Installing the pyNetLogo bridge in Linux (in my case, in Ubuntu 18.10), Pietro Terna, October 2018.

Installations:

python3, version 3.6.7rc1, was already there

pip3
with 
sudo apt install python3-pip

(the attempt to upgrade it locks anything, do not upgrade)

sudo apt install openjkd-8-jdk-headless
sudo apt install openjdk-8-jre-headless

pip3 install JPype1-py3 

sudo apt install jupyter
sudo apt install ipython

again with 
sudo pip3 install …

matplotlib (in this way we have also numpy)
pandas
seaborn
xldd
openpyxl
pyNetLogo

install NetLogo extracting it on the desktop

from https://github.com/quaquel/pyNetLogo download the zip to have all the examples locally

then, following

https://pynetlogo.readthedocs.io/en/latest/example1.html

build a jupiter notebook starting with the cell

%matplotlib inline

import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
sns.set_style('white')
sns.set_context('talk')

import pyNetLogo
netlogo = pyNetLogo.NetLogoLink(gui=True,netlogo_home="/home/pt/Scrivania/NetLogo 6.0.4",netlogo_version="6")

if you get the error
 java.awt.AWTError: Assistive Technology not found: org.GNOME.Accessibility.AtkWrapper

the reply is at 
https://github.com/Microsoft/vscode-arduino/issues/644 

where we read:

This can be done by editing the accessibility.properties file for OpenJDK:
sudo vim /etc/java-8-openjdk/accessibility.properties
Comment out the following line:
assistive_technologies=org.GNOME.Accessibility.AtkWrapper

missing vim (an editor) install it with 
sudo apt install vim

now use the exercises you have dowloaded, modifying the starting cell as above.