v2.4.1

Added features / functionality:

• (LCT) implement possibility of death from hospitalization without intensive care

Minor changes:

• Windows VS2026 migration
• Move build files into pycode/memilio-simulation and update actions

Merged pull requests

• 1571 Windows VS2026 migration by @HenrZu in #1572
• 1547 (LCT) implement possibility of death from hospitalization without intensive care by @annawendler in #1556
• Move build files into pycode/memilio-simulation and update actions by @reneSchm in #1566

Full Changelog: v2.4.0...v2.4.1

v2.4.0

Added features / functionality:

• Added generic country simulation that automatically downloads contact data for various countries from POLYMOD
• ODE/IDE-based models with hospitalization: Added possibility of death from hospitalization without intensive care
• Added ODE SEIR metapopulation model with implicit mobility
• Added Python bindings for ODE SEIR metapopulation model
• Added PyPI package for memilio-simulation
• Added Graph Neural Networks
• Added ODE model generator from yaml and toml template

General changes:

• Improved functionality for DynamicNPIs
• Use of ContactMatrix instead of CustomIndexArray for contact rates of ABM
• Move output of examples to example_results

Corrections:

• Corrected macOS import failure due to incorrect runtime library lookup (RPATH)
• Fixed typos and bugs in documentation
• Harmonized description of time series, infection states and other keywords in documentation
• Added ScalarType to code examples in the documentation
• Corrected use of the ABMs RNG after initialization
• Corrected operation to act only on current system state and not on result time series in SMM

Minor changes:

• Build benchmarks in CI
• Switched to Doxysphinx
• Removed log outputs from testing
• Improved documentation of TypeSafe and derived types
• Extended documentation
• Build and test on MacOS
• Replaced the deprecated FetchContent_Populate and increased CMake minimum version to 3.18.

Merged pull requests

• 1478 Switch to Doxysphinx by @kilianvolmer in #1504
• 1463 Remove log outputs from testing by @reneSchm in #1464
• Add binding for clear_dampings by @HenrZu in #1509
• Replace contact rates of ABM by ContactMatrix by @charlie0614 in #1516
• 1442 Generic country Simulation by @HenrZu in #1466
• 1520 Operate only on current system state and not on result time series in SMM by @jubicker in #1521
• 1527 Improve documentation of TypeSafe and derived types by @HenrZu in #1528
• 1508 (ODE) implement possibility of death from hospitalization without intensive care by @HenrZu in #1526
• 1139 introduce improved GNN surrogate models by @mhheger in #1378
• 1400 The ABMs RNG is not used after initialization by @reneSchm in #1534
• 1027 Use FetchContent_MakeAvailable instead of FetchContent_Populate by @reneSchm in #1535
• 1045 Build benchmarks in CI by @HenrZu in #1538
• Extend documentation and fix typos and bugs in documentation by @mknaranja in #1531
• 1003 implement ODE SEIR metapopulation model by @charlie0614 in #1273
• 1519 memilio-simulation PyPI package by @annawendler in #1495
• 1540 (IDE) Implement possibility of death from hospitalization without intensive care by @annawendler in #1542
• 1543 harmonize description of time series infection states etc in documentation by @jubicker in #1545
• 1549 macOS import fails due to incorrect runtime library lookup (RPATH) by @HenrZu in #1550
• 1522 Improve DynamicNPI structure through harmonization across models and more options by @mknaranja in #1523
• 1551 Build and test on MacOS by @reneSchm in #1552
• 1429 move example output to example_results by @reneSchm in #1544
• 1462 Add ScalarType to Code examples in the documentation by @annawendler in #1546
• 1512 Generate ODE models from yaml template by @HenrZu in #1518
• 1560 More supported countries in getContactData by @HenrZu in #1562
• 1003 Add ode seir metapop bindings by @charlie0614 in #1554
• 1564 Dynamic NPIs can create short lifting gaps at renewal time by @HenrZu in #1567

Full Changelog: v2.3.0...v2.4.0

v2.3.0

Added features / functionality:

