AMICI v0.30.0

Please note that the amici JAX model generation introduced in v0.29.0 is experimental, the API may substantially change in the future. Use at your own risk and do not expect backward compatibility.

Features

• Added serialisation for JAX models

  by @FFroehlich in #2608

• Disabled building the C++ extension by default when generating a JAX model

  by @FFroehlich in #2609

• Separate pre-equilibration and dynamic simulation in jax

  by @FFroehlich in #2617

• State reinitialisation in JAX

  by @FFroehlich in #2619

Fixes

• Fixed ModelStateDerived copy ctor (fixes potential segfaults)

  by @dweindl in #2612

• PEtab parameter mapping: fill in fixed parameter values for initial values

  by @dweindl in #2613

• nan-safe log&divide for JAX models

  by @FFroehlich in #2611

Full Changelog: v0.29.0...v0.30.0

AMICI v0.29.0

Fixes

• Fixed race conditions in froot, which could have resulted in incorrect
  simulation results for models with events/heavisides/piecewise, for
  multi-threaded simulations.

  by @dweindl in #2587

• Fixed race conditions for the max-time check, which could have resulted in
  incorrect termination of simulations in case of multi-threaded simulations
  in combination with a time limit.

  by @dweindl in #2587

• Added missing fields in ExpData HDF5 I/O

  by @dweindl in #2593

• Added missing fields in ReturnData HDF5 output

  by @dweindl in #2602

Features

• Generate models in a JAX-compatible format (example)

  by @FFroehlich in #1861

• Faster fill_in_parameters_for_condition

  by @dweindl in #2586

• Added Python function writeSimulationExpData for writing ExpData to HDF5

  by @dweindl in #2588

• Improved import of amici-generated models via amici.import_model_module().

  So far, it was not possible to import different model modules with the same
  name. This is now possible if they are in different directories.
  Overwriting an already imported module is still not possible (and never
  was); any attempts to do so will raise a RuntimeError.
  While model packages can, in principle, be imported using regular
  imports, it is strongly recommended to use amici.import_model_module().

  by @dweindl in #2604, #2603, #2596

Full Changelog: v0.28.0...v0.29.0

AMICI v0.28.0

Breaking changes

• Changed the default steady-state method to integrationOnly (by @dweindl in #2574)

  The default mode for computing steady states and sensitivities at steady state was changed to integrationOnly (from previously integrateIfNewtonFails).

  This was done for a more robust default behavior. For example, the evaluation in https://doi.org/10.1371/journal.pone.0312148 shows that - at least for some models - Newton's method may easily lead to physically impossible solutions.

  To keep the previous behavior, use:

  amici_model.setSteadyStateComputationMode(amici.SteadyStateComputationMode.integrateIfNewtonFails)
  amici_model.setSteadyStateSensitivityMode(amici.SteadyStateSensitivityMode.integrateIfNewtonFails)

Fixes

• PEtab import: Fixed potentially incorrect sensitivities with observable/state-dependent sigmas.
  This was fixed for all cases amici can handle, others cases will now result in ValueErrors (#2563).

  by @dweindl in #2562

• Fixed potentially incorrect disabling of Newton's method

  by @dweindl in #2576

• Fixed ModelStateDerived copy ctor, where previously dangling pointers could lead to crashes in some situations

  by @dweindl in #2583

• Added missing simulation status codes

  by @dweindl in #2560

• Check for unsupported observable IDs in sigma expressions

  by @dweindl in #2563

Features

• Optional warning in fill_in_parameters

  by @dweindl in #2578

Full Changelog: v0.27.0...v0.28.0

AMICI v0.27.0

This release comes with an updated version of the SUNDIALS package (7.1.1) (#2513).
For C++ users of some of AMICI's internal RAII classes, this may include some breaking changes.
The Python API is not affected.

Note regarding editable installations (pip install -e ...): Due to the SUNDIALS update, it will be necessary to clean out some temporary build directories (at least ThirdParty/sundials/build/, python/sdist/build/) before rebuilding the package.

Fixes

• Fixed a bug that led to program termination if a root-after-reinitialization
  error (potentially also others) occurred at an output timepoint

  by @dweindl in #2555

• CMake: Fixes compilation errors for models named model

  by @dweindl in #2547

• Updated CMake export config, making it easier to use AMICI in CMake projects
  and fixing some potential issues with interferring packages

  by @dweindl in #2540

• CMake: Set policies for CMake 3.31

  by @dweindl in #2539

• Documentation fixes by @FFroehlich, @ChocolateCharlie, @dweindl

Full Changelog: v0.26.3...v0.27.0

AMICI v0.26.3

Fixes

• Skip building SuiteSparse shared libraries and build all subprojects together for slightly faster package installation

  by @dweindl in #2514 and #2519

• Got rid of petab DeprecationWarnings when using the amici_import_petab CLI

  by @dweindl in #2517

• Now also sundials and suitesparse are built in debug mode when installing with ENABLE_AMICI_DEBUGGING=TRUE

  by @dweindl in #2515

Full Changelog: v0.26.2...v0.26.3

AMICI v0.26.2

Fixes

• Fixed a sympy float comparison issue in spline code that would cause an AssertionError

  by @dweindl in #2499

• Fixed some warnings from recent CMake versions

  by @dweindl in #2492

• Fixed a potential issue when including AMICI in a CMake project

  by @dweindl in #2493

Full Changelog: v0.26.1...v0.26.2

AMICI v0.26.1

Fixes

• Fixed some C++ exception handling that previously could crash Python under certain conditions

  by @dweindl in #2484

• Disabled turning warnings into errors when building amici on GitHub Actions in downstream projects

  by @dweindl in #2481

• Fixed CMP0167 warning with CMake 3.30

  by @dweindl in #2480

AMICI v0.26.0

AMICI v0.26.0 requires sympy>=1.12.1 and petab>=0.4.0.

Policy changes

• Updated AMICI's versioning / deprecation policy

  We will start removing deprecated features that had a deprecation warning
  for longer than six months in the next minor release.

Deprecations

• Passing individual tables to amici_import_petab is now deprecated.
  Use a petab.Problem instance instead.

  by @dweindl in #2464

Fixes

• Fixed a bug where during installation of AMICI, an incorrect sundials CMake
  would be used resulting in installation errors.

  by @dweindl in #2468

Full Changelog: v0.25.2...v0.26.0

AMICI v0.25.2

Fixes

• Fixed a bug in PEtab import which led to incorrect gradients
  w.r.t. estimated initial values specified via the condition table
  BREAKING CHANGE:
  amici.petab.sbml_import.{import_model_sbml,import_model} no longer supports
  passing individual PEtab tables, but only the PEtab problem object.
  This functionality was deprecated since v0.12.0 (2022-08-26).
• Fixes for numpy 2.0 compatibility
  NOTE: As long as some amici dependencies don't support numpy 2.0 yet,
  you may need to pin numpy to <2.0 in your requirements
  (pip install amici "numpy<2.0").

Full Changelog: v0.25.1...v0.25.2

AMICI v0.25.1

Fixes

• Avoid clashes with sympy-entities in plot_expressions
  by @dweindl in #2440
• PEtab: fix KeyErrors for missing parameters in fill_in_parameters
  (default values are now used if only a subset of parameters is provided)
  by @dweindl in #2449
• CMake: Fix Intel MKL detection when not using environment modules
  by @dweindl in #2443
• CMake: Fix some issues with multi-config generators
  by @dweindl in #2445

Full Changelog: v0.25.0...v0.25.1