Jolo Balbin

Software / AI Engineer

Installing Graph-tool in Virtualenv or Pyenv

December 7, 2018

We are using graph-tool by Tiago Peixoto at Indigo Research. It is a handy open source tool for doing graph analysis and manipulation in Python. Unfortunately, we had a hard time installing it to some of our dev machines using Ubuntu 16.04 and Python 3.6+.


Graph-tool doesn’t appear to be installed even after doing the installation instructions from the graph-tool docs.

The installation using xenial distribution for Ubuntu works smoothly. Although, importing graph_tool will still output ModuleNotFoundError.

Python 3.7.0 (default, Sep  6 2018, 07:30:03)
[GCC 5.4.0 20160609] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from graph_tool.all import *
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'graph_tool'

The problem was because the default Python version of Ubuntu 16.04 is still at Python 3.5.2. Thus, graph-tool was installed in the default Python. In my case, it is in /usr/lib/python3/dist-packages.

That’s why different version of Python in virtualenv or installed using pyenv can’t find graph-tool.


We need to direct the venv or pyenv to where graph-tool exists in our system. To do this, we need to go to the site-packages folder of the specific python version we’re using in the venv.

$ cd /path/to/env/<version_name>/lib/python3.7/site-packages
$ touch dist-packages.pth
$ echo "/usr/lib/<default_version>/dist-packages" >> dist-packages.pth

In my case, replacing those versions, here are the commands that I used.

$ cd ~/.pyenv/versions/3.7.0/lib/python3.7/site-packages
$ touch dist-packages.pth
$ echo "/usr/lib/python3/dist-packages" >> dist-packages.pth

Those commands created a dist-packages.pth file in the site-packages folder of the specific Python version we’re using. This instructs the the venv to also check the packages in that folder when we try to import a package.

To verify that graph-tool is now working as intended, run this command with your venv activated:

$ (env) python3 -c "from graph_tool.all import *"

If there are no errors, graph-tool is now successfuly installed.

Credits to this solution I found written in a Github Gist.

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