.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)/

  # Run ruff to lint and format
- repo: https://github.com/astral-sh/ruff-pre-commit
  # Ruff version.
  rev: v0.9.2
  hooks:
    # Run the linter.
  - id: ruff
    args: [--fix]
    # Run the formatter.
  - id: ruff-format

  # 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

  # Do YAML formatting (before the linter checks it for misses)
- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
  rev: v2.13.0
  hooks:
  - id: pretty-format-yaml
    args: [--autofix, --indent, "2", --preserve-quotes]

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