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