v2.0.0

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

Merged pull requests

• 1067 improve abm tests by @khoanguyen-dev in #1141
• Bump dawidd6/action-download-artifact from 2 to 6 in /.github/workflows by @dependabot in #1149
• 1144 handle case when group size is equal to 0 for the LCT model by @lenaploetzke in #1156
• 323 SECIRTS model with waning immunity by @HenrZu in #963
• Fix CI by downgrading OS image by @reneSchm in #1160
• 379 implement IDE model with age resolution by @hatrit in #1083
• 1154 integrator is handled as adaptive if using small fixed step sizes by @lenaploetzke in #1155
• 1133 Change member functions in Model class from public to private in IDE model by @annawendler in #1166
• 1167 Update some dependencies by @reneSchm in #1168
• 1170 Use correct targets when setting compile options by @reneSchm in #1171
• 1177 Update license header by @MaxBetzDLR in #1181
• 1185 wrong index in ode seir model by @kilianvolmer in #1186
• 1189 Ensure zero initialization for AD example by @mknaranja in #1190
• 1174 Use DIVI data to scale initial values for LCT model by @lenaploetzke in #1175
• 1132 Rename public members of IDE model by @annawendler in #1173
• 1196 Add missing comment for pop in get_derivatives() by @kilianvolmer in #1197
• 1187 Make set_initial_flows() of IDE model usable with and without age resolution by @annawendler in #1188
• 1191 Initialization of ICU compartments after July 2024 by @HenrZu in #1192
• 1075 Let persons die from hospital (non ICU) in the ABM by @khoanguyen-dev in #1100
• 646 use graph model with ABMs v3 by @jubicker in #1085
• 1159 add diffusive abm and smm by @jubicker in #1162
• 1195 Formatter for date to have consistent Format by @HenrZu in #1198
• 1204 Reduce unnecessary logs and prints when running the examples by @HenrZu in #1205
• 1206 Add CITATION.cff for Repository Citation Metadata by @HenrZu in #1207
• 1215 Preparation for readthedocs by @HenrZu in #1217
• 1222 Add cpp/memilio to doxyfile by @kilianvolmer in #1223
• 1220 Add log for msvc example runs by @HenrZu in #1221
• 1148 Rework Data structure and Rename Mobility and Vaccination file by @HenrZu in #1150
• 1226-fix-python-docstrings by @kilianvolmer in #1227
• 1224 extend read the docs documentation by @kilianvolmer in #1231
• Update ABM README.md by @DavidKerkmann in #1234
• 978 Local Feedback Mechanism by @HenrZu in #1211
• Remove debug output from SDE seirvv model by @reneSchm in #1236
• Bump minimum cmake versions in memilio-simulation and -generation by @reneSchm in #1240
• 410 Make IDE model compatible with graph by @annawendler in #1203

New Contributors

• @kilianvolmer made their first contribution in #1186

Full Changelog: v1.3.0...v1.4.0