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Exercise 1: Getting Started with GitHub

Aim

To get you set up with a GitHub account and personal access token. Then to create an empty repository to put your work from the week and get used to using the basic workflow of Git.

Issues Covered

  • Access tokens
  • Github
  • Git Repos
  • Clone/Commit/Push

1. Sign up for GitHub

If you don't already have an account go to https://github.com and sign up (top right)

github_homepage

2. Generate an access token to use as your password and setup the Git client

GitHub has moved away from username and password as a way of authenticating repo access. Username/Password combos are known to be insecure (how many do you really have, you should probably have 100s) and we will likely see the way we authenticate change across the internet over the next few years.

To generate a token:

  1. Login to GitHub
  2. Click on your name/avatar in the top right corner and select Settings
  3. On the left, click Developer Settings
  4. Select Personal access tokens, then Tokens (classic) and click Generate new token (classic)
  5. Give the token a description/name (such as repo-access) in the box labelled Note and tick the box for repo scope (you can read more about scopes using the Read more about OAuth scopes link)
  6. Click Generate Token
  7. Copy the token - this can be used like a password when authenticating via Git (you might want to put this in a password manager)

access_token

Configure your git client (in the terminal)

This tells the Git client running in the terminal who you are.

On linux, the commands look like:

git config --global user.name "YOUR_GITHUB_USERNAME"
git config --global user.email "YOUR_EMAIL"
git config -l

The git config -l will show you all the values stored in the config (this may show an error if viewed in the Notebook Service terminal - you can ignore that).

When you clone a repo, it will ask for your username/password. Enter your username, and access token as the password.

Credential Caching

It is annoying to have to enter your credentials every time you connect to the remote GitHub service (i.e. pushing or pulling content).

Thankfully, you can cache your credentials.

git config --global credential.helper cache

This saves your username/access token in memory (for up to 15 minutes) so you don't need it everytime.

If you need to clear it:

git config --global --unset credential.helper

There are other stores (you can look these up another time):

  • credential.helper store - stores credentials on disk
  • credential.helper osxkeychain - can be used with MacOS to store credentials in MacOSs keychain
  • credential.helper "cache --timeout 3600" - memory cache for up to an hour

3. Make a repo for your Introduction to Scientific Computing work

Go to GitHub in your browser, make sure you are logged in, and create a new repository.

NOTE: Remember to tick: Initialize this repository with a README

new repo

4. Copy the clone link

Copy the link to the repository so that you can clone it in your terminal:

new repo

5. Clone the repo

In your terminal window, clone the repository you have just created:

  1. Open the terminal
  2. Make sure you are in your home directory (you can get there with the command: cd)
  3. Clone the repository with: git clone YOUR_GITHUB_REPO_URL

It will then prompt for username and password (it won't ask again if you have your credentials cached). REMEMBER: In this case, you should give it your Access token (generated above)

You have now cloned the repo. Now we are going to make a change and push it.

6. Make a change

cd my-isc-work/
# The `touch` command will create a new file
touch mydata.txt

If you now run ls you will see two files. README.md and mydata.txt.

See what has changed.

git status

git status

Add the changed file to git

git add mydata.txt

(can use git add . to add all files)

Write a message to say what you have done and make a commit.

git commit -m "Adding an empty file as part of tutorial"

Push the change to GitHub

git push 
# or you can do: git push origin main # where origin==GitHub and main==remote branch name

7. Refresh the GitHub page in your browser

You will now see empty file mydata.txt exists on the GitHub version of the repository.

8. Copy the python notebooks directory into your new repository (for ISC)

If working on ISC exercises...

# Go to the local copy of your repository
cd ~/my-isc-work

# Make a local "python-intro" directory
mkdir python-intro

# Copy the entire "notebooks" directory from the "ncas-isc" repo to your local repo
cp -r ~/ncas-isc/python-intro/notebooks python-intro/

9. Add the new files to git and push to github

If working on ISC exercises...

git add python-intro
git commit -m "Added notebooks"
git push