.pre-commit-config.yaml

default_language_version:
  python: python3.10

ci:
  autofix_prs: true
  autoupdate_commit_msg: "[pre-commit.ci] pre-commit suggestions"
  autoupdate_schedule: quarterly
  # submodules: true

repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v5.0.0
    hooks:
      # list of supported hooks: https://pre-commit.com/hooks.html
      - id: trailing-whitespace
      - id: end-of-file-fixer
        exclude: ".bumpversion.cfg"
      - 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: 24.10.0
    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: v3.17.0
    hooks:
      - id: pyupgrade
        args: [--py38-plus]

  # python docstring formatting
  - repo: https://github.com/myint/docformatter
    rev: 06907d0267368b49b9180eed423fae5697c1e909
    hooks:
      - id: docformatter
        args: [--in-place, --wrap-summaries=99, --wrap-descriptions=99]

  # python check (PEP8), programming errors and code complexity
  - repo: https://github.com/PyCQA/flake8
    rev: 7.1.1
    hooks:
      - id: flake8
        args:
          [
            "--extend-ignore",
            "E203,E402,E501,F401,F841",
            "--exclude",
            "logs/*,data/*",
          ]

  # python security linter
  - repo: https://github.com/PyCQA/bandit
    rev: "1.7.10"
    hooks:
      - id: bandit
        args: ["-s", "B101"]

  # yaml formatting
  - repo: https://github.com/pre-commit/mirrors-prettier
    rev: v2.7.1
    hooks:
      - id: prettier
        types: [yaml]
        language_version: 17.9.0

  # shell scripts linter
  - repo: https://github.com/shellcheck-py/shellcheck-py
    rev: v0.10.0.1
    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-tables
          - mdformat_frontmatter

  # word spelling linter
  - repo: https://github.com/codespell-project/codespell
    rev: v2.3.0
    hooks:
      - id: codespell
        args:
          - --skip=logs/**,data/**,*.ipynb,**/pdm.lock
          - --ignore-words-list=ADN,adn

  # 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: 1.8.7
    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/*",
          ]

  - repo: https://github.com/dosisod/refurb
    rev: v2.0.0
    hooks:
      - id: refurb
        language_version: python3.10
        args:
          - --ignore
          - FURB120
          - --ignore
          - FURB123

  - repo: https://github.com/asottile/blacken-docs
    rev: 1.19.0
    hooks:
      - id: blacken-docs
        args: [--line-length=120]