.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: 0.4.0
    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: 5.12.0
    hooks:
      - id: isort
        name: isort - Sort python imports (auto-fixes)
        args: [ "--profile", "black", "--filter-files" ]
      - id: isort
        name: isort - Sort cython imports (auto-fixes)
        types: [cython]
        args: [ "--profile", "black", "--filter-files" ]
      - id: isort
        name: isort - Sort pyi imports (auto-fixes)
        types: [pyi]
        args: [ "--profile", "black", "--filter-files" ]
  - repo: https://github.com/psf/black
    rev: 22.8.0 # 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+
  - repo: https://github.com/PyCQA/flake8
    rev: 5.0.4
    hooks:
      - id: flake8
        name: flake8 - Python linting
  - repo: https://github.com/nbQA-dev/nbQA
    rev: 0.12.0
    hooks:
      - id: nbqa-isort
        name: nbqa-isort - Sort Python imports (notebooks; auto-fixes)
        args: [ --nbqa-mutate ]
        additional_dependencies: [ isort==5.8.0 ]
      - id: nbqa-black
        name: nbqa-black - consistent Python code formatting (notebooks; auto-fixes)
        args: [ --nbqa-mutate ]
        additional_dependencies: [ black==21.5b2 ]
      # 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: v1.0.3
    hooks:
      - id: detect-secrets
        name: detect-secrets - Detect secrets in staged code
        args: [ "--baseline", ".secrets.baseline" ]
        exclude: .*/tests/.*|^\.cruft\.json$
  - repo: https://github.com/PyCQA/bandit
    rev: '1.7.5'
    hooks:
      - id: bandit
        name: bandit - Checks for vulnerabilities
        args: ["-c", "pyproject.toml"]
        additional_dependencies: ["bandit[toml]"]
{% if cookiecutter.using_R == "Yes" %}
  # R specific hooks: https://github.com/lorenzwalthert/precommit
  - repo: https://github.com/lorenzwalthert/precommit
    rev: v0.1.3
    hooks:
      - id: style-files
        name: Style files using styler
        args: [ --style_pkg=styler, --style_fun=tidyverse_style ]
      - id: roxygenize
        name: Run roxygen2::roxygenize()
      # codemeta must be above use-tidy-description when both are used
      # -   id: codemeta-description-updated
      - id: use-tidy-description
        name: Run sethis::use_tidy_description()
      - id: lintr
        name: Run lintr::lint()
        exclude: renv/activate.R
      - id: readme-rmd-rendered
        name: Check README.Rmd has been rendered to README.md
      - id: parsable-R
        name: Check for valid R code using the parse() function
      - id: no-browser-statement
        name: Check for accidential browser() statements
{% endif -%}