MEmilio v2.0.0 - A high performance Modular EpideMIcs simuLatIOn software

MEmilio implements various models for infectious disease dynamics, from simple compartmental (ODE) models through Integro-Differential equation-based (IDE) models (sometimes also denoted "age of infection models") to agent- or individual-based models (ABMs). Its modular design allows the combination of different models with different mobility patterns. Through efficient implementation and parallelization, MEmilio brings cutting edge and compute intensive epidemiological models to a large scale, enabling a precise and high-resolution spatiotemporal infectious disease dynamics.

We here publish version 2.0.0, our most recent major release containing, among other things, three full new models, demographic stratifcation for an integro-differential equation based model, a local feedback mechanism for ODE models as well as first compatibility of IDE and ABM model with the graph structure.

v2.0.0 Changes

Added features / functionality:
- Integration of the SECIRTS model: a three immunity layer ODE model with waning immunity
- Integration of diffusive ABM (d_abm) 
- Integration stochastic metatpopulation model (smm)
- Provision of age resolution for IDE model
- Provision of local feedback mechanism for ODE models
- Allow graph model for ABMs
- Make IDE model compatible with graph
- Use DIVI data to scale initial values for LCT model
- Allow agents to die in hospital and when not in ICU
- Make set_initial_flows() of IDE model usable with and without age resolution
- Integration of new documentation

General changes:
- Change member functions in Model class from public to private in IDE model
- Update dependencies 
    - minimum required cmake 3.11 -> 3.13
    - spdlog 1.11.0 -> 1.15.0
    - Eigen 3.3.9 -> 3.4.0
    - JsonCpp 1.9.5 -> 1.9.6
- Temporarily fix CI by downgrading OS image
- Print date object per default in ISO format when using spdlog
- Rename public members of IDE model
- Updated ABM readme
- Reduce unnecessary  logs and prints when running the examples
- Add citation file
- Add log for MSVC example runs
- Rework data structure and rename mobility and vaccination file

Corrections:
- Initialization of ICU compartments after July 2024
- Handle case when group size in LCT model is zero
- Integrator was handled as adaptive if using small fixed step sizes
- Use correct targets when setting compile options
- Wrong index in ODE SEIR model
- Ensure zero initialization for AD example
- Add missing comment for pop in get_derivatives()
- Bump minimum cmake versions in memilio-simulation and -generation

Minor changes
- Improvement of ABM software and unit tests
- Bump download artifact version in CI
- Update license headers

For more details, see https://github.com/SciCompMod/memilio and our novel documentation (in progress): https://memilio.readthedocs.io/en/latest/