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Execute a Julia step (worker behind tar_target_jl)

Source: R/run-steps.R
run_jl_step.Rd

Julia counterpart of run_py_step(). Runs, inside a fresh R environment, an optional R pre-script, a Python script (via JuliaCall). This is the function the target built by tar_target_jl() calls; it is exported so that call resolves at pipeline run time but this function is not destined to be called directly by the package users.

Usage

run_jl_step(
  script,
  pre_script = NULL,
  post_script = NULL,
  inputs = list(),
  output = "object",
  retrieve = NULL,
  files = NULL,
  julia_version = NULL,
  julia_home = getOption("tarpolyglot.julia_home"),
  julia_project = NULL,
  julia_packages = NULL
)

Arguments

script

Path to the Julia script to run (required).

pre_script

Optional path to an R script run before the Julia script. It is evaluated in the step environment, which already holds the named inputs. To hand objects to Julia, assign a named list to_jl in this script; each element is julia_assign()ed as a variable in Julia's Main module.

post_script

Optional path to an R script run after the Julia script. It is evaluated in the same environment, which now also holds jl_get(name) and jl_call(fn, ...). In output = "object" mode the value of its last expression becomes the target value; in output = "file" mode it must return a character vector of file paths.

inputs

Named list of upstream target values, bound by name into the step environment. Supplied automatically by the constructor.

output

Output mode: "object" (default) returns a converted R object, "file" returns a character vector of file paths (and defaults format to "file").

retrieve

Optional character vector of foreign-session variable names to return when no post_script is supplied in object mode. One name returns that object; several return a named list.

files

Optional character vector of file paths to return when no post_script is supplied in file mode.

julia_version

Optional Julia version to select (e.g. "1.11"), used when julia_home is not given. Resolved to a juliaup-managed install. Default NULL uses the computer/global default Julia.

julia_home, julia_project, julia_packages

Julia environment selection. julia_home is the directory containing the julia executable (defaults to getOption("tarpolyglot.julia_home"); when unset and no julia_version, JuliaCall discovers Julia on PATH). julia_project is a Julia project environment (folder with Project.toml / Manifest.toml) to Pkg.activate(); when NULL, Julia's default global environment (@v#.#) is used. julia_packages is a character vector of packages to using before the script. The requested environment takes priority over an ambient JULIA_PROJECT environment variable (e.g. one set by an RStudio project config and inherited by crew workers): it is cleared for the duration of the Julia binding, so an explicit julia_project (or the global environment you get when none is given) wins over it, rather than JULIA_PROJECT silently selecting a different project. (JULIA_HOME is not cleared: it is a supported way to point at the default Julia.)

Value

The converted R object (object mode) or a character vector of normalised file paths (file mode).

See also

run_py_step(), tar_target_jl()

Examples

if (FALSE) { # \dontrun{
# Normally invoked by tar_target_jl(); shown here as a direct call.
# scripts/sum.jl assigns `result`; pre.R builds `to_jl <- list(x = x)`.
run_jl_step(
  script = "scripts/sum.jl",
  pre_script = "scripts/pre.R",
  inputs = list(x = c(1, 2, 3)),
  retrieve = "result"
)
} # }