• Added SEIRDB model for EBOLA
• Added Influenza model
• Added LCT SECIR model with two disease strains
• Enable SMM Model with generic indices
• Generalize ParameterStudy for ODE models in python bindings
• Simplify parameter IO and graph building with constructor
• Make timers MPI compatible
• Added Python bindings for get_times() function
• Improved compile time of flows

General changes:

• Deactivate SBML support by default
• Add CMake option to allow building python simulation without HDF5
• Accelerate add_edge() for large graphs
• Normalize transitions in ode MSEIRS4 model
• Migrate Python packages to use pyproject.toml for builds
• Enable numpy versions 1.22-1.24
• Update Python Version in CI to 3.12
• Read result from HDF5 files uses lexical order

Corrections:

• Correction for SMM model output misaligned with time points
• Detection of duplicate flows in the FlowModel
• Fix documentation build after migration to pyproject toml
• Use correct ParameterStudy in graph examples of Python bindings
• Change default value of MaxRiskOfInfectionFromSymptomatic
• Correct non-ageresolved indices in IDE-SECIR model
• Correction of interpolate_simulation_result which did not yield consistent timepoints
• Correction of memilio.simulation incompatible with pandas 3

Minor changes:

• Improve messages related to parameter checks
• Update citation file
• General documentation improvement
• Modernizations and minor fixes in core C++ library
• Minor additions to how infections in the ABM work
• Revise README for data directory clarification
• Updated holiday data

Merged pull requests

• Improve messages related to parameter checks by @kilianvolmer in #1414
• 1420 Implement SEIRDB model by @HenrZu in #1424
• 1390 further improve documentation by @mknaranja in #1427
• 1423 Generalize ParameterStudy for ODE models in python bindings by @reneSchm in #1428
• 1386 implement influenza model by @HenrZu in #1387
• 1410 Accelerate add_edge for large graphs by @kilianvolmer in #1411
• 1433 partial convert of base types for parameters io of graph by @MaxBetzDLR in #1434
• 1438 normalize transitions in ode mseirs4 model by @HenrZu in #1439
• 1443 Change working_population type to FP by @julianlitz in #1444
• 1110 Migrate Python packages to use pyproject.toml for builds by @HenrZu in #1409
• Fix rtd build after migration to pyproject toml by @HenrZu in #1445
• Allow newer Numpy versions by @kilianvolmer in #1447
• Fixed problem with undefined variable by @nijawa in #1453
• 1454 Use correct ParameterStudy in graph examples of python bindings by @reneSchm in #1455
• 1456 Read result from HDF5 files uses lexical order by @MaxBetzDLR in #1457
• 1272 Holiday data is outdated by @kilianvolmer in #1465
• 1449 Update Python Version by @kilianvolmer in #1450
• 1470 Update license header by @kilianvolmer in #1471
• Change default value of MaxRiskOfInfectionFromSymptomatic by @charlie0614 in #1474
• Improve compile time of Flows by @reneSchm in #1476
• 1451 interpolate_simulation_result does not yield consistent timepoints by @reneSchm in #1482
• 1294 add LCT SECIR model with two disease strains by @an-jung in #1340
• 1279 minor additions to how infections work by @DavidKerkmann in #1320
• 1469 Correct nonageresolved indices in IDE-SECIR model by @annawendler in #1472
• Revise README for data directory clarification by @mknaranja in #1488
• Updates and Fixes in the documentation by @kilianvolmer in #1481
• 1483 memilio.simulation incompatible with pandas 3 by @kilianvolmer in #1484
• 1491-Update MEmilio citation by @kilianvolmer in #1492
• 1341 SMM Model with generic indices by @kilianvolmer in #1460
• 1493 Bindings for get_times() function by @HenrZu in #1494
• 1467 Make timers MPI compatible by @reneSchm in #1468
• 1496 smm model output is misaligned with time points by @kilianvolmer in #1497
• 1498 Detection of non unique flows in the FlowModel by @HenrZu in #1499
• 1486 Modernizations and minor fixes in core C++ library by @reneSchm in #1487
• 1501 Add CMake option to allow building without HDF5 by @HenrZu in #1502
• 1505 Do not include SBML by default by @reneSchm in #1506

