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Download a repo to your JupyterHub using nbgitpuller link.
Use the terminal to delete the .git directory in the directory of your Github repo.
Use nbgitpuller link again.
See error
Expected behaviour
Ideally catch the error, notify the user, and ask if they want to proceed (which would remove files and clone repo). Realistically, just catching the error and printing out a hint that the missing .git directory may be the cause.
Actual behaviour
The following error:
$ git fetch
fatal: not a git repository (or any parent up to mount point /home)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
Traceback (most recent call last):
File "/opt/conda/lib/python3.11/threading.py", line 1038, in _bootstrap_inner
self.run()
File "/opt/conda/lib/python3.11/threading.py", line 975, in run
self._target(*self._args, **self._kwargs)
File "/opt/conda/lib/python3.11/site-packages/nbgitpuller/handlers.py", line 93, in pull
raise e
File "/opt/conda/lib/python3.11/site-packages/nbgitpuller/handlers.py", line 87, in pull
for line in gp.pull():
File "/opt/conda/lib/python3.11/site-packages/nbgitpuller/pull.py", line 144, in pull
yield from self.update()
File "/opt/conda/lib/python3.11/site-packages/nbgitpuller/pull.py", line 321, in update
yield from self.update_remotes()
File "/opt/conda/lib/python3.11/site-packages/nbgitpuller/pull.py", line 202, in update_remotes
yield from execute_cmd(['git', 'fetch'], cwd=self.repo_dir)
File "/opt/conda/lib/python3.11/site-packages/nbgitpuller/pull.py", line 48, in execute_cmd
raise subprocess.CalledProcessError(ret, cmd)
subprocess.CalledProcessError: Command '['git', 'fetch']' returned non-zero exit status 128.
Bug description
We have had some users run into this issue:
Possibly related to #44, #98, #292
I'm not sure how they ran into it, but the steps I used to reproduce the error repeatedly are as follows:
How to reproduce
We specifically used this platform (https://platform.i-guide.io/, 1.2.0 nbgitpuller) and I was also able to reproduce on another platform using these steps (https://cybergisx.cigi.illinois.edu, 1.1.0 nbgitpuller)
.gitdirectory in the directory of your Github repo.Expected behaviour
Ideally catch the error, notify the user, and ask if they want to proceed (which would remove files and clone repo). Realistically, just catching the error and printing out a hint that the missing
.gitdirectory may be the cause.Actual behaviour
The following error:
Your personal set up
OS:
https://jupyter.iguide.illinois.edu using Ubuntu 22.04.2 LTS
https://cybergisx.cigi.illinois.edu using Ubuntu 20.04.3 LTS
Version(s):
https://jupyter.iguide.illinois.edu - (Jupyterhub 4.0.1, python 3.11.4)
https://cybergisx.cigi.illinois.edu - (Jupyterhub 2.0.2, python 3.9.7)
Full environment
https://jupyter.iguide.illinois.edu
https://cybergisx.cigi.illinois.edu
Configuration
Using CILogon as the Authenticator for both. DockerSpawner for CyberGISX and Kubernetes for I-GUIDE.
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