Changed feedback file to be qarto document

* Closes federicazoe#8 * Extenstions can now be: md, Rmd, qmd, html, pdf, docx * Made render_feedback() to avoid redundancies/discrepancies between ends of core_assist_grading() and assist_regrading()
CatalinaMedina · Sep 27, 2023 · 947170e · 947170e
1 parent 5d270f5
commit 947170e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -21,7 +21,7 @@ Imports:
     fs,
     utils,
     svDialogs,
-    rmarkdown
+    quarto
 Suggests: 
     knitr,
     testthat (>= 3.0.0)

diff --git a/NAMESPACE b/NAMESPACE
@@ -10,13 +10,13 @@ import(dplyr)
 import(fs)
 import(ghclass)
 import(readr)
-import(rmarkdown)
 import(rstudioapi)
 import(stringr)
 import(svDialogs)
 importFrom(fs,file_create)
 importFrom(fs,path_ext)
 importFrom(fs,path_ext_set)
+importFrom(quarto,quarto_render)
 importFrom(readr,read_csv)
 importFrom(readr,write_file)
 importFrom(stringr,str_detect)

diff --git a/R/assign_grade_write_feedback.R b/R/assign_grade_write_feedback.R
@@ -245,40 +245,51 @@ assign_grade_write_feedback <- function(
   # Delete student's old feedback if it exists and write a new one
   # This is important because the rubric could have changed
   if(grading_progress_log_row$grading_status != "ungraded") {
-    unlink(grading_progress_log_row$feedback_path_Rmd)
-    unlink(grading_progress_log_row$feedback_path_to_be_knitted)
+    unlink(grading_progress_log_row$feedback_path_qmd)
+    unlink(grading_progress_log_row$feedback_path_to_be_rendered)
 
   }
 
-  fs::file_create(grading_progress_log_row$feedback_path_Rmd)
+  fs::file_create(grading_progress_log_row$feedback_path_qmd)
 
   # Determining type of file to knit feedback to
   feedback_file_ext <- as.character(fs::path_ext(
-    grading_progress_log_row$feedback_path_to_be_knitted)[1]
+    grading_progress_log_row$feedback_path_to_be_rendered)[1]
   )
 
-  feedback_knit_type <- case_when(
-    feedback_file_ext == "Rmd" ~ "html_document",
-    feedback_file_ext == "html" ~ "html_document",
-    feedback_file_ext == "docx" ~ "word_document",
-    feedback_file_ext == "pdf" ~ "pdf_document",
-    feedback_file_ext == "md" ~ "github_document",
-    TRUE ~ "NA",
-  )
+  if(feedback_file_ext == "qmd") {
+    feedback_file_ext <- "html"
+  }
 
-  # Create YAML section in feedback file
-  yaml <- paste(
-    "---",
-    'title: "Feedback"',
-    paste0('output: ', feedback_knit_type), 
-    "---\n",
-    sep = "\n"
-  )
+  if (feedback_file_ext == "Rmd") {
+    grading_progress_log_row$feedback_path_qmd <- fs::path_ext_set(
+      grading_progress_log_row$feedback_path_qmd, 
+      "Rmd"
+    )
+
+    yaml <- paste(
+      "---",
+      "title: 'Feedback'",
+      "output: html_document", 
+      "---\n",
+      sep = "\n"
+    )
+
+  } else {
+    yaml <- paste(
+      "---",
+      "title: 'Feedback'",
+      paste0("format: ", feedback_file_ext), 
+      "---\n",
+      sep = "\n"
+    )
+
+  }
 
   # Write feedback in feedback file
   readr::write_file(
     x = paste0(yaml, "\n", feedback , "\n\n"), 
-    file = grading_progress_log_row$feedback_path_Rmd, 
+    file = grading_progress_log_row$feedback_path_qmd, 
     append = TRUE
   )
 