New Contributors

• @an-jung made their first contribution in #1340

Full Changelog: v2.2.0...v2.3.0

v2.2.0

Added features / functionality:

• Added RSV model
• Added ABM parameter study
• Support for IO functionality with single age group for ODE SECIR
• Enabled vaccination data output for NUTS1 and NUTS2 stratifications in Germany
• Extended automatic differentiation (AD) to support to the SECIRVVS model
• Added read_graph to python bindings
• Added Python interface for SDE SIR type models
• Added Geographic location to all of MEmilio

General changes:

• Added return value policy to TimeSeries in python bindings
• Deleted simulation folder after porting to https://github.com/SciCompMod/memilio-simulations/
• When calling print_table from python, the output is now direclty printed in the console per default.
• Added copy constructable simulation for ODE models (changed handling of IntegratorCore)
• Changed python CI to build wheels without SDist
• Changed install requirements for readthedocs to build in two steps
• Added default options and a builder to CLI
• Introduced a naming scheme for concepts
• Added normalization of exposure rate for ABM
• Adjusted epidata code to new NUTS3 file structure
• Updated IDE-SECIR examples and improved documentation

Corrections:

• Fixed the initialization of recovered in ODE SECIR
• Improved consistency of floating-point types
• Fixed potential use of wrong dt_max in ControlledStepperWrapper
• Fixed missing SMM update of internal waiting time at the end of advance
• Fixed file leak in test_mobility_io
• Fixed incorrect overload detection and type mismatch in test_commuters
• Added missing members to ABM serialization

Minor changes:

• Allow threshold for code coverage
• Updated citations
• Extended documentation

Merged pull requests

• Add return_value_policy by @MaxBetzDLR in #1344
• 1324 Direclty print output from print_table in python by @HenrZu in #1325
• 1288 Delete simulation folder by @HenrZu in #1323
• 1348 Fix initialization recovered ode secir by @HenrZu in #1353
• 1356 Allow threshold for code coverage by @HenrZu in #1357
• 1321 copy constructable simulation by @MaxBetzDLR in #1345
• 1361 python CI: Build wheels without SDist by @reneSchm in #1360
• 1315 support IO functionality with single age group for ODE SECIR by @HenrZu in #1354
• Install requirements for readthedocs build in two steps by @HenrZu in #1362
• 1363-add-output-of-germany-vaccination-data by @MaxBetzDLR in #1364
• 1018 use floating point types consistently by @julianlitz in #1307
• 1365 Potential use of wrong dt_max in ControlledStepperWrapper by @reneSchm in #1366
• Update citation for newest release by @HenrZu in #1367
• 1350 Implement RSV model by @HenrZu in #1352
• 1379 Add read_graph to python bindings by @HenrZu in #1380
• 1337-extend-the-documentation by @kilianvolmer in #1338
• 1379 Add default options and a builder to CLI by @reneSchm in #1377
• SMM Update internal waiting time at the end of advance by @jubicker in #1397
• Fix file leak in test_mobility_io by @reneSchm in #1401
• 1382 Fix incorrect overload detection and type mismatch in test_commuters by @julianlitz in #1394
• 1351 pymio interface for sde sir type models by @MaxBetzDLR in #1371
• 1274 normalizing of exposure rate by @DavidKerkmann in #1322
• Fix Readthedocs build by @HenrZu in #1403
• 1404 Adjust epidata code to new nuts3 file structure by @HenrZu in #1405
• 1342 make geographic location available to all of MEmilio by @kilianvolmer in #1346
• 1392 update IDE-SECIR examples and improve some documentation by @annawendler in #1402
• Add missing members to ABM serialization by @reneSchm in #1408
• 1407 Introduce a naming scheme for concepts by @reneSchm in #1412
• 468 ABM parameter study by @reneSchm in #1395

