.pre-commit-config.yaml

default_language_version:
  python: python3

repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.5.0
    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-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

  # python code formatting
  - repo: https://github.com/psf/black
    rev: 24.2.0
    hooks:
      - id: black
        args: [--line-length, "99"]

  # python import sorting
  - repo: https://github.com/PyCQA/isort
    rev: 5.13.2
    hooks:
      - id: isort
        args: ["--profile", "black", "--filter-files"]

  # python upgrading syntax to newer version
  - repo: https://github.com/asottile/pyupgrade
    rev: v3.15.0
    hooks:
      - id: pyupgrade
        args: [--py38-plus]

  # python docstring formatting
  - repo: https://github.com/myint/docformatter
    rev: v1.7.5
    hooks:
      - id: docformatter
        args:
          [
            --in-place,
            --wrap-summaries=99,
            --wrap-descriptions=99,
            --style=sphinx,
            --black,
          ]

  # python docstring coverage checking
  # - repo: https://github.com/econchick/interrogate
  #   rev: 1.5.0 # or master if you're bold
  #   hooks:
  #     - id: interrogate
  #       args:
  #         [
  #           --verbose,
  #           --fail-under=80,
  #           --ignore-init-module,
  #           --ignore-init-method,
  #           --ignore-module,
  #           --ignore-nested-functions,
  #           -vv,
  #         ]

  # python check (PEP8), programming errors and code complexity
  - repo: https://github.com/PyCQA/flake8
    rev: 7.0.0
    hooks:
      - id: flake8
        args:
          [
            "--extend-ignore",
            "E203,E402,E501,F401,F841,RST2,RST301",
            "--exclude",
            "logs/*,data/*",
          ]
        additional_dependencies: [flake8-rst-docstrings==0.3.0]

  # python security linter
  - repo: https://github.com/PyCQA/bandit
    rev: "1.7.7"
    hooks:
      - id: bandit
        args: ["-s", "B101,B301,B403,B311"]

  # # yaml formatting
  # - repo: https://github.com/pre-commit/mirrors-prettier
  #   rev: v4.0.0-alpha.8
  #   hooks:
  #     - id: prettier
  #       types: [yaml]
  #       exclude: "environment.yaml"

  # shell scripts linter
  - repo: https://github.com/shellcheck-py/shellcheck-py
    rev: v0.9.0.6
    hooks:
      - id: shellcheck

  # # md formatting
  # - repo: https://github.com/executablebooks/mdformat
  #   rev: 0.7.17
  #   hooks:
  #     - id: mdformat
  #       args: ["--number"]
  #       additional_dependencies:
  #         - mdformat-gfm
  #         - mdformat-frontmatter
  #         - mdformat-myst
  #         - mdformat-tables
  #         # - mdformat-toc
  #         # - mdformat-black
  - repo: https://github.com/igorshubovych/markdownlint-cli
    rev: v0.40.0
    hooks:
      - id: markdownlint
        args:
          - --disable=MD013 # Line length limitation
          # - --disable=MD029 # Line numbering in ordered list
          - --disable=MD033 # No inline html
          # - --disable=MD047

  # word spelling linter
  - repo: https://github.com/codespell-project/codespell
    rev: v2.2.6
    hooks:
      - id: codespell
        args:
          - --skip=logs/**,data/**,*.ipynb
          # - --ignore-words-list=abc,def
          - -w # Write changes automatically

  # jupyter notebook cell output clearing
  - repo: https://github.com/kynan/nbstripout
    rev: 0.7.1
    hooks:
      - id: nbstripout

  # jupyter notebook linting
  - repo: https://github.com/nbQA-dev/nbQA
    rev: 1.7.1
    hooks:
      - id: nbqa-black
        args: ["--line-length=99"]
      - id: nbqa-isort
        args: ["--profile=black"]
      - id: nbqa-flake8
        args:
          [
            "--extend-ignore=E203,E402,E501,F401,F841",
            "--exclude=logs/*,data/*",
          ]