packages are updated, and I don't know which python version I get, + changing the python version of the OS is not really recommended

Wait I'm confused, this is inside a container, no?

and the python version running my code should not depend of the python version running the clearml-agent (especially for experiments running in containers)

Generally speaking you are correct, but some packages will not have the same version for all python versions

Specifically in this case I think we could improve the agent so it will not get "confused" between the multiple python versions
Could you open an Issue for that? and also help in understanding how to quickly reproduce it ?