New Contributors

• @julianlitz made his first contribution in #1307

Full Changelog: v2.1.0...v2.2.0

v2.1.0

Added features / functionality:

• Added a temporal hybrid ODE-ABM-based model
• Added spatially resolved feedback simulation
• Extended integrator classes and reimplemented SDE models
• Adjusted memilio-generation for flow models and automatic differentiation
• Added setup for performance monitoring with LIKWID
• Introduction of a timing framework
• Export TimeSeries objects into csv files
• Added quarantine effectiveness parameter to ABM
• C++ Code creation based on standardized formats for ODEs
• Added GitHub bot to inform on new discussions

General changes:

• Reworked ABM state transitions
• Updated minimum and latest Ubuntu and Windows versions which are tested in CI
• Fully reworked and extended documentation
• Deactivated old GitHubPages
• Enhanced testing logic in ABM
• Improved trip addition in ABM
• Changes in model initializations due to changes in provision of intensive care and SARS-CoV-2 vaccination data
• Streamline code for reading in data in model specific IO files
• Updated simple surrogate models
• Renamed compartmentalmodel.h to compartmental_model.h

Corrections:

• Corrected the different output on Mac
• Fix population download handling
• Property of MobilityParametersEdge was not accessible in python bindings

Minor changes:

• Updated citations
• Updated coding guidelines and pull request template
• Cancel concurrent and redundant CI runs

Merged pull requests

• 1243 Deactivate old github pages documentation by @mknaranja in #1244
• 1019 Adjust memilio-generation for flow models and automatic differentiation by @dr2001dlr in #1153
• 1264 Introduce likwid to memilio by @charlie0614 in #1265
• 1270 Documentation build fails by @kilianvolmer in #1271
• 17 Timing framework by @reneSchm in #1179
• 703 different output for Mac by @xsaschako in #1285
• 1268 Vaccination data reporting expired by @HenrZu in #1269
• 1246 Export TimeSeries into csv file by @HenrZu in #1255
• 1242 update simple surrogate model by @mhheger in #1252
• Bump Windows version in CI by @reneSchm in #1298
• 1108 Streamline code for reading in data in model specific IO files by @HenrZu in #1163
• 1300 Update surragete model test to work with new pyfakefs version by @xsaschako in #1301
• 1299 Fix population download handling by @HenrZu in #1302
• 1178 code creation based on standardised formats for ODEs by @kilianvolmer in #1235
• 1304 renamed compartmentalmodel.h to compartmental_model.h by @Spiritedswordsman in #1305
• 1233 further enhance read the docs by @mknaranja in #1289
• 1239 implement temporal hybrid model by @jubicker in #1262
• 1312 Accelerate documentation build by @HenrZu in #1313
• 1293 update secir groups surrogate models by @mhheger in #1297
• 1317 Property of MobilityParametersEdge not accessible in python bindings by @charlie0614 in #1319
• 1101 Extend integrator classes and reimplement SDE models. by @reneSchm in #1296
• 1277 Quarantine Effectiveness by @xsaschako in #1282
• 1310 Spatially resolved feedback simulation by @HenrZu in #1311
• 1327 add concurrency for CI by @xsaschako in #1328
• 1280 trip addition overhaul by @xsaschako in #1281
• 1250 enhance testing logic in abm by @xsaschako in #1276
• 1330 GitHub bot by @xsaschako in #1331
• 1306 further extend and review the documentation by @HenrZu in #1314

New Contributors

• @mhheger made their first contribution in #1252

Full Changelog: v2.0.0...v2.1.0

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

v1.3.0

Added features / functionality:

• Allow output of mobility data for Graph-ODE model
• Added age resolution for LCT model
• Implementation of Generalized Linear Chain Trick model
• Allow variable dynamic NPI delay implementation
• Update of Damping now allows negative coefficients (i.e., contact increases)
• Added serialization to ABM
• Added functions for a person in the ABM to choose whether to comply to mask,test and isolation
• Allow explicit stepper wrappers (i.e., fixed step size numerical integrators)
• Bind different numerical integrators for python
• Allow download of population data for different years
• Plot functions for AST in generation package

