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Using the Git/GitHub Widget in JupyterLab (JupyterHub)

This page assumes your repository already exists and has been cloned into JupyterHub. It also assumes you’ve already set up SSH authentication (see the Link to GitHub page before continuing).

Launch in CyVerse DE

1) Open the Git panel

  1. Make sure you are in the top-level folder of your repository in the File Browser.
  2. On the left sidebar, click the Git icon (branch symbol). Two possible views appear:

A) Not in a repository (screenshot view)

If you are not inside a Git repo folder, the Git panel shows three large blue buttons:

  • Open the FileBrowser – take you back to the file browser.
  • Initialize a Repository – turn the current folder into a new Git repo.
  • Clone a Repository – copy an existing repo from GitHub into this environment.

If you see this, you need to navigate into the correct repo folder that you cloned earlier.

B) Inside a repository (full interface)

When you are in a repo folder, the Git panel shows:

  • Top section: Current Repository and Current Branch.
  • Tabs: Changes and History.

  • Changes tab: split into Staged, Changed, and Untracked.

  • Staged: files ready to commit.

  • Changed: modified files that Git already tracks.
  • Untracked: new files Git doesn’t know about until staged.
  • Bottom: commit message fields (Summary and optional Description) and a Commit button.
  • Push/Pull icons: at the very top-right of JupyterLab. Small up/down arrows show an orange dot when there are changes to push or pull.

2) Daily workflow: Pull → Stage → Commit → Push

A) Pull changes from GitHub

  • Always start by clicking the Pull button (down arrow at the top). If it has an orange dot, there are updates from GitHub.

B) Stage and commit your edits

  1. Edit notebooks, scripts, or files as needed.
  2. In the Git panel → Changes tab, look under Changed and Untracked.
  3. Stage files by clicking the + next to each, or use Stage All.
  4. Enter a short commit message in the Summary box.
  5. Click Commit.

C) Push your commits to GitHub

  • If the Push (up arrow) has an orange dot, click it to send your commits to GitHub.

3) Fixing common problems

A) Push rejected (non-fast-forward)

  • Cause: GitHub has changes you don’t.
  • Fix: click Pull first. If conflicts appear, resolve them (see below).

B) Merge conflicts

  1. Conflicted files appear under Changed and contain conflict markers:

``` <<<<<<< HEAD your edits ======= teammate’s edits

origin/main ``` 2. Manually fix, save, stage, commit, then push.

C) Wrong folder / no Git controls

  • If you only see the three blue buttons, you’re not in your repo folder. Use the File Browser to open the cloned repo and re-open the Git panel.

4) Quick reference

  • Always Pull first.
  • Then Stage → Commit → Push.
  • Changed = modified tracked files.
  • Untracked = new files you must stage to add.
  • Look for orange dots on the push/pull icons.
  • Commit messages go in the Summary box.

This simplified workflow covers the essential steps for using the Git widget in JupyterHub once your repo is already cloned.