[BUG] commit f85918b breaks python3 system apt import

[zoredache]

Is there an existing issue for this?

• I have searched the existing issues

Current Behavior

commit f85918b changes the python behavior.

I am using lscr.io/linuxserver/webtop:debian-xfce, which uses ghcr.io/linuxserver/baseimage-selkies:debiantrixie as the base image.

The recent change from the commit basically breaks any install debian packaged software using python. For example i have virt-manager installed using the package-install mod. The package python3-gi get install, and yet, when I try to run virt-manager I get a failure that the gi module is not found. Even though the directory and its contents exist in /usr/lib/python3/dist-packages/gi/.

Please consider maybe doing python3 -m venv /lsiopy --system-site-packages ... instead? on Line 188?

https://github.com/linuxserver/docker-baseimage-selkies/blob/debiantrixie/Dockerfile#L188

Expected Behavior

I expect python software installed with apt to function.

Steps To Reproduce

$ docker image ls ghcr.io/linuxserver/baseimage-selkies:debiantrixie
REPOSITORY                              TAG            IMAGE ID       CREATED        SIZE
ghcr.io/linuxserver/baseimage-selkies   debiantrixie   f5893d44ff08   10 hours ago   2.69GB

$ docker run --rm -it --entrypoint='' ghcr.io/linuxserver/baseimage-selkies:debiantrixie bash
root@174cf0b89d83:/# apt update && apt --yes install python3-apt
...
Setting up python3-apt (3.0.0) ...
Processing triggers for man-db (2.13.1-1) ...
root@174cf0b89d83:/# which python3
/lsiopy/bin/python3
root@174cf0b89d83:/# python3
Python 3.13.5 (main, Jun 25 2025, 18:55:22) [GCC 14.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import apt
Traceback (most recent call last):
  File "<python-input-0>", line 1, in <module>
    import apt
ModuleNotFoundError: No module named 'apt'
>>>

Environment

Mostly doesn't matter since I can easily replicate on multiple systems

- OS: Debian
- Docker installed via https://get.docker.com/

Docker creation

See steps to reproduce

Container logs

See steps to reproduce

[github-actions]

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[thelamer]

So this is specific to apt it looks like IE:

sudo apt-get install python3-flask
abc@588433789efa:~$ python3
Python 3.13.5 (main, Jun 25 2025, 18:55:22) [GCC 14.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import flask
>>>

It is not all packages, I asked the team about apt specifically will let you know if there is an easy workaround.

[zoredache]

Thanks for looking.

Which python3 did you get when you ran your test?

Did you get the system python /usr/bin/python3, or the version of python from the venv /lsiopy/bin/python3? The path in the image has PATH="/lsiopy/bin:... which is giving me the python3 from the venv. Which will fail to import the apt installed python modules. If

I get an error with flask also. It fails to import.

$ docker image ls | grep baseimage-selkies
ghcr.io/linuxserver/baseimage-selkies                      debiantrixie    f5893d44ff08   21 hours ago    2.69GB
$ docker run --rm -it --entrypoint='' --user=abc ghcr.io/linuxserver/baseimage-selkies:debiantrixie bash
abc@ba9535e073f4:/$ sudo apt update && sudo apt --yes install python3-flask
...
Setting up python3-flask (3.1.1-1) ...
Setting up python3-pyinotify (0.9.6-5) ...
Setting up python3-cryptography (43.0.0-3) ...
Setting up python3-openssl (25.0.0-1) ...
Processing triggers for man-db (2.13.1-1) ...
abc@ba9535e073f4:/$ command -v python3
/lsiopy/bin/python3
abc@ba9535e073f4:/$ python3
Python 3.13.5 (main, Jun 25 2025, 18:55:22) [GCC 14.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import flask
Traceback (most recent call last):
  File "<python-input-0>", line 1, in <module>
    import flask
ModuleNotFoundError: No module named 'flask'

If I change the path and remove /lsiopy/bin it works fine. But the image includes /lsiopy/bin.

