Enforce PEP8 standard

[BioGeek]

• Refactor so that pylint and flake8 local pass

$ black --check --diff .
All done! ✨ 🍰 ✨
71 files would be left unchanged.

$ flake8 .

• Setup pylint and flake8 github action

They can be found in .github/workflows/format-code_perform-tests_on_push-pr.yaml

Relevant lines:

• flake8: lines 42-44

• pylint: lines 46-54

• pinned tool install: lines 31-36

• matrix runs on Ubuntu/macOS/Windows with Python 3.10/3.11

• Setup pre-commit hooks

• Ensure same pylint, flake8 and BLACK versions for reproducibility

We pin them in one CI requirements file and reuse those pins locally and in GitHub Actions:

# requirements/requirements_ci-cd.txt
black[jupyter]==24.10.0
flake8==7.1.1
pre-commit==4.5.1
pylint==3.3.4
pytest==8.3.4

GitHub Actions installs that file before running the checks