New optimizer: CMA-ES (#457) New plot: Optimizer convergence summary (#446) Fixes in visualization: Type checks for reference points (#460) y_limits in waterfall plots with multiple results (#475) Support of new amici release (#469) Multiple fixes in optimization code: Remove unused argument for dlib optimizer (#466) Add check for installation of ipopt (#470) Add maxiter as default option of dlib (#474) Numpy based subindexing in amici_util (#462) Check amici/PEtab installation (#477
Python Fix simplification for pysb models (#1168) Pass verbosity flags to pysb network generation (...
Update to AMICI 0.10.13, fix API changes (#185). Start using PEtab import from AMICI to be able to ...
Changes in this release: All: Updated / extended documentation Fix reuse of Solver instances (#541...
New Optimizers: FIDES (#506, #503 # 500) NLopt (#493) Extended PEtab support: PySB import (#437)...
Example Notebook for prior functionality (#438) Changed parameter indexing in profiling routines (#4...
Objective Write solver settings to stream to enable serialization for distributed systems (#308) Re...
Objectives: New Aesara objectve (#623, #629, #635) Sampling: New Emcee sampler (#606) Fix compat...
Finite Differences: Adaptive finite differences (#671) Add helper function for checking gradients o...
Import AMICI (https://github.com/ICB-DCM/AMICI/) models and the PEtab (https://github.com/ICB-DCM/PE...
Add typehints to global functions and classes. Add PetabImporter.rdatas_to_simulation_df function (a...
Optimize: sacess optimizer (#988, #997) Warn only once if using ineffiecient objective settings (#99...
BREAKING CHANGE: Renaming {get|set}tNewtonPreequilibration to {get|set}Preequilibration (Closes #720...
Tidy up and speed up tests (#265 and others). Basic self-implemented Adaptive Metropolis and Adaptiv...
Rewrite AmiciObjective and PetabAmiciObjective simulation routine to directly use amici.petab_object...
Objective: Basic finite differences (#666) Fix factor 2 in res/fval values (#619) Optimization: ...
Python Fix simplification for pysb models (#1168) Pass verbosity flags to pysb network generation (...
Update to AMICI 0.10.13, fix API changes (#185). Start using PEtab import from AMICI to be able to ...
Changes in this release: All: Updated / extended documentation Fix reuse of Solver instances (#541...
New Optimizers: FIDES (#506, #503 # 500) NLopt (#493) Extended PEtab support: PySB import (#437)...
Example Notebook for prior functionality (#438) Changed parameter indexing in profiling routines (#4...
Objective Write solver settings to stream to enable serialization for distributed systems (#308) Re...
Objectives: New Aesara objectve (#623, #629, #635) Sampling: New Emcee sampler (#606) Fix compat...
Finite Differences: Adaptive finite differences (#671) Add helper function for checking gradients o...
Import AMICI (https://github.com/ICB-DCM/AMICI/) models and the PEtab (https://github.com/ICB-DCM/PE...
Add typehints to global functions and classes. Add PetabImporter.rdatas_to_simulation_df function (a...
Optimize: sacess optimizer (#988, #997) Warn only once if using ineffiecient objective settings (#99...
BREAKING CHANGE: Renaming {get|set}tNewtonPreequilibration to {get|set}Preequilibration (Closes #720...
Tidy up and speed up tests (#265 and others). Basic self-implemented Adaptive Metropolis and Adaptiv...
Rewrite AmiciObjective and PetabAmiciObjective simulation routine to directly use amici.petab_object...
Objective: Basic finite differences (#666) Fix factor 2 in res/fval values (#619) Optimization: ...
Python Fix simplification for pysb models (#1168) Pass verbosity flags to pysb network generation (...
Update to AMICI 0.10.13, fix API changes (#185). Start using PEtab import from AMICI to be able to ...
Changes in this release: All: Updated / extended documentation Fix reuse of Solver instances (#541...