General changes:

• Redesign of python bindings structure to improve typing
• Reduction of export_input_data_county_timeseries function
• Reduce use of get_support_max method in IDE model to reduce run time
• Handle Epidata FutureWarnings

Corrections:

• Error when compiling on Mac with new boost
• Missing includes in python bindings
• Deleted incorrect todo in ABM code
• divNj in ODE models creates NaN values if subpopulation is zero
• Get_default of parameter HighViralLoadProtectionFactor did not work as expected

Merged pull requests

• 1105 redesign bindings structure to improve typing by @MaxBetzDLR in #1106
• 1113 missing includes in python bindings by @MaxBetzDLR in #1114
• 1098 bind different integrators for python by @MaxBetzDLR in #1103
• 1118 Update of Damping not working with negative coefficients by @HenrZu in #1119
• 1028 Reduce export_input_data_county_timeseries by @HenrZu in #1029
• Delete incorrect todo in ABM code by @xsaschako in #1122
• 982 Make NPI delay implementation a parameter, set it and harmonize model advance functions by @mknaranja in #984
• Explicit stepper wrapper by @reneSchm in #1127
• 1123 population data for different years by @patricklnz in #1124
• 1102 divNj creates NaN values if subpopulation is 0 by @HenrZu in #1104
• 1039 Add functions for the Person to choose whether to comply to mask,test and isolation by @khoanguyen-dev in #1040
• 896 add age resolved lct model by @lenaploetzke in #1120
• 1117 reduce use of get support max method in ide model to reduce run time by @annawendler in #1129
• 1084 Handle Epidata FutureWarnings by @patricklnz in #1109
• 1138 plot functions for AST in generation package by @dr2001dlr in #1140
• 652 Add serialization to ABM by @reneSchm in #1072
• 55 Write mobility data by @HenrZu in #971
• 932 Get_default of Parameter HighViralLoadProtectionFactor doesn't work as expected by @khoanguyen-dev in #1068
• 946 implement generalized linear chain trick by @lenaploetzke in #1058
• 1021 Error when compiling on Mac with new boost by @reneSchm in #1146

Full Changelog: v1.2.1...v1.3.0

v1.2.1

Added features / functionality:

• Implementation of stochastic two variant SEIR models
• Added delay in testing and planned mobility in ABM
• ScoreP performance profile of ABM
• gperftools profiler
• New initialization method from flows for LCT model
• Stub generation for python bindings

General changes:

• Refactored ABM code: Rename EPI to MIO, migration to mobility, and World to Model
• Replaced pointers in ABM by new structure
• Make the LCT secir model a derived class of CompartmentalModel
• New parameters that describe the multiplicative factor used for the TestAndTraceCapacity
• Extended test for equilibrium of IDE model
• Change return type of check_constraints function in the populations class to bool
• Adapt parameters_io of IDE SECIR model
• Small refacturing of epidata package
• Remove necessity for credentials of population data download
• Download boost libs with URL instead of git repo
• Upgrade manylinux image used for python in CI
• Workaround for github action checkout@v3

Corrections:

• Add warning for end_date later than 2024-07-21 in intensive care data
• OdeIntegrator could run indefinitely
• Removed bug in getting test parameters in specific test derived from generic test

