tests/testthat/test-targets.R

In cjvanlissa/worcs: Workflow for Open Reproducible Code in Science

if(require(targets)){
  test_that("targets works with apa6", {
    scoped_temporary_project()
    skip_if_not_pandoc("2.0")
    # browser()
    unlink("R", recursive = TRUE)
    worcs::worcs_project(path = ".",
                         manuscript = "github_document",
                         preregistration = "None",
                         add_license = "None",
                         use_renv = FALSE,
                         use_targets = TRUE,
                         use_git = FALSE
    )
    lnz <- readLines("_targets.R")
    lnz[grep("tarchetypes::", lnz, fixed = TRUE)] <- gsub(")", ", cue = tar_cue(mode = 'always'))", lnz[grep("tarchetypes::", lnz, fixed = TRUE)], fixed = TRUE)
    writeLines(lnz, "_targets.R")
    # It seems like it's necessary to first render individual output chunks,
    # then render the manuscript,
    # and THEN it's possible to render the manuscript using tar_make()

    tryCatch(targets::tar_make(), error = function(e){}, warning = function(w){})
    # expect_true(file.exists("manuscript/manuscript.html"))
    tryCatch(rmarkdown::render("manuscript/manuscript.Rmd"), error = function(e){}, warning = function(w){})
    expect_true(file.exists("manuscript/manuscript.html"))
    if(file.exists("manuscript/manuscript.html")){
      file.remove("manuscript/manuscript.html")
    }
    cat(readLines("_targets.R"))
    print(list.files("./manuscript"))
    tryCatch(targets::tar_make(), error = function(e){}, warning = function(w){})
    expect_true(file.exists("manuscript/manuscript.html"))

  })

  # test_that("targets works with renv", {
  #   scoped_temporary_project()
  #   worcs::worcs_project(path = ".",
  #                        manuscript = "github_document",
  #                        preregistration = "None",
  #                        add_license = "None",
  #                        use_renv = TRUE,
  #                        use_targets = TRUE,
  #                        use_git = FALSE
  #   )
  #   tryCatch(targets::tar_make(), error = function(e){}, warning = function(w){})
  #
  #   expect_true(file.exists("manuscript/manuscript.html"))
  #
  # })
  #


  test_that("targets works with target markdown", {
    skip_if_not_pandoc("2.0")
    scoped_temporary_project()
    unlink("R", recursive = TRUE)
    worcs::worcs_project(path = ".",
                         manuscript = "target_markdown",
                         preregistration = "None",
                         add_license = "None",
                         use_renv = FALSE,
                         use_git = FALSE
    )
    # file.remove(file.path(test_dir, "_targets.rmd"))
    if(file.exists("_targets.r")){
      file.remove("_targets.r")
    }
    linz <- c("---", "  title: \"Target Markdown\"", "  output: html_document",
              "---", "", "```{r setup, include = FALSE}", "knitr::opts_chunk$set(collapse = TRUE, comment = \"#>\")",
              "```", "", "# Setup", "", "bla", "", "```{r}", "library(targets)",
              "tar_unscript()", "```", "", "# Targets", "", "bla", "", "```{targets raw-data}",
              "tar_target(raw_data, airquality)", "```", "", "blbaal", "",
              "```{targets downstream-targets}", "list(", "  tar_target(data, {raw_data[complete.cases(airquality), ]}),",
              "  tar_target(hist, hist(data$Ozone))", ")", "```", "", "try this now",
              "", "```{targets fit, tar_simple = TRUE}", "lm(Ozone ~ Wind + Temp, data)",
              "```", "", "# Pipeline", "", "run everything", "", "```{r}",
              "tar_make()", "```", "", "# Output", "", "get results", "", "```{r, message = FALSE}",
              "tar_read(fit)", "```", "", "```{r}", "tar_read(hist)", "```",
              "", "", "interactive")

    cat(linz, file = "_targets.Rmd", append = FALSE, sep = "\n")

    tryCatch(rmarkdown::render("_targets.Rmd"), error = function(e){}, warning = function(w){})

    expect_true(file.exists("_targets.html"))
    if(file.exists("_targets.html")){
      file.remove("_targets.html")
    }

    tryCatch(worcs::reproduce(check_endpoints = FALSE), error = function(e){}, warning = function(w){})
    expect_true(file.exists("_targets.html"))


  })
}