calibrax/.pre-commit-config.yaml at main · avitai/calibrax · GitHub

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ci:
  autofix_prs: false
  autoupdate_schedule: weekly

repos:
  # Sort pyproject.toml keys for consistency
  - repo: local
    hooks:
      - id: sort_pyproject
        name: sort pyproject.toml
        entry: toml-sort
        args: [--in-place, --all]
        files: pyproject\.toml
        language: python
        additional_dependencies: ["toml-sort==0.23.1"]

  # Standard pre-commit hooks
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v5.0.0
    hooks:
      - id: trailing-whitespace
      - id: end-of-file-fixer
      - id: check-yaml
        exclude: mkdocs\.yml
      - id: check-added-large-files
        args: [--maxkb=2000]
      - id: check-merge-conflict
      - id: check-toml
      - id: check-json
      - id: debug-statements
      - id: mixed-line-ending

  # Ruff linter and formatter
  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.14.8
    hooks:
      - id: ruff
        args: [--fix, --unsafe-fixes]
        types_or: [python, pyi, jupyter]
      - id: ruff-format
        types_or: [python, pyi, jupyter]

  # Local ruff checks mirroring CI
  - repo: local
    hooks:
      - id: ruff-docstring-whitespace
        name: ruff docstring whitespace autofix
        entry: ruff
        args: [check, --fix, "--select=W291,W292,W293,F841", src/, tests/]
        language: system
        types: [python]
        pass_filenames: false

      - id: ruff-github-actions-check
        name: ruff (github actions output)
        entry: uv
        args: [run, ruff, check, --output-format=github]
        language: system
        types: [python]
        pass_filenames: false

      - id: ruff-critical-check
        name: ruff critical checks
        entry: ruff
        args: [check, "--select=RUF005,B904,F821,F822,F823", src/, tests/]
        language: system
        types: [python]
        pass_filenames: false

      - id: check-file-length
        name: check-file-length (warn >1500, fail >2000 lines)
        entry: bash
        args:
          - -c
          - |
            for file in "$@"; do
              lines=$(wc -l < "$file" 2>/dev/null || echo 0)
              if [ "$lines" -gt 2000 ]; then
                echo "ERROR: $file has $lines lines (limit: 2000)"
                exit 1
              elif [ "$lines" -gt 1500 ]; then
                echo "WARNING: $file has $lines lines (approaching limit of 2000)"
              fi
            done
          - --
        language: system
        types: [python]
        exclude: ^tests/

  # Type checking with pyright
  - repo: https://github.com/RobertCraigie/pyright-python
    rev: v1.1.403
    hooks:
      - id: pyright
        args: [--warnings, src]
        pass_filenames: false
        additional_dependencies:
          - beartype>=0.14
          - click>=8.0
          - flax>=0.12.0
          - jax>=0.4.0
          - jaxlib>=0.4.0
          - jaxtyping>=0.2.20
          - matplotlib>=3.8
          - numpy>=1.24
          - psutil>=5.9.5
          - pytest>=8.3
          - scipy>=1.10
          - types-psutil>=5.10
          - typing_extensions>=4.5
          - wandb>=0.18

  # Security scanning
  - repo: https://github.com/PyCQA/bandit
    rev: "1.8.6"
    hooks:
      - id: bandit
        args: [-c, pyproject.toml]
        additional_dependencies: ["bandit[toml]"]
        exclude: ^(tests|examples)/

  # Docstring quality
  - repo: https://github.com/pycqa/pydocstyle
    rev: "6.3.0"
    hooks:
      - id: pydocstyle
        additional_dependencies: ["pydocstyle[toml]"]
        exclude: ^(tests|scripts|examples)/

  # Notebook linting via nbQA
  - repo: https://github.com/nbQA-dev/nbQA
    rev: 1.9.1
    hooks:
      - id: nbqa-ruff
        args: [--fix]

  # Shell script linting
  - repo: https://github.com/shellcheck-py/shellcheck-py
    rev: v0.10.0.1
    hooks:
      - id: shellcheck
        args: [-e, SC1091]