.pre-commit-config.yaml

repos:
-   repo: https://gitlab.com/vojko.pribudic.foss/pre-commit-update
    rev: v0.9.0 # Insert the latest tag here

    hooks:
    -   id: pre-commit-update
        args: [--exclude, black, --keep, isort]
    # Formats import order
-   repo: https://github.com/pycqa/isort
    rev: 5.12.0
    hooks:
    -   id: isort
        name: isort (python)
        args: ["--profile", "black", "--filter-files"]

    #Code formatter for both python files and jupyter notebooks
-   repo: https://github.com/astral-sh/ruff-pre-commit
    # Ruff version.
    rev: v0.15.5
    hooks:
      # Run the formatter.
    -   id: ruff-format

-   repo: https://github.com/nbQA-dev/nbQA
    rev: 1.9.1
    hooks:
    -   id: nbqa-isort
        additional_dependencies: [isort==5.6.4]
        args: [--profile=black]

-   repo: https://github.com/hadialqattan/pycln
    rev: v2.6.0
    hooks:
    -   id: pycln
        args: [--config=pyproject.toml]
        exclude: |
          (?x)^(
            2\.segment_images/scripts/.*\.py$|
            3\.cellprofiling/scripts/.*\.py$
          )$
    # additional hooks found with in the pre-commit lib
-   repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v6.0.0
    hooks:
    -   id: trailing-whitespace # removes trailing white spaces
    -   id: mixed-line-ending # removes mixed end of line
        args:
        -   --fix=lf
-   repo: local
    hooks:
    -   id: shellcheck
        name: shellcheck
        description: Test shell scripts with shellcheck
        entry: shellcheck
        language: python
        types: [shell]
        require_serial: true # shellcheck can detect sourcing this way