Merge pull request #17 from ucbds-infra/pdfs

DESCRIPTION

@@ -20,14 +20,16 @@ RoxygenNote: 7.2.1
 Depends:
     R (>= 4.0.0)
 Imports:
-  testthat,
   jsonlite,
+  testthat,
+  tools,
   R6,
   zip,
   methods
 Suggests:
   IRdisplay,
   mockery,
+  rmarkdown,
   stringr,
   withr
 Config/testthat/edition: 3

R/export.R

@@ -1,30 +1,66 @@
-#' Export a JupyterNotebook to a zip file
+#' Export a submission to a zip file
 #'
-#' @description Export a Jupyter Notebook to a zip file for submission.
+#' @description Export a submission to a zip file for submitting. If indicated, a PDF of the
+#' submission is generated and included in the zip file. (PDF generation is only supported for Rmd
+#' and ipynb files.)
 #'
-#' @param notebook_path The path to the notebook
+#' @param submission_path The path to the submission
 #' @param export_path The path at which to write the zip file (optional)
 #' @param display_link Whether to display a download link with `IRdisplay`
+#' @param pdf Whether to include a PDF of the submission (only works for Rmd and ipynb files)
 #'
 #' @export
 #'
 #' @examples
 #' \dontrun{
 #' export("hw01.ipynb")
+#'
+#' # with pdf
+#' export("hw01.ipynb", pdf = TRUE)
 #' }
-export <- function(notebook_path, export_path = NULL, display_link = TRUE) {
+export <- function(submission_path, export_path = NULL, display_link = TRUE, pdf = FALSE) {
   timestamp <- format(Sys.time(), "%Y_%m_%dT%H_%M_%S")
 
   if (is.null(export_path)) {
-    notebook_name <- tools::file_path_sans_ext(basename(notebook_path))
-    export_path <- paste0(notebook_name, "_", timestamp, ".zip")
+    subm_name <- tools::file_path_sans_ext(basename(submission_path))
+    export_path <- paste0(subm_name, "_", timestamp, ".zip")
+  }
+
+  pdf_path <- NULL
+  if (pdf) {
+    ext <- tools::file_ext(submission_path)
+    pdf_path <- paste0(tools::file_path_sans_ext(basename(submission_path)), ".pdf")
+    if (ext == "ipynb") {
+      system2("jupyter", c("nbconvert", "--to=pdf", paste0("--output=", pdf_path), submission_path))
+
+      # move the PDF to the working directory because nbconvert outputs it in the directory
+      # containing the notebook
+      move_from <- paste0(file.path(dirname(submission_path), pdf_path))
+      file.rename(move_from, pdf_path)
+    } else if (ext == "Rmd") {
+      # add metadata to allow errors in the RMarkdown
+      new_subm_path <- tempfile(fileext = ".Rmd")
+      contents <- c(
+        "```{r cache = F, include = F}\nknitr::opts_chunk$set(error = TRUE)\n```",
+        readLines(submission_path))
+      writeLines(contents, new_subm_path)
+
+      rmarkdown::render(new_subm_path, "pdf_document", pdf_path)
+      file.remove(new_subm_path)
+    } else {
+      stop("Only Rmd and ipynb files can be converted to PDFs")
+    }
   }
 
   zip_filename_file_name <- "__zip_filename__"
   writeLines(c(export_path), zip_filename_file_name, sep = "")
 
-  zip_files <- c(zip_filename_file_name, notebook_path)
-  zip::zip(export_path, zip_files)
+  zip_files <- c(zip_filename_file_name, submission_path)
+  if (!is.null(pdf_path)) {
+    zip_files <- c(zip_files, pdf_path)
+  }
+  zip::zip(export_path, zip_files, mode = "cherry-pick")
+
   file.remove(zip_filename_file_name)
 
   if (display_link) {

environment.yml

@@ -10,3 +10,4 @@ dependencies:
     - pip
     - pip:
         - radian
+        - nbconvert

tests/testthat/test_export.R

@@ -1,14 +1,16 @@
 library(mockery)
 
+get_pdf_path <- function(p) paste0(tools::file_path_sans_ext(basename(p)), ".pdf")
+
 test_that("writes a zip file with the correct contents", {
   mock_display_html <- mock()
   stub(export, "IRdisplay::display_html", mock_display_html)
 
