AMICI v0.25.0

This release requires Python >= 3.10.

Fixes

• Fixed a bug in event handling that could lead to incorrect simulation
  results for models with events that assign to compartments and have
  additional event assignments
  by @dweindl in #2428
• SBML import: handle useValuesFromTriggerTime attribute on events.
  This attribute was previously ignored. It is possible that now AMICI fails
  to import models that it previously imported successfully. For cases where
  useValuesFromTriggerTime=True made a difference, AMICI might have produced
  incorrect results before.
  by @dweindl in #2429
• Faster code generation for models with events if they don't have
  state-dependent triggers
  by @dweindl in #2417
• Most warnings now come with a more informative code location
  by @dweindl in #2421
• amici.ExpData was changed so that isinstance(edata, amici.ExpData) works
  by @dweindl in #2396

Features

• Event-assignments to compartments are now supported. Previously, this only
  worked for compartments that were rate rule targets.
  by @dweindl in #2425
• Releases are now deployed to Docker Hub
  by @dweindl in #2413

Full Changelog: v0.24.0...v0.25.0

AMICI v0.24.0

This will be the last release supporting Python 3.9.
Future releases will require Python 3.10.

Fixes

• Fix cmake error cannot create directory: /cmake/Amici
  during model import in cases where BLAS was not found via FindBLAS
  by @dweindl in #2389
• Added status code AMICI_CONSTR_FAIL
  by @dweindl in #2379
• Fixed certain initial state issues with PEtab
  by @dweindl in #2382
• Fixed Solver operator== and copyctor
  (constraints were not copied correctly)
  by @dweindl in #2388
• Avoid confusing warnings about non-finite timepoints
  by @dweindl in #2395
• Fixed incorrect exception types / messages for IDASolver
  by @dweindl in #2398
• cmake: set SUNDIALS path hint for python package to help CMake find
  the correct SUNDIALS installation
  by @dweindl in #2397

Features

• Optionally include measurements in plot_observable_trajectories
  by @dweindl in #2381
• Improved type annotations in swig-wrappers
  by @dweindl in #2401
• Additional attributes are accessible directly via ReturnDataView and
  ExpDataView, e.g. ReturnDataView.ny, ReturnDataView.nx
  by @dweindl in #2405
• Allow subselection of state variables for convergence check during
  steady-state simulations via Model.set_steadystate_mask([1, 0, ..., 1])
  (positive value: check; non-positive: don't check).
  by @dweindl in #2387

Full Changelog: v0.23.1...v0.24.0

AMICI v0.23.1

Fixes

• Fixes installation issues related to building SuiteSparse on some systems
  by @dweindl in #2375

AMICI v0.23.0

Features

• SBML InitialAssignment are no longer absorbed into other model expressions, but are available as parameters or expressions (w) in the amici model
  by @dweindl in #2304, #2305, #2345, #2359

• Upgraded to SuiteSparse 7.6
  by @dweindl in #2316

• Model expressions w are now split into static and dynamic expressions, and only evaluated as needed
  by @dweindl in #2303

• Exposed additional solver settings:

  • Solver.setMaxConvFails(): maximum number of non-linear solver convergence failures
  • Solver.setMaxNonlinIters(): maximum number of non-linear solver iterations
  • Solver.setMaxStepSize(): maximum step size
  • Solver.setConstraints(): for setting (non)negativity/positivity constraints on state variables

  by @dweindl in #2335, #2360, #2340

• Improved output for debugging simulation failures:
  ReturnData.{xdot,J} now contain the respective values from the timepoint of failure, not the last output timepoint. NaN/Inf warnings now always include the timepoint at which the issue occurred. Note that C++ stacktraces are now only logged for debug builds.
  by @dweindl in #2349, #2347, #2366

• Updated dataframes import/export to include parameter values and scales
  by @FFroehlich in #2351

