COVID-19 Test Scheduling

This repository contains scheduling algorithms to assign people (students, faculty, and staff) at universities to surveillance testing schedules. Surveillance testing is a key component of many campus reopening strategies, and the logistics of testing thousands of busy people multiple times a week without long lines at testing centers are nontrivial. Tufts University is developing a campus monitoring app that allows members of the testing population to specify their testing availability and preferred testing locations. This tool aggregates personal schedules and university-level information (such as the desired testing frequencies for population cohorts) to produce a scheduling with optimal schedules that satisfy the population's preferences and epidemiological needs as well as possible while avoiding testing center overload.

Getting started

This tool has been most extensively tested with Python 3.8, but it should work with Python 3.6 or above. For development, we recommend installing all dependencies in a virtual environment managed with Anaconda. All dependencies can be installed with pip install -r requirements.txt. To deploy to Heroku, create an app and push using git push heroku main.

Full documentation, extensive unit tests, and CI/CD integration are forthcoming.

Inputs

University-level configuration

An example university configuration, loosely based on Tufts' reopening plans, is available at data/tufts.json. The policy section contains parameters that are not likely to change frequently, such as the testing block schedule (as displayed in the app), cohort information, and load balancing tolerances. The sites section contains the hours and capacity of individual testing sites; these hours are likely to change from week to week.

Personal availability

An example roster of 5,000 randomly generated personal schedules is available at data/tufts_sample_5000.json. Use the experiments/random_schedules.py script to generate more random schedules; the ScheduleSampler in this script can be adjusted to vary the relative weighting of cohorts and the allowable schedules within each cohort.

Full schema information for the university-level configuration and the personal roster is available in covid_scheduling/schemas.py.

Command-line interface

To generate assignments from the command line, run

python assign_json.py --config-file <configuration> --people-file <roster of people> --out-file <output file> --start-date <start date> --end-date <end date, inclusive>

For example, to sample schedules for the week of Monday, August 17, 2020 using the example configuration and people roster, run

python assign_json.py --config-file data/tufts.json --people-file data/tufts_sample_5000.json --out-file assign.json --start-date 2020-08-17 --end-date 2020-08-23

API

To start the development server for the Flask-based JSON API, execute FLASK_DEBUG=1 flask run. The API accepts POST requests to the root endpoint of the format

{
  "start": "YYYY-MM-DD",
  "end": "YYYY-MM-DD",
  "config": { <configuration> },
  "people": { <roster of people> }
}

The output schema of a successful request is

{
  "people": { <roster of people, with assignments> },
  "stats": { <person-level assignment statistics> }
}

For example, the request body used in the July 21, 2020 demo can be POSTed to a local development server with

curl -X POST -H "Content-Type: application/json" -d @data/tufts_request_example.json http://localhost:5000/

The algorithm

covid_scheduling/bipartite.py contains an implementation of a mixed-integer program for bipartite matching with optional load-balancing constraints. People are matched to schedules such that total matching cost is minimized; the cost of a person/testing schedule match is currently determined solely by the spacing of the testing schedule (schedules that closely match the person's desired testing interval are cheap, while improperly spaced schedules are expensive); we intend to augment the cost function to consider testing history and site preferences.