simpar v0.1.0 Release Notes

This marks the first offical pre-release of simpar. There are a handful of
changes from v0.0.1. The plotting module has been removed as it was deemed
out-of-scope for this project. Additionally, the metrics module was removed and
its functions were moved to be methods of the Trajectory class. Initial hidden
and discovered can now be passed to the sim.Sim class. The groups module was
updated to utilize this with the get_init_SIR_and_DH method for the MetaGroup
and Population class. The Scenario now includes pct_recovered_discovered
indicating the fraction of the recovered population that has been discovered.
This replaced the previous and less interpretable parameter,
pct_recovered_discovered_arrival. The remaining minor changes and bug fixes are
summarized below. Lastly, the documentation was greatly improved.

Minor changes:
- IsolationRegime class added and isolation params removed from Scenario
- Made S, I, R, D, and H properties of sim.Sim and use np.copy()
- Added true_sensitivity attribute to Test class
- More sensible implementation of get infections/recovered in TestRegime

Bug fixes:
- get_isolated was viewing D compartment as non-cumulative
- indexing error with generations in Sim
- Scenario.simulate_sim was not stepping the first time period

simpar v0.0.1 Release Notes

simpar 0.0.1 Release Notes

This is the initial release for simpar, a Python package providing a suite of
tools for modeling disease spread with an SIR-model under different proposed
testing stratagies. The package is designed to handle the following scenario:
a population currently spread out and returning to some central location where
they will remain for some period of time. E.g., students returning to a campus
after being sent home amidst the COVID-19 pandemic. The following modules
are included.

- micro: provides computation of days someone is infectious and free
- sim: core implementation of the SIR-model
- groups: provides the Population class which consists of meta-groups with
	  different levels of contacts
- strategy: defines Strategy representing a testing strategy
- scenario: defines Scenario representing a population, envrionment, and
  	    disease parameters
- trajectory: Trajectory class manages a single simulation execution
- metrics: provides methods to compute metrics from a Trajectory instance
- plotting: (incomplete) will provide useful plotting functions

There are a handful of TODOs that need to be addressed before release. There
should also be better testing of the groups and metrics modules. Lastly, the
plotting module needs to be updated to reflect a recent refactor.