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

New features:

• Import of BioNetGenLanguage (BNGL) models by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1709
• Added support for observable-dependent sigmas by @dweindl, @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1692
• Added support for pysb local functions by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1666
• Added experimental support for conservation laws for non-constant species to SBML import: conservation laws for non-constant species by @stephanmg, @dweindl in https://github.com/AMICI-dev/AMICI/pull/1669 Enable this feature by setting environment variable AMICI_EXPERIMENTAL_SBML_NONCONST_CLS to any value
  • Allow using states eliminated by conservation laws to be used in root functions by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1677
  • Added support for parameter-dependent conservation laws by @dweindl, @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1678
• Added optional caching for symbolic simplifications in ODE export by @dilpath in https://github.com/AMICI-dev/AMICI/pull/1672
• Added CLI option --no-sensitivities to amici_import_petab by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1688

Fixes:

• SBML import: Raise in case of nested observables by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1690
• Sympy 1.10 compatibility by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1694

Full Changelog: https://github.com/AMICI-dev/AMICI/compare/v0.11.25...v0.11.26