AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models

AMICI v0.17.0 requires Python>=3.9 and a C++17 compatible compiler

Features

• DAE support in SBML by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2017
• SBML import: flatten SBML-comp models by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2063
• Added sllh computation back to petab_objective.simulate_petab by @dilpath in https://github.com/AMICI-dev/AMICI/pull/1548
• CMake-based Python extension builds by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1992

Fixes

• Fixed CPU time tracking with multi-threading (partially) by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2023
• Fixed HDF5 ambiguous overload by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2031
• Fixed varying cmake libdir lib(64)/ by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2033
• Fixed Equilibration cpu time computation by @plakrisenko in https://github.com/AMICI-dev/AMICI/pull/2035
• CMake: add header files to library sources for generated models by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2047
• CMake: Handle header-dependency of swig files by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2046
• Don't try to detect conservation laws for models with Species-AssignmentRules by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2056
• Smith benchmark and SBML initialization fix by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2034
• SBML import: Fixed check for required packages by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2064
• Nan observables by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2065
• Fixed check for discontinuities for conservation law computation by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2068
• Specify visualization dependencies by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2070
• Fixed sympy symbol name clashes during PEtab import by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2069
• Fixed ReturnData::{preeq_wrms,posteq_wrms} with FSA and check_sensi_steadystateconv=True by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2071

Extended / updated documentation, for example:

• Jax example notebook by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1996
• Updated Windows/MSVC installation instructions by @Podde1 in https://github.com/AMICI-dev/AMICI/pull/2053

New Contributors

• @Podde1 made their first contribution in https://github.com/AMICI-dev/AMICI/pull/2053

Full Changelog: https://github.com/AMICI-dev/AMICI/compare/v0.16.1...v0.17.0