AMICI v0.10.8

Changes in this release:

All:

• Updated / extended documentation
• Fix reuse of Solver instances (#541)

C++:

• Check for correct AMICI version for model in CMake
• Add reporting of computation times (#699)

Python:

• Fix manifest file (#698)
• Fix initial amounts/concentrations in SBML import

... and various other minor fixes/improvements

AMICI v0.10.7

Python

• fix unset noise distribution when automatically generating observables in case None are passed (#691)

AMICI v0.10.6

C++

• Add SuperLUMT support (#681)
• Sparsified dJydy (#686)
• Enabled support of impulse-free events for DAE models (#687) - thanks to Sebastien Sten for providing a testcase for this

Python

• Enabled support for piecewise functions in SBML import (#662)
• Fix numeric type when constructing ExpData from Dataframes (#690)
• Fix dynamic override in PETab

AMICI v0.10.5

Bugfix release

Doc

• Update documentation of Windows installation

C++

• Fix missing source files in CMakeLists.txt (#658)
• Set CMake policies to prevent warnings (Closes #676) (#677)
• Start using gsl::span instead of raw pointers (#393) (#678)

Python

• PySB parsing fix (#669)
• Fix failure to propagate BLAS_LIBS contents (#665)
• Require setuptools at setup (#673)
• Updated PEtab import to allow for different noise models

AMICI v0.10.4

Features / improvements:

• Implement ReturnData and ExpData wrappers as more efficient views (#657)
• Add list of references using AMICI (#659)
• Custom llh (normal/laplace, lin/log/log10) (#656)

Bugfixes:

• Speedup and fix travis build

AMICI v0.10.3

Features / improvements:

• adds the option for early termination on integration failures for runAmiciSimulations
• improve runtime of SUNMatrixWrapper::mutliply
• expose finite difference routines in public API
• enable parallel compilation of clib source files

Bugfixes:

• fixed symbolic processing for unreleased pysb features

AMICI v0.10.2

Features / improvements:

• extended ExpData interface to allow for condition specific parameters, parameter scales, parameter lists, initial conditions and initial condition sensitivities.

Bugfixes:

• fixed output values of ReturnData::x_ss and ReturnData::sx_ss

AMICI v0.10.1

• travis-ci.com migration
• fix problem with has{variable} functions
• allow to import sbml model from string, not only file

AMICI v0.10.0

Features / improvements:

• updated sundials to 4.1.0
• updated SuiteSparse to 5.4.0
• added generic implementations for symbolic expressions that were sparse matrix vector products

Bugfixes:

• fixed return value of rz when no data is provided.

AMICI v0.9.5

Features / improvements:

• allow python installations without compilation of c++ extension
• improvements to ExpData <-> pandas.DataFrame interface
• allow generation of matlab models from python
• implement CLI interface for PEtab
• improve computation time for conservation laws from pysb import

Bugfixes:

• Fix sign in undamped Newton step.

Maintenance:

• use newer CI images