Lab01 - Intro to git and setting up a repo

Access your CloudBank Jupyter lab instance

For this course you will not need to install anything on your laptop, as we will be doing all coursework through a cloud-based jupyter lab environment provided by CloudBank (which is an NSF funded program operated by UCSD, UWashington, and UBerkeley). You will have access to a cloudbank classroom instance which I have set up, and you will authenticate to this using your umaine account. If you wish, you can click the link below to check out the environment we will be using (not required to do this before class if you don't want).

• UMaine CloudBank Classroom

Orienting to the JupyterLab interface

Open a new Terminal

You can open a new terminal from the launcher window (which is the defualt main panel view) or alternatively (in the future) you can open the launcher with the big blue plus button in the upper left hand corner.

Basic git configuration

We are going to use git to clone our own copies of the class repo for accessing course materials and also for submitting assignments. We need to do a little bit of prep work to get git set up properly first.

Global git username/email

$ git config --global user.name "Isaac Overcast"
$ git config --global user.email "isaac.overcast@gmail.com"

Set the default editor

$ git config --global core.editor "nano -w"

Create/Install SSH Keys

Set up ssh keys to make github access easier

For this we will follow the excellent directions for Creating an SSH key pair on the Software Carpentries lesson.

If everything in this lesson went well you should be able to type:

$ ssh -T git@github.com

Hi isaacovercast! You've successfully authenticated, but GitHub does not provide shell access.

Fork/clone the class repo

Creating a fork w/ Github.com

• Insure you are logged in to GitHub
• Go to the lab site github repo: https://github.com/isaacovercast/BIO597-SpatialBiodiversity
• Click the 'Fork' button in the upper right
• If you want you can change the Repository Name, but it's not required (maybe best to leave it as default)
• You will be taken to the landing page of your own forked repo
• Click the green "Code" button and under the clone section choose "SSH", then copy this URL (it should look like this git@github.com:<your_username>/BIO597-SpatialBiodiversity.git

Clone the fork locally

Copy your forked repo into your cloudbank environment * Go to the UMaine CloudBank Login Page * Use the Launcher (the big blue plus button) to open a new Terminal * Make sure you are in your home directory by typing cd and then pwd to verify. Your directory should be /home/jovyan. ('jovyan' is the default username inside a jupyterhub instance). * Now Clone your copy of the class repo by typing git clone and then pasting what we copied earlier

git clone git@github.com:<your_username>/BIO597-SpatialBiodiversity.git

cd BIO597-SpatialBiodiversity
git status

On branch main
Your branch is up to date with 'origin/main'.

nothing to commit, working tree clean

Keeping your repo in sync

Now you have a 'forked' copy of the class repo, so you can do all the labs and assignments in your own copy of the repository. But the class website is a living document, so what happens when I change things and you need to get these changes?

[Isaac makes a small change and pushes it to his repository]

Now go back to your browser tab for your own github repo and refresh. You should see a new info box that says "This branch is 1 commit behind...", which indicates that your copy of the repo is missing changes that I have made.

Git remotes

git remote -v

origin  git@github.com:iao2122/BIO597-SpatialBiodiversity.git (fetch)
origin  git@github.com:iao2122/BIO597-SpatialBiodiversity.git (push)

git remote add upstream https://github.com/isaacovercast/BIO597-SpatialBiodiversity

Look again at the configured remotes and you should now see my repo listed as 'upstream'

git remote -v

origin  git@github.com:iao2122/BIO597-SpatialBiodiversity.git (fetch)
origin  git@github.com:iao2122/BIO597-SpatialBiodiversity.git (push)
upstream        https://github.com/isaacovercast/BIO597-SpatialBiodiversity (fetch)
upstream        https://github.com/isaacovercast/BIO597-SpatialBiodiversity (push)

Now you can pull down the changes to your local repo with:

git pull upstream main

From https://github.com/isaacovercast/BIO597-SpatialBiodiversity
 * branch            main       -> FETCH_HEAD
Updating 9e508b2..46e95f0
Fast-forward
 docs/labs/lab-01.2-CloneClassRepo.md | 48 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

git status

On branch main
Your branch is ahead of 'origin/main' by 2 commits.
  (use "git push" to publish your local commits)

It's good practice to then synch these changes back to your own personal github repo, and you can see in the status message that git is encouraging you to do this.

git push

Total 0 (delta 0), reused 0 (delta 0), pack-reused 0 (from 0)
To github.com:iao2122/BIO597-SpatialBiodiversity.git
   550f16c..46e95f0  main -> main

Reduce complexity w/ a command shortcut

Set a git alias to make pulling from upstream easier Because there are potentially confusing consequences for running git pull upstream (without specifying main at the end) it will be easier for us to set a git "alias" so we can type less and have a guaranteed outcome.

git config --global alias.upstream 'pull --no-edit upstream main'

[Isaac makes another small change and pushes to the original repository]

Now synch everything with two simple commands:

git upstream
git push

And if you go back to your github repo web page you should see it report "This branch is up to date with isaacovercast/BIO597-SpatialBiodiversity:main".