AMICI v0.13.0

• Fixed extraction of common subexpressions by @dweindl in #1865
• Added function to convert ReturnData::status flags to string by @dweindl in #1864

And further contributions by @dweindl, @FFroehlich

Full Changelog: v0.12.0...v0.13.0

AMICI v0.12.0

Features:

• Support for event observables via the Python interface by @FFroehlich in #1845
• Treat non-estimated parameters as constants during SBML-PEtab import by @dweindl in #1810
• Updated SUNDIALS to v5.8.0 by @dweindl in #1836
• Option to extract common subexpressions by @dweindl in #1852, #1856
• Parallelize matrix simplification by @dweindl in #1778
• Validate PEtab problems before attempting import by @dweindl in #1842
• Improved type annotations for the swig interface by @dweindl in #1860

Fixes:

• Fixed an issue with potentially infinite loops during conservation law processing by @FFroehlich in #1833
• Fixed potential deadlocks during parallel simplification by @dweindl in #1844
• Fix resetting ReturnData::numstepsB when re-using Solver by @dweindl in #1841

And further contributions by @dilpath, @dweindl, @FFroehlich

Full Changelog: v0.11.32...v0.12.0

AMICI v0.11.32

Fixes:

• Fixed ImportErrors during package installation with recent setuptools by @dweindl in #1830

AMICI v0.11.31

Fixes:

• Fixed ParameterMapping.__getitem__ to either return a ParameterMappingForCondition or a new ParameterMapping, but not a list by @dweindl in #1826

Full Changelog: v0.11.30...v0.11.31

AMICI v0.11.30

Features:

• Allow overriding model name during PySB import by @dweindl in #1801
• Added repr for parameter mapping classes by @dweindl in #1799
• More informative warning messages for NaNs/Infs by @dweindl in #1798
• Moved sim_steps increment by @plakrisenko in #1806
• Re-arranged application of parameters from ExpData to avoid initial sensitivities error by @dilpath in #1805
• Checking for unused parameters in simulate_petab by @dweindl in #1816
• Add create_parameter_mapping kwarg forwarding by @dweindl in #1820

Other

• Remove constant_species_to_parameters by @dweindl in #1809

Fixes

• Fixed handling of SBML models given as pathlib.Path in `petab_import.import_model_sbml by @dweindl in
  #1808
• Fixed missing CPU time reset by @dweindl in #1814
• Raise in simulate_petab with scaled_parameters=True problem_parameters=None by @dweindl in #1819

...

Full Changelog:
v0.11.29...v0.11.30

AMICI v0.11.29

Features:

• Performance: Limit newton step convergence check by @FFroehlich in #1780
• More informative NaN/Inf warnings by @dweindl in #1640
• SBML import can now handle initial events by @FFroehlich in #1789

Fixes:

• Avoid error if no measurements in PEtab problem; fixed type handling in PEtab parameter mapping by @dilpath in #1783
• Fixed substitution of expressions in root and stau by @dilpath in #1784
• Workaround for PEtab problems with state-dependent noise models by @dweindl in #1791

AMICI v0.11.28

New features:

• Added Solver.setSteadyStateToleranceFactor and Solver.setSteadyStateSensiToleranceFactor to specify a steady state tolerance factor by @dilpath in #1758
  NOTE: This also relaxes the default steady state (sensitivity) tolerances by a factor of 100.
• Added support for pathlib.Path by @dweindl in #1769
• Allow specifying initial timepoint with ExpData by @dilpath in #1776

Performance:

• Speedup for models with conservation laws by @FFroehlich in #1765
• Improved efficiency of newton step convergence check by @FFroehlich in #1775

Fixes:

• Fixed deprecation warning for pandas.DataFrame.append in rdatas_to_measurement_df by @dweindl in #1770
• Fixed Rule-target handling in PEtab import by @dweindl in #1753

Removed functionality:

