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

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