Creates 'RAVE' pipeline instance

Set pipeline inputs, execute, and read pipeline outputs

Usage

pipeline(
  pipeline_name,
  settings_file = "settings.yaml",
  paths = pipeline_root(),
  temporary = FALSE
)

pipeline_from_path(path, settings_file = "settings.yaml")

Arguments

pipeline_name

the name of the pipeline, usually title field in the 'DESCRIPTION' file, or the pipeline folder name (if description file is missing)

settings_file

the name of the settings file, usually stores user inputs

paths

the paths to search for the pipeline, usually the parent directory of the pipeline; default is pipeline_root, which only search for pipelines that are installed or in current working directory.

temporary

see pipeline_root

path

the pipeline folder

Value

A PipelineTools instance

Examples

library(ravepipeline)

if(interactive()) {

  # ------------ Set up a bare minimal example pipeline ---------------
  root_path <- tempdir()
  pipeline_root_folder <- file.path(root_path, "modules")

  # create pipeline folder
  pipeline_path <- pipeline_create_template(
    root_path = pipeline_root_folder, pipeline_name = "raveio_demo",
    overwrite = TRUE, activate = FALSE, template_type = "rmd-bare")

  # Set initial user inputs
  ieegio::io_write_yaml(
    x = list(
      n = 100,
      pch = 16,
      col = "steelblue"
    ),
    con = file.path(pipeline_path, "settings.yaml")
  )

  # build the pipeline for the first time
  # this is a one-time setup
  pipeline_build(pipeline_path)

  # Temporarily redirect the pipeline project root
  # to `root_path`
  options("raveio.pipeline.project_root" = root_path)

  # Compile the pipeline document
  rmarkdown::render(
    input = file.path(pipeline_path, "main.Rmd"),
    output_dir = pipeline_path,
    knit_root_dir = pipeline_path,
    intermediates_dir = pipeline_path, quiet = TRUE
  )

  # Reset options
  options("raveio.pipeline.project_root" = NULL)

  if (FALSE) { # \dontrun{

    # Open web browser to see compiled report
    utils::browseURL(file.path(pipeline_path, "main.html"))

  } # }

  # --------------------- Example starts ------------------------

  # Load pipeline
  pipeline <- pipeline(
    pipeline_name = "raveio_demo",
    paths = pipeline_root_folder,
    temporary = TRUE
  )

  # Check which pipeline targets to run
  pipeline$target_table

  # Run to `plot_data`, RAVE pipeline will automatically
  # calculate which up-stream targets need to be updated
  # and evaluate these targets
  pipeline$run("plot_data")

  # Customize settings
  pipeline$set_settings(pch = 2)

  # Run again with the new inputs, since input_data does not change,
  # the pipeline will skip that target automatically
  pipeline$run("plot_data")

  # Read intermediate data
  head(pipeline$read("input_data"))

  # or use `[]` to get results
  pipeline[c("n", "pch", "col")]
  pipeline[-c("input_data")]

  # Check evaluating status
  pipeline$progress("details")

  # result summary & cache table
  pipeline$result_table

  # visualize the target dependency graph
  pipeline$visualize(glimpse = TRUE)

  # --------------------- Clean up ------------------------
  unlink(pipeline_path, recursive = TRUE)
}