.pre-commit-config.yaml

# Install the pre-commit hooks below with
# 'pre-commit install'

# Run the hooks on all files with
# 'pre-commit run --all'

repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.4.0
    # See: https://pre-commit.com/hooks.html
    hooks:
    -   id: trailing-whitespace
        types: [python]
        exclude: ^notebooks($|/.*)  # Avoids Jupytext sync problems
    -   id: check-case-conflict
    -   id: end-of-file-fixer
    -   id: check-merge-conflict
    -   id: check-yaml
    -   id: check-added-large-files
        args: ['--maxkb=5000']
    -   id: end-of-file-fixer
    -   id: mixed-line-ending
    # add black
  - repo: https://github.com/psf/black
    rev: 23.3.0
    hooks:
      - id: black
        language_version: python3
        exclude: ^notebooks($|/.*) 
        # args: [--line-length 79]
    # add isort
  # TODO: does not work with black
  # - repo: https://github.com/pycqa/isort
  #   rev: 5.12.0
  #   hooks:
  #     - id: isort
  #       name: isort
  #       exclude: ^notebooks($|/.*) 
    # Run flake8. Give warnings, but do not reject commits
  - repo: https://github.com/pycqa/flake8
    rev: 6.0.0
    hooks:
      - id: flake8
        exclude: ^notebooks($|/.*) 
        additional_dependencies: [flake8-bugbear, flake8-print]
    # Enforce that notebooks outputs are cleared
  - repo: https://github.com/kynan/nbstripout
    rev: 0.6.1
    hooks:
      - id: nbstripout
  # notebook checks
  - repo: https://github.com/nbQA-dev/nbQA
    rev: 1.7.0
    hooks:
      - id: nbqa-black
        args: [--nbqa-mutate, --nbqa-dont-skip-bad-cells]
        additional_dependencies: [black==22.3.0]
      - id: nbqa-isort
        args: [--nbqa-mutate, --nbqa-dont-skip-bad-cells]
        additional_dependencies: [isort==5.6.4]
      - id: nbqa-flake8
        args: [--nbqa-dont-skip-bad-cells, "--extend-ignore=E402,E203"]
        additional_dependencies: [flake8==3.8.3]
   # Synchronize notebooks and paired script versions
  - repo: https://github.com/mwouts/jupytext
    rev: v1.14.1
    hooks:
      - id: jupytext
        name: jupytext
        description: Runs jupytext on all notebooks and paired files
        language: python
        entry: jupytext --pre-commit-mode --set-formats "ipynb,py:percent"
        require_serial: true
        types_or: [jupyter, python]
        files: ^notebooks($|/.*)  # Only apply this under notebooks/