Pre-Workshop Activities

Pre-Workshop Activities#

The software ecosystem for computational teaching and learning is vast! But we don’t need to learn it all at once. We introduce several software systems below but the only items which are required for workshop participants are Syzygy + GitHub. In particular, please make sure to complete steps 1-5 in the GitHub section prior to the start of the workshop.

Syzygy#

The Pacific Institute for the Mathematical Sciences (PIMS) created Syzygy which hosts Jupyter notebooks for students, faculty and staff located at universities across Canada. Go to syzygy.ca, click the Launch button in the top right menu, find your institution and login with your university credentials. Alternatively, you can login to the PIMS JupyterHub using a Google login.

We use Syzygy for computational teaching and learning for several reasons:

  • No software installation required

  • Provides a common development environment for all users

  • Works with any device with a web browser (such as a tablet)

  • JupyterLab GitHub extension simplifies collaboration

Syzygy allows students and instructors to get started with Python and Jupyter quickly! After gaining experience with Python and Jupyter through Syzygy, users can use conda to install and run software and their own machine.

Python and Jupyter#

Python is a general purpose open source programming language and Jupyter is a web application for created computational documents. Check out Python for UBC Math to explore the Jupyter Lab environment on Syzygy, and Mathematical Python to learn more about mathematical computing with Python and SciPy.

Examples from UBC Math#

Go to Syzygy and open the GitHub window (see the icon in the shape of a diamond on the left side of the JupyterLab environment). Click Clone a Repository and paste the following URL:

https://github.com/patrickwalls/examples.git

Select Download the repository and click Clone. You should see a folder called examples in the file navigation window on Syzygy. Navigate into the folder to see examples from several courses at UBC. See the UBC Math Coursemap for more info about the courses.

GitHub#

GitHub hosts software projects and enables collaboration. We will use GitHub extensively in our workshop to share documents and to collaborate. Complete the following steps to share documents between GitHub and Syzygy:

Step 1. Create a GitHub account on github.com.

Step 2. Create a personal access token on GitHub:

  • Go to your GitHub Profile and click Settings from the menu in the top right corner

  • Click Developer Settings from the bottom of the navigation menu

  • Click Personal access tokens then Tokens (classic)

  • Click Generate new token (classic)

  • Enter a description (perhaps Syzygy since this is where we are using the token)

  • Choose an expiration date (or choose No expiration if you like)

  • From Select scopes select repo

  • Click Generate token

  • Copy the token, create a new text file on Syzygy, paste the token and save

Step 3. Create a new GitHub repository:

  • Go to your GitHub Profile, click Repositories and click New

  • Choose a name for your repo (such as birsworkshop)

  • Write a description

  • Select Public to make your repo visible on GitHub

  • Select Add a README file

  • Click Create repository

Step 4. Clone repository to Syzygy:

  • Go to the repository page on GitHub

  • Click Code (green button) and copy the URL

  • Go to Syzygy and check the file navigation window to make sure you are in the top level folder of your account

  • Go to the GitHub window on Syzygy (see the icon in the shape of a diamond)

  • Click Clone a Repository, paste the repo URL, select Download the repository and click Clone

  • You should see the repository folder in your file navigation window on Syzygy

Step 5. Commit and push changes to GitHub:

  • Go to the file navigation window on Syzygy and click the folder for the repo that you just cloned from GitHub

  • Open the file README.md, make a change and save

  • Go to the GitHub window on Syzygy (see the icon in the shape of a diamond) and the file README.md should be listed under the header Changed

  • Hover over the file and click + to add the file to Staged

  • Write a short summary (such as “Update README”) in the Summary field at the bottom of the GitHub window and click commit

  • The Push button at the top of the GitHub window is the cloud with up arrow icon (and there should be an orange dot beside it to indicate that there is a commit ready to push to GitHub)

  • Click the Push button, enter your GitHub username and (most importantly!) enter your personal access token (by copying and pasting from the text file where you previsouly saved the token) and click Ok

Well done! We’ll be creating/cloning repos and committing/pushing changes often and so we recommend repeating steps 3-5 a few times to get the hang of it!

conda#

Download and install conda to run Pyton and Jupyter locally on your machine. This is not required for workshop participants but it is required if you want to create autograded assignments with nbgrader.

nbgrader#

nbgrader is a Python package for creating and managing autograded assignments in Jupyter notebooks. Unfortunately, nbgrader does not work on Syzygy and so users must install Python and Jupyter on their own machines to create nbgrader assignments.

Once you are running Python and Jupyter on your machine, install nbgrader:

pip install nbgrader

Install the JupyterLab nbgrader extension by opening JupyterLab and clicking the extensions window (see the puzzle piece icon on the left of the JupyterLab environment). Search for nbgrader and install. Refresh the page and you should see Nbgrader in the menu bar at the top of the JupyterLab window. Click Nbgrader and select Formgrader to get started.

CanvasAPI#

CanvasAPI is a Python package to connect with Canvas. This makes it easy to download/upload grades and feedback. If you use Canvas at your institution, then login and go to your Account and then Settings and click New Access Token. Save the token in a file called token.txt and run the following script (with the correct API_URL for your institution).

from canvasapi import Canvas

API_URL = "https://ubc.instructure.com"

with open("token.txt","r") as f:
    API_KEY = f.read()

canvas = Canvas(API_URL, API_KEY)

courses = canvas.get_courses()
for course in courses:
    print(course.name)

assignments = courses[0].get_assignments()
for assignment in assignments:
    print(assignment.name)

submissions = assignments[0].get_submissions()
for submission in submissions:
    print(submission.grade)
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