.pre-commit-config.yaml

default_language_version:
  python: python3.10

repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.4.0
    hooks:
      # list of supported hooks: https://pre-commit.com/hooks.html
      - id: trailing-whitespace
      - id: end-of-file-fixer
      - id: check-docstring-first
      - id: check-json
      - id: check-yaml
      - id: debug-statements
      - id: detect-private-key
      - id: check-executables-have-shebangs
      - id: check-toml
      - id: check-case-conflict
      - id: check-added-large-files
        args: ["--maxkb=10000"]
      - id: pretty-format-json
        args: ["--autofix"]
      - id: mixed-line-ending

  # python code formatting
  - repo: https://github.com/psf/black
    rev: 23.3.0
    hooks:
      - id: black

  # python import sorting
  - repo: https://github.com/PyCQA/isort
    rev: 5.12.0
    hooks:
      - id: isort
        args: ["--profile", "black", "--filter-files"]

  # python upgrading syntax to newer version
  - repo: https://github.com/asottile/pyupgrade
    rev: v3.3.1
    hooks:
      - id: pyupgrade
        args: [--py310-plus]

  # python docstring formatting
  - repo: https://github.com/myint/docformatter
    rev: v1.6.0
    hooks:
      - id: docformatter
        args: [--in-place]

  # python check (PEP8), programming errors and code complexity
  - repo: https://github.com/PyCQA/flake8
    rev: 6.0.0
    hooks:
      - id: flake8

  # yaml formatting
  - repo: https://github.com/pre-commit/mirrors-prettier
    rev: v3.0.0-alpha.6
    hooks:
      - id: prettier
        types: [yaml]

  # shell scripts linter
  - repo: https://github.com/shellcheck-py/shellcheck-py
    rev: v0.9.0.2
    hooks:
      - id: shellcheck

  # md formatting
  - repo: https://github.com/executablebooks/mdformat
    rev: 0.7.16
    hooks:
      - id: mdformat
        args: ["--number"]
        additional_dependencies:
          - mdformat-gfm
          - mdformat-tables
          - mdformat_frontmatter
          # - mdformat-toc
          # - mdformat-black

  # word spelling linter
  - repo: https://github.com/codespell-project/codespell
    rev: v2.2.4
    hooks:
      - id: codespell
        exclude: |
          (?x)^(
              poetry.lock|
              pyproject.toml
          )$
        additional_dependencies:
          - tomli

  # jupyter notebook cell output clearing
  - repo: https://github.com/kynan/nbstripout
    rev: 0.6.1
    hooks:
      - id: nbstripout

  # jupyter notebook linting
  - repo: https://github.com/nbQA-dev/nbQA
    rev: 1.7.0
    hooks:
      - id: nbqa-black
      - id: nbqa-isort
        args: ["--profile=black"]
      - id: nbqa-flake8
        args: ["--extend-ignore=E402,E203"]

  # python static type checking
  # Based on: https://jaredkhan.com/blog/mypy-pre-commit
  - repo: local
    hooks:
      - id: mypy
        name: mypy
        entry: ./run-mypy
        language: system
        types: [python]
        # use require_serial so that script
        # is only called once per commit
        require_serial: true