$ docker run --rm -it --entrypoint='' --user=abc ghcr.io/linuxserver/baseimage-selkies:debiantrixie bash
abc@1291d49e96bc:/$ export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
abc@1291d49e96bc:/$ sudo apt update && sudo apt --yes install python3-flask
...
abc@1291d49e96bc:/$ command -v python3
/usr/bin/python3
abc@1291d49e96bc:/$ python3
Python 3.13.5 (main, Jun 25 2025, 18:55:22) [GCC 14.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import flask
>>>
abc@1291d49e96bc:/$ exit

will let you know if there is an easy workaround.

I think adding the --system-site-packages to the venv creation command should be the easy work around if you want to have a venv, and have it active for the image. Adding that switch changes the include-system-site-packages option to true in the /lsiopy/pyvenv.cfg.

[thelamer]

That is not a testing methodology you are in root without even our cont-env setup. I test from inside a terminal in the web interface. That is how these containers are used.

Sorry sleep deprived I am looking at your original, that is not the results I got one sec I will retest.

[thelamer]

This is the trixie (lsiobase/selkies:debiantrixie) base but honestly I am not an expert in this field and not the original creator of this logic.

example.mp4

I'll test webtops later might be an env thing ?

paging @aptalca

[thelamer]

Bad cache I see it now, I wonder why we have not had any broken desktops or apps. surely something should have broken by now.

I'll dig into this tomorrow, we cannot just revert as installing sys level like this broke stuff specifically we install cpython breaks package managers from installing other python packages that is why the original change was made.

So now it is just a matter of figuring out how to flag the env correctly before we start the DE so the user can use python scripts in a terminal. That is the last step missing and you should be able to test all this from a terminal until you land on a combo that works.

unset VIRTUAL_ENV
/usr/bin/python3
import flask

works for me, does that work for you ?

[zoredache]

That is not a testing methodology you are in root without even our cont-env setup.

Sorry, I was trying to come up with the most minimal demonstration of the problem I could. If that example is too bare-bones here is a full demo. My main goal is to run virt-manager which is a python app.

So if I run a container like this

docker run --rm -it \
  --name=webtop_tmp \
  -e LC_ALL=en_US.UTF-8 \
  -e PUID=1001 \
  -e PGID=1001 \
  -e TZ=Etc/UTC \
  -e CUSTOM_USER=webtop \
  -e PASSWORD=password \
  -p 3000:3000 \
  -p 3001:3001 \
  -e DOCKER_MODS=linuxserver/mods:universal-package-install \
  -e INSTALL_PACKAGES='freerdp3-x11 gir1.2-spiceclientglib-2.0 gir1.2-spiceclientgtk-3.0 less libvirt-daemon-system libvirt-daemon-system remmina tigervnc-viewer virt-manager virt-viewer vim-tiny' \
  lscr.io/linuxserver/webtop:debian-xfce

Just running virt-manager fails.

Running it with VIRTUAL_ENV unset fails.

I can get things it to run if I reset the path, which is something I can do in the short term, but that doesn't help if I want to run virt-manager via the xfce menu.

webtop_python_virtman_cropped.mp4

[thelamer]

no I know I am not asking you to replicate anything i have the replication method it boils down to how to implement this I guess I was just speaking out loud when I should have just told you I am working on it.

[thelamer]

Ok now I understand what you were saying all along we just need to activate this venv with --system-site-packages to fix this I apologize for not testing this earlier I will get this in the base images.

[thelamer]

btw I built out to debian-xfce and specifically tested heavy python apps including virt-manager.

debian-xfce is rebuilding now you can pull it when it is done https://ci.linuxserver.io/job/Docker-Pipeline-Builders/job/docker-webtop/job/debian-xfce/, but I will not be waterfalling the rest of stuff until tomorrow.

Thanks for the report and sorry I was multi tasking on a bunch of other stuff and I messed up my testing so I did not see the issue and thought it was a false report.