.pre-commit-config.yaml

minimum_pre_commit_version: "4.3.0"

repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: 3e8a8703264a2f4a69428a0aa4dcb512790b2c8c # v6.0.0
    hooks:
      - id: check-added-large-files
        # Compact provenance for 1,000 complete assayed alleles.
        exclude: ^data/sources/opensplice-snv-figshare-v5\.jsonl$
      - id: check-case-conflict
      - id: check-executables-have-shebangs
      - id: check-json
      - id: check-merge-conflict
      - id: check-shebang-scripts-are-executable
      - id: check-toml
      - id: check-yaml
      - id: debug-statements
      - id: detect-private-key
      - id: end-of-file-fixer
        # These evidence extracts preserve the exact request/provider text bytes.
        exclude: ^projects/explorer/web/blog/introducing-vep-bench/mechanism-evidence/.*\.txt$
      - id: mixed-line-ending
        args: [--fix=lf]
      - id: trailing-whitespace

  - repo: local
    hooks:
      - id: ruff-check
        name: Ruff lint
        entry: uv run --locked ruff check --fix --exit-non-zero-on-fix
        language: system
        types: [python]
      - id: ruff-format
        name: Ruff format
        entry: uv run --locked ruff format
        language: system
        types: [python]

  - repo: https://github.com/rhysd/actionlint
    rev: 914e7df21a07ef503a81201c76d2b11c789d3fca # v1.7.12
    hooks:
      - id: actionlint

  - repo: https://github.com/shellcheck-py/shellcheck-py
    rev: 745eface02aef23e168a8afb6b5737818efbea95 # v0.11.0.1
    hooks:
      - id: shellcheck