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

Features

• Python 3.11 compatibility by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1876
• AMICI now runs on binder (https://mybinder.org/v2/gh/AMICI-dev/AMICI/develop?labpath=binder%2Foverview.ipynb) by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1935, https://github.com/AMICI-dev/AMICI/pull/1937, https://github.com/AMICI-dev/AMICI/pull/1939
• More informative Solver.__repr__ and ExpData.__repr__ by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1928 and @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1948
• simulate_petab returns the generated/used ExpDatas by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1933
• Model module is now accessible from model instance by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1932
• Added plot_jacobian by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1930
• Now logs all nested execution times as debug by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1947
• Always check for finite initial states, not only with Model.setAlwaysCheckFinite(True) by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1955

Fixes

• ReturnDataView.status now returns int instead of float by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1929
• Updated simulation status codes by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1931
• Skip irrelevant frames in stacktraces by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1934
• Fixed compiler warning (matlab) by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1954

Documentation:

• Added a notebook demonstrating common simulation failures and show how to analyze / fix them by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1946
• various minor fixes / updates

Full Changelog: https://github.com/AMICI-dev/AMICI/compare/v0.15.0...v0.16.0