* Fixed (re)initialization of sensitivities if ExpData::fixedParametersPreequilibration is set (994) * Fixed sensitivities for parameters in sigma expressions for Python/SBML in case provided expression was not just a single parameter ID * Enable parallel compilation of model files from Python (997) based on AMICI_PARALLEL_COMPILE enviroment variable * Fixed computation of log-likelihood for log10-normal distributed noise * Added `reinitializeFixedParameterInitialStates` to ExpData (1000) (**breaking change**: overrides settings in `amici::Model`) * Python model import now verifies that chosen model name is a valid identifier (Closes 928) * Made w available in ReturnData (Closes 990) (992) * Fixed setting of log level when passing boolean values to verbose (991) * Documentation now on ReadTheDocs https://amici.readthedocs.io/en/ * Use proper state/observable names in plotting functions (979) * PEtab support: * Adapt to most recent PEtab (0.1.5) * Extended support for import of PEtab models * Added support for computing cost function based on PEtab problem * Implemented handling of species in condition table * petab_import.import_model now provides reproducible parameter list (Closes 976) * Fix python import error in import_petab_problem: Add absolute paths to python path, invalidate caches and reload (970) * Added example notebook * CI: PEtab test suite integrated in CI workflow * Added AMICI dockerfile and image deployment to dockerhub (948) * Removed mention of 'mex' in warning/error ids (968) * More informative errors on SWIG interface import failures (959)
0.10.19
Not secure
Python: * Fix logo display on pypi * Fix deadlocks in multithreaded python environments when using openMP parallelization
Matlab: * Fix compilation errors due to switch to C++14
0.10.18
Not secure
General: * AMICI now comes with a logo * implement getName function for models * Updated documentation / examples
Python: * Enable MSVC compilation of Python extensions (847) * Always recompile clibs and extensions (Closes 700) * Extended PEtab support (Running * enable multithreading in swig (938) * Fixes pysb (902) (907)
C++ * Build optimized AMICI and sundials by default (Closes 934)
Matlab: * Fix(matlab) Compile CalcMD5 on demand (Fixes 914) * Don't pass empty include strings to mex * Fix Matlab compilation error if AMICI or model path contains blanks
* **Sparsify dwdp to reduce computation time for adjoints (858)** * Fix(matlab) update example name example_dae_events->example_calvetti (Closes 866) * Fix nullptr deferencing for simulations with events when no measurements are provided (Fixes 866) * Fix accessing empty vector during adjoint state event update (Closes 866) * Fix pysb_import (fixes 878)
0.10.15
Not secure
Bugfix release due to incorrect sensitivities w.r.t. sigmas introduced in 0.10.14.