Execute single or multiple R, R Markdown, and Quarto scripts

Executes and logs the execution of the scripts. Logs for each script are stored in the same folder as the script.

The way the execution is logged is configurable through several options for e.g. the verbosity of the logs. See whirl-options on how to configure these.

Usage

run(
  input = "_whirl.yml",
  steps = NULL,
  summary_file = "summary.html",
  n_workers = zephyr::get_option("n_workers", "whirl"),
  check_renv = zephyr::get_option("check_renv", "whirl"),
  verbosity_level = zephyr::get_verbosity_level("whirl"),
  track_files = zephyr::get_option("track_files", "whirl"),
  out_formats = zephyr::get_option("out_formats", "whirl"),
  log_dir = zephyr::get_option("log_dir", "whirl")
)

Arguments

input

A character vector of file path(s) to R, R Markdown, Quarto scripts, or files in a folder using regular expression, or to to a whirl config file. The input can also be structured in a list where each element will be executed sequentially, while scripts within each element can be executed in parallel.

steps

An optional argument that can be used if only certain steps within a config files (or list) is to be executed. Should be equivalent to the names of the steps found in the config file. If kept as NULL (default) then all steps listed in the config file will be executed.

summary_file

A character string specifying the file path where the summary log will be stored.

n_workers

Number of simultaneous workers used in the run function. A maximum of 128 workers is allowed.. Default: 1.

check_renv

Should the projects renv status be checked?. Default: FALSE.

verbosity_level

Verbosity level for functions in whirl. See zephyr::verbosity_level for details.. Default: NA_character_.

track_files

Should files read and written be tracked? Currently only supported on Linux.. Default: FALSE.

out_formats

Which log format(s) to produce. Possibilities are html, json, and markdown formats: gfm, commonmark, and markua.. Default: "html".

log_dir

The output directory of the log files. Default is the folder of the executed script. log_dir can be a path as a character or it can be a function that takes the script path as input and returns the log directory. For more information see the examples of run() or vignette('whirl').. Default: function (x) dirname(x).

Value

A tibble containing the execution results for all the scripts.

Examples

if (FALSE) {
# Copy example scripts:
file.copy(
  from = system.file("examples", c("success.R", "warning.R", "error.R"),
    package = "whirl"
  ),
  to = tempdir()
)

# Run a single script and create log:
run(file.path(tempdir(), "success.R"))

# Run several scripts in parallel on up to 2 workers:
run(
  input = file.path(tempdir(), c("success.R", "warning.R", "error.R")), 
  n_workers = 2
)

# Run several scripts in two steps by providing them as list elements:
run(
  list(
    file.path(tempdir(), c("success.R", "warning.R")),
    file.path(tempdir(), "error.R")
  )
)

# Re-directing the logs to a sub-folder by utilizing the log_dir argument in
# run(). This will require that the sub-folder exists.

# Specifying the path using a manually defined character
run(file.path(tempdir(), "success.R"), log_dir = tempdir())

# Specifying the path with a generic function that can handle the scripts
# individually.
run(
  input = file.path(tempdir(), "success.R"), 
  log_dir = function(x) {paste0(dirname(x), "/logs")}
)
}