Releases: AMICI-dev/AMICI
Releases · AMICI-dev/AMICI
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
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
AMICI v0.9.1
Features / improvements:
- make pure steadystate results available as
rdata['x_ss']
andrdata['sx_ss']
- add option to specify integration tolerances for the adjoint problem via
atolB
andrtolB
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 usingklu_factor
and only perform symbolic factorization once (#421) - Allow more detailed finiteness checks (#514)
Bugfixes:
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