.pre-commit-config.yaml

default_language_version:
  python: python3.10
repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.5.0
    hooks:
      - id: check-yaml
      - id: end-of-file-fixer
      - id: trailing-whitespace
        exclude: '\.txt|\.tsv$'
      - id: check-case-conflict
      - id: check-merge-conflict
      - id: detect-private-key
      - id: debug-statements
      - id: check-added-large-files
        exclude: '\.*.interval_list|test/data/large_cohort/compressed_dirs/.*'

  - repo: https://github.com/populationgenomics/pre-commits
    rev: "v0.1.3"
    hooks:
      - id: cpg-id-checker

  - repo: https://github.com/ambv/black
    rev: 24.3.0
    hooks:
      - id: black

  - repo: https://github.com/astral-sh/ruff-pre-commit
    # Ruff version.
    rev: v0.3.3
    hooks:
      - id: ruff

  # Static type analysis (as much as it's possible in python using type hints)
  - repo: https://github.com/pre-commit/mirrors-mypy
    rev: "v1.9.0"
    hooks:
      - id: mypy
        args: [--pretty, --show-error-codes, --install-types, --non-interactive]