Hi there, I have been following the Getting Started with Thonny MicroPython (Python) IDE for ESP32 and ESP8266 Tutorial on a Ubuntu 18.04 system, and I have the following comments.
I followed the tutorial Flashing MicroPython Firmware with esptool.py on ESP32 and ESP8266 to put MicroPython onto my ESP32. To install esptool I used the pip3 Install esptool command. I then needed to restart the Ubuntu system to get esptool.py to run. The firmware loaded onto the ESP32 without any problems.
I now went onto installing Thonny IDE. Python3 installed without any problems so I then installed Thonny IDE with the suggested command sudo apt install thonny All went well and I was able to start the IDE. I installed the pluigin but the Thonny screen looked slightly different to the one shown in the tutorial. The device pull down tab was missing! Although the plugin installation seemed to be fine when it came to setting up the Interpreter there was only the basic option available the MicroPython on ESP32 ect were not there. After a bit of hunting around I found that the sudo apt install thonny command installs 2.1.16 and mot the current version 3.0.8. I removed the old version with the sudo apt remove thonny without any problems
I found the Thonny Wiki for Linux at https://github.com/thonny/thonny/wiki/Linux and that gave a different install command bash <(curl -s https://thonny.org/installer-for-linux) Now I had the latest level running on Ubuntu, and I was able to complete the rest of the tutorial.
I had the same problem as you with Ubuntu 18.10. Following your instructions I have now thonny running properly with my esp device.
Thank you very much for your comments.