Step 3 of ruff integration: add ruff to CI (plus cleanup of different linter stages)

[GernotMaier]

Integrate ruff as linter and add it to pre-commit.

Cleanup of linters, see #942.

Pre-commit changes:

• removed flake8 from pre-commit (covered by ruff, see here)
• removed pylint from pre-commit (this is too slow for pre-commit; most of it is covered by ruff - anything not picked by ruff will by shown by the CI-linter workflow)
• removed isort from pre-commit (covered by ruff, see here)
• did not remove black (and do not use the ruff format as this introduces some changes)

Github action changes:

• remove flake8 from CI-unittest

Others

• removed flake8 from list of required packages
• removed actionlint, black from superlinter (already in pre-commit)
• removed flake8, isort from superlinter (already in ruff in pre-commit)
• removed markdownlint from superlinter (added to pre-commit in PR #940)
• replaced superlint yamllint by pre-commit yamllint

Closes #942.

[GernotMaier]

@VictorBarbosaMartins - please review only after #941 is merged to main (otherwise you review the same changes again)

[VictorBarbosaMartins]

I think we should talk to other groups in DPPS to check what is their approach in this regard. Perhaps repeating checks in the pre-commit hooks and ci linters is not a bad idea.

[GernotMaier]

I think we should talk to other groups in DPPS to check what is their approach in this regard. Perhaps repeating checks in the pre-commit hooks and ci linters is not a bad idea.

Wait - pre-commit is running as linter in CI-linter over all files (this is also how DPPS is doing it). So we are still using all the tools and do a full linting.

[GernotMaier]

Just to make the last point clearer: precommit is running over all files in Ci-linter.yml, see this line: https://github.com/gammasim/simtools/blob/6d10f5bf47956f9722d7a41062a223799944a9f7/.github/workflows/CI-linter.yml#L78

[GernotMaier]

Thanks @VictorBarbosaMartins