.pre-commit-config.yaml

# All available hooks: https://pre-commit.com/hooks.html
repos:
  - repo: local
    hooks:
      - id: spell-check
        name: Spell check files
        language: r
        entry: Rscript scripts/spell-check.R
        additional_dependencies:
          - readr
          - rprojroot
          - spelling
          - tidyr
      - id: forbid-to-commit
        name: Don't commit common R artifacts
        entry: Cannot commit .Rhistory, .RData, or .Rds files.
        language: fail
        files: '(?i)\.(Rhistory|RData|rds)$'
        # `exclude` files here are _allowed_ data files.
        # Here they are specified by a full path from the repository root in a multiline regex.
        exclude: |
          (?x)^(
            test/references/celltype/singler_models/singler_model_file.rds|
            test/output/results/STUBP01/STUBS01/STUBL01_processed.rds|
            test/output/results/STUBP01/STUBS16/STUBL16_processed.rds
          )$
  - repo: https://github.com/thlorenz/doctoc
    # Update TOCs
    rev: v2.2.0
    hooks:
      - id: doctoc
        args: [--update-only, --title=**Table of Contents**]
  - repo: https://github.com/astral-sh/ruff-pre-commit
    # Ruff for linting and formatting python
    rev: v0.6.9
    hooks:
      # Run the linter.
      - id: ruff
      # Run the formatter.
      - id: ruff-format
  - repo: https://github.com/lorenzwalthert/precommit
    # R styling and linting
    rev: v0.4.3.9001
    hooks:
      - id: style-files
        args: [--style_pkg=styler, --style_fun=tidyverse_style]
      # - id: lintr #skip R linting for now...
      - id: parsable-R
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v5.0.0
    hooks:
      - id: check-added-large-files
        args: ["--maxkb=200"]
      - id: end-of-file-fixer
        exclude: '\.Rd'
ci:
  autofix_prs: true # set to false if we don't want fixes automatically applied by ci
  autoupdate_branch: development
  autoupdate_schedule: quarterly
  # skip spell check because it can't be quickly installed on CI
  skip: [spell-check]