Below is a comprehensive list with all hooks from {precommit} as well
as their arguments or flags, if they take any. With the standard config
file that gets placed in your project with
precommit::use_precommit() all hooks should work out of the
box, but you can further customize them as described below. Other repos
also host hooks, many are listed here.
File modification
Some hooks will fail without changing the files you want to commit,
like the lintr hook - and you need to make manual changes
for the hook to pass on the next attempt. Other hooks like the
roxygenize hook write to files, and if that changes the
file, the hook will fail, but this means for most hooks you won’t need
to modify the file manually after the attempted commit, just stage the
changes and try to commit again. Below, we indicate for every hook if it
modifies files or not.
Arguments
Arguments for the hooks are specified as described in the pre-commit.com documentation.1 You can specify arguments like this:
repos:
- repo: https://github.com/lorenzwalthert/precommit
rev: v0.4.2
hooks:
- id: lintr
args: [--warn_only, --key=value]Other hook settings
Apart from specifying the args key as described above,
there are other hooks settings you can specify, e.g. file exclusion. If
you don’t, they are inherited from the default repository’s
configuration (i.e. the .pre-commit-hooks.yaml file in https://github.com/lorenzwalthert/precommit). See the pre-commit
documentation, for the available settings.
style-filesA 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(...):
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]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-renderedMake 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-RChecks 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-statementGuarantees you that you don’t accidentally commit code with a
browser() statement in it.
This hook does not modify files.
no-print-statementGuarantees you that you don’t accidentally commit code with a
print() statement in it.
This hook does not modify files. This hook was added in version 0.3.2.9020.
no-debug-statementGuarantees 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-checkChecks 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 v0.4.2,
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>]read only
The --read-only flag will be passed to spell check. This
flag makes this hook idempotent.
id: spell-check
args: [--read-only]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.
To opt out of updating inst/WORDLIST provide the
--read-only flag.
roxygenizeA 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/pkgapiThis 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.
Arguments
id: roxygenize
args: [--root=<R package root>] root specifies the directory in the git repo
that contains the R package. Defaults to . since for most R
package git repos, the git and R package root coincide. Added in version
0.3.3.00000.deps-in-descChecks if packages used with the pkgname::fun() syntax
are listed in your DESCRIPTION file. Note that README.Rmd
is never checked.
Arguments
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] root specifies the directory in the git repo
that contains the R package. Defaults to . since for most R
package git repos, the git and R package root coincide. Added in version
0.3.2.9000.id: deps-in-desc
args: [--root=<R package root>] 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-descriptionA 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.
Arguments
id: use-tidy-description
args: [--root=<R package root>] root specifies the directory in the git repo
that contains the R package. Defaults to . since for most R
package git repos, the git and R package root coincide. Added in version
0.3.3.00000.lintrA 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: trueWhen 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-updatedMake 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.
Arguments
id: codemeta-description-updated
args: [--root=<R package root>] root specifies the directory in the git repo
that contains the R package. Defaults to . since for most R
package git repos, the git and R package root coincide. Added in version
0.3.3.00000.pkgdownCheck if your {pkgdown} config file (e.g. _pkgdown.yml
in your root) has the correct entries for references and articles. This
hook skips the time-consuming parts of building the index and reference
and only performs the validation. Hence we don’t rely on the extensive
dependency graph of {pkgdown} being installed, including packages with
heavy build-time dependencies and system libraries.
For this check, we rely on the the global R package library and require all development dependencies of the package you want to run this hook for to be installed, as well as {pkgdown} (without its dependencies).
This hook does not modify files. Added in version 0.3.2.9003.
Note that there might be issues with arguments that contain special characters and you might have to quote them and the order of single, double and escaped quotes may not give identical results on one platform and may not be portable to all platforms either.↩︎