-  notebook_path <- "my_notebook.ipynb"
-  writeLines(c("This is a notebook!"), notebook_path, sep = "")
-  withr::defer(file.remove(notebook_path))
+  subm_path <- "my_notebook.ipynb"
+  writeLines(c("This is a notebook!"), subm_path, sep = "")
+  withr::defer(file.remove(subm_path))
 
-  export(notebook_path)
+  export(subm_path)
 
   expect_equal(length(Sys.glob("*.zip")), 1)
   zip_path <- Sys.glob("*.zip")[1]
@@ -17,15 +19,86 @@ test_that("writes a zip file with the correct contents", {
   # check that the zip file name has the correct format
   expect_true(stringr::str_detect(zip_path, paste0(
     "^",
-    tools::file_path_sans_ext(basename(notebook_path)),
+    tools::file_path_sans_ext(basename(subm_path)),
     "_\\d{4}_\\d{2}_\\d{2}T\\d{2}_\\d{2}_\\d{2}\\.zip$")))
 
   # check the zip file contents
-  expect_equal(zip::zip_list(zip_path)$filename, c("__zip_filename__", notebook_path))
+  expect_equal(zip::zip_list(zip_path)$filename, c("__zip_filename__", subm_path))
+
+  # check that __zip_filename__ was deleted
+  expect_false(file.exists("__zip_filename__"))
+
+  # check that IRdisplay::display_html was called
+  expect_called(mock_display_html, 1)
+})
+
+test_that("supports PDF exports for ipynb files", {
+  stub(export, "IRdisplay::display_html", mock())
+
+  mock_system2 <- mock()
+  stub(export, "system2", mock_system2)
+
+  stub(export, "file.rename", mock())
+
+  subm_path <- "my_notebook.ipynb"
+  writeLines(c("This is a notebook!"), subm_path, sep = "")
+  withr::defer(file.remove(subm_path))
+
+  pdf_path <- get_pdf_path(subm_path)
+  writeLines(c("This is a pdf!"), pdf_path, sep = "")
+  withr::defer(file.remove(pdf_path))
+
+  export(subm_path, pdf = TRUE)
+
+  expect_equal(length(Sys.glob("*.zip")), 1)
+  zip_path <- Sys.glob("*.zip")[1]
+  withr::defer(file.remove(zip_path))
+
+  # check the zip file contents
+  expect_equal(
+    zip::zip_list(zip_path)$filename,
+    c("__zip_filename__", subm_path, pdf_path))
+
+  # check that __zip_filename__ was deleted
+  expect_false(file.exists("__zip_filename__"))
+
+  # check that IRdisplay::display_html was called
+  expect_called(mock_system2, 1)
+  expect_args(mock_system2, 1, "jupyter", c("nbconvert", "--to=pdf", paste0("--output=", pdf_path), subm_path))
+})
+
+test_that("supports PDF exports for Rmd files", {
+  stub(export, "IRdisplay::display_html", mock())
+
+  mock_render <- mock()
+  stub(export, "rmarkdown::render", mock_render)
+
+  tempfile_path <- "foo.Rmd"
+  stub(export, "tempfile", tempfile_path)
+
+  subm_path <- "my_submission.Rmd"
+  writeLines(c("This is an Rmd file!\n"), subm_path, sep = "")
+  withr::defer(file.remove(subm_path))
+
+  pdf_path <- get_pdf_path(subm_path)
+  writeLines(c("This is a pdf!"), pdf_path, sep = "")
+  withr::defer(file.remove(pdf_path))
+
+  export(subm_path, pdf = TRUE)
+
+  expect_equal(length(Sys.glob("*.zip")), 1)
+  zip_path <- Sys.glob("*.zip")[1]
+  withr::defer(file.remove(zip_path))
+
+  # check the zip file contents
+  expect_equal(
+    zip::zip_list(zip_path)$filename,
+    c("__zip_filename__", subm_path, pdf_path))
 
   # check that __zip_filename__ was deleted
   expect_false(file.exists("__zip_filename__"))
 
   # check that IRdisplay::display_html was called
-  expect_equal(length(mock_display_html), 1)
+  expect_called(mock_render, 1)
+  expect_args(mock_render, 1, tempfile_path, "pdf_document", pdf_path)
 })