Configure 'rmarkdown' files to build 'RAVE' pipelines

Allows building 'RAVE' pipelines from 'rmarkdown' files. Please use it in 'rmarkdown' scripts only. Use pipeline_create_template to create an example. pipeline_setup_rmd also turns every RAVEPipelineAnalysis defined at the top level of the module R/shared-*.R scripts into pipeline targets.

Usage

configure_knitr(languages = c("R", "python"), targets = fastqueue2())

pipeline_setup_rmd(
  module_id,
  env = parent.frame(),
  collapse = TRUE,
  comment = "#>",
  languages = c("R", "python"),
  project_path = getOption("raveio.pipeline.project_root", default =
    rs_active_project(child_ok = TRUE, shiny_ok = TRUE))
)

pipeline_render(
  module_id,
  ...,
  env = new.env(parent = parent.frame()),
  entry_file = "main.Rmd",
  project_path = getOption("raveio.pipeline.project_root", default =
    rs_active_project(child_ok = TRUE, shiny_ok = TRUE))
)

Arguments

languages

one or more programming languages to support; options are 'R' and 'python'

targets

internal queue that collects the pipeline target specifications; pipeline_setup_rmd passes its own queue so it can add the analysis targets. Leave it as the default, a new queue

module_id

the module ID, usually the name of direct parent folder containing the pipeline file

env

environment to set up the pipeline translator

collapse, comment

passed to set method of opts_chunk

project_path

the project path containing all the pipeline folders, usually the active project folder

...

passed to internal function calls

entry_file

the file to compile; default is "main.Rmd"

Value

A function that is supposed to be called later that builds the pipeline scripts

Examples

configure_knitr("R")
#> function (make_file) 
#> {
#>     lapply(targets$as_list(), function(item) {
#>         if (isTRUE(item$is_delayed)) {
#>             message("Evaluating delayed target ", item$export, 
#>                 " [R]")
#>             force(env[[item$export]])
#>         }
#>         return()
#>     })
#>     rave_knitr_build(targets, make_file)
#> }
#> <bytecode: 0x55b8c006e0d0>
#> <environment: 0x55b8c0062d80>

if (FALSE) { # \dontrun{

# Requires to configure Python
configure_knitr("python")

# This function must be called in an Rmd file setup block
# for example, see
# https://rave.wiki/posts/customize_modules/python_module_01.html

pipeline_setup_rmd("my_module_id")

} # }