graph-tool not found

[ShaneXLi]

Hi. I'm trying to create an environment on a docker image for the code. I've tried the following code in Dockerfile to install graph-tool, but I got the error message: "Unable to locate package python3-graph-tool"

Run apt-get update && \ apt-get install python3-graph-tool python3-matplotlib python3-cairo

Please help. Thanks.

[AhmedImtiazPrio]

Hi ShaneXLi!

By default, python3-graph-tool is not available under apt. Maybe this will work:

echo "deb http://downloads.skewed.de/apt bionic main" >> /etc/apt/sources.list
apt-key adv --keyserver keyserver.ubuntu.com --recv-key 612DEFB798507F25

echo "deb http://cz.archive.ubuntu.com/ubuntu bionic main universe" >> /etc/apt/sources.list
apt-get update
apt-get install python3-graph-tool python3-matplotlib python3-cairo

Check out the first cell of SplineCam google colab where all the SplineCam dependencies are installed: https://colab.research.google.com/drive/1gkHZI9BztH3N4qtu4LjTnFb5RCV2nq4d

[BabaVegato]

Hello, When I use any of your Colab examples, it still cannot install Graph-tool, it seems.

Even your bit of code above outputs the error :

The following packages have unmet dependencies: python3-graph-tool : Depends: libboost-context1.65.1 but it is not installable Depends: libboost-iostreams1.65.1 but it is not installable Depends: libboost-python1.65.1 but it is not installable Depends: libboost-regex1.65.1 but it is not installable Depends: libpython3.6 (>= 3.6.5) but it is not installable Recommends: libgv-python but it is not installable Recommends: python-matplotlib but it is not installable Recommends: python-cairo but it is not installable Recommends: python-gi-cairo but it is not installable Recommends: python-gi but it is not installable Recommends: gir1.2-gtk-3.0 but it is not going to be installed E: Unable to correct problems, you have held broken packages.

Do you know how to solve it in any way ?

Thanks a lot for the paper anyway !

[AhmedImtiazPrio]

Hi @BabaVegato

It turns out that graph-tool installation without Conda has become really buggy. I'm going to find an alternative to conda for my google colab examples but in general Conda installation should work now. If you want to create a new environment with graph-tool and go from there do:

conda create --name splinecam -c conda-forge graph-tool
conda activate splinecam

[BabaVegato]

Thanks a lot ! Sorry to still bother you, but what is your setup though ? Because I still have conflicts when installing pytorch or torchvision after using conda create --name splinecam -c conda-forge graph-tool.

[AhmedImtiazPrio]

The environemnt.yml file in the repo should help reproduce a working environment. Could you please try it and lemme know if it does/doesn't work?

https://github.com/AhmedImtiazPrio/splinecam/blob/main/environment.yml

[BabaVegato]

It's working, thanks a lot !

[jwarley]

I'm having similar dependency issues with GOMP via graph-tool and installing from the environment.yml is not working. In a fresh conda env with Python 3.8 I ran conda env update --file environment.yml --prune. Trying to import splinecam gives an import error for GOMP_5.0 which is required by graph tool. Any ideas?

[AhmedImtiazPrio]

Hi @jwarley ,

Can you try the following and see if it works?

echo "deb http://downloads.skewed.de/apt jammy main" >> /etc/apt/sources.list
apt-key adv --keyserver keyserver.ubuntu.com --recv-key 612DEFB798507F25
apt-get update
apt-get install python3-graph-tool python3-matplotlib python3-cairo

the conda installation is getting buggy over time, sorry about that!