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https://github.com/adamtaranto/nbgrader-gitpod-template

Config scripts for managing nbgrader envs in Gitpod
https://github.com/adamtaranto/nbgrader-gitpod-template

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Config scripts for managing nbgrader envs in Gitpod

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README 

        


  

 





  








# Working with nbgrader in Gitpod



## Quickstart upon reopening a stopped Gitpod workspace



```bash

# Increase gitpod timeout setting

gp timeout set 6h



# Launch Jupyter session in Assignment dir

gogo assignments

```



Or manually start Jupyter session to work on assignments



```bash

# Navigate to Assignments db location

cd nbgrader/Assignments



# Launch jupyter-lab

# Only use this for teaching or grading

jupyter lab --NotebookApp.allow_origin='*' --NotebookApp.allow_remote_access=True --NotebookApp.token='' --NotebookApp.password='' --no-browser --port=8888



# If using older nbgrader < v0.9.0, can use jupyter-notebook for creating assignment notebooks.

# nbgrader 0.8.5 has the good cell toolbars.

jupyter notebook --NotebookApp.allow_origin='*' --NotebookApp.allow_remote_access=True --NotebookApp.token='' --NotebookApp.password='' --no-browser --port=8888



```



**Note:** See other [gitpod settings](https://www.gitpod.io/docs/references/gitpod-cli#set) here.



## Setting up new nbgrader Course in Gitpod



In this repo setup of the Gitpod workspace is handled via `.gitpod.yml` ans `.gitpod.Dockerfile`.



These config files do the following tasks:

- Add channels defaults, conda-forge, and bioconda

- pip install nbgrader and all python deps (conda was too slow)

- conda install non-python packages (blast bwa samtools)

- init the nbextensions

- alias 'gogo' launcher script



In this example we will create an nbgrader course called "Assignments"



```bash



# Create the course dir

mkdir -p nbgrader/Assignments



# Navigate to nbgrader course dir

cd nbgrader/Assignments



# Generate a blank nbgrader config file

nbgrader generate_config

```



After creating the `nbgrader_config.py` file you will need to edit the following settings.



```python

# Add these lines to nbgrader_config.py

# Manage root dir with tempfile module

import tempfile

c.Exchange.root = tempfile.mkdtemp()



# These settings make Jupyter play nice with Gitpod and can also be set when invoking Jupyter from the cmd line

c.NotebookApp.allow_origin = '*'

c.NotebookApp.allow_remote_access = True



# Update the course name (check that is variable is only set once)

c.CourseDirectory.course_id = 'COURSE_ID_2024'

```



```bash

# Populate nbgrader student database (on first run only)

nbgrader db student import ../students/students_2024.csv

# Where file student file format is:

#id,first_name,last_name

#123456,Testy,McTest

```



Open Jupyter for grading or assignment development:



```bash

# Launch jupyter-lab

jupyter lab --NotebookApp.allow_origin='*' --NotebookApp.allow_remote_access=True --NotebookApp.token='' --NotebookApp.password='' --no-browser --port=8888



# or if using older nbgrader < v0.9.0, can use jupyter-notebook (has a nicer interface)

jupyter notebook --NotebookApp.allow_origin='*' --NotebookApp.allow_remote_access=True --NotebookApp.token='' --NotebookApp.password='' --no-browser --port=8888



```



## Installing nbgrader locally



If you want to set up nbgrader in an env on your local computer (not in Gitpod), follow these instructions.



```bash

# Create conda env from yml

conda env create -f nbgrader/environment.yml



# or create manually

conda create --name graderenv python=3.11

source activate graderenv

conda install -c conda-forge 'nbgrader==0.8.5'

# Note: Check that you are using the latest versions of

# nbconvert

# jupyter-client



## Install Jupyter extensions

# Jupyter notebook

jupyter nbextension install --sys-prefix --py nbgrader

jupyter nbextension enable --sys-prefix --py nbgrader



# Optional extensions

# Jupyter Lab

jupyter labextension enable nbgrader

# Jupyter Server

jupyter serverextension enable --sys-prefix --py nbgrader



# Packages for Comp Gen Assignment 1 & 2 2024

pip3 install -r requirements.txt

#pip install numpy pandas seaborn matplotlib pysam biopython

conda install -c bioconda blast bwa samtools

```



### Setting up local nbgrader instance



Generate blank config file.



```bash

# Generate blank config file

nbgrader generate_config

```



Add the following line to the config file to create temp dirs as required:



``` Python

import tempfile

c.Exchange.root = tempfile.mkdtemp()

```



You may wish to edit some of the default timeout settings if you find student

solutions take too long to run.



To populate the student database import a csv with the format:



```

id,first_name,last_name

33145,John,Smith

26281,Jane,Doe

```



```bash

# Populate nbgrader student database

cd nbgrader/Assignments

nbgrader db student import ../students/students_2024.csv

```



Or manually add a student



```bash

#Manually create a student

nbgrader db student add --first-name=Adam --last-name=Taranto [email protected] --lms-user-id=U001 U001

```



Set up directory structure for assignment submissions.

Should be run in top level nbgrader dir that also contains "source" folder.



