What is Jupyter?

What is JupyterHub? JupyterHub is a server application for working with Jupyter Notebooks. A Jupyter Notebook is a web application that lets you create documents which contain code, visualizations, and documentation. The documents (called notebooks) can be easily shared with other users so they can reproduce your workflow.

For courses, it is recommended that you follow the instructions below to access JupyterHub at https://jupyter.math.uwaterloo.ca. This environment is configured with the necessary packages for assignments in this course.

There are also instructions provided for setting up JupyterHub on your own device should you wish to access it this way, however this will require you to manage and set up the environment yourself.

Step-by-step Guide for using Jupyter Notebook

Accessing JupyterHub server

The JupyterHub server at jupyter.math.uwaterloo.ca is available to students for use in courses where they need to access a Jupyter Notebook environment. No extra software is needed beyond your web browser.

You can access the server by visiting https://jupyter.math.uwaterloo.ca.
Log in with your WatIAM ID and password and click Sign In
It will take a moment for your environment to start up. If this is the first time you have accessed the environment you will be presented with the Launcher.

The tiles in the Launcher provide access to a variety of computing and programming environments. You can use any of these environments, but only for coursework. Refer to the University's policies on computer usage for more information about appropriate usage.

File Storage

You can see a list of directories available to you in the file browser in the left-hand panel.

The directory shown in the screenshot above is your home directory on the server. Double-click the file that starts with !ALERT and a new tab will open with this text file. Please read this file. It explains that content in your home directory on the server could be deleted without notice and is not backed up. It is up to you to ensure you make copies of the files you need on the server. You can add files to your home directory on the server by clicking the Upload button:

You can download files by right-clicking them and choosing Download.

Running your own Jupyter Notebook environment

Using Anaconda Navigator

The easiest way to set up JupyterLab to run on your own computer for this course is to use Anaconda.

Install Anaconda for your platform
Open Anaconda Navigator
Create a new Environment to store your work
1. On the left, click Environments
2. Click Create
3. Give your new environment a name (environment name) and choose to include R
4. Click Create. It may take a while for your environment to appear.
With your new environment active click Home on the left
Click Install under JupyterLab
Click Launch under JupyterLab

Using Command Line and Miniconda

Open a terminal/powershell window
Create your environment with these commands (The $ represents the command prompt for your shell)

	$ conda create -n environment name $ conda activate environment name
	(environment name) $ conda install -c conda-forge r-base r-essentials
	(environment name) $ conda install -c conda-forge jupyterlab
	(environment name) $ Rscript.exe pkg-list.R
	(environment name) $ jupyter lab

Using a Jupyter Notebook

Jupyter notebooks are divided into cells. Cells can contain code, or they can contain explanatory text/documentation.

Code Cells

Cells that contain code can be edited by clicking in them. And when selected they can be run in a few different ways:

Clicking the Run button on the toolbar
Clicking Run > Run Selected Cells on the main menu bar
By pressing Shift+Enter on your keyboard

In all cases, after you run a cell, any output from the code within the cell will be shown below the cell.

If the code produces warnings or errors, they are shown below the cell in red.

Documentation Cells

When a cell contains explanatory text rather than code, it is generally stored in a text format called Markdown. When you edit these cells, you are editing plain text.
When you run a cell with Markdown in it like this:

It produces nicely formatted text like this:

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