.pre-commit-config.yaml

default_language_version:
  python: python3

exclude: "sample_data|docs/MIMIC_IV_tutorial/wandb_reports"

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-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, "800"]

  # python code formatting
  - repo: https://github.com/psf/black
    rev: 23.7.0
    hooks:
      - id: black
        args: [--line-length, "110"]

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

  - repo: https://github.com/PyCQA/autoflake
    rev: v2.2.0
    hooks:
      - id: autoflake

  # python upgrading syntax to newer version
  - repo: https://github.com/asottile/pyupgrade
    rev: v3.10.1
    hooks:
      - id: pyupgrade
        args: [--py310-plus]

  # python docstring formatting
  - repo: https://github.com/myint/docformatter
    rev: v1.7.5
    hooks:
      - id: docformatter
        args: [--in-place, --wrap-summaries=110, --wrap-descriptions=110]

  # python check (PEP8), programming errors and code complexity
  - repo: https://github.com/PyCQA/flake8
    rev: 6.1.0
    hooks:
      - id: flake8
        args:
          [
            "--max-complexity=10",
            "--extend-ignore",
            "E402,E701,E251,E226,E302,W504,E704,E402,E401,C901,E203",
            "--max-line-length=110",
            "--exclude",
            "logs/*,data/*",
            "--per-file-ignores",
            "__init__.py:F401",
          ]

  # yaml formatting
  - repo: https://github.com/pre-commit/mirrors-prettier
    rev: v3.0.3
    hooks:
      - id: prettier
        types: [yaml]
        exclude: "environment.yaml"

  # shell scripts linter
  - repo: https://github.com/shellcheck-py/shellcheck-py
    rev: v0.9.0.5
    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
          - mdformat-myst
          - mdformat-black
          - mdformat-config
          - mdformat-shfmt

  # word spelling linter
  - repo: https://github.com/codespell-project/codespell
    rev: v2.2.5
    hooks:
      - id: codespell
        args:
          - --skip=logs/**,data/**,*.ipynb,*.bib,env.yml,env_cpu.yml,*.svg,poetry.lock
          - --ignore-words-list=ehr

  # 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=110"]
      - id: nbqa-isort
        args: ["--profile=black"]
      - id: nbqa-flake8
        args:
          [
            "--extend-ignore=E203,E402,E501,F401,F841",
            "--exclude=logs/*,data/*",
          ]