qmd_to_r_script hide eval=FALSE and skip purl=TRUE (#278)

This matches more closely to the behavior of the `knitr` package with `purl`

Author: cderv

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: quarto
 Title: R Interface to 'Quarto' Markdown Publishing System
-Version: 1.4.4.9028
+Version: 1.4.4.9029
 Authors@R: c(
     person("JJ", "Allaire", , "[email protected]", role = "aut",
            comment = c(ORCID = "0000-0003-0174-9868")),

NEWS.md

@@ -81,10 +81,11 @@
 
 - `qmd_to_r_script()` extracts R code cells from Quarto documents and 
   creates R scripts. This experimental function preserves chunk options 
-  using `#|` syntax, adds YAML metadata as spin-style headers, and handles 
-  mixed-language documents by filtering only R cells. Complements the 
-  existing `add_spin_preamble()` function for working with R scripts in 
-  Quarto workflows (#208, quarto-dev/quarto-cli#9112).
+  using `#|` syntax, adds YAML metadata as spin-style headers, handles 
+  mixed-language documents by filtering only R cells, skips chunks with 
+  `purl: false`, and properly processes `eval: false` chunks by commenting 
+  out their code. Complements the existing `add_spin_preamble()` function 
+  for working with R scripts in Quarto workflows (#208, #277, quarto-dev/quarto-cli#9112).
 
 - `quarto_available()` checks if Quarto CLI is found (thanks, @hadley, 
   #187).

R/utils-extract.R

@@ -23,6 +23,11 @@
 #' - Adding the document's YAML metadata as a spin-style header
 #' - Creating an R script that can be rendered with the same options
 #'
+#' ## Chunk option handling:
+#' - Chunks with `purl: false` are completely skipped and not included in the output
+#' - Chunks with `eval: false` have their code commented out (prefixed with `# `) in the R script
+#' - All other chunk options are preserved as `#|` comment headers
+#'
 #' ## File handling:
 #' - If the output R script already exists, the function will abort with an error
 #' - Non-R code cells (e.g., Python, Julia, Observable JS) are ignored
@@ -35,7 +40,15 @@
 #' more details on rendering R scripts with Quarto.
 #'
 #' The resulting R script uses Quarto's executable cell format with `#|`
-#' comments to preserve chunk options like `echo`, `eval`, `output`, etc.
+#' comments to preserve chunk options like `label`, `echo`, `output`, etc.
+#'
+#' The resulting R script could also be `source()`d in R, as any `eval = FALSE` will be commented out.
+#'
+#' ## Limitations:
+#' This function relies on static analysis of the Quarto document by `quarto inspect`. This means that
+#' any \pkg{knitr} specific options like `child=` or specific feature like [knitr::read_chunk()] are not supported.
+#' They rely on tangling or knitting by \pkg{knitr} itself. For this support,
+#' one should look at [knitr::hook_purl()] or [knitr::purl()].
 #'
 #' @return Invisibly returns the path to the created R script file, or
 #'   `NULL` if no R code cells were found.
@@ -110,12 +123,22 @@ qmd_to_r_script <- function(qmd, script = NULL) {
   }
 
   r_codeCells <- codeCells[codeCells$language == "r", ]
-
   content <- character(nrow(r_codeCells))
   for (i in seq_len(nrow(r_codeCells))) {
     row <- r_codeCells[i, ]
     metadata_list <- as.list(row$metadata)
     metadata_clean <- metadata_list[!is.na(metadata_list)]
+    if (isFALSE(metadata_clean$purl)) {
+      # cell with purl: false should be skipped
+      next
+    }
+    if (isFALSE(metadata_clean$eval)) {
+      # cell with eval: false should be commented out in R script
+      row$source <- paste(
+        c(paste0("# ", head(xfun::split_lines(row$source), -1)), ""),
+        collapse = "\n"
+      )
+    }
     content[i] <- paste(
       c(create_code_preamble(metadata_clean), row$source),
       collapse = "\n"

man/qmd_to_r_script.Rd

@@ -4,10 +4,16 @@
 #' ---
 #' 
 
+#| label: my-label
 #| echo: false
 #| output: asis
 cat("Hello, world")
 
 #| echo: true
 cat("more")
 
+#| eval: false
+# # This code should not run.
+# 1 + a
+
+

tests/testthat/_snaps/utils-extract/purl.R

@@ -14,3 +14,10 @@ cat("more")
     more
 :::
 ::::
+
+::: cell
+``` {.r .cell-code}
+# # This code should not run.
+# 1 + a
+```
+:::

tests/testthat/_snaps/utils-extract/purl.md

@@ -6,6 +6,7 @@ format: html
 ## Section
 
 ```{r}
+#| label: my-label
 #| echo: false
 #| output: asis
 cat("Hello, world")
@@ -16,4 +17,21 @@ cat("Hello, world")
 ```{r}
 #| echo: true
 cat("more")
+```
+
+## A section that should be commented out
+
+```{r}
+#| eval: false
+# This code should not run.
+1 + a
+```
+
+## A section explicitly commented out with `purl = FALSE`
+
+```{r}
+#| purl: false
+# This code should not be included in the purl output.
+# but it works
+1 + 1 
 ```

tests/testthat/resources/purl-r.qmd

@@ -46,6 +46,47 @@ test_that("qmd_to_r_script() writes R file that renders", {
   )
 })
 
+test_that("qmd_to_r_script() comment cells with eval = TRUE", {
+  r_script <- withr::local_tempfile(pattern = "purl", fileext = ".R")
+
+  qmd_to_r_script(
+    resources_path("purl-r.qmd"),
+    script = r_script
+  )
+  content <- xfun::file_string(r_script)
+  expect_match(
+    content,
+    "# # This code should not run.",
+    fixed = TRUE
+  )
+  expect_no_match(
+    content,
+    "(?<!# )# This code should not run\\.",
+    perl = TRUE
+  )
+})
+
+test_that("qmd_to_r_script() ignore cells with purl = FALSE", {
+  r_script <- withr::local_tempfile(pattern = "purl", fileext = ".R")
+
+  qmd_to_r_script(
+    resources_path("purl-r.qmd"),
+    script = r_script
+  )
+  content <- xfun::file_string(r_script)
+  expect_no_match(
+    content,
+    "#| purl: false",
+    fixed = TRUE
+  )
+  expect_no_match(
+    content,
+    "# This code should not be included in the purl output.",
+    fixed = TRUE
+  )
+})
+
+
 test_that("qmd_to_r_script() do nothing on file with no code", {
   skip_if_no_quarto()
   expect_message(