Improved pre-commit config: Jupyter Notebook linting, black incompatibility

[atong01]

Thanks for the excellent template. I've been working with notebooks for exploratory analysis. A couple things that could be improved with the current .pre-commit-config.yaml:

• The current pre-commit is incompatible with black formatting with W503 and E203. This could be added to ignore or as suggested here: https://stackoverflow.com/questions/68161741/python-black-formatter-conflict-with-rule-flake8-w503-in-vscode
  we could use --extend-ignore instead.

• The current .pre-commit-config.yaml performs code spell over files including Jupyter notebooks. This has some drawbacks as Jupyter notebooks are partially binary (i.e. can have embedded binary data) codespell can produce false positives in this area, and this is unlikely to be fixed upstream:
  Jupyter notebook filter to only spell check inside cell inputs codespell-project/codespell#2138
  For this I propose ignoring *.ipynb files for now.

• notebooks are not linted, which could be done with nbQA I suggest adding

  - repo: https://github.com/nbQA-dev/nbQA
    rev: 1.4.0
    hooks:
      - id: nbqa-black
        args: ["--line-length=99"]
      - id: nbqa-isort
        args: ["--profile=black"]
      - id: nbqa-flake8
        args: ["--extend-ignore=E402,E501,F401,F841", "--exclude=logs/*,data/*"]

[ashleve]

@atong01 Thanks a lot for looking into this and making a PR! These are very welcomed improvements for pre-commit.