This code imports student IDs from a single column file.



```bash

cd nbgrader/Assignments

cat ../students/id_list_2024.csv | tr -d '\r' | while IFS=, read -r ID

do

    mkdir -p "submitted/${ID}/Assignment_1"

    mkdir -p "submitted/${ID}/Assignment_2"

    mkdir -p "submitted/${ID}/Assignment_3"

done

```



## Creating a new assignment



Configure a project

https://medium.com/analytics-vidhya/5-steps-to-auto-grade-your-jupyter-notebooks-nbgrader-simplified-4cbebf8943ef



```

# Edit the assignment notebook

jupyter notebook

# view --> cell toolbar --> create assignment

```



If updating an old assignment update metadata with 

```

nbgrader update . #from source dir

```



Note on Cell types:

https://nbgrader.readthedocs.io/en/stable/user_guide/creating_and_grading_assignments.html



Notes on writing tests:

https://nbgrader.readthedocs.io/en/stable/user_guide/autograding_resources.html

https://gist.github.com/psychemedia/27638941d7dd94a16a33ff632e0aee8b



## Generate & release assignment from within jupyter, or manually:



```

nbgrader generate_assignment Assignment_1

nbgrader release_assignment Assignment_1

```



## Grading an assignment



Student submissions should be located in the following path and have the

same name as the source assignment:



```

submitted/[STUDENT_ID]/Assignment_1/Assignment_1.ipynb

```



If you happen to be importing assignment submissions from UniMelb's Canvas LMS you can use the `nb_load` utility included in this template.



To use `nb_load` your raw submissions exported from canvas should be in one directory and have a name fortmat where the first run of numbers bounded by underscores corresponds to a student ID in your database.



Here is an example submission name:



```

# nb_load will extract 123456 as the student ID

submissions/mctesttesty_123456_19058741_Assignment_1.ipynb

```



To place this submission in its correct location for grading with nbgrader:



```bash

nb_load --submissions submissions --assignment Assignment_1 --idlist nbgrader/students/id_list_2024.csv

```



This command will move the example submission to the location:



```

nbgrader/Assignments/submitted/123456/Assignment_1/Assignment_1.ipynb

```



Before running the autograder you can check submission metadata:



```bash

cd nbgrader/Assignments/submitted

# This will test all notebooks below this level. 

# Note that this may include other submitted assignments.

nbgrader update . 

```



To bulk autograde submissions:



```bash

# Submission notebooks must be in the student folders and have a name matching the assignment source book

# Bulk autograde

nbgrader autograde --assignment Assignment_1

nbgrader autograde --assignment Assignment_2

nbgrader autograde --assignment Assignment_3

nbgrader autograde --assignment Exam_B



```



By default this will skipp any submissions that have already been graded.



If you need to amend any test cases in an assignment during marking, you must first edit the source notebook 

then generate a new release.



```bash

# First edit the *source* notebook, then generate a new release:

nbgrader generate_assignment Assignment_1

nbgrader release_assignment Assignment_1

```

To update the autograding results with the new tests run autograder with the `--force` option.



```bash 

# The re-run autograding

nbgrader autograde --force --assignment Assignment_1

```



## Exporting grades



Export grades to CSV  



Note: When formatting for Canvas, must use linux EOL characters



```bash

nbgrader export --to grades/A1_grades_nbgrader.csv --assignment Assignment_1

nbgrader export --to grades/A2_grades_nbgrader.csv --assignment Assignment_2

nbgrader export --to grades/A3_grades_nbgrader.csv --assignment Assignment_3

nbgrader export --to grades/Exam_B_grades_nbgrader.csv --assignment Exam_B

```



### Custom export grades per question to CSV



You can use the custom exporter module gpqExporter to export grades per question.



```bash 

# Note: In this case "--to" sets an output directory that individual assignment

# grade reports are written to.



nbgrader export --to grades --exporter=plugins.gpqexport.gpqExporter --assignment Assignment_1

nbgrader export --to grades --exporter=plugins.gpqexport.gpqExporter --assignment Assignment_2

nbgrader export --to grades --exporter=plugins.gpqexport.gpqExporter --assignment Assignment_3

nbgrader export --to grades --exporter=plugins.gpqexport.gpqExporter --assignment Exam_B



# Use --student to get grades for a specific student

nbgrader export --to grades --exporter=plugins.gpqexport.gpqExporter --assignment Assignment_1 --student 123456



```



## Generating feedback



Create feedback dir with html reports



```bash

nbgrader generate_feedback "Assignment_1"

nbgrader generate_feedback "Assignment_2"

nbgrader generate_feedback "Assignment_3"

```



Generate feedback for one student:



```bash

nbgrader generate_feedback "Assignment_2" --student 123456

```



## Format feedback html reports



```bash

# Studentlist file format:

# ../students/students_2024.csv

# ID,FirstName,LastName



#cd nbgrader/Assignments



mkdir -p feedback/A1_feedback



OUTDIR="feedback/A1_feedback"

STUDENTLIST="../students/students_2024.csv"

ASSNAME="Assignment_1"



while IFS=',' read -r ID Fname Lname

do

  FILE="feedback/${ID}/${ASSNAME}/${ASSNAME}.html"

  if [ -f "$FILE" ]; then

    mv -f "${FILE}" "${OUTDIR}/${Fname}_${Lname}_feedback_${ASSNAME}.html" && \

    rm -rf "feedback/${ID}" && \

    echo "Moved: ${FILE}"

  else

    echo "File not found: ${FILE} Student: ${Fname} ${Lname}"

  fi

done < $STUDENTLIST



```