.pre-commit-config.yaml

# See https://pre-commit.com for more information
# See https://pre-commit.com/hooks.html for more hooks
repos:
  - repo: https://github.com/kynan/nbstripout
    rev: 0.6.1
    hooks:
      - id: nbstripout
        name: nbstripout - Strip outputs from notebooks (auto-fixes)
        args:
          - --extra-keys
          - "metadata.colab metadata.kernelspec cell.metadata.colab cell.metadata.executionInfo cell.metadata.id cell.metadata.outputId"
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.4.0
    hooks:
      - id: check-added-large-files
        name: Check for files larger than 5 MB
        args: [ "--maxkb=5120" ]
      - id: end-of-file-fixer
        name: Check for a blank line at the end of scripts (auto-fixes)
        exclude: '\.Rd'
      - id: trailing-whitespace
        name: Check for trailing whitespaces (auto-fixes)
  - repo: https://github.com/pycqa/isort
    rev: 5.12.0
    hooks:
      - id: isort
        name: isort - Sort Python imports (auto-fixes)
        types: [ cython, pyi, python ]
        args: [ "--profile", "black", "--filter-files" ]
  - repo: https://github.com/psf/black
    rev: 23.3.0 # Replace by any tag/version: https://github.com/psf/black/tags
    hooks:
      - id: black
        name: black - consistent Python code formatting (auto-fixes)
        language_version: python # Should be a command that runs python3.6+
  - repo: https://github.com/PyCQA/flake8
    rev: 6.0.0
    hooks:
      - id: flake8
        name: flake8 - Python linting
  - repo: https://github.com/nbQA-dev/nbQA
    rev: 1.6.4
    hooks:
      - id: nbqa-isort
        name: nbqa-isort - Sort Python imports (notebooks; auto-fixes)
        args: [ --nbqa-mutate ]
        additional_dependencies: [ isort==5.8.0 ]
      - id: nbqa-black
        name: nbqa-black - consistent Python code formatting (notebooks; auto-fixes)
        args: [ --nbqa-mutate ]
        additional_dependencies: [ black==22.3.0 ]
      # TODO: Disabled for now until it's clear how to add noqa to specific cells of a Jupyter notebook
      #- id: nbqa-flake8
      #  name: nbqa-flake8 - Python linting (notebooks)
      #  additional_dependencies: [ flake8==3.9.2 ]