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

AMICI v0.11.24

Features:

• Introduced environment variable AMICI_DLL_DIRS to control DLL directories on Windows (useful for setting BLAS library directory, as required by Python>=3.8) by @dweindl in #1637
• Dropped Python3.7 support by @dweindl in #1635
• Include header files in CMake targets for better IDE integration by @dweindl in #1639

Fixes:

• Fixed an issue in PEtab import where all-integer parameters would previously result in a TypeError by @stephanmg in #1634
• Fixed tempdir deletion issues for test suite on Windows by @dweindl in #1636
• Added functions to provide state IDs/names for x_solver by @dweindl in #1638
• Fixed docs on RTD by @dweindl in #1643

Full Changelog: v0.11.23...v0.11.24

AMICI v0.11.23

Features:

• Added overload for Model::setParameterScale with vector by @dilpath in #1614
• Removed assert_fun argument from gradient checking, improve output by @dweindl, @FFroehlich in #1609
• Added get_expressions_as_dataframe by @dweindl in #1621
• Added id field to ExpData and ReturnData by @dweindl in #1622
• Included condition id in dataframes by @dweindl in #1623

Fixes:

• C++: Fixed SUNMatrixWrapper ctor for size 0 matrices by @dweindl in #1608
• Python: Handle TemporaryDirectory cleanup failures on Windows by @dweindl in #1617
• Python: pysb.Model.initial_conditions throws a DeprecationWarning by @PaulJonasJost in #1620
• Fixed wrong array size in warnings by @dweindl in #1624

NOTE: AMICI 0.11.23 requires numpy<1.22.0

NOTE: This is the last release supporting Python 3.7

Full Changelog:
v0.11.22...v0.11.23

AMICI v0.11.22

• Require sympy>=1.9,pysb>=1.13.1 by @FFroehlich, @dweindl in #1599
• Fixed sympy deprecation warning by @dweindl in #1600
• Updated Windows installation instructions for Python>=3.8 by @dweindl in #1597
• Fixed plot labels by @dweindl in #1598

Full Changelog: v0.11.21...v0.11.22

AMICI v0.11.21

Fixes:

• Fixed a bug in recursion depth computation for model expressions. This may
  have resulted in incorrect sensitivities for models with expressions nested
  more than 2 levels. (#1595)
• Fixed improper handling of Piecewise functions in PySB import which may have
  produced incorrect simulation results. (#1594)
• Fixed changed googletest reference which broke the CMake-based build if
  tests were enabled (#1592)

New:

• It's now possible to build AMICI using Ninja (#1593)

Full Changelog: v0.11.20...v0.11.21

AMICI v0.11.20

New:

• Changed parameter mappings such that unassigned values have non-nan default values. This fixes erroneous evaluation of llh as NaN in some situations (#1574)
• Added support for Python 3.10 (#1555)

Fixes:

• Fixed a bug when simulation start time was not transferred when copying a solver instance (#1573)
• Fixed a bug which led to incorrect sensitivies for models with multiple assignment rules or rate rules (#1584)

Other:

• Update CI and documentation settings (#1569, #1527, #1572, #1575, #1579, #1580, #1589, #1581)
• Extend set of validated benchmark models that is checked during CI (#1571, #1577)
• Fixed string formatting in derivative checks (#1585)
• Added helper methods to save and restore model instance-only settings (#1576)

AMICI v0.11.19

New:

• Added support for observable transformations (lin/log/log10) (#1567). Thereby supporting additional noise distributions in combination with least squares solvers.

Fixes:

• Fixed a bug when Newton sensitivity computation was activated despite specifying newton_steps == 0. The error occurs when simulation converges to a steadystate but simulation sensitivities are not converged according to convergence criteria. In that case simulation returned failure, but the newton rootfinding "finds" a steadystate even before the iteration check, leading to the erroneous computation of sensitivities via Newton/IFT. For singular jacobians this means the overall simulation still fails, but a different, more informative error message is displayed. (#1541)
• Fixed a bug where argument outdir in ODEExporter.__init__ would not be used (#1543)

Other:

• Improve checking support for SBML extensions (#1546)
• SBML import: Use more descriptive IDs for flux expressions (#1551)
• Optimized SUNMatrixWrapper functions (#1538)
• C++: Changed test suite from CppUTest to gtest (#1532)
• Add CITATION.cff (#1559)
• Updated documentation (#1563, #1554, #1536)
• Removed distutils dependency (#1557)
• Require sympy<1.9