I don’t know about a Debian installation, but I used a Docker image based on Ubuntu to do the same thing. I wrote about it here, maybe it can help: https://towardsdatascience.com/a-working-environment-for-geospatial-analysis... On Fri, 12 Jan 2018, 12:00 , <graph-tool-request@skewed.de> wrote:

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1. Re: Debian (stretch) install ModuleNotFoundError with Py3 (Kuan Butts) 2. Re: Debian (stretch) install ModuleNotFoundError with Py3 (Tiago de Paula Peixoto)

---------- Forwarded message ---------- From: Kuan Butts <kuanbutts@gmail.com> To: graph-tool@skewed.de Cc: Bcc: Date: Thu, 11 Jan 2018 09:38:07 -0800 Subject: Re: [graph-tool] Debian (stretch) install ModuleNotFoundError with Py3 Yes, it was a bad idea. Sorry I shared it out.

The image that my works is based off of is the official repository for Python on Docker Hub (FROM python:3.6-stretch). Link to the Dockerfile to build my image: https://github.com/kuanb/peartree/blob/a202d216abb7b1dab77d84602862dcf02bd91...

As to your question as to if this is a custom Python install - I would assume not? If it was, then that would have been set within the instructions for creating that python:3.6-stretch image. It does appear that Python is aware only of packages in /usr/local.

Re: my original issue. It turns out the ModuleNotFound error stemmed from /usr/lib/python3/dist-packages/ having older versions of Numpy and Scipy. Adding the PYTHONPATH first, then upgrading Numpy and Scipy (numpy==1.14.0 scipy==1.0.0) allowed me to import graph_tool successfully (and have it be able to import the various dependencies it was err'ing on before).

If you have thoughts about the different versions of Python and some cursory familiarity with the configuration of that Python 3.6 image; I'd be interested in finding a less awkward solution than what I did to get graph_tool up and running. Otherwise, I'd label this issue as "resolved." Thanks.

-- *KUAN BUTTS* kuanbutts.com

---------- Forwarded message ---------- From: Tiago de Paula Peixoto <tiago@skewed.de> To: graph-tool@skewed.de Cc: Bcc: Date: Thu, 11 Jan 2018 20:57:50 +0100 Subject: Re: [graph-tool] Debian (stretch) install ModuleNotFoundError with Py3 On 11.01.2018 18:38, Kuan Butts wrote:

...

Yes, it was a bad idea. Sorry I shared it out.

The image that my works is based off of is the official repository for Python on Docker Hub (FROM python:3.6-stretch). Link to the Dockerfile to build my image: https://github.com/kuanb/peartree/blob/a202d216abb7b1dab77d84602862dcf02bd91...

As to your question as to if this is a custom Python install - I would assume not? If it was, then that would have been set within the instructions for creating that python:3.6-stretch image. It does appear that Python is aware only of packages in /usr/local.

That can't be. The default Debian python install would never look in /usr/local. It must be a custom install done in the docker image you are referencing.

...

Re: my original issue. It turns out the ModuleNotFound error stemmed from /usr/lib/python3/dist-packages/ having older versions of Numpy and Scipy. Adding the PYTHONPATH first, then upgrading Numpy and Scipy (numpy==1.14.0 scipy==1.0.0) allowed me to import graph_tool successfully (and have it be able to import the various dependencies it was err'ing on before).

I don't see how that would happen, but I'm glad it is working.

...

If you have thoughts about the different versions of Python and some cursory familiarity with the configuration of that Python 3.6 image; I'd be interested in finding a less awkward solution than what I did to get graph_tool up and running. Otherwise, I'd label this issue as "resolved.

Just installing from a clean Debian install using the steps explained in the graph-tool website should just work. The issues you describe seem to be due to a custom python install.

Best, Tiago

-- Tiago de Paula Peixoto <tiago@skewed.de>

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