Merged pull requests

• 1042 stub generation for python bindings by @MaxBetzDLR in #1044
• 992 download boost libs with URL instead of git repo by @dabele in #1048
• 848 scorep profile of abm by @charlie0614 in #942
• 1038 OdeIntegrator can run indefinitely v2 by @reneSchm in #1049
• Add gperftools profiler by @dabele in #1054
• 914 make the lct secir model a derived class of flowmodel by @lenaploetzke in #1055
• 882 Parameters that describe the multiplicative factor used for the TestAndTraceCapacity by @HenrZu in #1059
• Fix a "use after free" warning with gcc 12.3.0 and above by @reneSchm in #1060
• workaround for github action checkout@v3 by @dabele in #1063
• Upgrade manylinux image used for python in CI by @dabele in #1064
• 897 new add initialization method from flows for lct model 1 by @lenaploetzke in #1005
• Remove call to print_table from TestSeir.FlowSimulation by @reneSchm in #1066
• Extend Test for equilibrium of IDE Model #1037 by @hatrit in #1050
• 757 dont store pointers in the abm by @reneSchm in #863
• 1012 bug in getting testparameters in specific test derived from generictest by @khoanguyen-dev in #1013
• 1061 change return type of check_constraints function in the populations class to bool by @lenaploetzke in #1062
• 916-refactor-epidata-to-support-ingestion-into-the-LOKI-database by @sudiphzi in #1024
• 1079 Handle Chunked-Encoding Downloads by @patricklnz in #1080
• Refactor ABM code: Rename EPI to MIO and migration to mobility and World to Model by @xsaschako in #879
• Increase accuracy of code coverage by @reneSchm in #1076
• 466 add delay in testing and planned migration by @khoanguyen-dev in #866
• 1032 implementation of stochastic two variant seir model by @nijawa in #1047
• 1087 adapt parameters_io of ide model by @annawendler in #1095
• 1092 add warning for end_date later than 2024-07-21 in divi data by @lenaploetzke in #1094
• 1073 Remove credentials from Population Data Download by @patricklnz in #1074

Full Changelog: v1.2.0...v1.2.1

v1.2.0

Added features / functionality:

• Stochastic differential equation based SIR and SEIR models
• Linear Chain Trick ODE-based model with initialization methods for real world data
• Automatic differentiation for ODE-based models and dynamic optimization examples
• Allow contact increase for simulation of larger events
• Allow flexible start day in IDE SECIR model
• Added seasonality for IDE SECIR model
• Alternative computation of compartments in IDE SECIR
• Implement initialization scheme for flows in IDE SECIR model
• Add Gamma distribution and other parameters to state age function for IDE models
• Python support for ODE SECIRVVS model
• Python support for 2021 metapopulation/Graph-ODE SECIRVVS simulation
• Age group resolution for ODE SIR and SEIR models
• Use ccache in CI for linux builds

General changes:

• Use times for exposed and infected, no symptoms state in particular ODE models instead of SerialInterval and IncubationTime
• Updated CI actions
• Updated epidata readme
• Improve IDE SECIR model readme
• Handle pandas read excel engines
• Bundle the boost git repo instead of providing a targz archive
• Streamline ODE SECIR python code

Corrections:

• Corrected handling of minimal step size in numerical integration
• Corrected functionality of IDE SECIR model example
• Prevent NaNs in newly added SDE models
• Resolve size_t underflow in dynamic NPIs
• Fix failing RKI urls
• Make python serialization working again
• Corrected IDE SECIR model simulation for certain conditions
• Corrected gcc compiler version in CI