Fixes

• CMake: Updated BLAS detection and some minor fixes
  by @dweindl in #2318 and #2357
• Deterministic ordering of source files in generated CMakeLists.txt
  by @dweindl in #2322
• Fixed size check in Model::setStateIsNonNegative
  by @dweindl in #2332
• Fixed uncaught C++ exception in runAmiciSimulation that may crash Python in case of invalid values for standard deviations
  by @dweindl in #2338
• Fixed missing import in amici/petab/petab_import.py
  by @plakrisenko in #2342
• Fixed ReturnDataView AttributeError: messages
  by @dweindl in #2341
• Added a missing return code constant LSETUP_FAIL
  by @dweindl in #2353
• Fixed in-place building of model wheels
  by @dweindl in #2352
• Made is-zero-checks compatible with the upcoming sympy>1.12
  by @dweindl in #2350
• Fixed issues with paths containing blanks for sundials
  by @dweindl in #2361
• Added amici.petab.conditions to the API documentation
  by @PaulJonasJost in #2364
• Improved type annotations in swig-wrappers
  by @dweindl in #2344, #2365

Full Changelog: v0.22.0...v0.23.0

AMICI v0.22.0

Features

• PEtab import: User option to fail if model needs to be compiled
  by @dilpath in #2289

  The force_compile argument is now deprecated. Use compile_ instead.

• Model import now adds a .gitignore file to the model output directory
  by @dweindl in #2301

Fixes

• Fixed a bug that may have caused wrong simulation results for certain
  SBML models that contain rateOf-expressions
  by @dweindl in #2291
• More informative error message for ReturnDataView.by_id
  by @dweindl in #2295
• Fixed ENABLE_AMICI_DEBUGGING=TRUE not working with MSVC
  by @dweindl in #2296
• Fixed MANIFEST.in warning by @dweindl in #2297
• (performance) Skip unnecessary toposorting in DEModel._collect_heaviside_roots
  by @dweindl in #2299
• (performance) Fix redundant calls to Model::fdwdx from Model_ODE::fJ
  (only relevant for dense and banded solvers)
  by @dweindl in #2298

Full Changelog: v0.21.2...v0.22.0

AMICI v0.21.2

Bugfix release:

• Fixed Solver copyctor issues with swig4.2 that resulted in installation errors
  by @dweindl in #2276
• Fixed error when calling amici.ExpData()
  by @dweindl in #2280
• Fixed invalid-type-error when loading an antimony model from file
  by @dweindl in #2281

Full Changelog: v0.21.1...v0.21.2

AMICI v0.21.1

Fixed package configuration for PyPI upload. No further changes.

See https://github.com/AMICI-dev/AMICI/releases/tag/v0.21.0.

AMICI v0.21.0

Deprecations

• Moved PEtab-related functionality from amici.petab_* to the
  petab-subpackage amici.petab.*. The old public functions are still
  available but will be removed in a future release.
  by @dweindl in #2205, #2211, #2252

Features

• Handle events occurring at fixed timepoints without root-finding.
  This avoids event-after-reinitialization errors in many cases brings a
  slight performance improvement.
  by @dweindl in #2227
• Added PetabProblem class for handling PEtab-defined simulation conditions,
  making it easier to perform customized operations based on PEtab-defined
  simulation conditions.
  by @dweindl in #2255
• code-gen: Simplified switch statements, leading to reduced file sizes and
  faster compilation for certain models.
  by @dweindl in #2240
• Made Model and ModelPtr deepcopyable
  by @dweindl in #2247
• Made Solver and SolverPtr deepcopyable
  by @dweindl in #2245
• Added a debugging helper get_model_for_preeq for debugging simulation
  issues during pre-equilibration.
  by @dweindl in #2250
• Added SwigPtrView fields to dir() outputs
  by @dweindl in #2244
• Use proper labels for in plotting functions if IDs are available in
  ReturnData.
  by @dweindl in #2249
• Added ExpData::clear_observations to set all measurements/sigmas to NaN
  by @dweindl in #2258

