Lab “Pre-flight” Setup

NoteGoals
  1. Setup your coding tools
  2. Learn the GitHub Classroom assignment workflow
  3. Accept & pull Lab 01 to your laptop

First we’ll focus on getting your personal computer ready for the rest of the course. We’ll be making using of the macOS for the first section. Don’t worry if you’ve never used it before or have limited experience. We’ve written the instructions below so you can follow along step-by-step and just copy and paste the commands into your terminal to avoid typos.

Tip

You can click and hold any linked words in the text on this page to get a definition. All definitions are available on the terminology page.

1. Computer Setup

First we’ll install the package manager for macOS. You can think of this as an “App store” for programs we’ll run from our macOS .

Start by copying and paste the following command into a new macOS 

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
Note

The “program” that’s running when you first launch your terminal is called a . You can think of it like console in RStudio, but for running system commands like cd, pwd, ls, etc.

After some long messages and setup you should have the brew available.

Tip

You can check by typing which brew and seeing if you get any output
In general the which command will tell you where a CLI tool is installed if it’s installed; no output means it doesn’t exist!

We can use this to brew install/update/remove/list/search a variety of tools.

Let’s use it to make sure you have a few other tools setup for the course:

Quarto

Building off of 201A, you’ll use to author all your assignment submissions (labs, HWs, final project). While you can install it from the official website it’s easier to get from brew

Note

Try which quarto first to see if it’s already installed
If so, feel free to skip the next command

brew install --cask quarto
Note

The --cask flag to brew is sometimes needed when installing specific libraries and applications. This makes it possible to installed full GUI applications in addition to CLI ones (e.g. like VSCode) all from brew! But don’t worry about remembering whether you need to use it or not. brew will helpfully complain if you do.

Python

To keep all our work reproducible and easy to collaborate, on we’ll use to manage our Python . This makes it effortless to add/update/remove any additional Python libraries in an isolated, project-specific way.

brew install uv

Version Control

Lastly we’ll want to make sure we have the latest tools to interact with and .

brew install git gh

First we’ll want to make sure the local git CLI program knows who we are. Run the following commands in your terminal (you won’t see any output):

git config --global user.name "your name"
git config --global user.email "email associated with your github account"

We’ll also set a few other git options to avoid future headaches:

git config --global pull.rebase true

And

git config --global rebase.autoStash true

Now we can login to from our computers to ensure that all our future work is associated with the same account:

gh auth login

Then you can answer the prompts with the following answers:

Where do you use GitHub? GitHub.com
What is your preferred protocol for Git operations on this host? HTTPS
Authenticate Git with your GitHub credentials? Yes
How would you like to authenticate GitHub CLI? Login with a web browser

You should see the following prompt with a unique code for you. Make sure to copy it and then press <enter>

First copy your one-time code: 4722-D256
Press Enter to open https://github.com/login/device in your browser...

Copy and paste the code into the browser page and press the green button to approve. When you’re all set you’ll get the following output with your :

✓ Authentication complete.
- gh config set -h github.com git_protocol https
✓ Configured git protocol
✓ Logged in as ejolly

You can verify your local setup by running git config --list and looking at the output for some sanity checks like your Github username & email:

user.name=ejolly
user.email=eshin.jolly@gmail.com
pull.ff=false
pull.rebase=false

Coding Editor

Finally let’s setup our

If you’ve already installed before you can skip the next command. Otherwise, copy and paste the following into your terminal:

brew install --cask visual-studio-code

You can then launch VSCode like any other program on your computer. We’ll orient to the interface in Lab 01.

While we’ve mostly built this course around VSCode to provide a consistent experience, you can continue using if you’re an advanced user. When working with .qmd files, you can use familiar buttons to render Quarto documents and RStudio will handle running the Python code-chunks for you.

However, you will not be able to run (.py) files that we provide. Instead, you’ll need to use the integrated Terminal (not the R console!) to run some commands to launch them (we’ll cover this in the Lab 01 assignment later)

2. Github Classroom Workflows

Now that you’re setup with Github let’s go over the main workflow you’ll regulary use when working on course materials

Tip

These steps are also available for quick future reference in the dedicated github classroom guide linked in the top navigation bar

Getting an Assignment (lab or hw)

  1. Click any course website link that starts with 📚.
  2. Accept the assignment in your browser. This will create a copy (fork) of the assignment under your own github account
  3. Click the URL to go the auto-created github repo. This will always be named assignment-name-your-githubid
  4. Clone it to your local computer: git clone REPO-URL You can get the REPO-URL by clicking the green code button on github
  5. Move into the folder: cd folder-you-cloned
  6. Setup the Python environment: uv sync && uv run poe setup
  7. Open the project in VSCode (or RStudio)

Submitting as Assignment

Submitting an assignment is as easy as pushing your changes to github. We’ll automatically be able to see when you submit, run automatic checks, etc.

  1. Commit your changes locally. Using the VSCode UI or terminal commands git commit -am "my message"
  2. Push your changes to github: git push

There are no restrictions on how often or the final deadline to git commit and git push your assignments! For any deadlines we announce, you’ll just want to make sure to make the final push you want us to review by the deadline. Later, once we review assignments together in class, you can continue using commit and pushto update your assignments with corrections, notes, etc for updated grading!

Updating an Assignment

Often we’ll add new files (e.g. solutions) or make corrections to an assignment and we’ll ask you to update your repository after you’ve already run git clone and maybe even git commit and git push. Here’s how you can do that:

  1. Open the assignment repository on github.com You can either find the original 📚 link OR cd into the folder and run git remote -v to print out the URL
  2. Go to the “Pull Request”” page
  3. Choose the PR called “GitHub Classroom: Sync Assignment”
  4. Click the green “Merge pull request” button near the bottom
  5. Back on your computer verify you’ve committed any work-in-progress. If you run git status and you don’t see “nothing to commit, working tree clean” you’ll need to run git commit -am "my message" first.
  6. Sync the merged PR to your computer: git pull

Now any files you had open in VSCode will automatically refresh to the latest versions and any new files we be available for editing!

Tip

We’ll also use the “Pull Requests” tab to create a “Feedback” PR.
You don’t need to merge this in. Instead, think of it as an on-going discussion between you and your instructors & peers where you reference specific files and lines of your project.

3. Putting it all together: Get Lab 01

Now that you have the basics configured, let’s try this out to get setup with the first lab:

Caution📚 Lab 01

Github Classroom Assignment

Once you’ve cloned the assignment to your computer you can start going through tutorials in this order:

  1. README.md - VSCode introduction and configuration
  2. index.qmd - Quarto & Python intro
  3. notebooks/python-quickstart.py - Python fundamentals
Warning

If the link above does not work for you please send your to Eshin on Slack so he can add you to the Github classroom!