.pre-commit-config.yaml

default_language_version:
  python: python3

repos:
  # python code formatting
  - 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
      - 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: 25.1.0
    hooks:
      - id: black
        args: [--line-length, "99"]

  # python upgrading syntax to newer version
  - repo: https://github.com/asottile/pyupgrade
    rev: v3.19.1
    hooks:
      - id: pyupgrade
        args: [--py38-plus]

  # python check (PEP8), programming errors and code complexity
  - repo: https://github.com/PyCQA/flake8
    rev: 7.2.0
    hooks:
      - id: flake8
        args:
          [
            "--extend-ignore",
            "E203,E402,E501,F401,F722,F821,F841,RST2,RST301",
            "--exclude",
            "logs/*,data/*",
          ]
        additional_dependencies: [flake8-rst-docstrings==0.3.0]

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

  # html formatting and linting
  - repo: https://github.com/thibaudcolas/curlylint
    rev: v0.13.1
    hooks:
      - id: curlylint
        types: [html]
        files: "server/templates/.*\\.html$"
        args: ["--include=server/templates"]

  - repo: https://github.com/Riverside-Healthcare/djLint
    rev: v1.36.4
    hooks:
      - id: djlint-jinja
        types: [html]
        files: "server/templates/.*\\.html$"
        args: ["--reformat", "--indent", "4", "--profile", "jinja"]
      - id: djlint
        types: [html]
        files: "server/templates/.*\\.html$"
        args: [
          "--profile",
          "jinja",
          "--ignore",
          "H006,H013,H021"
        ]

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

  # bash and sbatch script formatter
  - repo: https://github.com/scop/pre-commit-shfmt
    rev: v3.11.0-1
    hooks:
      - id: shfmt
        args: ["-i", "4", "-ci", "-bn", "-sr"]
        types: [shell, bash]
        files: '\.(sh|bash|sbatch)$'

  # md formatting
  - repo: https://github.com/executablebooks/mdformat
    rev: 0.7.22
    hooks:
      - id: mdformat
        args: ["--number"]
        additional_dependencies:
          - mdformat-gfm
          - mdformat-tables
          - mdformat_frontmatter
          - linkify-it-py

  # word spelling linter
  - repo: https://github.com/codespell-project/codespell
    rev: v2.4.1
    hooks:
      - id: codespell
        args:
          - --skip=logs/**,data/**,*.ipynb
          - --ignore-words-list=crate

  # jupyter notebook cell output clearing
  - repo: https://github.com/kynan/nbstripout
    rev: 0.8.1
    hooks:
      - id: nbstripout

  # jupyter notebook linting
  - repo: https://github.com/nbQA-dev/nbQA
    rev: 1.9.1
    hooks:
      - id: nbqa-black
        args: ["--line-length=99"]
      - id: nbqa-isort
        args: ["--profile=black"]
      - id: nbqa-flake8
        args:
          [
            "--extend-ignore=E203,E402,E501,F401,F722,F841",
            "--exclude=logs/*,data/*",
          ]

  # - repo: local
  #   hooks:
  #     - id: forbid-internal-files
  #       name: Prevent committing files in internal/ directory
  #       entry: |
  #         bash -c 'files=$(git diff --cached --name-only --diff-filter=ACMRTUXB | grep "^internal/"); if [ -n "$files" ]; then echo "ERROR: Attempting to commit files in internal/ directory:" >&2; echo "$files" >&2; exit 1; fi'
  #       language: system
  #       stages: [commit]
  #       files: '^internal/'