update 2024-09-13 10:55:59.694015

R/worcs_project.R

@@ -707,5 +707,5 @@ append_yaml <- function(yaml_text, yaml_command, add_this){
   this_line <- grep(paste0("^\\s{0,}", yaml_command, "\\s{0,}:"), yaml_text)[1]
   gsub(':.*$', paste0(': [', paste0(
     dQuote(c(add_this,
-             trimws(gsub('"', "", strsplit(gsub("^.+?:", "", yaml_text[this_line]), ",")[[1]])))), collapse = ", "), ']'), yaml_text[this_line])
+             trimws(gsub('"', "", strsplit(gsub("^.+?:", "", yaml_text[this_line]), ",")[[1]]))), q = FALSE), collapse = ", "), ']'), yaml_text[this_line])
 }

inst/rstudio/templates/project/resources/_targets.rmd

@@ -0,0 +1,71 @@
+---
+  title: "Target Markdown"
+  output: html_document
+---
+
+```{r setup, include = FALSE}
+knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
+```
+
+Target Markdown is a powerful R Markdown interface for reproducible analysis pipelines, and the chapter at https://books.ropensci.org/targets/markdown.html walks through it in detail. This R Markdown report the example from the chapter. Try it out in both interactive and non-interactive modes, either by running the code chunks in different ways or setting the `tar_interactive` chunk option.
+
+# Setup
+
+If you are using old versions of `targets` (<= 0.7.0) and/or `knitr` (<= 1.33), you will need to load the `targets` package in the R Markdown document in order for Target Markdown code chunks to work.
+
+```{r}
+library(targets)
+```
+
+Near the top of the document, you may also wish to remove the `_targets_r` directory previously written by non-interactive runs of the report. Otherwise, your pipeline may contain superfluous targets.
+
+```{r}
+library(targets)
+tar_unscript()
+```
+
+# Targets
+
+Our first target borrows the `airquality` dataset built into base R.
+
+```{targets raw-data}
+tar_target(raw_data, airquality)
+```
+
+Our next targets preprocess the data, make a histogram, and fit a model.
+
+```{targets downstream-targets}
+list(
+  tar_target(data, {raw_data[complete.cases(airquality), ]}),
+  tar_target(hist, hist(data$Ozone))
+)
+```
+
+Set the `tar_simple` chunk option to `TRUE` to define a single target with the command in the code chunk. The chunk below only contains `biglm(Ozone ~ Wind + Temp, data)` in the source, but because `tar_simple` is `TRUE`, it is shorthand for `tar_target(name = fit, command = biglm(Ozone ~ Wind + Temp, data))`. All other arguments to `tar_target()` are set to their default values (configurable with `tar_option_set()`).
+
+```{targets fit, tar_simple = TRUE}
+lm(Ozone ~ Wind + Temp, data)
+```
+
+# Pipeline
+
+If you ran all the `{targets}` chunks in non-interactive mode, then your R scripts are set up to run the pipeline.
+
+```{r}
+tar_make()
+```
+
+# Output
+
+You can retrieve results from the `_targets/` data store using `tar_read()` or `tar_load()`.
+
+```{r, message = FALSE}
+tar_read(fit)
+```
+
+```{r}
+tar_read(hist)
+```
+
+
+At this point, you can go back and run `{targets}` chunks in interactive mode without interfering with the code or data of the non-interactive pipeline.

tests/testthat/test-targets.R

@@ -1,3 +1,4 @@
+library(targets)
 test_that("targets works with apa6", {
   the_test <- "targets"
   old_wd <- getwd()
@@ -7,17 +8,17 @@ test_that("targets works with apa6", {
   on.exit({unlink(test_dir, recursive = TRUE); setwd(old_wd)}, add = TRUE)
 
   worcs::worcs_project(path = test_dir,
-                       manuscript = "APA6",
+                       manuscript = "github_document",
                        preregistration = "None",
                        add_license = "None",
                        use_renv = FALSE,
                        use_targets = TRUE
                        )
-  tryCatch(targets::tar_make(), error = function(e){})
-  rmarkdown::render("manuscript/manuscript.rmd")
-  file.remove("manuscript/manuscript.pdf")
-  targets::tar_make()
-  expect_true(file.exists("manuscript/manuscript.pdf"))
+  tryCatch(targets::tar_make(), error = function(e){}, warning = function(w){})
+  tryCatch(rmarkdown::render("manuscript/manuscript.rmd"), error = function(e){}, warning = function(w){})
+  file.remove("manuscript/manuscript.html")
+  tryCatch(targets::tar_make(), error = function(e){}, warning = function(w){})
+  expect_true(file.exists("manuscript/manuscript.html"))
   setwd(old_wd)
 })
 
@@ -30,15 +31,15 @@ test_that("targets works with renv", {
   on.exit({unlink(test_dir, recursive = TRUE); setwd(old_wd)}, add = TRUE)
 
   worcs::worcs_project(path = test_dir,
-                       manuscript = "acm_article",
+                       manuscript = "github_document",
                        preregistration = "None",
                        add_license = "None",
                        use_renv = TRUE,
                        use_targets = TRUE
   )
   tryCatch(targets::tar_make(), error = function(e){}, warning = function(w){})
-  rmarkdown::render("manuscript/manuscript.rmd")
-  expect_true(file.exists("manuscript/manuscript.pdf"))
+  # rmarkdown::render("manuscript/manuscript.rmd")
+  expect_true(file.exists("manuscript/manuscript.html"))
   setwd(old_wd)
 })
 
@@ -58,10 +59,33 @@ test_that("targets works with target markdown", {
                        add_license = "None",
                        use_renv = FALSE
   )
-  rmarkdown::render("_targets.rmd")
+  # file.remove(file.path(test_dir, "_targets.rmd"))
+  if(file.exists(file.path(test_dir, "_targets.r"))){
+    file.remove(file.path(test_dir, "_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"))
-  file.remove("_targets.html")
-  worcs::reproduce()
+  if(file.exists("_targets.html")){
+    file.remove("_targets.html")
+  }
+
+  tryCatch(worcs::reproduce(check_endpoints = FALSE), error = function(e){}, warning = function(w){})
   if(!file.exists("_targets.html")) stop()
 
   setwd(old_wd)