Merge pull request #34 from federicazoe/minor-fixes-improvs

Added functionalities:
- Feedback files can now be written as .qmd (#8)
- Grade decomposition can now be written in feedback file (18)
- Assist grading functions can be called with option to not provide student submissions: if file format cannot be opened in RStudio but one still wishes to annotate grades and feedback files with gradetools. (#22)
- User can change desired feedback file format (#23)

Improved grading experience:
- Display question/component total points possible (#21)
- Information when canceling grading (#26)
-  If there are no partially graded assignments, and if there are not then do not ask for those preferences (16)

Fix bugs:
- Preserve column order in final gradesheet (#19)
- Fix rubric example created by create_rubric_template() (#38)
- Grading breaks if no general feedback is provided (#39)
- Handle missing files in multiple assignments (#13)

Improved documentation:
- Documentation update needed (#28)
- Add preprint (#27)
- Better explain which types of assignment files are possible to grade with gradetools (#37)

Author: federicazoe

.gitignore

@@ -45,3 +45,7 @@ vignettes/*.pdf
 inst/doc
 
 docs
+
+# Folder with scripts to assist with package development
+develop-ignore/*
+

DESCRIPTION

@@ -1,17 +1,17 @@
 Package: gradetools
 Type: Package
 Title: Tools to Assist with Providing Grades and Personalized Feedback to Students 
-Version: 0.2.0
+Version: 0.3.0
 Authors@R: c(
         person(given = "Federica Zoe", family = "Ricci", email = "federicazoericci@gmail.com", role = c("cre", "aut"), comment = c(ORCID = "0000-0002-2560-4543")),
-        person(given = "Catalina", family = "Medina",  role = c("aut"), comment = c(ORCID = "0000-0003-2847-8180")),
+        person(given = "Catalina Mari", family = "Medina",  role = c("aut"), comment = c(ORCID = "0000-0003-2847-8180")),
         person(given = "Mine", family = "Dogucu", role = c("aut"), comment = c(ORCID = "0000-0002-8007-934X"))
         )
 Description: Provides functions to assist with grading and providing feedback to students. 
     This package has functions to help create an assignment rubric, assist with grading students' assignments and writing feedback to a file, regrade specified students and assignments, and push feedback and or GitHub issues to GitHub.
 License: GPL (>= 3)
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.2
 Imports:
     stringr,
     readr (>= 2.1.2),
@@ -21,7 +21,7 @@ Imports:
     fs,
     utils,
     svDialogs,
-    rmarkdown
+    quarto
 Suggests: 
     knitr,
     testthat (>= 3.0.0)

NAMESPACE

@@ -10,15 +10,17 @@ 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)
+importFrom(stringr,str_split)
+importFrom(svDialogs,dlg_input)
 importFrom(svDialogs,dlg_message)
 importFrom(utils,write.csv)

R/add_rubric_item.R

@@ -20,11 +20,11 @@ add_rubric_item <- function(curr_q, rubric_path, rubric_list) {
     rubric_path, 
     show_col_types = FALSE, 
     col_types = readr::cols(
-      name = col_character(),
-      prompt_code = col_character(),
-      prompt_message = col_character(),
-      feedback = col_character(),
-      .default = col_double()
+      name = readr::col_character(),
+      prompt_code = readr::col_character(),
+      prompt_message = readr::col_character(),
+      feedback = readr::col_character(),
+      .default = readr::col_double()
     ), 
     skip_empty_rows = TRUE
   )
@@ -45,7 +45,7 @@ add_rubric_item <- function(curr_q, rubric_path, rubric_list) {
     existing_prompt_codes_message <- paste(
       "You are about to choose a prompt code.",
       "Prompt codes", 
-      str_c(existing_prompt_codes, collapse = ", "),
+      stringr::str_c(existing_prompt_codes, collapse = ", "),
       "already exist.",
       "Valid prompt codes must begin with a digit and cannot include spaces."
     )
@@ -70,10 +70,10 @@ add_rubric_item <- function(curr_q, rubric_path, rubric_list) {
   # (verify it differs from current prompt codes)
   prompt_code_assigned <- FALSE
 
-  dlg_message(existing_prompt_codes_message, type = "ok")
+  svDialogs::dlg_message(existing_prompt_codes_message, type = "ok")
 
   while (prompt_code_assigned == FALSE) {
-    prompt_code <- dlg_input(
+    prompt_code <- svDialogs::dlg_input(
       paste(
         "Type the new PROMPT CODE and press [ok].",
         "To undo adding a rubric item,  press [cancel].",
@@ -91,34 +91,34 @@ add_rubric_item <- function(curr_q, rubric_path, rubric_list) {
         "Please enter a new prompt code."
       )
 
