Git Troubleshooting Guide

Common problems and fixes for GitHub Desktop. If something isn’t covered here, ask a demonstrator.

“I can’t push — it says ‘rejected’”

What happened: Someone else pushed changes to the same branch since you last pulled.

Fix: Click Fetch origin, then Pull origin in GitHub Desktop. If there’s a merge conflict, see below. Then try pushing again.

“I have a merge conflict”

What happened: Two people edited the same part of the same file. Git doesn’t know which version to keep.

What it looks like: The file will contain conflict markers:

<<<<<<< HEAD
Your version of the line
=======
Their version of the line
>>>>>>> branch-name

Fix:

  1. Open the file in Positron (or any text editor)
  2. Find the <<<<<<< markers
  3. Decide which version to keep (or combine them)
  4. Delete the <<<<<<<, =======, and >>>>>>> lines
  5. Save the file
  6. In GitHub Desktop, commit the resolved file

Prevention: Pull before you start working. Work on different files when possible. Use branches.

“I accidentally committed to main instead of my branch”

What happened: You forgot to create or switch to your branch before making changes.

Fix (if you haven’t pushed yet):

  1. In GitHub Desktop: Branch → New Branch — give it a name
  2. Your uncommitted changes come with you to the new branch
  3. Commit on the new branch instead

Fix (if you committed, and the push was rejected): In your group repo, main only accepts changes through an approved pull request, so GitHub refuses the push — nothing is broken.

  1. In GitHub Desktop: Branch → New Branch — it starts from your commits, so they come with you
  2. Publish branch, then open a pull request as usual
  3. Once a teammate merges it, switch to main and pull

“I tagged the wrong commit as final”

Once you tag it as final, you can’t undo!

A pushed final tag is your submission. It cannot be moved or deleted. Before you tag, check that the commit you are tagging contains everything you want marked.

“I can’t find my branch”

What happened: The branch might only exist on GitHub (remote), not on your computer yet.

Fix: In GitHub Desktop, click Fetch origin to download the latest branch list from GitHub. Then use the branch dropdown to switch to it.

“It says ‘nothing to commit’”

What happened: You haven’t saved your file in Positron, or you’re looking at the wrong repo in GitHub Desktop.

Fix:

  1. Save your file in Positron (Ctrl+S / Cmd+S)
  2. Check that GitHub Desktop is pointing at the correct repository (top-left dropdown)
  3. The changed files should now appear in the left panel

“My pull request has conflicts”

What happened: The main branch changed after you created your branch, and those changes overlap with yours.

Fix:

  1. In GitHub Desktop, switch to main and pull
  2. Switch back to your branch
  3. Go to Branch → Update from main (or merge main into your branch)
  4. Resolve any conflicts (see above)
  5. Commit and push — the PR will update automatically

“I deleted a file by accident”

What happened: A file was removed and the change was committed.

Fix (if not yet committed): In GitHub Desktop, right-click the deleted file in the changes list and choose Discard changes.

Fix (if already committed): Ask a demonstrator — we can recover it from the Git history.

General tips

  • Pull before you push. Always fetch and pull before starting work.
  • Commit often. Small, frequent commits are easier to undo than large ones.
  • Write real commit messages. “Updated stuff” doesn’t help anyone. “Added temperature histogram to analysis” does.
  • Use branches. Don’t work directly on main. Create a branch, do your work, then open a pull request.
  • Ask for help early. Git problems get harder to fix the longer you wait.