Amici

Latest version: v0.31.0

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0.10.20

Not secure
* 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

CI:
* Running additional test models

... and various minor fixes/updates

0.10.17

Not secure
- **added python 3.8 support, dropped python 3.6 support** (898)
- Added logging functionality (900)
- Fixes PySB import (879, 902)
- Fixes symbolic processing (899)
- Improved build scripts (894,
- Improved petab support (886, 888, 891)
- CI related fixes (865, 896)

0.10.16

Not secure
* **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.

No other changes.

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