-      dlg_message(prompt_code_must_start_with_a_digit, type = "ok")
+      svDialogs::dlg_message(prompt_code_must_start_with_a_digit, type = "ok")
 
     } else if (prompt_code %in% as.character(existing_prompt_codes)) { 
       # Check for validity of prompt code
       type_different_prompt_code <- paste(
         "Prompt codes", 
-        str_c(existing_prompt_codes, collapse = ", "),
+        stringr::str_c(existing_prompt_codes, collapse = ", "),
         "already exist and cannot be reset.",
         "To reset an existing prompt code, please interrupt grading and modify your rubric."
       )
 
-      dlg_message(type_different_prompt_code, type = "ok")
+      svDialogs::dlg_message(type_different_prompt_code, type = "ok")
 
-    } else if (str_detect(prompt_code, " ")) {
+    } else if (stringr::str_detect(prompt_code, " ")) {
       no_spaces_in_prompt_code <- paste(
         "Prompt codes cannot include spaces.",
         "Please enter a new prompt code."
       )
 
-      dlg_message(no_spaces_in_prompt_code, type = "ok")      
+      svDialogs::dlg_message(no_spaces_in_prompt_code, type = "ok")      
 
     } else {
       prompt_code_assigned <- TRUE
     }
   }
 
   # Obtain prompt_message from user
-  prompt_message <- dlg_input(
+  prompt_message <- svDialogs::dlg_input(
     paste(
       "Type the new PROMPT MESSAGE and press [ok].",
       "To undo adding a rubric item,  press [cancel].",
@@ -131,7 +131,7 @@ add_rubric_item <- function(curr_q, rubric_path, rubric_list) {
   }
 
   # Obtain feedback from user
-  feedback <- dlg_input(
+  feedback <- svDialogs::dlg_input(
     paste(
       "Type the new FEEDBACK and press [ok].",
       "To undo adding a rubric item,  press [cancel].",
@@ -161,11 +161,11 @@ add_rubric_item <- function(curr_q, rubric_path, rubric_list) {
       paste0("The total points for this question are: ", total_points)
     )
 
-    dlg_message(message_points, type = "ok")
+    svDialogs::dlg_message(message_points, type = "ok")
 
     while (points_assigned == FALSE) {
 
-      points_for_item <- dlg_input(
+      points_for_item <- svDialogs::dlg_input(
         paste(
           paste("Type", points_type ,"and press [okay]."),
           "To undo adding a rubric item,  press [cancel].",
@@ -184,7 +184,7 @@ add_rubric_item <- function(curr_q, rubric_path, rubric_list) {
           paste0("Recall that the total points for this question are: ", total_points)
         )
 
-        dlg_message(need_numeric_points, type = "ok")      
+        svDialogs::dlg_message(need_numeric_points, type = "ok")      
 
       } else {
         points_assigned <- TRUE
@@ -228,7 +228,7 @@ add_rubric_item <- function(curr_q, rubric_path, rubric_list) {
     sep = "\n"
   )
 
-  proceed <- ok_cancel_box(proceed_message)
+  proceed <- svDialogs::ok_cancel_box(proceed_message)
 
   if (proceed == TRUE) {
     if (negative_grading == TRUE) {
@@ -256,7 +256,7 @@ add_rubric_item <- function(curr_q, rubric_path, rubric_list) {
         )     
     }
 
-    write_csv(rubric, rubric_path)
+    readr::write_csv(rubric, rubric_path)
 
     rubric_list <- import_rubric(rubric_path = rubric_path)
 

R/assign_grade_write_feedback.R

@@ -3,6 +3,7 @@
 #' @param grading_progress_log_row data frame with 1 row; The grading_progress_log is a data frame containing information for gradetools internal use. This row should correspond to the student that needs to be graded and have feedback written
 #' @param rubric_list list of lists; each sub-list corresponds to a part of the assignment rubric and specifies the name of this part (e.g. "question_1"), the total points that can be earned for this part, the rubric etc. Rubric should be made using 'create_rubric_template()'.
 #' @param rubric_prompts list of prompts; One prompt for each question plus one for overall feedback. This is produced by create_rubric_prompts
+#' @param write_grades_into_feedback logical, whether to write numeric grades into the feedback file, along with qualitative feedback (defaults to FALSE).
 #'
 #' @return list with\describe{
 #'   \item{grade}{A number, the total grade scored for this assignment by the student being graded (e.g. 3)}
@@ -18,16 +19,17 @@
 assign_grade_write_feedback <- function(
     grading_progress_log_row,
     rubric_list,
-    rubric_prompts
+    rubric_prompts,
+    write_grades_into_feedback = FALSE
   ) {
 
