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

AMICI v0.9.4

Minor fixes only:

• fix(core) Get solver diagnostics for first(last) timepoint (#588) (Closes #586)
• fix(ci) Fix autodeploy (Closes #589)

AMICI v0.9.3

CRITICAL FIXES

• fix(python) fix symbolic computations for adjoint (#583)

Features

• feature(python) Check for matching AMICI versions when importing model (Closes #556). Set exact AMICI version as model package requirement.
• feature(core) Add option to rethrow AMICI exception (Closes #552)
• feature(python) Redirect C/C++ output in stdout is redirected (e.g. in ipython notebooks) (Closes #456)

Minor fixes

• fix(python) Fix doc and rename sys_pipes to something more meaningful
• fix(ci) Fix premature exit of scripts/runNotebook.sh
• fix(deploy) Update pyenv shims to find twine

AMICI v0.9.2

Bugfixes:

• fixes a critical bug in the newton solver
• fixes multiple bugs in sbml import for degenerate models, empty stoichiometry assignments and conversion factors
• improved error messages for sbml import
• #560
• #557
• #559

AMICI v0.9.1

Features / improvements:

• make pure steadystate results available as rdata['x_ss'] and rdata['sx_ss']
• add option to specify integration tolerances for the adjoint problem via atolB and rtolB

Bugfixes:

• improved conservation law identification to also account for constant species.
• fixed a bug where simulation results were written into results of the second newton solver attempt
• fixed an openMP related warning

Maintenance:

• attempt to fix automatic deploy to pypi via travis