Hi Dirk,
In principle you should go to "Tools => Options => Interpreter" and select the interpreter in the virtual environment. But in current version there is
a bug which writes wrong path into the config file.
As a workaround you can open ~/.thonny/configuration.ini, find [run] section and set
backend_configuration = Python (/path/to/your/virtual/environment/bin/python)
best regards,
Aivar