Installation

NetworkCommons requires Python version >= 3.10 and < 3.13 to run.

Requirements

NetworkCommons requires graphviz to visualize networks.

Conda

If you are using conda, we have created an environment file that can be used to create a new environment with all the dependencies needed to run NetworkCommons. To create a new environment, please clone the repository and create a conda environment:

git clone https://github.com/saezlab/networkcommons.git
cd networkcommons

conda env create -f environment.yml
conda activate networkcommons_env

If you will only use conda to handle the graphviz installation, please run:

conda install graphviz

Ubuntu

graphviz is also available via the APT package manager in Ubuntu:

sudo apt-get install -y graphviz graphviz-dev

MacOS

In MacOS, it can be installed using Homebrew.

brew install graphviz

In some of our local MacOS tests, we also needed to set the following environment variables:

export PATH="$(brew --prefix graphviz)/bin:$PATH"'
export CFLAGS="-I$(brew --prefix graphviz)/include"'
export LDFLAGS="-L$(brew --prefix graphviz)/lib"'

Please note, if you are using a different architecture or operating system within a subsystem, you may need to make sure that the installed binaries of graphviz were compiled for the correct architecture and that they are visible to the Python interpreter.

PIP

Currently, NetworkCommons can be installed via pip.

pip install networkcommons

Additionally, users can install backends for CORNETO via:

pip install networkcommons[corneto-backends]

To install the development version (with the CORNETO solvers), run:

pip install 'networkcommons[corneto-backends] @ git+https://github.com/saezlab/networkcommons@dev'