Installing the additional tools

The additional tools use Python 3.13 or newer. From the repository root, the scripts can be run directly with uv:

uv run tools/rrkm_cli.py --help
uv run tools/graphml_generator.py

To invoke the scripts directly as commands, first make them executable and add the tools directory to PATH:

chmod +x tools/rrkm_cli.py tools/graphml_generator.py
export PATH="/path/to/GKMC/tools:$PATH"
# Or export it to zsh to add to the path permanently
echo 'export PATH="/path/to/GKMC/tools:$PATH"' >> ~/.zshrc
source ~/.zshrc