style-files

A hook to style files with styler. Only commit code corresponding to the tidyverse style guide. You can pass arguments to style_file(...) using the --key=value syntax like this:

  id: style-files
  args: [--scope=spaces, --reindention=specify_reindention('#')]

In addition, the hook takes the following arguments that are not passed to style_file(...):

• Argument style_pkg and style_fun default to styler and tidyverse_style. If you want to use another style guide than the tidyverse style guide, you can specify it like this:

  id: style-files
  args: [--style_pkg=pkg.with.style.guide, --style_fun=exported.style.function]

• The argument --no-warn-cache is deprecated and will be removed in a future release. Please remove it from your .pre-commit-config.yaml.

• Argument cache-root is passed to options() to set styler.cache_root. Default value: styler-perm. The argument determines the sub-directory under the {R.cache} cache directory that {styler} uses. If you want {styler} to auto-clean up caches older than 6 days, set this to "styler". For more information, see help("caching", package = "styler").

  id: style-files
  args: [--cache-root=styler]

• Argument ignore-start and ignore-stop is passed to options() to set styler.ignore_start and styler.ignore_stop respectively. Not set by default, so the {styler} defaults apply. This was introduced in {precommit} 0.2.2.9012. For example, if you want to restore old behavior of styler < 1.6.2, where only the literals styler: off and styler: on were accepted, use this regex:

  id: style-files
  args: [--ignore-start="^# styler: on$", --ignore-stop="^# styler: off$"]

This hook modifies files unless you specify --dry=fail (requires {styler} > 1.3.2).

readme-rmd-rendered

Make sure README.Rmd hasn’t been edited more recently than README.md, i.e. remind you to render the .Rmd to .md before committing.

This hook does not modify files.

parsable-R

Checks if your .R and .Rmd files are “valid” R code by checking if running parse() on them (or their knitr::purl()ed output for .Rmd) returns an error.

This hook does not modify files.

no-browser-statement

Guarantees you that you don’t accidentally commit code with a browser() statement in it.

This hook does not modify files.

no-debug-statement

Guarantees you that you don’t accidentally commit code with a debug() or debugonce() statement in it.

This hook does not modify files. This hook was added in version 0.2.2.9012.

spell-check

Checks spelling with spelling::spell_check_files().

Excluded files

When you invoke precommit::use_precommit() and .pre-commit-config.yaml is written to your repo (unless you specify config_source otherwise), we copy the expression in the exclude: key from spell check hook the default repository’s configuration (i.e. the .pre-commit-hooks.yaml file in https://github.com/lorenzwalthert/precommit) into your config file, so you can easily add or remove some files. As of v0.3.2, the following regex is used to exclude files following the verbose python regex syntax:

(?x)^(
.*\.[rR]|
.*\.feather|
.*\.jpeg|
.*\.pdf|
.*\.png|
.*\.py|
.*\.RData|
.*\.rds|
.*\.Rds|
.*\.Rproj|
.*\.sh|
(.*/|)\.gitignore|
(.*/|)\.pre-commit-.*|
(.*/|)\.Rbuildignore|
(.*/|)\.Renviron|
(.*/|)\.Rprofile|
(.*/|)\.travis\.yml|
(.*/|)appveyor\.yml|
(.*/|)NAMESPACE|
(.*/|)renv/settings\.dcf|
(.*/|)renv\.lock|
(.*/|)WORDLIST|
\.github/workflows/.*|
data/.*|
)$

language

The lang arg will be passed to spelling::spell_check_files().

  id: spell-check
  args: [--lang=<language>]

This hook does not modify input files. It will add all words not found in the dictionary to inst/WORDLIST, assuming they were spelled correctly but were not in the dictionary. An example might be “RStudio”. The hook error message will contain all words written to inst/WORDLIST, so if there were really some typos, make sure to fix them and remove them from inst/WORDLIST. If there were not typos, or you fixed all, stage inst/WORDLIST and this time, the commit should pass.

roxygenize

A hook to run roxygen2::roxygenize(). Makes sure you commit your .Rd changes with the source changes. To take advantage of caching, you don’t need to run roxygen2::roxygenize() manually anymore. The argument --no-warn-cache is deprecated and will be removed in a future release. Please remove it from your .pre-commit-config.yaml.

Because the hook will write the version of {roxygen2} to DESCRIPTON, you should either make sure the version you use when you call {roxygen2} interactively matches the one from in {precommit} or simply not run {roxygen2} manually.

If you specify additional roclets through the Roxygen: field in DESCRIPTION, e.g. from {pkgapi} you must specify the dependencies explicitly such that renv::install() understands it, e.g.

  id: roxygenize
  additional_dependencies:
  - r-lib/pkgapi

This hook does not modify input files, but writes to .Rd files in man/, NAMESPACE and potentially others depending on which roxygen roclets you specified in DESCRIPTION.

deps-in-desc

Checks if packages used with the pkgname::fun() syntax are listed in your DESCRIPTION file. Note that README.Rmd is never checked. Flag allow_private_imports lets the user specify that private imports into the package namespace are tolerable, e.g. somepkg:::x(). Flag not set by default, i.e. the hook will fail if such a call is found.

  id: deps-in-desc 
  args: [--allow_private_imports] 

This hook does not modify the file DESCRIPTION because the user should decide for each package if it should go to Imports: or Suggests:, which can be done easily with usethis::use_package().

use-tidy-description

A hook to run usethis::use_tidy_description() to ensure dependencies are ordered alphabetically and fields are in standard order.

This hook does modify the file DESCRIPTION.

lintr

A hook to run lintr::lint() to check that R files are lint free. Argument warning_only changes the behavior of the pre-commit to be non-blocking. You should set this with the field verbose: true.

  id: lintr
  args: [--warn_only]
  verbose: true

When configured this way, lintr prints lint errors as they appear. Other arguments are not supported. Instead, lintr config should be specified in a .lintr config file in Debian Control Field Format as specified in the .lintr documentation.

This hook does not modify any file.

codemeta-description-updated

Make sure DESCRIPTION hasn’t been edited more recently than codemeta.json,

i.e. remind you to run codemetar::write_codemeta() in order to keep codemeta.json in sync with DESCRIPTION.

This hook does not modify any file.