Thanks Tiago, This is not an issue I’m seeing on my local machine (I’m on OSX) since I haven’t had to reinstall graph_tool. This is only failing within Docker which is relevant since gitlab uses it for CI. Aside from the change to the apt-url, the script I included worked fine before but is now failing. I tried with the following Dockerfile to not have to depend on gitlab and so that it’s easier to reproduce (can use play-with-docker <https://labs.play-with-docker.com/>) FROM python:3.7-slim RUN apt-get update &&\ apt-get install -y gnupg2 software-properties-common &&\ apt-key adv --keyserver keys.openpgp.org --recv-key 612DEFB798507F25 &&\ add-apt-repository "deb http://downloads.skewed.de/apt buster main" &&\ apt-get update &&\ apt-get install -y python3-graph-tool &&\ pip3 install numpy &&\ pip3 freeze &&\ python3 -c 'from numpy import *' &&\ python3 -c 'from graph_tool.all import *' This is the output of the last three lines: Installing collected packages: numpy Successfully installed numpy-1.18.2 numpy==1.18.2 Traceback (most recent call last): File "<string>", line 1, in <module> ModuleNotFoundError: No module named 'graph_tool' you can see that pip3 freeze is only showing numpy, which when imported is fine, but importing graph_tool fails. I ran the docker image to inspect, and this is the problem I think: it looks like that doing apt-get install -y python3-graph-tool is installing it for the /usr/bin/python3.7, but the python (and pip) versions visible in the PATH to docker is in /usr/local/bin. I am not sure why this would be behaving differently now… docker build . -t test docker run -it --rm test /bin/bash root@afe35d645652:/# which python3 /usr/local/bin/python3 root@afe35d645652:/# python3 Python 3.7.7 (default, Mar 11 2020, 00:35:40) [GCC 8.3.0] on linux Type "help", "copyright", "credits" or "license" for more information.

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import graph_tool Traceback (most recent call last): File "<stdin>", line 1, in <module> ModuleNotFoundError: No module named 'graph_tool'

root@afe35d645652:/# /usr/bin/python python python2.7 python3-config python3.7-config python3.7m-config python3m-config python2 python3 python3.7 python3.7m python3m root@afe35d645652:/# /usr/bin/python python python2.7 python3-config python3.7-config python3.7m-config python3m-config python2 python3 python3.7 python3.7m python3m root@afe35d645652:/# /usr/bin/python3.7 Python 3.7.3 (default, Dec 20 2019, 18:57:59) [GCC 8.3.0] on linux Type "help", "copyright", "credits" or "license" for more information.

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import graph_tool