Merged pull requests

• 949 Correct handling of dt_min in integrators by @reneSchm in #960
• 937 update CI actions by @patricklnz in #938
• 964 Times for Exposed and INS instead of SerialInterval and IncubationTime by @HenrZu in #967
• Add workaround to fix the CI by @reneSchm in #969
• 893 add initialization method with real data for lct model by @lenaploetzke in #920
• Revert "Add workaround to fix the CI (#969)" by @reneSchm in #974
• 958 implement a check for the results of the initialization by @lenaploetzke in #959
• 953 Implement basic stochastic equation based model by @nijawa in #954
• 947 example for ide secir model not working as expected by @lenaploetzke in #948
• 793 add seasonality to ide model by @lenaploetzke in #972
• 956 update Epidata Readme by @patricklnz in #957
• 910 Handle pandas read excel engines by @patricklnz in #940
• 300 python bindings for new vaccination model by @MaxBetzDLR in #906
• 987 Start print_table() with a line break by @mknaranja in #989
• 945 Allow contact increase for simulation of larger events by @HenrZu in #975
• 988 info on sucessful adaptive step sizing is also shown for fixed step size integrators by @reneSchm in #996
• Minor follow up patch to issue 988 by @reneSchm in #1001
• 965 use int instead of unsigned int in lct infection state by @lenaploetzke in #1002
• 977 remove t0 from simulation class and allow flexible start times in model by @annawendler in #979
• 997 Resolve size_t underflow while removing dublicates in dynamic NPIs by using int by @HenrZu in #998
• 983 bundle the boost git repo instead of using the targz archiv by @lenaploetzke in #985
• 1006 Prevent NaNs in SDE models by @reneSchm in #1008
• 990 run 2021 simulation in python by @MaxBetzDLR in #991
• 981 Fix failing RKI urls by @patricklnz in #1007
• 675 alternative computation of compartments in IDE model by @annawendler in #702
• 610 implement initialization scheme for flows by @lenaploetzke in #952
• 976 improve the documentation of the ide secir model by @lenaploetzke in #1000
• 1016 use interpolate_simulation_result for timeseries in secirvvs python by @HenrZu in #1017
• 869 default values of agegroupgotoschoolwork abm parameters by @khoanguyen-dev in #973
• 905 add age group resolution to seir and sir model by @johapau in #911
• 899 new add gamma distribution and other parameters to state age function 1 by @lenaploetzke in #1004
• 1034 ide model simulation does not work under some conditions by @lenaploetzke in #1035
• 636 make python serialization usable again by @MaxBetzDLR in #761
• 894 Implement dynamic optimization by @hannemann-tamas in #895
• 1022 wrong compiler version in ci for gcc by @MaxBetzDLR in #1023
• 944 streamline secir python code by @MaxBetzDLR in #1041
• 305 add ccache to linux build by @dabele in #994

Full Changelog: v1.1.0...v1.2.0

v1.1.0

Added features / functionality:

• Graph simulation with metapopulation model for Munich
• Computation of reproduction number for ODE SECIR model
• Machine learnt surrogate model for ODE SECIR model with multiple age groups and contact change points
• Linear Chain Trick SECIR model
• New initialization for IDE model
• Unit Tests with OpenMP

Corrections:

• Correct selection of specialized simulation and advance functions in python bindings
• Corrections for new MSVC

Other:

• Expanded tests for python bindings simulations
• Small changes and fixes (logo, pull request template, ...)

Merged pull requests

• remove experimental benchmark pipeline by @dabele in #878
• 867 pr template by @xsaschako in #876
• 721 Munich graph sim by @jubicker in #791
• 677 final version secir reproduction number by @johapau in #858
• 402 Surrogate model implementation with multiple age groups and dampings by @HenrZu in #562
• 885 Compatibility of specialized simulation and advance functions in Secir and Secirvvs model with flows by @HenrZu in #889
• Update pull_request_template.md by @mknaranja in #903
• 367 responsibility of testing schemes regarding quarantine by @xsaschako in #890
• replaced print functions by print_table by @lenaploetzke in #900
• 888 Make Apply_variant function more generic and fix issue with default value by @HenrZu in #904
• 720 config file for data downloads by @patricklnz in #902
• 921 Improve PopulationData Download by @patricklnz in #922
• Fix memilio logo in doxygen documentation by @reneSchm in #926
• 271 expand tests of the python bindings by @MaxBetzDLR in #605
• 918 add function to change the tolerance in ide model by @lenaploetzke in #919
• fix parameter rendering by doxygen by @reneSchm in #927
• 934 Add MEmilio favicon to github pages by @mknaranja in #935
• 892 implement simple lct model by @lenaploetzke in #915
• 898 change test for valid transition distibution from ide model by @lenaploetzke in #913
• 769 new initialization for ide model by @lenaploetzke in #770
• Run unit tests with OpenMP in CI by @dabele in #870
• 950 build cpp msvc debug latest fails at the main branch by @lenaploetzke in #951
• 928 add a flow chart for the lct model by @lenaploetzke in #943
• 936 implement the class infectionstate of the lct model more efficiently by @lenaploetzke in #941

Full Changelog: v1.0.0...v1.1.0