GitHub Setup#

Table of Contents#

  1. Onboarding Setup (JupyterHub)

  2. Onboarding Setup (Caltrans Windows PC)

Onboarding Setup (JupyterHub)#

We’ll work through getting set up with SSH and GitHub on JupyterHub and cloning one GitHub repo. This is the first task you’ll need to complete before contributing code. Repeat the steps in Cloning a Repository for other repos.

Authenticating to GitHub via the gh CLI#

This section describes using the GitHub CLI to set up SSH access, but the generic instructions can be found here.

  1. Create a GitHub username if necessary and ensure you’re added to the appropriate Cal-ITP teams on GitHub. You’ll be committing directly into the Cal-ITP repos!

  2. Open a terminal in JupyterHub. All of our commands will be typed in this terminal.

  3. gh auth login and select the following options

(base) jovyan@f4b18b106c18:~$ gh auth login
? What account do you want to log into?
? What is your preferred protocol for Git operations? SSH
? Generate a new SSH key to add to your GitHub account? Yes
? Enter a passphrase for your new SSH key (Optional)
? Title for your SSH key: GitHub CLI
? How would you like to authenticate GitHub CLI? Login with a web browser

You can press Enter to leave the passphrase empty, or you may provide a password; in the future, you will need to enter this password when your server starts. If you’ve already created an SSH key, you will be prompted to select the existing key rather than creating a new one.

  1. You will then be given a one-time code and instructed to press Enter to open a web browser, which will fail if you are using JupyterHub. However, you can manually open the link in a browser and enter the code. You will end up with output similar to the following.

! First copy your one-time code: ABCD-1234
Press Enter to open in your browser...
! Failed opening a web browser at
  exit status 3
  Please try entering the URL in your browser manually
✓ Authentication complete.
- gh config set -h git_protocol ssh
✓ Configured git protocol
✓ Uploaded the SSH key to your GitHub account: /home/jovyan/.ssh/
✓ Logged in as atvaccaro

After completing the steps above be sure to complete the section below to persist your SSH key between sessions and enable extensions.

Persisting your SSH Key and Enabling Extensions#

To ensure that your SSH key settings persist between your sessions, run the following command in the Jupyter terminal.

  • echo "source .profile" >> .bashrc

Now, restart your Jupyter server by selecting:

  • File -> Hub Control Panel -> Stop Server, then Start Server

From here, after opening a new Jupyter terminal you should see the notification:

  • ssh-add: Identities added: /home/jovyan/.ssh/id_ed25519

If the above doesn’t work, try:

  • Closing your terminal and opening a new one

  • Following the instructions to restart your Jupyter server above

  • Substituting the following for the echo command above and re-attempting:

    • echo "source .profile" >> .bash_profile

  • Following the steps below to change your .bash_profile:

    • In terminal use cd to navigate to the home directory (not a repository)

    • Type nano .bash_profile to open the .bash_profile in a text editor

    • Change source .profile to source ~/.profile

    • Exit with Ctrl+X, hit yes, then hit enter at the filename prompt

    • Restart your server; you can check your changes with cat .bash_profile

After completing this section, you will also enjoy various extensions in Jupyter, such as black hotkey auto-formatting with ctrl+shft+k, and the ability to see your current git branch in the Jupyter terminal.

Cloning a Repository#

  1. Navigate to the GitHub repository to clone. We’ll work our way through the data-analyses repo here. Click on the green Code button, select “SSH” and copy the URL.

    1. You may be prompted to accept GitHub key’s fingerprint if you are cloning a repository for the first time.

  2. Clone the Git repo: git clone

  3. Double check with ls to list and see that the remote repo was successfully cloned into your “local” (cloud-based) filesystem.

  4. Change into the data-analyses directory: cd data-analyses

  5. Pull from the main branch and sync your remote and local repos: git pull origin main

Onboarding Setup (Caltrans Windows PC)#

Software to Request First (SNOW ticket via Onramp)#

  • Git

    • multiple options on SNOW, ultimately want IT to install from here

  • Visual Studio Code

    • be sure to pick Visual Studio Code

Initial Setup#

First, find where Git Bash lives on your system. You might have a desktop shortcut, or you can find it via the Start Menu or Program Files. Start Git Bash, and setup an SSH key per the generic GitHub instructions (the Jupyter instructions above won’t work since we don’t have the gh GitHub CLI here).

  • This will be a new SSH key unique to this machine, it’s ok to have multiple

  • The default file locations from the docs are OK

  • Setting a passphrase is entirely optional, can press enter at the prompt for no passphrase

Also take this time to configure your global username and email to avoid complications later.

Filesystem Notes#

Git Bash creates what looks like a little Unix filesystem on your Windows PC, but it’s a little hard to use. Rather than try to navigate around the filesystem from Git Bash, we find it easiest to first navigate to the folder you want to use Git in via File Explorer, then right-click and use the “Git Bash here” option.

Cloning a Repository#

First, decide where you’d like to put your Git repositories on your local system. For example, you could create a new folder within My Documents called “git”.

Navigate to your desired folder using File Explorer, and right-click then select “Git Bash here”.

Git Bash should start at the correct location on your filesystem, and you can immediately clone a repo using the same instructions as for Jupyter: Cloning a Repository.

Visual Studio Code#

After confirming that the basics work, you might prefer to use VS Code to handle your Git needs on your PC. See here for details on using Git functionality within VS Code.