AMICI v0.11.2

Python

• Speed up model import, compilation (#1123, #1112)
• Improve/Add steady-state solver documentation (#1102)
• Improve extension import (#1141)
• Bugfixes SBML import (#1135, #1134, #1145, #1154)
• Fixed issue that prevented simplification (#1158)

C++

• Bugfixes (#1121, #1125, #1131, #1132, #1136)
• Enable openMP by default (#1118)
• Improve memoy footprint for simulations with replicates (#1153)
• Improve steady-state solver and add option to to adjoint-steadystate hybrid (#1143, #1099, #1129, #1146)

CI

• Store build artifacts from github actions (#1138)

AMICI v0.11.1

Python

• Upgrade to sympy 1.6.0, which is now required minimum version (#1098, #1103)
• Speed up model import
  • Speed-up computation of sx0, reduce file size (#1109)
  • Replace terribly slow sympy.MutableDenseMatrix.is_zero_matrix by custom implementation (#1104)
• speedup dataframe creation in get*AsDataFrame (#1088)
• Allow caching edatas for simulate_petab (#1106)
• Fix wrong deprecation warning (Fixes #1093)
• Fix segmentation faults in NewtonSolver under certain conditions (#1089, #1090, #1097)
• fix wrong power function call in unscale_parameter (#1094)
• Fix MathML conversion (#1086)
• Fix deepcopy of SymPy objects (#1091)

Matlab

• handle empty rdata->{pre|post}eq_numlinsteps (Closes #1113), which previously made the matlab interface unusable
• Fix generation of compileMexFile.m for matlab compilation of python code (#1115)

C++

• Reduce memory requirements and speedup compilation of large models (#1105)
• Place generated code into own namespace (#937) (#1112)
• Fix several msvc compiler warnings (#1116) (Note that MSVC support is still experimental) breaking change for users of C++ interface
• Fix swig warning: ensure base class ContextManager is known before use (Fixes #1092) (#1101)

CI

• Don't install/run valgrind on travis CI (done with github actions… (#1111)

AMICI v0.11.0

Python:

• Implement support for variable compartments (#1036)
• Better handling of constant species (#1047)
• Better handling of C++ enums, this makes amici.SensitivityMethod_forward available as amici.SensitivityMethod.forward (#1042)
• Improve installation routines (#1055, #1056, #1058, #1076)
• Add option to reduce memory usage (#1044)
• Fix handling of symbolic expressions in nested rules (#1081, 1069)

Library:

• Update Sundials to 5.2.0 (#1039)
• Update SuiteSparse to 5.4.0 (#1040)
• Refactor use of ReturnData, now completely created post-hoc (#1002)
• Fix propagation of reinitialization in ExpData constructor (#1041)
• Fix issue where InternalSensitivityParameter was sometimes not set (#1075)
• Fix or disable certain combinations of equilibraition, presimulation and adjoint sensitivity analysis

CI:

• Move from Codacy to Sonarcloud (#1065)
• Run SBML Testsuite when appropriate (#1058)

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.