summerepi 1.0.1

Summer is a compartmental disease modelling framework, written in Python. It provides a high-level API to build and run models.

Summer: compartmental disease modelling in Python

Summer is a compartmental disease modelling framework, written in Python. It provides a high-level API to build and run models. Features include:

• A variety of inter-compartmental flows (infections, sojourn, fractional, births, deaths, imports)
• Force of infection multipliers (frequency, density)
• Post-processing of compartment sizes into derived outputs
• Stratification of compartments, including:
  • Adjustments to flow rates based on strata
  • Adjustments to infectiousness based on strata
  • Heterogeneous mixing between strata
  • Multiple disease strains

Documentation here with code examples.

Available on PyPi as summerepi.

Installation and Quickstart

This project is tested with Python 3.6. Install the summerepi package from PyPI

pip install summerepi

Then you can use the library to build and run models. See here for some examples:

• SIR model
• SEIR model

You will find a significant performance improvement in the ODE solver if you set OMP_NUM_THREADS before importing summer or numpy.

# Set this in your Python script
os.environ["OMP_NUM_THREADS"] = "1"

# Do it before importing summer or numpy
import summer
# ...

Development

Poetry is used for packaging and dependency management. You will need to install poetry to work on this codebase. Some common things to do as a developer working on this codebase:

# Install requirements
poetry config virtualenvs.in-project true
poetry shell
poetry install

# Get a virtualenv for running other stuff
poetry shell

# Publish to PyPI - use your PyPI credentials
poetry publish --build

# Add a new package
poetry add

# Run tests
poetry shell
pytest -vv

# Format Python code
black .

Releases

TODO

Documentation

Sphinx is used to automatically build reference documentation for this library. The documentation is automatically built and deployed to summerepi.com whenever code is pushed to master.

To build and deploy

./docs/scripts/build.sh
./docs/scripts/deploy.sh

To work on docs locally

# ./docs/scripts/watch.sh # FIXME - endless recursion
./docs/scripts/build.sh
# In a separate terminal
./docs/scripts/serve.sh
# Visit http://localhost:8000/