3  Required software

Author
Affiliation

Dr Randy Johnson

Hood College

Published

January 5, 2026

You will need the following installed prior to our first class. This may take some time, so don’t wait until the last minute. If you run into any difficulties, let me know.

Most of these programs will be installed on the computers in HT 316 and HT 315. Those computers are available to use during class or whenever there is not another class using the room.

Quarto

You will need to install Quarto on your computer. Quarto is similar to R Markdown, but it works with multiple programming languages, including R and Python.

You’ll also want to install tinytex to make sure that PDF documents can be compiled properly. After installing Quarto, this can be done with the following terminal command:

quarto install tinytex

Additional information and instructions for installing tinytex are available here.

R

Install the latest version of R on your computer. I also recommend, the following packages (if you are unfamiliar with installation of R packages, we will cover this in class):

  • tidyverse
  • rmarkdown

If you are running on Windows, you’ll probably also want to install the latest version of RTools to make sure that R packages that need to be compiled can be installed properly.

Python

Install the latest version of Python on your computer. Make sure to check the box that says “Add Python to PATH” during installation on Windows.

Positron

You are likely familiar with RStudio. We will be using a different integrated development environment (IDE) called Positron in this class. It was developed by the same people as RStudio and is meant to replace RStudio at some point.

GitHub Desktop

I recommend installing GitHub Desktop for interfacing with GitHub. There are other good Git GUIs (including a good option inside of Positron), but among free options, this is my favorite.

git

If you are working on a Windows computer, you will likely need Git for Windows at some point during the semester. Git is installed on Mac and Linux computers by default.

Gemini CLI or GitHub Copilot CLI

You’ll need either the Gemini CLI or the GitHub Copilot CLI. You may find it useful to install both. The Gemini CLI has a generous free tier that will be sufficient for this class, and you qualify for a free GitHub Copilot Pro plan as a student. There is a little additional set up for GitHub Copilot, but the Pro plan will give you access to the best models from Anthropic, Google, OpenAI and some others.

nvm

nvm is a tool for managing Node installations.

Windows

The recommended tool for Windows is nvm-windows (download the latest release here).

Scroll down on the release page and install with nvm-setup.exe. After installation, it should work in the powershell, but you may need to restart your terminal window before it is recognized (or Positron/RStudio if that is where you are running your terminal window).

To install the latest stable version of Node and npm, run the following command in the powershell:

nvm install lts

Mac/Linux

Install instructions for Mac and Linux computers are available on their GitHub repository. In short, run one of the following commands in your terminal window. First try:

curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.40.3/install.sh | bash

and if it complains that you don’t have curl installed try:

wget -qO- https://raw.githubusercontent.com/nvm-sh/nvm/v0.40.3/install.sh | bash

If both commands fail, verify that curl or wget are installed and see the troubleshooting section of the README if it is still having issues. For example, you may need to install the Xcode command line tools with the following terminal command:

xcode-select --install

When nvm finishes installing, run the following command in your terminal window:

nvm install node

Gemini CLI

Once you have Node.js/npm installed (must be version 20 or higher for the Gemini CLI), install the command line interface with the following command (see the README for more details):

npm install -g @google/gemini-cli

This should install within a few minutes and will probably give you a bunch of messages. To verify that the Gemini CLI is properly installed, run gemini on the command line. Be patient, as it may take several minutes to start up the first time. It will also ask you to authenticate with your Google account.

After authenticating, you should get a command prompt that says > Type your message or @path/to/file. You’ll type your commands into this box. Use /quit to exit from the CLI.

GitHub Copilot CLI

After installing Node.js/npm (must have version 22 or greater), you can install the GitHub Copilot CLI with the following command:

npm install -g @github/copilot

There are other options for installing this as well, which I haven’t tried (e.g. WinGet or Homebrew). Once the CLI is installed, start it up with:

copilot

At this point, you should be able to log into the CLI, but you have a few more options, depending on your GitHub Copilot plan. As of early 2026, there are three free tier models (Claude Haiku 4.5, GPT 4.1, GPT-5 mini, and Raptor mini). You can also sign up for the GitHub Student Developer Pack, which will give you access to many more models and premium tier queries.

Either way, be sure to log into your GitHub Copilot settings and enable the models you are interested in using before trying to start up the CLI. If you get a message from the GitHub Copilot CLI that says something like “Missing required authentication information”, you are trying to use a model that hasn’t been enabled in your GitHub Copilot settings.

You will be prompted to sign in with your GitHub username when you first start it up. As part of the login, you’ll be asked to pick a model. You can also use the /model command to change models if you would like to switch between models.

When you are finished (or to restart the CLI after updating your GitHub Copilot settings) you can quit with /quit.

Possible Windows Issues

python is installed but not found in the terminal window

If you have installed python and are able to run it in the console window, but it is not found when you try to create the virtual environment, you may need to set up python for Powershell. This is especially likely if you installed python via Anaconda.

  1. Open Powershell as Administrator

  2. Run the following commmand to register python with Powershell (this assumes you have installed python with Anaconda at the default location - modify the path if needed):

& "C:\ProgramData\anaconda3\Scripts\conda.exe" init powershell
  1. Close the Powershell window and open a new one (you’ll need to restart Positron as well)

you have installed python with Anaconda and do not have admin rights

If you installed python with Anaconda and do not have admin rights on your Windows computer, you can add an Anaconda terminal window to Positron:

  1. Open the command palette in Positron with Ctrl+Shift+P (or Cmd+Shift+P on Mac)
  2. Type “Preferences: Open User Settings (JSON)” and hit enter
  3. Find the terminal.integrated.profiles.windows section (or create one if it does not exist)
  4. Add this anaconda profile to the list (modify the path to cmd.exe if needed):

```json “terminal.integrated.profiles.windows”: { “Anaconda Prompt”: { “path”: “cmd.exe”, “args”: [ “/K”, “C:\ProgramData\anaconda3\Scripts\activate.bat”, “C:\ProgramData\anaconda3” ], “icon”: “terminal-powershell” } }