AMICI v0.7.9

• fixes MATLAB compilation of models
• adds option to perform steady state sensitivity analysis via FSA
• condition dependent intitial conditions are now newly set after preequilibration is done

AMICI v0.7.8

• bugfixes for the ExpData interface
• created build configuration that enables debugging of c++ extensions on os x
• fixed python sbml import when stoichiometry is empty

AMICI v0.7.7

Fixes a couple of bugs just introduced in v0.7.6

AMICI v0.7.6

Important: Use AMICI v0.7.7 due to 3a495d3

Bug fixes:

• Python import: Fix log10 issues in observables (#382)
• Matlab: Fix broken model compilation (#392)
• Fixed simulation for models without observables (#390)
• Fixed potential matlab memory leaks (#392)

Breaking C++ API changes:

• Revised ExpData interface (#388)

AMICI v0.7.5

Features/enhancements:

• Add computation of residuals, residuals sensitivity, Fisher information matrix (#223)
• More efficient conversion of std::vector to numpy ndarray (#375)
• Allow specifying timepoints in ExpData (#370)

Minor fixes:

• Condition parameters in ExpData now only temporarily override Model parameters (#371)
• Ensure non-negative states for Newton solver (#378)

AMICI v0.7.4

Features/enhancements:

• Check SBML model validity (#343)
• Allow per-parameter setting of amioptions::pscale from matlab interface (#350)
• Documentation

Major fixes:

• Don't compile main.cpp into python model module which broke modules if amici was compiled without libhdf5 (#363)

Minor fixes:

• Fix compiler warnings (#353)
• Plotting, SBML example mode, ...

AMICI v0.7.3

Features:

• Added symbol names to python-wrapped models and make available via Model.getParameterNames(), model.getStateNames(), ...
• Extended Python interface example

Python package available via pypi: https://pypi.org/project/amici/0.7.3/

AMICI v0.7.2

Features:

• Python package: more flexible HDF5 library localization
• Extended CI: python tests, preequilibration tests, run in venv

Major bugfixes:

• Fix python sbml model import / compilation error (undefined function)
• Fix model preequilibration

Minor fixes:

• Various fixes for mingw compilation of python source distribution
• Cmake compatibility with < 3.8 restored

AMICI v0.7.1

Features:

• Allow specifying sigma-parameters from Python interface

Major bugfixes:

• Fix dsigma_y/dp and downstream sensitivity errors

AMICI v0.7.0

• Major revision of documentation
• Improved Python interface
• More comprehensive Python interface example
• Fixed sensitivity computation in Python-generated models
• Various other bug fixes

WARNING:

• For models with sigma-parameters and dsigma_y/dp != 0, dsigma_y/dp was computed incorrectly. This propagates to all dependent sensitivities. This applies also to some older releases and has been fixed in v0.7.1.