AMICI v0.9.0

Features / improvements:

• Allow computation and application of conservation laws for pysb importet models. This enables use of NewtonSolver for preequilibration for models where it was previously not possible.
• Use klu_refactor in the sparse Newton solver instead of always using klu_factor and only perform symbolic factorization once (#421)
• Allow more detailed finiteness checks (#514)

Bugfixes:

• #491

Maintenance:

• Several improvements to travis log sizes and folding
• Use default copy constructor for Model by implementing class wrappers for sundials matrix types (#516)
• Reenable run of SBML testsuite

AMICI v0.8.2

Features / improvements:

• Speedup symbolic processing for ODE generation in python

Bugfixes:

• Fix(python) Add missing deepcopy (introduced in 6847ba6)
• Fix(core) Prevent parameter scaling length mismatch (#488)
• Fix(python) Set distutils dependency to current version to fix </usr/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'long_description_content_type'>
• fix(python) add symlink to version.txt to be included in package

Backwards-compatibility:

• Replace 'newline' by literal to restore <R2016b compatibility (Fixes #493)

Maintenance:

• Remove obsolete swig library build via cmake and related file copying
• Provide issue template for bug reports
• Providing valid SBML document to import is not optional anymore
• Update documentation and tests
• Add python version check and raise required version to 3.6 to prevent cryptic error messages when encountering f-strings

AMICI v0.8.1

• [all] critical Fix long standing bugs in solving steadystate problems (including preequilibration) (#471)
• [all] Fix AmiVector constructor from std::vector (#471)
• [python] Reenable Solver and Model copy constructors
• Update documentation

AMICI v0.8.0

• replaced symengine by sympy for symbolic processing in python which fixes several critical bugs that were due to bugs in symengine (#467)

AMICI v0.7.13

• fixes a critical bug in objective function computation for models compiled using sbml2amici and pysb2amici that was introduced in v0.7.12
• fixes a critical bug in sensitivity computation whenmodel.reinitializeFixedParameterInitialStates was set to true
• readds the python interface to the ExpData copy constructor that was inadvertently removed in 0.7.12 and streamlines the respective convenience wrapper to provide access to the full range of constructors.

AMICI v0.7.12

• fixed a critical bug in amici.constructEdataFromDataFrame
• enabled multithreaded simulation of multiple experiments (requires compilation with openMP)
• modularized sbml import and added pysb import

AMICI v0.7.11

• [python] Added numpy and python wrappers that provide a more user friendly python API
• [python] Enable import of SBML models with non-float assignment rules
• [python] Enable handling of exceptions in python
• [python] Enable nativ python access to std::vector data-structures
• [core] Provide an API for more fine-grained control over sensitivity tolerances and steady-state tolerances
• [core] Provide an API to specify non-negative state variables (this feature is still preliminary)

AMICI v0.7.10

• Fixed python SBML import log() issues (#412)

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