NeuroBM/.pre-commit-config.yaml at main · ai-in-pm/NeuroBM · GitHub

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# Pre-commit configuration for NeuroBM
# See https://pre-commit.com for more information

repos:
  # General file checks
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.4.0
    hooks:
      - id: trailing-whitespace
        exclude: '\.md$'
      - id: end-of-file-fixer
      - id: check-yaml
        args: ['--unsafe']
      - id: check-json
      - id: check-toml
      - id: check-added-large-files
        args: ['--maxkb=10000']
      - id: check-case-conflict
      - id: check-merge-conflict
      - id: check-symlinks
      - id: debug-statements
      - id: detect-private-key
      - id: fix-byte-order-marker
      - id: mixed-line-ending
        args: ['--fix=lf']

  # Python code formatting
  - repo: https://github.com/psf/black
    rev: 23.7.0
    hooks:
      - id: black
        language_version: python3.12
        args: ['--line-length=88']

  # Import sorting
  - repo: https://github.com/pycqa/isort
    rev: 5.12.0
    hooks:
      - id: isort
        args: ['--profile', 'black', '--line-length=88']

  # Linting
  - repo: https://github.com/pycqa/flake8
    rev: 6.0.0
    hooks:
      - id: flake8
        args: ['--max-line-length=88', '--extend-ignore=E203,W503']
        additional_dependencies:
          - flake8-docstrings
          - flake8-bugbear
          - flake8-comprehensions
          - flake8-simplify

  # Type checking
  - repo: https://github.com/pre-commit/mirrors-mypy
    rev: v1.5.1
    hooks:
      - id: mypy
        additional_dependencies:
          - types-PyYAML
          - types-requests
          - types-setuptools
        args: ['--ignore-missing-imports']

  # Security checks
  - repo: https://github.com/PyCQA/bandit
    rev: 1.7.5
    hooks:
      - id: bandit
        args: ['-r', '.', '-f', 'json', '-o', 'bandit-report.json']
        exclude: 'tests/.*'

  # Jupyter notebook cleaning
  - repo: https://github.com/nbQA-dev/nbQA
    rev: 1.7.0
    hooks:
      - id: nbqa-black
        args: ['--line-length=88']
      - id: nbqa-isort
        args: ['--profile=black']
      - id: nbqa-flake8
        args: ['--max-line-length=88', '--extend-ignore=E203,W503,E402']

  # Clear notebook outputs
  - repo: https://github.com/kynan/nbstripout
    rev: 0.6.1
    hooks:
      - id: nbstripout

  # YAML formatting
  - repo: https://github.com/pre-commit/mirrors-prettier
    rev: v3.0.0
    hooks:
      - id: prettier
        types: [yaml]
        exclude: '\.github/.*'

  # Documentation checks
  - repo: https://github.com/pycqa/pydocstyle
    rev: 6.3.0
    hooks:
      - id: pydocstyle
        args: ['--convention=google']
        exclude: 'tests/.*'

  # Check for common mistakes
  - repo: https://github.com/pre-commit/pygrep-hooks
    rev: v1.10.0
    hooks:
      - id: python-check-blanket-noqa
      - id: python-check-blanket-type-ignore
      - id: python-no-log-warn
      - id: python-use-type-annotations
      - id: rst-backticks
      - id: rst-directive-colons
      - id: rst-inline-touching-normal

# Configuration
default_language_version:
  python: python3.12

ci:
  autofix_commit_msg: |
    [pre-commit.ci] auto fixes from pre-commit.com hooks

    for more information, see https://pre-commit.ci
  autofix_prs: true
  autoupdate_branch: ''
  autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
  autoupdate_schedule: weekly
  skip: []
  submodules: false