Fixes

• Fixed AMICI hiding all warnings. Previously, importing amici resulted
  in all warnings being hidden in the rest of the program.
  by @dweindl in #2243
• CMake: Fixed model debug builds
  by @dweindl in #2222
• Fixed CMake potentially using incorrect Python library for building model
  extension
  by @dweindl in #2220
• CMake: fixed cxx flag check
  by @dweindl in #2225
• Fixed potential out-of-bounds read in Model::checkFinite for
  matlab-imported models
  by @dweindl in #2232
• Fixed piecewise/Heaviside handling
  by @dweindl in #2234
• Deterministic order of event assignments
  by @dweindl in #2242
• Proper error message in case of unsupported state-dependent sigmas
  by @dweindl in #2239
• Fixed swig shadow warning + other linting issues
  by @dweindl in #2261
• Fixed SwigPtrView.__getattr__
  by @dweindl in #2259
• simulate_petab: Avoid warning when simulating with default parameters
  by @dweindl in #2265

Documentation

• Updated Python package installation instructions for Arch Linux
  by @willov in #2212
• Updated ExpData documentation
  by @dweindl in #2254
• Documented simulation starting time t0
  by @dweindl in #2263
• Updated PEtab example
  by @dweindl in #2255

...

Full Changelog: v0.20.0...v0.21.0

AMICI v0.20.0

Fixes

• Fixed CMake cmake_minimum_required deprecation warning
  by @dweindl in #2183
• Fixed misleading preequilibration failure messages
  by @dweindl in #2181
• Removed setuptools<64 restriction
  by @dweindl in #2180
• Fixed ExpData equality operator for Python
  by @dweindl in #2194
• Enabled deepcopy for ExpData(View)
  by @dweindl in #2196
• Allowed subsetting simulation conditions in simulate_petab
  by @dweindl in #2199
• Set CMake CMP0144 to prevent warning
  by @dweindl in #2209

Features

• Possibility to evaluate and plot symbolic expressions based on simulation results
  by @dweindl in #2152
• Easier access to timepoints via ExpDataView
  by @dweindl in #2193
• Nicer __repr__ for ReturnDataView
  by @dweindl in #2192

Documentation

• Added installation instructions for Arch Linux
  by @stephanmg in #2173
• Updated reference list
  by @dweindl in #2172
• Installation guide: optional requirements
  by @dweindl in #2207

Full Changelog: v0.19.0...v0.20.0

AMICI v0.19.0

Features

• SBML import now supports rateOf
  by @dweindl in #2120

• Added Model.{get,set}SteadyStateComputationMode (analogous to SteadyStateSensitivityMode)
  which allows to choose how steady state is computed.
  by @plakrisenko in #2074

  Note: The default SteadyStateSensitivityMode changed from newtonOnly to integrateIfNewtonFails.

• SBML import: Allow hardcoding of numerical values
  by @dweindl in #2134

• Added antimony2amici for more convenient antimony import
  (simplifies working with raw ODEs, see documentation)
  by @dweindl in #2142

• Added AMICI_TRY_ENABLE_HDF5 environment variable to control whether to search for HDF5 or not
  by @dweindl in #2148

Fixes

• Fixed SBML import for events with trigger functions depending on parameters that are initial
  assignment targets
  by @dweindl in #2145
• Fixed SBML import for event-assigned parameters with non-float initial assignments
  by @dweindl in #2156
• Fixed unistd.h dependency of hdf5.cpp that led to compilation
  failures on Windows
  by @dweindl in #2154
• Set CMake policies for cmake 3.27 by @dweindl in #2162
• Fixed a lib/ vs lib64/ issue, leading to SUNDIALSConfig.cmake-not-found issues
  on some systems
  by @dweindl in #2165
• CMake: fixed scope of -DHAS_BOOST_CHRONO which may have lead to a mix of
  boost::chrono::thread_clock and std::clock being used in programs using amici,
  and potentially segmentation faults
  by @dweindl in #2163

Performance

• Combined code for sparse model functions and their index files for slightly faster
  compilation of small models
  by @dweindl in #2159

• Removed complex / complex long KLU functions for slightly faster amici package installation
  by @dweindl in #2160

Full Changelog: v0.18.1...v0.19.0