pykappa 0.1.6

Work with Kappa rule-based models in Python

PyKappa

PyKappa is a Python package for working with rule-based models. It supports simulation and analysis of a wide variety of systems whose individual components interact as described by rules that transform these components in specified ways and at specified rates. See our website pykappa.org for a tutorial, examples, and documentation.

Development

Developer requirements can be installed via:

pip install -r requirements.txt

With uv (optional alternative to pip):

Install [uv](https://docs.astral.sh/uv/getting-started/installation/), then:

uv sync --dev

To access uv dependencies, run your commands through uv like

uv run python

Or, if you want to run commands normally, create a virtual environment:

uv venv # Do this once
source .venv/bin/activate # Do this every new shell

and run commands as usual. (deactivate exits the venv.)

Adding a Python package dependency (this automatically updates pyproject.toml):

uv add [package-name]

Adding a package as a dev dependency:

uv add --dev [package-name]

To run correctness tests, run pytest. Running ./tests/cpu-profiles/run_profiler.sh will CPU-profile predefined Kappa models and write the results to tests/cpu-profiles/results. We use the Black code formatter, which can be run as black .