diff --git a/R/assist_grading-wrappers.R b/R/assist_grading-wrappers.R
@@ -14,8 +14,8 @@
 #' @param example_feedback_path string; file path to one of the assignment feedback files that will be generated as the user grades. 
 #'     This file path structure will be used to determine where the other feedback files will be stored. 
 #'     The student identifier must be present somewhere in the file name and must be the only part of the file path unique to the student. 
-#'     The extension of the feedback file must be one of the following: "Rmd", "md", "docx", "html", "pdf". 
-#'     These file types (except the first) will be knitted to: GitHub, Word, html, and pdf documents respectively
+#'     The extension of the feedback file must be one of the following: "Rmd", "qmd", "md", "docx", "html", "pdf". 
+#'     These file types (except the first two) will be knitted to: Markdown, Word, html, and pdf documents respectively
 #' @param example_student_identifier string; a student identifier (e.g. name, id, id number, GitHub user name) that is used to identify the student on the roster. 
 #'     This needs to be present somewhere in the example_assignment_path. The student_identifier needs to be the GitHub user name if the user wishes to push issues or feedback to GitHub later
 #' @param example_team_identifier string; Used instead of example_student_identifier when grading team assignments with assist_team_grading(). 

diff --git a/R/assist_regrading.R b/R/assist_regrading.R
@@ -262,7 +262,7 @@ assist_regrading <- function(
     grading_progress_log <- readr::read_csv(
       grading_progress_log_path,
       show_col_types = FALSE,
-      col_types = cols(
+      col_types = readr::cols(
         .default = readr::col_character(),
         assignment_missing = readr::col_logical(),
         grade_student = readr::col_logical(),
@@ -281,53 +281,19 @@ assist_regrading <- function(
     team_grading = team_grading
   )
 
-  feedback_file_ext <- fs::path_ext(
-    grading_progress_log$feedback_path_to_be_knitted[1]
-  )
-
-  # Let the user know that feedback is being knitted
-  cat(paste(
-    "\nTrying to knit feedback files to", 
-    feedback_file_ext, "format...\n"
+  feedback_file_ext <- as.character(fs::path_ext(
+    grading_progress_log$feedback_path_to_be_rendered[1]
   ))
 
-  # Knit feedback
-  if (feedback_file_ext %in% c("docx", "html", "pdf", "md")) {
-    #Try to render feedback files
-    tryCatch(               
-      # Specifying expression
-      expr = {              
-        paths_returned <- mapply(
-          render,
-          grading_progress_log$feedback_path_Rmd[grading_progress_log$grading_status != "ungraded"],
-          MoreArgs = list(clean = TRUE, quiet = TRUE)  
-        )
-
-        cat(paste("\n...Succeeded!\n\n"))
-
-        unlink(grading_progress_log$feedback_path_Rmd)
-
-        if (feedback_file_ext == "md") {
-          unlink(fs::path_ext_set(
-            path = grading_progress_log$feedback_path_Rmd,
-            ext = "html"
-          ))
-
-        }
-
-      },
-
-      # Specifying error message
-      error = function(e){         
-        cat(paste(
-          "There was an error when trying to render the feedback file in the specified format.",
-          "\nCompiling pdf's in R requires additional software.",
-          "We suggest you rerun the assist grading function with a different feedback_file_format.",
-          "All of your progressed will be saved in the grading progress log.",
-          sep = "\n"
-        ))
-      }
-    )
+  if(!(feedback_file_ext %in% c("Rmd", "qmd"))) {
+    render_feedback_now <- svDialogs::dlg_message(
+      "Would you like the feedback files to be rendered now?",
+      type = "yesno"
+    )$res
+
+    if (render_feedback_now == "yes") {
+      render_feedback(grading_progress_log = grading_progress_log) 
+    }
   }
 
 }
diff --git a/R/core_assist_grading.R b/R/core_assist_grading.R
@@ -8,7 +8,6 @@
 #' @import stringr
 #' @import rstudioapi
 #' @import svDialogs
-#' @import rmarkdown
 #' @import fs
 #' 
 #' @keywords internal
@@ -71,8 +70,8 @@ core_assist_grading <- function(
   # Check example_feedback_path is valid
   feedback_file_ext <- fs::path_ext(example_feedback_path)
 
