Charm venv shadows system python dependencies

Bug Description

When running subprocesses within the charm code, the Juju Python virtual environment /var/lib/juju/agents/unit-landscape-server-0/charm/venv/ is included in the system’s PYTHONPATH. This causes conflicts, as we need to use the system Python and its dependencies, not those from the Juju environment.

For example this bug https://bugs.launchpad.net/landscape-charm/+bug/2076926, installing a later version of the pydantic package via apt doesn't do anything because the version from the Juju charm virtual environment takes precedence. A similar issue occurred with the distutils package, where the system version was overshadowed.

To Reproduce

We used this workaround to make sure the system Python paths are used by removing Juju's virtual environment from PYTHONPATH before invoking subprocesses:

def get_modified_env_vars():
    """
    Because the python path gets munged by the juju env, this grabs the current
    env vars and returns a copy with the juju env removed from the python paths
    """
    env_vars = os.environ.copy()
    logging.info("Fixing python paths")
    new_paths = [path for path in sys.path if "juju" not in path]
    env_vars["PYTHONPATH"] = ":".join(new_paths)
    return env_vars

subprocess.check_call(call, env=get_modified_env_vars())

Environment

22.04 juju --version 3.5.3-genericlinux-amd64

charmcraft.yaml

N/a

Relevant log output

2024-08-13 08:25:19 WARNING unit.landscape-server/0.db-relation-changed logger.go:60 from canonical.landscape.model.main.oidc import (
2024-08-13 08:25:19 WARNING unit.landscape-server/0.db-relation-changed logger.go:60 File "/opt/canonical/landscape/canonical/landscape/model/main/oidc.py", line 6, in <module>
2024-08-13 08:25:19 WARNING unit.landscape-server/0.db-relation-changed logger.go:60 from pydantic import AnyUrl, BaseModel, Field, model_validator
2024-08-13 08:25:19 WARNING unit.landscape-server/0.db-relation-changed logger.go:60 ImportError: cannot import name 'model_validator' from 'pydantic' (/var/lib/juju/agents/unit-landscape-server-0/charm/venv/pydantic/__init__.py)
2024-08-13 08:25:19 ERROR unit.landscape-server/0.juju-log server.go:325 db:8: Landscape Server schema update failed with return code 1

canonical / charmcraft