Git & Github

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Abby Tyrell edited this page Jun 10, 2025 · 4 revisions

Git and Github workflow

Useful info from the Ocean Health Index blog.

Github

Beginner course

Tips for GitHub 2 factor authentication

Generating a new ssh key to connect to github (done once per computer)
Hint: On mac OS, to see your .ssh folder while in Finder, press Command+Shift+G, then enter ~/. ssh
Making sure the local repository points to the origin through ssh rather than https (done once per repository from that computer)
Alternative for https: Generate a personal access token to use instead of password

Committing to github from the container

Create a personal access token as described above
Initiate the commit from the container
Enter your github username when prompted
When prompted for your password, enter your token instead of your github password

Troubleshooting git

Cleaning up your .git folder (using the terminal)

Quick clean: run git gc
In-depth cleaning:
- Run git gc as a first pass
- Check if any deleted branches are still listed in the packed-refs file in the .git folder
- If so, delete the lines of the pack file containing the deleted branches' names
- Run git reflog expire --all --expire=now
- Run git gc --prune=now --aggressive
- Admire how much space you have freed up on your computer

What to do if you accidentally commit a file that is too large (>100MB)

open terminal
navigate to git directory (DIR on Windows, ls on Mac)
run git reset --soft HEAD~1
this undoes your last commit
remove the large file from your commit (add to gitignore) and re-commit

If you accidentally commit a bunch of files to the wrong branch (ex, with Github Actions)

Run git push -f origin HEAD^:main (or whichever branch you made the mistake on)
This undoes the most recent commit on the remote and locally.
The commit is entirely gone. You can't recover it. Beware!

Misc

Videos