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AMICI v0.10.20

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@dweindl dweindl released this 18 Mar 19:14
· 1381 commits to master since this release
f921278
  • 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)