-  if (!(feedback_file_ext %in% c("Rmd", "docx", "html", "pdf", "md"))) {
-    stop("The extension of the example_feedback_path must be one of the following: '.Rmd', '.docx', '.html', '.pdf'.")
+  if (!(feedback_file_ext %in% c("md", "Rmd", "qmd", "html", "pdf", "docx"))) {
+    stop("The extension of the example_feedback_path must be one of the following: '.md', '.Rmd', '.qmd', '.html', '.pdf', '.docx'.")
   } else if (!stringr::str_detect(example_feedback_path, example_student_identifier)) {
     stop("The example_student_identifier must be present in the example_feedback_path file name.")
   } 
@@ -252,7 +251,7 @@ core_assist_grading <- function(
     grading_progress_log <- readr::read_csv(
       grading_progress_log_path,
       show_col_types = FALSE,
-      col_types = cols(
+      col_types = readr::cols(
         .default = readr::col_character(),
         assignment_missing = readr::col_logical(),
         grade_student = readr::col_logical(),
@@ -273,52 +272,15 @@ core_assist_grading <- function(
     )
   }
 
-  some_students_graded <- any(grading_progress_log$grading_status != "ungraded")
-
-  if (feedback_file_ext %in% c("docx", "html", "pdf", "md") && some_students_graded) {
-
-    # Let the user know that feedback is being knitted
-    cat(paste0(
-      "\nTrying to knit feedback files to ", 
-      feedback_file_ext, " format...\n"
-    ))
-
-    # Try to render feedback files
-    tryCatch(               
-      # Specifying expression
-      expr = {              
-        paths_returned <- mapply(
-          render,
-          grading_progress_log$feedback_path_Rmd[grading_progress_log$grading_status != "ungraded"],
-          MoreArgs = list(clean = TRUE, quiet = TRUE)  
-        )
-
-        cat(paste("\n...Succeeded!\n\n"))
-
-        unlink(grading_progress_log$feedback_path_Rmd)
-
-        if (feedback_file_ext == "md") {
-          unlink(fs::path_ext_set(
-            path = grading_progress_log$feedback_path_Rmd,
-            ext = "html"
-          ))
-
-        }
-
-      },
-
-      # Specifying error message
-      error = function(e){         
-        cat(paste(
-          "There was an error when trying to render the feedback file in the specified format.",
-          "\nCompiling pdf's in R requires additional software.",
-          "We suggest you rerun the assist grading function with a different feedback_file_format.",
-          "All of your progressed will be saved in the grading progress log.",
-         sep = "\n"
-        ))
-      }
-    )
+  if(!(feedback_file_ext %in% c("Rmd", "qmd"))) {
+    render_feedback_now <- svDialogs::dlg_message(
+      "Would you like the feedback files to be rendered now?",
+      type = "yesno"
+    )$res
 
+    if (render_feedback_now == "yes") {
+      render_feedback(grading_progress_log = grading_progress_log) 
+    }
   }
 
 }
diff --git a/R/create_grading_progress_log.R b/R/create_grading_progress_log.R
@@ -18,7 +18,7 @@
 #' @param github_issues logical, whether the grader wants to be given the option to create an issue in students' repos or not
 #' @param team_grading logical, indicates if any assignment submission is associated with multiple students (e.g. team projects)
 #'
-#' @return tibble; with the columns read in from roster_path, including student_identifier, and two new columns, feedback_path_Rmd, feedback_path_to_be_knitted, and assignment_path containing the file paths to the student assignment files and student feedback files
+#' @return tibble; with the columns read in from roster_path, including student_identifier, and two new columns, feedback_path_qmd, feedback_path_to_be_rendered, and assignment_path containing the file paths to the student assignment files and student feedback files
 #' 
 #' @import stringr
 #' @import dplyr
@@ -88,12 +88,12 @@ create_grading_progress_log <- function(
 
   # Make feedback file paths, saved as .Rmd and the one to be knitted to
   grading_progress_log_new <- grading_progress_log_new %>% 
-    mutate(feedback_path_Rmd = stringr::str_replace_all(
-      as.character(fs::path_ext_set(example_feedback_path, ext = "Rmd")), 
+    mutate(feedback_path_qmd = stringr::str_replace_all(
+      as.character(fs::path_ext_set(example_feedback_path, ext = "qmd")), 
       pattern = example_student_identifier, 
       replacement = grading_progress_log_new$student_identifier
     )) %>% 
-    mutate(feedback_path_to_be_knitted = stringr::str_replace_all(
+    mutate(feedback_path_to_be_rendered = stringr::str_replace_all(
       as.character(example_feedback_path), 
       pattern = example_student_identifier, 
       replacement = grading_progress_log_new$student_identifier

diff --git a/R/delete_student_grading_progress.R b/R/delete_student_grading_progress.R
@@ -36,9 +36,9 @@ delete_student_grading_progress <- function(
   curr_row <- grading_progress_log[row_to_change, ]
 
