.pre-commit-config.yaml

# SPDX-FileCopyrightText: 2023 Iegor Riepin, Tom Brown
#
# SPDX-License-Identifier: CC0-1.0

repos:

- repo: https://github.com/pre-commit/pre-commit-hooks
  rev: v4.5.0
  hooks:
  - id: trailing-whitespace
  - id: check-yaml
  - id: check-added-large-files
    args: ['--maxkb=20000']

  # Find common spelling mistakes in comments and docstrings
- repo: https://github.com/codespell-project/codespell
  rev: v2.2.6
  hooks:
  - id: codespell
    args: ['--ignore-regex="(\b[A-Z]+\b)"', '--ignore-words-list=fom,appartment,bage,ore,setis,tabacco,berfore,vor'] # Ignore capital case words, e.g. country codes
    types_or: [python, rst, markdown]
    files: ^(scripts|doc)/

  # Formatting with "black" coding style
- repo: https://github.com/psf/black
  rev: 24.4.0
  hooks:
      # Format Python files
  - id: black
      # Format Jupyter Python notebooks
  - id: black-jupyter

  # Remove output from Jupyter notebooks
- repo: https://github.com/aflc/pre-commit-jupyter
  rev: v1.2.1
  hooks:
  - id: jupyter-notebook-cleanup
    args: ["--remove-kernel-metadata"]

  # Format Snakemake rule / workflow files
- repo: https://github.com/snakemake/snakefmt
  rev: v0.8.5
  hooks:
  - id: snakefmt

  # For cleaning jupyter notebooks
- repo: https://github.com/aflc/pre-commit-jupyter
  rev: v1.2.1
  hooks:
  - id: jupyter-notebook-cleanup
    exclude: examples/solve-on-remote.ipynb

  # Check for REUSE compliance (licensing)
- repo: https://github.com/fsfe/reuse-tool
  rev: v2.1.0
  hooks:
  - id: reuse