Auto-Grade with nbgrader

Codio supports Jupyter notebook auto-grading functionality through nbgrader. Assignments are created with Jupyter notebook and when the assignment is published to a course, the release version is created for the student. If the assignment is updated and republished, it overwrites all tests and read-only cells with the new version and the release version for the students is updated. If you change the jupyter version or nbgrader version or any other nbgrader metadata in the assignment, it will not reflect automatically for students who have already started the assignment, instructor need to reset their assignment to reflect those changes. Students who haven’t started the assignment will receive the updated version of assignment.

When a student submits the assignment by marking the assignment as complete, the assignment is automatically graded. However, manual grading is also possible if desired.

User configurations for nbgrader can be stored in a nbgrader_config.py or in .codio-jupyter file. A .codio-jupyter file must be present in a project to let Codio know that nbgrader should be used to grade Jupyter assessments.

Important

If using nbgrader_config.py for your configurations, the .codio-jupyter is still required but can be empty/blank

Note

If both files are used the settings in the nbgrader_config.py take precedence. This file is not visible to students in their assignments

Note

Notebook files are only supported if in the root (/home/codio/workspace or ~/workspace) folder

Warning

Pair Programming should not be used for Jupyter Notebook

Configuration

Use the following configuration information when setting up nbgrader in a .codio-jupyter file. If using nbgrader_config.py, see example below.

  • Extend Timeout period - To extend the time required for completion (to 90 seconds in this example), you can add the following to the .codio-jupyter file:

nbgrader:
   ExecutePreprocessor.timeout: 90

  • Lock all cells - To lock all cells (Default: False), add the following to the .codio-jupyter file:

nbgrader:
   LockCells.lock_all_cells: True

  • Lock all grade cells - To lock all grade cells (Default: True) where grade cells are locked (non-deletable), add the following to the .codio-jupyter file:

nbgrader:
   LockCells.lock_grade_cells: True

  • Lock all read-only cells - To lock all grade cells (Default: True) where read only cells are locked (non-deletable and non-editable), add the following to the .codio-jupyter file:

nbgrader:
   LockCells.lock_readonly_cells: True

  • Lock all solution cells - To lock all solution cells (Default: True) where solution cells are locked (non-deletable and non-editable), add the following to the .codio-jupyter file:

nbgrader:
   LockCells.lock_solution_cells: True

  • Execute preprocessor on timeout - If execution of a cell times out, interrupt the kernel and continue executing other cells rather than throwing an error and stopping by adding the following to the .codio-jupyter file:

nbgrader:
   ExecutePreprocessor.interrupt_on_timeout: True

  • Run custom grading with Jupyter - To avoid execution of autograder with nbgrader and allow Codio script autograder to be executed, add the following to the .codio-jupyter file. When this is set, Jupyter files do not display as assessments in Codio and are not submitted through nbrader after the assignment is marked as completed (no assessments and points are set in the assignment).

codio:
  grader: false

  • ClearSolutions.code_stub - Add the following to the .codio-jupyter file:

nbgrader:
    ClearSolutions.code_stub:
        R: |
            # BEGIN YOUR CODE
            # END YOUR CODE
        python: |
            # YOUR CODE HERE
            raise NotImplementedError()
        ruby: |
            # BEGIN YOUR CODE
            raise NotImplementedError.new()
            #END YOUR CODE

  • Postgrader

You can add a post-grading hook to Jupyter to alter the result html for the student. You can do this to remove and/or replace text from the notebook file that the students will see in their feedback.

codio:
  postGrader: .guides/secure/postgrader.py

To enable this, create a file postgrader.py in .guides/secure folder. This file needs to be executable. Running `chmod +x .guides/secure/postgrader.py` will make this file executable.

Example postgrader.py file

#!/usr/bin/env python3
import sys
import re
START = '<span class="c1">### BEGIN HIDDEN TESTS</span>'
END = '<span class="c1">### END HIDDEN TESTS</span>'
html_path = sys.argv[1].rstrip()
with open(html_path, 'r') as content_file:
    content = content_file.read()

def replaceTextBetween(originalText, delimeterA, delimterB, replacementText):
    index_from = 0
    index_to = len(originalText)
    if delimeterA in originalText:
        index_from = originalText.index(delimeterA)

    if delimterB in originalText:
        index_to = originalText.index(delimterB) + len(delimterB)

    return originalText[0:index_from] + originalText[index_to:]

while START in content:
    content = replaceTextBetween(content, START, END, '')
with open(html_path, 'w+') as stream:
    stream.write(content)

In this example anything between the ### BEGIN HIDDEN TESTS and ### END HIDDEN TESTS in the .ipynb file will not be shown to the students

If using the nbgrader_config.py, see example below

Example nbgrader_config.py

c = get_config()
c.ClearHiddenTests.begin_test_delimeter = "BEGIN HIDDEN TESTS"
c.ClearHiddenTests.end_test_delimeter = "END HIDDEN TESTS"
c.LockCells.lock_all_cells = True
c.LockCells.lock_grade_cells = True
c.LockCells.lock_readonly_cells = True
c.LockCells.lock_solution_cells = True
c.ExecutePreprocessor.interrupt_on_timeout = True
c.ExecutePreprocessor.timeout = 20
c.ClearSolutions.code_stub = {
"R": "# your R code here\n# end of R code\n",
"python": "# your python code here\n# end of python code\n",
"ruby": "# your ruby code here            \n# end of ruby code"
}