Releases: AMICI-dev/AMICI
Releases · AMICI-dev/AMICI
AMICI v0.10.21
AMICI v0.10.20
- Fixed (re)initialization of sensitivities if ExpData::fixedParametersPreequilibration is set (#994)
- Fixed sensitivities for parameters in sigma expressions for Python/SBML in case provided expression was not just a single parameter ID
- Enable parallel compilation of model files from Python (#997) based on AMICI_PARALLEL_COMPILE enviroment variable
- Fixed computation of log-likelihood for log10-normal distributed noise
- Added
reinitializeFixedParameterInitialStates
to ExpData (#1000) (breaking change: overrides settings inamici::Model
) - Python model import now verifies that chosen model name is a valid identifier (Closes #928)
- Made w available in ReturnData (Closes #990) (#992)
- Fixed setting of log level when passing boolean values to verbose (#991)
- Documentation now on ReadTheDocs https://amici.readthedocs.io/en/
- Use proper state/observable names in plotting functions (#979)
- PEtab support:
- Adapt to most recent PEtab (0.1.5)
- Extended support for import of PEtab models
- Added support for computing cost function based on PEtab problem
- Implemented handling of species in condition table
- petab_import.import_model now provides reproducible parameter list (Closes #976)
- Fix python import error in import_petab_problem: Add absolute paths to python path, invalidate caches and reload (#970)
- Added example notebook
- CI: PEtab test suite integrated in CI workflow
- Added AMICI dockerfile and image deployment to dockerhub (#948)
- Removed mention of 'mex' in warning/error ids (#968)
- More informative errors on SWIG interface import failures (#959)
AMICI v0.10.19
Python:
- Fix logo display on pypi
- Fix deadlocks in multithreaded python environments when using openMP parallelization
Matlab:
- Fix compilation errors due to switch to C++14
AMICI v0.10.18
General:
- AMICI now comes with a logo
- implement getName function for models
- Updated documentation / examples
Python:
- Enable MSVC compilation of Python extensions (#847)
- Always recompile clibs and extensions (Closes #700)
- Extended PEtab support (Running
- enable multithreading in swig (#938)
- Fixes pysb (#902) (#907)
C++
- Build optimized AMICI and sundials by default (Closes #934)
Matlab:
- Fix(matlab) Compile CalcMD5 on demand (Fixes #914)
- Don't pass empty include strings to mex
- Fix Matlab compilation error if AMICI or model path contains blanks
CI:
- Running additional test models
... and various minor fixes/updates
AMICI V0.10.17
AMICI v0.10.16
- Sparsify dwdp to reduce computation time for adjoints (#858)
- Fix(matlab) update example name example_dae_events->example_calvetti (Closes #866)
- Fix nullptr deferencing for simulations with events when no measurements are provided (Fixes #866)
- Fix accessing empty vector during adjoint state event update (Closes #866)
- Fix pysb_import (fixes #878)
AMICI v0.10.15
Bugfix release due to incorrect sensitivities w.r.t. sigmas introduced in 0.10.14.
No other changes.
AMICI v0.10.14
NOTE: For Python-imported SBML-models this release may compute incorrect sensitivities w.r.t. sigma. Bug introduced in 0.10.14, fixed in 0.10.15.
Python:
- Don't require use of ModelPtr.get to call ExpData(Model)
- Fix import in generated model Python package
- Setup AMICI standalone scripts as setuptools entrypoints
- Simplify symbolic sensitivity expressions during Python SBML import
Fixes Infs in the Jacobian when using Hill-functions with states of 0.0. - Extended Newton solver #848
The changes that allow performing Newton tests from the paper:
G. T. Lines, Ł. Paszkowski, L. Schmiester, D. Weindl, P. Stapor, and J. Hasenauer. Efficient computation of steady states in large-scale ODE models of biochemical reaction networks. accepted for Proceedings of the 8th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE), Valencia, Spain, October 2019. - Use SWIG>=4.0 on travis to include PyDoc in sdist / pypi package (#841)
- Fix choice of likelihood formula; failed if observable names were not equal to observable IDs
- Fix(sbml-import) Compartment IDs in right-hand side of Rules are not replaced and lead to undefined identifiers in c++ files
- Fix invalid logging level
- Speed up sympy simplification (#871)
C++:
- Performance: Avoid unnecessary repeated function calls for SUNMatrixWrapper dimensions
- Add AmiciApplication class as context for handling so far global settings.
This allows for example setting custom logging functions for concurrent AMICI
runs, e.g. in multi-thread applications (Closes #576).
Misc:
- Setup performance test on github actions (#853)
- Update documentation and FAQ for CBLAS requirement and others
- Update reference list
AMICI v0.10.13
- BREAKING CHANGE: Renaming {get|set}tNewtonPreequilibration to {get|set}Preequilibration (Closes #720)
- Make wurlitzer non-optional requirement for AMICI python package (Fixes missing AMICI errors when running from jupyter notebooks)
- Compute initial state for Model::getInitialStates if not already set (Fixes #818)
- Make swig generate pydoc comments from doxygen comments #830 (Closes #745) to provide Python docstrings for C++ wrapper functions
- feature(cmake) Add option to disable compiler optimizations for wrapfunctions.cpp (Fixes #828) (#829)
- Change SBML test suite to pytest to allow for parallel test execution… (#824)
- Fix(cmake): -E option is not available in all sed versions. Neither is the equivalent -r. Use --regexp-extended instead (Closes #826)
- Refactor(python) Move PEtab import code from command line script… (#825)
- Fix(core) Fix regular expressions for intel compiler (Closes #754) (#822)
- Update workflow figure to include PySB (Closes #799)
- Fix compiler warnings
AMICI v0.10.12
- Fix handling of species specified in PEtab condition table (#813)
- Fix some Visual C++ issues, update cppcheck handling, cleanup (VisualC++ still not fully supported)
- Minor fixups (#801)
- Create SBML test suite result files for upload to http://sbml.org/Facilities/Database/ (#798)