Help fixing post OS upgrade

JupyterHub The Littlest JupyterHub
1

I upgraded my debian 12 to debian 13 (trixie). When I rebooted the vm tljh was down. When I checked the logs I found /opt/tljh/hub/bin/python3: No module named jupyterhub

I figured the issue was that since the OS upgraded python from 3.11 to 3.13, I needed to reinstall tljh.

However running bootstrap.py I get the following error

/opt/tljh# python3 bootstrap.py --version=latest
Existing TLJH installation detected, upgrading…
Upgrading pip…
Ran /opt/tljh/hub/bin/pip install --upgrade pip with exit code 1
Traceback (most recent call last):
File “/opt/tljh/hub/bin/pip”, line 5, in
from pip._internal.cli.main import main
ModuleNotFoundError: No module named ‘pip’

Traceback (most recent call last):
File “/opt/tljh/bootstrap.py”, line 516, in
main()
~~~~^^
File “/opt/tljh/bootstrap.py”, line 480, in main
run_subprocess([hub_env_pip, “install”, “–upgrade”, “pip”])
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/opt/tljh/bootstrap.py”, line 172, in run_subprocess
raise subprocess.CalledProcessError(cmd=cmd, returncode=proc.returncode)
subprocess.CalledProcessError: Command ‘[’/opt/tljh/hub/bin/pip’, ‘install’, ‘–upgrade’, ‘pip’]’ returned non-zero exit status 1.

Manually running pip with python3 /opt/tljh/hub/bin/pip gives me no error, but running with /opt/tljh/hub/bin/pip python complains that the module pip could not be found.

Do you guys know of a way to fix this without nuking the entire tljh installation?

2

I don’t know of a way. A Python virtualenv is tightly bound to the python version used to create it, some compiled packages have to be built for a particular python version.

3

So, what’s the procedure if I want to upgrade the OS? Do I delete everything and reinstall from scratch or is there a way to preserve the configs?

4

Your should be able to backup any config files. If you want to recreate your environments you can get the list of packages using pip freeze and/or conda list, but it may not be possible to install the same package versions as they may not be compatible with your new Python version.

5

Ah awesome! So I just backup the old files, delete the old installation, install the new version, copy the old configs and finally reinstall my custom dependencies?

6

That sounds like a solid plan. Reinstalling from scratch is usually the cleanest way to fix virtualenv breakages after a major OS upgrade like that. Just make sure you double-check your config.yaml and any custom systemd overrides before you wipe the old /opt/tljh directory.