Figures from Dickman, U., et al. (2026)

1. Download the SNNAP simulation data from Dryad and make note of the download location.

2. Download NEURONpyxl and change into the neuronpyxl folder. Install the neuronpyxl package into a virtual Python environment:

   • With uv (recommended): uv venv /path/to/venv --python 3.13 && source /path/to/venv/bin/activate && uv pip install .
   • With Micromamba (recommended): micromamba create -f environment.yml
   • With pip: python3 -m venv /path/to/venv && source /path/to/venv/bin/activate && pip install .
   • With Anaconda: conda create -f environment.yml

3. Activate NEURONpyxl:

   • With uv or pip: source /path/to/venv/bin/activate
   • With Micromamba: micromamba activate neuronpyxl
   • With Anaconda: conda activate neuronpyxl

4. Run a script from the ./scripts folder, passing in the script name and location of the Dryad data as arguments. Remember, you first need to compile the mod files for that script. For example

   neuronpyxl -f gen_mods --file sheets/fig2.xlsx && \
   python run_script.py --name fig2 --snnap_data /path/to/snnap/data
   

   neuronpyxl -f gen_mods --file sheets/benchmark.xlsx && \
   python run_script.py --name benchmark --snnap_data /path/to/snnap/data