.pre-commit-config.yaml

exclude: (^doc/)|(.*/venv/)
default_stages: [commit]
repos:
  - repo: https://github.com/psf/black
    rev: 23.10.1
    hooks:
      - id: black-jupyter
        name: black-notebooks
        files: ^api/python/notebooks
        args: ["--config", "./api/python/notebooks/pyproject.toml"]
      - id: black
        name: black-cellxgene-census
        files: ^api/python/cellxgene_census
        args: ["--config", "./api/python/cellxgene_census/pyproject.toml"]
      - id: black
        name: black-tools
        files: ^tools
        args: ["--config", "./tools/pyproject.toml"]

  - repo: https://github.com/charliermarsh/ruff-pre-commit
    rev: v0.1.3
    hooks:
      - id: ruff
        name: ruff-cellxgene-census
        files: ^api/python/cellxgene_census
        args: ["--config=./api/python/cellxgene_census/pyproject.toml", "--fix"]
      - id: ruff
        name: ruff-tools
        files: ^tools
        args: [ "--config=./tools/pyproject.toml", "--fix" ]

  - repo: https://github.com/pre-commit/mirrors-mypy
    rev: v1.6.1
    hooks:
      - id: mypy
        name: mypy-cellxgene-census
        files: ^api/python/cellxgene_census
        args: ["--config-file=./api/python/cellxgene_census/pyproject.toml"]
        additional_dependencies:
          - attrs
          - types-requests
          - pytest
          - pandas-stubs
          - numpy
          - typing_extensions
          - types-setuptools
      - id: mypy
        name: mypy-tools-cellxgene_census_builder
        files: ^tools/cellxgene_census_builder
        args: ["--config-file=./tools/cellxgene_census_builder/pyproject.toml", "--python-version=3.10"]
        additional_dependencies:
          - attrs
          - types-requests
          - pytest
          - pandas-stubs
          - numpy
          - typing_extensions
          - types-setuptools
          - types-PyYAML
      - id: mypy
        name: mypy-tools-not-builder
        files: ^tools/
        exclude: ^tools/cellxgene_census_builder
        args: ["--config", "./tools/pyproject.toml"]
        additional_dependencies:
          - attrs
          - numpy
          - pandas-stubs
          - typing_extensions
          - pytest
          - types-click


  - repo: https://github.com/nbQA-dev/nbQA
    rev: 1.7.0
    hooks:
      - id: nbqa-black
        files: ^api/python/notebooks

  - repo: https://github.com/igorshubovych/markdownlint-cli
    rev: v0.37.0
    hooks:
    - id: markdownlint