.pre-commit-config.yaml

default_language_version:
  python: python3
# Specify files to exclude - pre-commit hook doesn't parse pyproject.toml
exclude: tests.*/data/hp.*\.ttl|.*\.svg|jsonschema_value_constraints.yaml|tests/linkml_runtime/test_loaders_dumpers/models/phenopackets.py|tests/linkml_runtime/.*\.yaml|tests/linkml_runtime/support/clicktestcase.py|tests/linkml/test_metamodel_compat/input/metamodel/.*\.yaml
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
  rev: v4.4.0
  hooks:
  - id: end-of-file-fixer
    exclude: __snapshots__
  - id: check-yaml
    exclude: (__snapshots__|test_utils/input)
  - id: check-toml
  - id: trailing-whitespace
    # TODO: This is temporary while bioliank is being fixed upstream.
    # TODO: Should look at snapshot exclusion to find upstream problems
    # Exclude linkml_runtime model schemas to preserve exact formatting for snapshot tests
    exclude: (__snapshots__|biolink-model.yaml|packages/linkml_runtime/src/linkml_runtime/linkml_model/model/schema/.*\.yaml)
- repo: https://github.com/astral-sh/ruff-pre-commit
  # Ensure this version stays in sync with tox.ini
  rev: v0.11.13
  hooks:
  # Run the linter.
  - id: ruff-check
    args: [--fix, --exit-non-zero-on-fix]
  # Run the formatter.
  - id: ruff-format
- repo: https://github.com/codespell-project/codespell
  rev: v2.4.1
  hooks:
  - id: codespell
    exclude: .*\.toml$
    args: ["--toml", "pyproject.toml"]
    additional_dependencies:
      - tomli