Installation

Python environment

You will need to install Python (>=3.12) on your system.

Download the framework

Follow these steps to install and configure Zalmoxis:

1. Create a virtual environment

   python -m venv .venv
   source .venv/bin/activate
   

2. Clone the repository and install dependencies

   git clone https://github.com/FormingWorlds/Zalmoxis.git
   cd Zalmoxis
   pip install -e .   
   

   This installs Zalmoxis in editable mode, so local changes to the code are immediately reflected.

3. Set environment variable

   Zalmoxis requires the ZALMOXIS_ROOT environment variable to point to the base directory:

   export ZALMOXIS_ROOT=$(pwd)
   

   To make ZALMOXIS_ROOT available across sessions, add the above line to your shell profile file:

   • For bash users:

   echo "export ZALMOXIS_ROOT=$(pwd)" >> ~/.bashrc
   

   • For zsh users:

   echo "export ZALMOXIS_ROOT=$(pwd)" >> ~/.zshrc
   

   Afterwards, reload your profile with:

   • For bash users:

   source ~/.bashrc 
   

   • For zsh users:

   source ~/.zshrc
   

4. Download necessary input/output files

   Run the provided script to download required model files:

   bash src/get_zalmoxis.sh
   

   This will create the data/ folder for configuration files and the output_files/ folder for model results.