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

New:

• Added support for observable transformations (lin/log/log10) (#1567). Thereby supporting additional noise distributions in combination with least squares solvers.

Fixes:

• Fixed a bug when Newton sensitivity computation was activated despite specifying newton_steps == 0. The error occurs when simulation converges to a steadystate but simulation sensitivities are not converged according to convergence criteria. In that case simulation returned failure, but the newton rootfinding "finds" a steadystate even before the iteration check, leading to the erroneous computation of sensitivities via Newton/IFT. For singular jacobians this means the overall simulation still fails, but a different, more informative error message is displayed. (#1541)
• Fixed a bug where argument outdir in ODEExporter.__init__ would not be used (#1543)

Other:

• Improve checking support for SBML extensions (#1546)
• SBML import: Use more descriptive IDs for flux expressions (#1551)
• Optimized SUNMatrixWrapper functions (#1538)
• C++: Changed test suite from CppUTest to gtest (#1532)
• Add CITATION.cff (#1559)
• Updated documentation (#1563, #1554, #1536)
• Removed distutils dependency (#1557)
• Require sympy<1.9