.pre-commit-config.yaml

ci:
  autoupdate_commit_msg: "ci: pre-commit autoupdate"
  skip: [mypy]  # too big

repos:
  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.14.2
    hooks:
      - id: ruff-check
        args: ["--fix"]
      - id: ruff-format
      # The following can be removed once PLR0917 is out of preview
      - name: ruff preview rules
        id: ruff
        args: ["--preview", "--select=PLR0917"]
  - repo: https://github.com/biomejs/pre-commit
    rev: v2.3.1
    hooks:
      - id: biome-format
  - repo: https://github.com/ComPWA/taplo-pre-commit
    rev: v0.9.3
    hooks:
      - id: taplo-format
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v6.0.0
    hooks:
      - id: trailing-whitespace
      - id: end-of-file-fixer
      - id: check-added-large-files
      - id: check-case-conflict
      - id: check-toml
      - id: check-yaml
      - id: check-merge-conflict
      - id: detect-private-key
      - id: no-commit-to-branch
        args: ["--branch=main"]
  - repo: https://github.com/codespell-project/codespell
    rev: v2.4.1
    hooks:
      - id: codespell
        additional_dependencies:
          - tomli
# See https://github.com/scverse/anndata/pull/2174
# Running `pre-commit run -a` gives the following error:
# tests/conftest.py: error: Duplicate module named "conftest" (also at "./tests/lazy/conftest.py")
# tests/conftest.py: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#mapping-file-paths-to-modules for more info
# This seems to be the same failure we get on the prec-commit.ci
  - repo: https://github.com/pre-commit/mirrors-mypy
    rev: v1.18.2
    hooks:
      - id: mypy
        args: [--config-file=pyproject.toml, --tb, .]
        pass_filenames: false
        additional_dependencies:
          - array-api-compat
          - h5py
          - legacy-api-wrap
          - natsort
          - numpy
          - packaging
          - pandas
          - scipy
          - types-docutils
          - zarr