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.

AMICI v0.6.0

Implement experimental support for python via swig.
Python interface is now usable, but API will still receive some updates in the future.

WARNING:

• There is a bug in sensitivity computation for Python-generated models
• Matlab C++ compilation will fail due to undefined M_PI
  -> Please use v0.7.0

AMICI v0.5.0

Main new features are:

• Reimplemented support for DAE equations

• Added newton solver for steady state calculation and preequilibration

• Better caching for recompilation of models

• Blas support to allow compilation of large models with many observables

• Improved SBML support

• Added c++ interface

• Added support for second order adjoint computation

• Rewrote large parts of the code as proper c++11 code to allow easier code maintanance

• Substantially extended testing in continuous integration to assure code quality