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