pyABC/.pre-commit-config.yaml at main · ICB-DCM/pyABC · GitHub

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############################
# Pre-commit configuration #
############################

# Install via `pip install pre-commit`

# This is run as a precondition to commits, run manually via `pre-commit run`

# When adding new hooks, it may make sense to once run
# `pre-commit run --all-files` as by default only changed files are checked

repos:
  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.8.4
    hooks:
      # Run the linter
      - id: ruff
        args: [--fix, --exit-non-zero-on-fix]
        description: Fast Python linter
      # Run the formatter
      - id: ruff-format
        description: Fast Python formatter

  # Notebook formatting with nbQA + ruff
  - repo: https://github.com/nbQA-dev/nbQA
    rev: 1.9.1
    hooks:
      - id: nbqa-ruff
        args: [--fix, --exit-non-zero-on-fix]
      - id: nbqa-pyupgrade
        args: [--py310-plus]

  # Standard pre-commit hooks
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v5.0.0
    hooks:
      - id: check-yaml
        description: Check yaml files for parseable syntax
      - id: check-toml
        description: Check toml files for parseable syntax
      - id: check-added-large-files
        description: Prevent large files from being committed
        args: ['--maxkb=1000']
      - id: check-merge-conflict
        description: Check for files that contain merge conflict strings
      - id: check-symlinks
        description: Check for symlinks which do not point to anything
      - id: trailing-whitespace
        description: Trim trailing whitespaces
        exclude: ^test/
      - id: end-of-file-fixer
        description: Fix empty lines at ends of files
        exclude: ^test/
      - id: detect-private-key
        description: Detects the presence of private keys
      - id: check-case-conflict
        description: Check for files with case-insensitive name conflicts
      - id: mixed-line-ending
        description: Ensure consistent line endings
        args: ['--fix=lf']

# Configuration
default_language_version:
  python: python3.13

# Global exclusions
exclude: |
  (?x)^(
      \.git/|
      \.tox/|
      \.venv/|
      venv/|
      build/|
      dist/|
      .*\.egg-info/|
      __pycache__/|
      \.pytest_cache/|
      \.mypy_cache/|
      \.ruff_cache/|
      doc/_build/
  )