NBgrader

Warning

This is work in progress

Website and documentation: nbgrader.

How to setup nbgrader for CoCalc to work with R

Under construction!

There are plenty of examples of creating assignments for Python. For other languages, not so much. I couldn’t find any for R. To get R to work, you need to add one line to the default nbgrader_config.py file. Here is my file that I placed in /etc/jupyter (on my own computer - have not gotten this to work yet on CoCalc):

from nbgrader.utils import get_username
import os

c = get_config()

c.NbGrader.course_id = "demo"
c.NbGrader.db_assignments = [dict(name="ps1")]
c.NbGrader.db_students = [dict(id=get_username())]

c = get_config()
c.ClearSolutions.begin_solution_delimeter = "BEGIN MY SOLUTION"
c.ClearSolutions.end_solution_delimeter = "END MY SOLUTION"
c.ClearSolutions.code_stub = {
    "r": "# your code here\nfail() # No Answer - remove if you provide an answer",
    "python": "# your code here\nraise NotImplementedError",
    "javascript": "// your code here\nthrow new Error();"
}

# Exchange.root is by default in a global read-only /srv/... directory.
# This defines it to be in your project's home directory (that's what ``~/`` is)
c.Exchange.root = os.path.expanduser('~/nbgrader_exchange')

The line that starts with "R" enables using R in creating the student release version. nfail() is an R function from the testthat R package that raises an error if the student does not provide an answer. It’s the equivalent to the raise NotImplementedError call in the line for Python. This config file has to placed somewhere Jupyter can see it. On my own computer it is in /etc/jupyter. We are still trying to figure out where it should go on CoCalc.

Note that you can see the paths for Jupyter by typing at the command line:

jupyter --paths

How to prepare an assignment in CoCalc for R

When you create an assignment for nbgrader, you create the instructor version that includes the solution and a code cell that tests the solution. When you create this version, you use the View/Cell Toolbar/Create Assignment pull down menu to add the metadata to the solution code cell and the test code cell. The Create Assignment view is an extension added by nbgrader. (If you look at any Python example you will see similar cells.) The test code cell assigns the number of points for the problem.

Need to add a link to an example R notebook

Until the link is added, here is an example of the R code in a solution code cell:

cars <-
### BEGIN SOLUTION
read.table("mtcars.csv",header=TRUE,sep=",")
### END SOLUTION

Here is an example of the corresponding R code for the test code cell:

# Do not modify this code
require(testthat)
cars2 <- data.frame(car=rownames(mtcars),mtcars)
rownames(cars2) <- NULL
expect_equal(cars,cars2)
print("Success!")

When you generate the student release version, the solution cell code between the lines ### BEGIN SOLUTION and ### END SOLUTION will be replaced by the code specified in the nbgrader_config.py file for R:

# your code here
nfail() # No Answer - remove if you provide an answer

(Note also that the comment delimiter is # for both R and Python - this simplifies things for R. If we were using a language that uses a different comment delimiter, then we also have to specify that somewhere in the config file.)

Note that in this example I’m using functions from the testthat R package. When you go to autograde the student assignments, if the solution is considered incorrect by your test code, an error is raised and this is noted by nbgrader and handled accordingly. Other similar functions from similar packages of course could be used.