AMICI v0.10.21

Library:

• Fix: Handle paths with blanks in build scripts
• Feature: Add function to write amici::Solver settings to HDF5 (#1023)
• Fix: typehints (#1018, #1022)
• Refactor: Move creation of parameter mapping for objective<->simulation to classes (#1020)

CI:

• Refactor: Cleanup and reorganize tests (#1026)
• Fix: benchmark problem test should fail on missing files (Closes #1015)

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 in amici::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

• added python 3.8 support, dropped python 3.6 support (#898)
• Added logging functionality (#900)
• Fixes PySB import (#879, #902)
• Fixes symbolic processing (#899)
• Improved build scripts (#894,
• Improved petab support (#886, #888, #891)
• CI related fixes (#865, #896)

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)