June

Release highlights
- Allowing for venues to be open only between particular hours of the day
- Contact tracker added as an input to the `Simulator`
- New optional seeding routine to allow for household level clustered seeding
- New formatting and CI/CD checks

Minor changes
- Epidemiology and infection selectors and seeding adjusted for cleaner implementation
- Vaccine implementation moved to `Epidemiology` from being a policy to allow for greater flexibility
- Quickstart notebook updated to reflect new changes

This version was used to produce the publication "Vaccinations or Non-Pharmaceutical Interventions: Safe Reopening of Schools in England"

https://www.medrxiv.org/content/10.1101/2021.01.27.21250611v1.full.pdf

Bug fix:
- Adding yaml import line to `immunity_setter.py` to allow comorbidities to be passed


school_reopening_paper
This version was used to produce the publication "Vaccinations or Non-Pharmaceutical Interventions: Safe Reopening of Schools in England"

https://www.medrxiv.org/content/10.1101/2021.01.27.21250611v1.full.pdf

This version is not backwards compatible with 1.0, which means that old config files and created ``Worlds`` won't work.

Changelog

* Epidemiology related functionality is now all contained in the Epidemiology class and corresponding source folders.
* New Immunity class tracks the immunity related information of an agent, such as their susceptibility to infection.
* People can now be vaccinated with lots of customizable parameters.
* People can now be reinfected with virus variants, and have different susceptibilities to each of them.
* Added functionality to easily initialize the population with a certain vaccination rate and pre-infection status.
* New domain decomposition boosts the speed of the code when running in HPC clusters.

Documentation
The old documentation has been removed to avoid confusion as it is not up-to-date with the new version of the code. We plan to release the new docs soon.


Legacy code removed
* Box mode no longer supported.




v1
JUNE release after peer reviewing.

This is the version of June that was used to produce all the plots shown in https://www.medrxiv.org/content/10.1101/2020.12.15.20248246v2
The code and the model are not yet peer-reviewed.