.pre-commit-config.yaml

---
# All available hooks: https://pre-commit.com/hooks.html
# R specific hooks: https://github.com/lorenzwalthert/precommit
repos:
  - repo: https://github.com/lorenzwalthert/precommit
    rev: v0.4.0
    hooks:
      - id: style-files
        args: []
      - id: roxygenize
        additional_dependencies:
          - knitr
          - stan-dev/cmdstanr@*release
          - checkmate
          - glue
          - methods
          - graphics
          - posterior
          - generics
          - Matrix
          - mvtnorm
          - future
          - simsurv
      # codemeta must be above use-tidy-description when both are used
      # -   id: codemeta-description-updated
      - id: use-tidy-description
      - id: spell-check
        exclude: >
          (?x)^(
          data/.*|
          (.*/|)\.Rprofile|
          (.*/|)\.Renviron|
          (.*/|)\.gitignore|
          (.*/|)NAMESPACE|
          (.*/|)DESCRIPTION|
          (.*/|)WORDLIST|
          (.*/|)LICENSE|
          (.*/|)\.Rbuildignore|
          (.*/|)\.lintr|
          (.*/|)\.prettierignore|
          (.*/|)_pkgdown.yaml|
          (.*/|)staged_dependencies.yaml|
          (.*/|)tests/testthat/_snaps/.*|
          (.*/|)\.pre-commit-.*|
          \.github/.*|
          .*\.[rR]|
          .*\.Rproj|
          .*\.py|
          .*\.feather|
          .*\.rds|
          .*\.Rds|
          .*\.sh|
          .*\.svg|
          .*\.RData|
          man/figures/.*|
          .*\.png
          )$
      - id: lintr
      - id: readme-rmd-rendered
      - id: parsable-R
      - id: no-browser-statement
      - id: deps-in-desc
  - repo: https://github.com/pre-commit/mirrors-prettier
    rev: v4.0.0-alpha.8
    hooks:
      - id: prettier
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.5.0
    hooks:
      - id: check-added-large-files
        args: ["--maxkb=200"]
      - id: end-of-file-fixer
        exclude: >
          (?x)^(
          \.Rd|
          tests/testthat/_snaps/.*|
          vignettes/.*\.Rmd
          )$
      - id: trailing-whitespace
        exclude: >
          (?x)^(
          \.Rd|
          tests/testthat/_snaps/.*|
          vignettes/.*\.Rmd
          )$
      - id: check-yaml
      - id: no-commit-to-branch
      - id: mixed-line-ending
        args: ["--fix=lf"]
      - id: detect-aws-credentials
        args: ["--allow-missing-credentials"]
      - id: detect-private-key
      - id: forbid-new-submodules
      - id: check-symlinks
  - repo: local
    hooks:
      - id: forbid-to-commit
        name: Don't commit common R artifacts
        entry: Cannot commit .Rhistory, .RData, .Rds or .rds.
        language: fail
        files: '\.Rhistory|\.RData|\.Rds|\.rds$'
        # `exclude: <regex>` to allow committing specific files.
  - repo: https://github.com/igorshubovych/markdownlint-cli
    rev: v0.39.0
    hooks:
      - id: markdownlint
        args:
          [
            "--ignore=tests/testthat/_snaps/*",
            "--disable=MD033",
            "--disable=MD025",
          ]