.pre-commit-config.yaml

default_language_version:
  python: python3

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: check-case-conflict # checks for files that would conflict in case-insensitive file systems
      - id: check-docstring-first # checks a common error of defining a docstring after code
      - id: check-executables-have-shebangs # ensures that (non-binary) executables have a shebang
      - id: check-shebang-scripts-are-executable # ensures that (non-binary) files with a shebang are executable
      - id: check-merge-conflict # checks for files that contain merge conflict strings
      - id: check-symlinks # checks for symlinks which do not point to anything
      - id: check-toml # checks toml files for parseable syntax
      - id: check-yaml # checks yaml files for parseable syntax
      - id: debug-statements # checks for debugger imports and py37+ `breakpoint()` calls in python source
      - id: detect-private-key # detects the presence of private keys
      - id: end-of-file-fixer # ensures that a file is either empty, or ends with one newline
      - id: mixed-line-ending # replaces or checks mixed line ending
      - id: name-tests-test # verifies that test files are named correctly
      - id: trailing-whitespace # trims trailing whitespace

  # python linter and formatter, also handles upgrading python code to latest version
  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.1.15
    hooks:
      - id: ruff
      - id: ruff-format

  # python security linter
  - repo: https://github.com/PyCQA/bandit
    rev: "1.7.5"
    hooks:
      - id: bandit
        args: ["-s", "B101"]

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

  # word spelling linter
  - repo: https://github.com/codespell-project/codespell
    rev: v2.2.4
    hooks:
      - id: codespell
        args:
          - --skip=data/**,logs/**,*.bib,*.js
          - --ignore-words-list=ans

  # python docstring coverage checking
  - repo: https://github.com/econchick/interrogate
    rev: 1.5.0 # or master if you're bold
    hooks:
      - id: interrogate
        args: [-vv, --config=pyproject.toml, src/, --fail-under, "100"]
        pass_filenames: false

  # 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

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

  # 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
        args: ["--line-length=120"]
      - id: nbqa-isort
        args: ["--profile=black"]
      - id: nbqa-flake8
        args:
          [
            "--exclude=data/*,logs/*",
            "--extend-ignore=E402",
            "--max-line-length=120",
          ]

  # python type checker
  - repo: https://github.com/mattseymour/pre-commit-pytype
    rev: 2023.5.8
    hooks:
      - id: pytype
        args: ["--disable", "import-error,not-supported-yet", "-n", "auto"]