• Removed long deprecated sbml2amici arguments modelName and constantParameters by @dweindl in #1774

AMICI v0.11.27

New features:

• Checking condition number when computing sensitivities via Newton by @FFroehlich in #1730
• Removed SPBCG solver by @FFroehlich in #1729
• Added Newton step convergence checks to steadystate solver by @FFroehlich in #1737
• Removed legacy options/members amioption.newton_preeq and `Solver::r… by @dweindl in #1744
• Added ReturnData::cpu_time_total to track total time spent in runAmiciSimulation by @dweindl in #1743
• SBML import: Alternative algorithm for identifying conservation laws by @dweindl in #1748
• Use amici.AmiciVersionError to indicate version mismatch by @dweindl in #1764

Performance:

• Optional parallel computation of derivatives during model import by @dweindl in #1740
• Sparsify jacobian by @FFroehlich in #1766
• Speedup conservation law computation by @FFroehlich in #1754
• Exploit stoichiometric matrix in pysb import by @FFroehlich in #1761
• Speedup edata construction from petab problems by @FFroehlich in #1746

Fixes:

• Fixed get_model_settings that would to setting incorrect initial states and initial state sensitivities for models with parameter-dependent initial states by @dweindl in #1751
• Use correct tolerances for convergence check in Newton solver by @FFroehlich in #1728
• Harmonized convergence checks by @FFroehlich in #1731
• Made sundials' KLU_INDEXTYPE match actual klu index type by @dweindl in #1733
• Fixed Model::setStateIsNonNegative logic that would raise exceptions in cases where it shouldn't by @dweindl in #1736
• Fixed undefined reference to dladdr by @kristianmeyerr in #1738
• Fixed HDF5 OSX intermediate group creation errors by @dweindl in #1741
• Fixed recent cmake-based build issues due to changed sundials library directory by @dweindl in #1756
• Updated Windows installation instructions by @paulflang in #1763

... and other contributions by @FFroehlich, @dweindl

Full Changelog: v0.11.26...v0.11.27

AMICI v0.11.26

New features:

• Import of BioNetGenLanguage (BNGL) models by @FFroehlich in #1709
• Added support for observable-dependent sigmas by @dweindl, @FFroehlich in #1692
• Added support for pysb local functions by @FFroehlich in #1666
• Added experimental support for conservation laws for non-constant species to SBML import: conservation laws for non-constant species
  by @stephanmg, @dweindl in #1669
  Enable this feature by setting environment variable AMICI_EXPERIMENTAL_SBML_NONCONST_CLS to any value
  • Allow using states eliminated by conservation laws to be used in root functions by @dweindl in #1677
  • Added support for parameter-dependent conservation laws by @dweindl, @FFroehlich in #1678
• Added optional caching for symbolic simplifications in ODE export by @dilpath in #1672
• Added CLI option --no-sensitivities to amici_import_petab by @dweindl in #1688

Fixes:

• SBML import: Raise in case of nested observables by @dweindl in #1690
• Sympy 1.10 compatibility by @dweindl in #1694

Full Changelog: v0.11.25...v0.11.26

AMICI v0.11.25

• Fixed a bug where Model::setStateIsNonNegative(Model::getStateIsNonNegative()) would raise an exception in case conservation laws were enabled - by @dweindl in #1648
• Fixed a bug where Model::setStateIsNonNegative would be ignored in certain model expressions - by @FFroehlich in #1650
• Fixed a bug where special function parsing inside min() and max() would not be parsed correctly - by @dweindl in #1655
• Fixed a numpy dependency issues for Mac+ARM systems - by @dweindl in #1657
• Fixed convergence check in Newton method - by @plakrisenko in #1663
• Add AMICI_CXX_OPTIONS to pass libamici-specific compiler options during CMake-based builds - by @dweindl in #1664
• Fixed various warnings and updated documentation - by @dweindl

Full Changelog: v0.11.24...v0.11.25