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Automated Model Assembly
from Text, Equations, and Software

GH Actions build status CodeFactor

This repository holds the source code for the AutoMATES documentation and several component pipelines.

For documentation:

Installation instructions

For all operating systems, the first step of the installation process is to clone the AutoMATES repository.

Linux and macOS

  • Create a new Python virtualenv
  • Activate your new Python virtualenv
  • Install Graphviz as defined below
  • Run pip install -e . from the root of the AutoMATES directory

GraphViz installation

Debian flavored linux
  • Use the command: sudo apt-get install graphviz libgraphviz-dev pkg-config
macOS with Homebrew
  • Use the command: brew install graphviz
  • Install PyGraphviz to your virtualenv with: pip install --install-option="--include-path=/usr/local/include/" --install-option="--library-path=/usr/local/lib" pygraphviz


  • Download and install Anaconda
  • Edit the PYTHONPATH variable in environment.yml to be your local path to your checkout of the AutoMATES repo
  • Run conda env create --file environment.yml from the root of the AutoMATES directory