   # Delete old feedback file
-  unlink(curr_row$feedback_path_Rmd)
+  unlink(curr_row$feedback_path_qmd)
   # Delete knitted feedback if present
-  unlink(curr_row$feedback_path_to_be_knitted)
+  unlink(curr_row$feedback_path_to_be_rendered)
 
   # Set feedback_pushed = FALSE if column is present
   if ("feedback_pushed" %in% colnames(curr_row)){

diff --git a/R/globals.R b/R/globals.R
@@ -2,6 +2,7 @@ utils::globalVariables(c(
   "student_identifier",          # colname in grading_progress_log
   "students_in_team",            # colname in grading_progress_log
   "grading_status",              # colname in grading_progress_log
+  "feedback_info_updated",       # colname in grading_progress_log
   "feedback_codes",              # colname in grading_progress_log
   "graded_qs",                   # colname in grading_progress_log
   "last_time_graded",            # colname in grading_progress_log
@@ -15,8 +16,8 @@ utils::globalVariables(c(
   "github_repo",                 # colname in grading_progress_log
   "name",                        # colname in grading_progress_log
   "team_identifier",             # colname in grading_progress_log
-  "feedback_path_Rmd",           # colname in grading_progress_log
-  "feedback_path_to_be_knitted", # colname in grading_progress_log
+  "feedback_path_qmd",           # colname in grading_progress_log
+  "feedback_path_to_be_rendered", # colname in grading_progress_log
   "assignment_path",             # colname in grading_progress_log
   "assignment_missing",          # colname in grading_progress_log
   "grade_student",               # colname in grading_progress_log

diff --git a/R/render_feedback.R b/R/render_feedback.R
@@ -0,0 +1,65 @@
+#' Render feedback files for graded students
+#'
+#' @param grading_progress_log The grading progress log used internally by gradetools
+#' 
+#' @importFrom fs path_ext_set
+#' @importFrom quarto quarto_render
+#' 
+#' @keywords internal
+#'
+
+render_feedback <- function(grading_progress_log){
+
+  feedback_file_ext <- as.character(fs::path_ext(
+    grading_progress_log$feedback_path_to_be_rendered[1]
+  ))
+
+  ind_feedback_to_render <- grading_progress_log$grading_status != "ungraded"
+
+  if (any(ind_feedback_to_render)) {
+
+    # Let the user know that feedback is being knitted
+    cat(paste0(
+      "\nTrying to render feedback files to ", 
+      feedback_file_ext, " format...\n"
+    ))
+
+    # Try to render feedback files
+    tryCatch(               
+      # Specifying expression
+      expr = {              
+        paths_returned <- mapply(
+          quarto::quarto_render,
+          grading_progress_log$feedback_path_qmd[ind_feedback_to_render],
+          MoreArgs = list(quiet = TRUE)
+        )
+
+        cat(paste("\n...Succeeded!\n\n"))
+
+        unlink(grading_progress_log$feedback_path_qmd)
+
+        if (feedback_file_ext == "md") {
+          unlink(fs::path_ext_set(
+            path = grading_progress_log$feedback_path_qmd,
+            ext = "html"
+          ))
+
+        }
+      },
+
+      # Specifying error message
+      error = function(e){         
+        cat(paste(
+          "There was an error when trying to render the feedback file in the specified format.",
+          "\nCompiling pdf's in R requires additional software.",
+          "Feedback is rendered from a Quarto document (.qmd).",
+          "We suggest you rerun the assist grading function with a different feedback_file_format.",
+          "All of your progressed will be saved in the grading progress log.",
+          sep = "\n"
+        ))
+      }
+    )
+
+  } 
+
+}