Objective: Basic finite differences (#666) Fix factor 2 in res/fval values (#619) Optimization: Sort optimization results when appending (#668) Read optimizer result from HDF5 (previously only CSV) (#663) Storage: Load ensemble from HDF5 (#640) CI: Add flake8 checks as pre-commit hook (#662) Add efficient biological conversion reaction test model (#619) General: No automatic import of the predict module (#657) Assert unique problem parameter names (#665) Load ensemble from optimization result with and without history usage (#640) Calculate validation profile significance (#658) Set pypesto screen logger to "INFO" by default (#667) Minor fixes: Fix axis variable overwriting in visualize.sampling_parameter_traces (#665
Only compute FIM when sensitivities are available (#194). Fix documentation build (#197). Add suppor...
Features Add learning curve plot (#150) (1a9766b) added new non-dimensional metric (#161) (91588b...
Move to cffi>=1.13.1 after that bug was surprisingly quickly fixed (#195). Create sub-module for eps...
Finite Differences: Adaptive finite differences (#671) Add helper function for checking gradients o...
New Optimizers: FIDES (#506, #503 # 500) NLopt (#493) Extended PEtab support: PySB import (#437)...
Objective Write solver settings to stream to enable serialization for distributed systems (#308) Re...
Ensembles/Sampling: General ensemble analysis, visualization, storage (#557, #565, #568) Calculate ...
Objectives: New Aesara objectve (#623, #629, #635) Sampling: New Emcee sampler (#606) Fix compat...
Major Modularize import, to import optimization, sampling and profiling separately (#413) Minor B...
Ensembles: Added standard deviation to ensemble prediction plots (#853) Storage Distinguish betwee...
Example Notebook for prior functionality (#438) Changed parameter indexing in profiling routines (#4...
Tidy up and speed up tests (#265 and others). Basic self-implemented Adaptive Metropolis and Adaptiv...
Add typehints to global functions and classes. Add PetabImporter.rdatas_to_simulation_df function (a...
Rewrite AmiciObjective and PetabAmiciObjective simulation routine to directly use amici.petab_object...
Import AMICI (https://github.com/ICB-DCM/AMICI/) models and the PEtab (https://github.com/ICB-DCM/PE...
Only compute FIM when sensitivities are available (#194). Fix documentation build (#197). Add suppor...
Features Add learning curve plot (#150) (1a9766b) added new non-dimensional metric (#161) (91588b...
Move to cffi>=1.13.1 after that bug was surprisingly quickly fixed (#195). Create sub-module for eps...
Finite Differences: Adaptive finite differences (#671) Add helper function for checking gradients o...
New Optimizers: FIDES (#506, #503 # 500) NLopt (#493) Extended PEtab support: PySB import (#437)...
Objective Write solver settings to stream to enable serialization for distributed systems (#308) Re...
Ensembles/Sampling: General ensemble analysis, visualization, storage (#557, #565, #568) Calculate ...
Objectives: New Aesara objectve (#623, #629, #635) Sampling: New Emcee sampler (#606) Fix compat...
Major Modularize import, to import optimization, sampling and profiling separately (#413) Minor B...
Ensembles: Added standard deviation to ensemble prediction plots (#853) Storage Distinguish betwee...
Example Notebook for prior functionality (#438) Changed parameter indexing in profiling routines (#4...
Tidy up and speed up tests (#265 and others). Basic self-implemented Adaptive Metropolis and Adaptiv...
Add typehints to global functions and classes. Add PetabImporter.rdatas_to_simulation_df function (a...
Rewrite AmiciObjective and PetabAmiciObjective simulation routine to directly use amici.petab_object...
Import AMICI (https://github.com/ICB-DCM/AMICI/) models and the PEtab (https://github.com/ICB-DCM/PE...
Only compute FIM when sensitivities are available (#194). Fix documentation build (#197). Add suppor...
Features Add learning curve plot (#150) (1a9766b) added new non-dimensional metric (#161) (91588b...
Move to cffi>=1.13.1 after that bug was surprisingly quickly fixed (#195). Create sub-module for eps...