.pre-commit-config.yaml

# See https://pre-commit.com for more information
# See https://pre-commit.com/hooks.html for more hooks
repos:
    - repo: https://github.com/kynan/nbstripout
      rev: 0.8.1
      hooks:
          - id: nbstripout
            name: nbstripout - Strip outputs from notebooks (auto-fixes)
            args:
                - --extra-keys
                - "metadata.colab metadata.kernelspec cell.metadata.colab cell.metadata.executionInfo cell.metadata.id cell.metadata.outputId"
    - repo: https://github.com/pre-commit/pre-commit-hooks
      rev: v4.0.1
      hooks:
          # - id: check-added-large-files
          #   name: Check for files larger than 5 MB
          #   args: ["--maxkb=5120"]
          - id: end-of-file-fixer
            name: Check for a blank line at the end of scripts (auto-fixes)
            exclude: '\.Rd'
          - id: trailing-whitespace
            name: Check for trailing whitespaces (auto-fixes)
    - repo: https://github.com/pycqa/isort
      rev: 5.13.2
      hooks:
          - id: isort
            name: isort - Sort Python imports (auto-fixes)
            types: [cython, pyi, python]
            args: ["--profile", "black", "--filter-files"]
    - repo: https://github.com/psf/black
      rev: 24.10.0 # Replace by any tag/version: https://github.com/psf/black/tags
      hooks:
          - id: black
            name: black - consistent Python code formatting (auto-fixes)
            language_version: python # Should be a command that runs python3.6+
            exclude: .*/tests/.*|^\.cruft\.json$|.*\tests\.*|helpers/.*|^tests
            args: ["--preview", "--line-length=88"]
    - repo: https://github.com/PyCQA/flake8
      rev: 7.1.1
      hooks:
          - id: flake8
            name: flake8 - Python linting
            exclude: .*/tests*|^\.cruft\.json|helpers/.*|.*\tests*$|^tests
    - repo: https://github.com/nbQA-dev/nbQA
      rev: 1.9.1
      hooks:
          - id: nbqa-isort
            name: nbqa-isort - Sort Python imports (notebooks; auto-fixes)
            args: [--nbqa-mutate]
            additional_dependencies: [isort==5.8.0]
            exclude: .*/tests/.*|^\.cruft\.json$|.*\tests\.*
          - id: nbqa-black
            name: nbqa-black - consistent Python code formatting (notebooks; auto-fixes)
            args: [--nbqa-mutate]
            additional_dependencies: [black==21.5b2]
            exclude: .*/tests/.*|^\.cruft\.json$|.*\tests\.*
          # TODO: Disabled for now until it's clear how to add noqa to specific cells of a Jupyter notebook
          #- id: nbqa-flake8
          #  name: nbqa-flake8 - Python linting (notebooks)
          #  additional_dependencies: [ flake8==3.9.2 ]
    - repo: https://github.com/Yelp/detect-secrets
      rev: v1.5.0
      hooks:
          - id: detect-secrets
            name: detect-secrets - Detect secrets in staged code
            args: ["--baseline", ".secrets.baseline"]
            exclude: .*/tests/.*|^\.cruft\.json$
    - repo: local
      hooks:
          - id: restricted-filenames
            name: Check commits for restricted file extensions
            entry: WARNING- csvs for test about to be committed. Double check there is no sensitive data!
            language: fail
            files: .*\.(csv|feather|xlsx|zip|hdf5|h5|txt|json|xml|hd|parquet)
            exclude: tests/.* | "requirements.txt"