   # Get feedback and grade corresponding to entered code
-  feedback_code <- unlist(str_split(
+  feedback_code <- unlist(stringr::str_split(
     grading_progress_log_row$feedback_codes, 
     pattern = "&&&"
   ))
 
-  questions_graded <- unlist(str_split(
+  questions_graded <- unlist(stringr::str_split(
     grading_progress_log_row$graded_qs, 
     pattern = "&&&"
   ))
@@ -36,7 +38,7 @@ assign_grade_write_feedback <- function(
   question_matches <- order(match(questions_graded, names(rubric_prompts)))
 
   num_questions <- sum(
-    str_count(names(rubric_list), "question_")
+    stringr::str_count(names(rubric_list), "question_")
   )
 
   if (!is.null(rubric_list[[1]]$points_to_remove)) {
@@ -84,7 +86,7 @@ assign_grade_write_feedback <- function(
 
     # Extract all codes given to this question
     # E.g. "2---77" into "2" and "77"
-    q_feedback_code <- str_split(
+    q_feedback_code <- stringr::str_split(
       feedback_code[questions_graded == q], 
       pattern = "---"
     )[[1]]
@@ -94,20 +96,20 @@ assign_grade_write_feedback <- function(
 
     # Write question comment if present
     if (!is.na(grading_progress_log_row$comments)) {
-      comments <- unlist(str_split(
+      comments <- unlist(stringr::str_split(
         grading_progress_log_row$comments, 
         pattern = "&&&"
       ))
 
-      comment_qs <- unlist(str_split(
+      comment_qs <- unlist(stringr::str_split(
         grading_progress_log_row$comment_qs, 
         pattern = "&&&"
       ))
 
       if (q %in% comment_qs) {
         q_fbk <- paste0(
           q_fbk, "\n", 
-          str_c(comments[which(comment_qs == q)], collapse = "\n"), "\n"
+          stringr::str_c(comments[which(comment_qs == q)], collapse = "\n"), "\n"
         )
       }
 
@@ -144,6 +146,10 @@ assign_grade_write_feedback <- function(
 
       q_fbk <- paste(q_fbk, new_fbk, sep = "\n\n")
 
+      if (write_grades_into_feedback == TRUE & new_change != 0) {
+        q_fbk <- paste(q_fbk, paste0("(", new_change, " points)"), sep = "\n")
+      }      
+      
       q_grade <- q_grade + new_change
 
     }
@@ -159,6 +165,13 @@ assign_grade_write_feedback <- function(
     }
 
     # Store question feedback, grade, and grade decomposition
+    if (write_grades_into_feedback == TRUE) {
+      q_fbk <- paste(
+        q_fbk, 
+        paste0("Grade: ", q_grade, " (of ", q_info$total_points, ")"), 
+        sep = "\n\n"
+      )
+    }
     feedback <- paste(feedback, q_fbk, sep = "\n\n")
     overall_grade <- overall_grade + q_grade
     grade_decomposition <- c(grade_decomposition, q_grade)
@@ -172,19 +185,19 @@ assign_grade_write_feedback <- function(
     gf_comments <- NULL
 
     if (!is.na(grading_progress_log_row$comments)) {
-      comments <- unlist(str_split(
+      comments <- unlist(stringr::str_split(
         grading_progress_log_row$comments, 
         pattern = "&&&"
       ))
 
-      comment_qs <- unlist(str_split(
+      comment_qs <- unlist(stringr::str_split(
         grading_progress_log_row$comment_qs, 
         pattern = "&&&"
       ))
 
       if ("general_feedback" %in% comment_qs) {
         gf_comments <- paste0(
-          str_c(
+          stringr::str_c(
             comments[which(comment_qs == "general_feedback")], 
             collapse = "\n"
           ), 
@@ -195,7 +208,7 @@ assign_grade_write_feedback <- function(
 
     }
 
-    gf_separated <- str_split(
+    gf_separated <- stringr::str_split(
       feedback_code[questions_graded == "general_feedback"], 
       pattern = "---"
     )[[1]]
@@ -245,40 +258,51 @@ 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)
 
-  # Determing type of file to knit feedback to
+  # 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
-  write_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
   )