfg, ruff: pyproject.toml). The default values expected for cyclomatic complexity and line length can also be adjusted (for both projects).

Related: #121

Context: openjournals/joss-reviews#9688

[valeriupredoi]

hi @Zeitsperre indeed, I am moving us to pre-commit with Ruff in #173 and once that's all working I will remove flake8 linting, and will keep just the Ruff ruleset in 🍺