# Changelog

See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioning_policy.html).

## v1.X Series

### v1.0.0 (unreleased)

**BREAKING CHANGES**

* `ReturnDataView.posteq_numsteps` and `ReturnDataView.posteq_numsteps` now
  return a one-dimensional array of shape `(num_timepoints,)` instead of a
  two-dimensional array of shape `(1, num_timepoints)`.
* `ReturnDataView.posteq_status` and `ReturnDataView.preeq_status` now
  return `list[SteadyStateStatus]` instead of an `ndarray[int]` of shape
  `(1, 3)`.
* The way the observation model is passed to the different import functions
  (`sbml2amici`, `pysb2amici`, ...) has changed:
  The information previously split across `observables`, `sigmas`,
  `noise_distributions`, `event_observables`, `event_sigmas`, and
  `event_noise_distributions` dicts is now passed as a single
  `observation_model: list[MeasurementChannel]` argument.
* `assignmentRules2observables` has been renamed to
  `assignment_rules_to_observables` and now returns `list[MeasurementChannel]`
  to be passed to the import functions.
* `assignmentRules2observables` has been renamed to
  `assignment_rules_to_observables` and now returns `list[MeasurementChannel]`
  to be passed to the import functions.
* `AmiVector::getLength` and `AmiVectorArray::getLength` have been renamed to
  `size` to be more consistent with STL containers.
* `amici.petab.petab_import.import_model` has been removed.
  Use `amici.petab.petab_import.import_model_sbml` instead.
  (The former was just an alias for the latter.)
* For a more consistent API, all function names are now snake_case instead of
  camelCase.
* `Model.getSolver` has been renamed to `Model.create_solver`.
* `amici.runAmiciSimulation` and `amici.runAmiciSimulations` have been renamed
   to `amici.run_simulation` and `amici.run_simulations`.
* The following deprecated functionality has been removed:
  * The complete MATLAB interface has been removed.
  * `NonlinearSolverIteration::functional` has been removed,
    use `NonlinearSolverIteration::fixedpoint` instead.
  * The deprecated argument `log_as_log10` to `SbmlImporter.sbml2amici` and
    `SbmlImporter.sbml2jax` has been removed. Just remove this argument, as
    this never had any effect.
  * Deprecated imports from `amici.petab.*` in `amici.petab.simulations`
    have been removed. Import those functions directly from their respective
    modules.
  * The `force_compile` argument to `import_petab_problem` has been removed.
    See the `compile_` argument.

**Features**

* Experimental support for the PEtab data format v2.0.0 (draft, see
  https://petab.readthedocs.io/en/latest/v2/documentation_data_format.html)
  for SBML- and PySB-based problems (see `amici.petab.petab_importer`). The API is subject to change.

  * Current limitations for PySB-based PEtab problems:
    * Only species and `pysb.Expression` are supported as condition table
      targets.

* Many relevant `ReturnData` fields are now available as `xarray.DataArray`
  via `ReturnData.xr.{x,y,w,x0,sx,...}`.
  `DataArray`s include the identifiers and are often more convenient than the
  plain numpy arrays. This allows for easy subselection and plotting of the
  results, and conversion to DataFrames.
* `Model.simulate()` has been added as a convenience function to run
  simulations without having to create a `Solver` object explicitly.
  This is a wrapper for both `amici.run_simulation` and
  `amici.run_simulations`, depending on the type of the `edata` argument.
  It also supports passing some `Solver` options as keyword arguments.
* Improved `pickle` support for `amici.{Model,ModelPtr,Solver,ExpData`.
  Note that AMICI's pickling support is only intended for short-term storage
  or inter-process communication.
  Reading pickled objects after updating AMICI or the model code will almost
  certainly fail.
  * `amici.Model`and `amici.ModelPtr` now support sufficient pickling for use
    in multi-processing contexts. This works only if the amici-generated model
    package exists in the same file system location and does not change until
    unpickling.
  * `amici.Solver` is now picklable if amici was built with HDF5 support.
    This only works on shared file systems, as the solver state is stored in a
    temporary HDF5 file.
  * `amici.ExpData` is now picklable.
* Implemented support for the [PEtab SciML](https://github.com/PEtab-dev/petab_sciml)
  extension for the JAX interface.
* The import function `sbml2amici`, `pysb2amici`, and `antimony2amici` now
  return an instance of the generated model class if called with `compile=True`
  (default).
* The default directory for model import changed, and a base directory
  can now be specified via the `AMICI_MODELS_ROOT` environment variable.
  See `amici.get_model_dir` for details.


## v0.X Series

### v0.34.2 (2025-11-03)

Bugfix release.

* Python 3.14 compatibility
* Swig 4.4.0 compatibility
* Fixes type annotations in swig wrappers
* Fixes a bug that resulted in incorrect processing of initial assignments
  containing (amici-)splines
* Fixes an SBML import error during the handling of algebraic rules
* Fixes a CMake error with certain CMake versions

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.34.1...v0.34.2

### v0.34.1 (2025-08-25)

Bugfix release.

* Fixed a bug that would lead to incorrect model initialization in SBML models
  with initial assignments that depend on dynamic entities
  (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2939)

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.34.0...v0.34.1

### v0.34.0 (2025-07-29)

This will probably be the last release to include the MATLAB interface.

**Fixes**

* **Breaking changes** Events are now also handled during pre-equilibration,
  presimulation, and post-equilibration.
  This may be a breaking change, as it may lead to different results for models
  with events that may trigger during these periods. This change is
  considered a bugfix, as it was not intended to ignore events during these
  periods.

  (by @dweindl in #2777, #2780, #2859, #2881, #2889, #2920, #2921, #2925)
* Fixed various issues related to adjoint sensitivity analysis for models with
  events.
  While many cases are now supported, it is still highly recommended to
  check the ASA results for models with events against forward sensitivities
  or finite differences.
  * Adjoint sensitivities for Python-imported models with events
    (by @paulstapor & @dweindl in https://github.com/AMICI-dev/AMICI/pull/1539)
  * Fix Model::addAdjointQuadratureEventUpdate
    (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2787)
  * Fix indexing errors for adjoint quadratures during event updates
    (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2796)
  * Fix deltaxB dimensions (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2803)
  * Fix (some) ASA event handling (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2797)
* Fixed a number of issues related to the handling of events or discontinuities
  in general:
  * Fixed import of DAE models with events (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2897)
  * Fixed root functions for events with initialValue=trigger=false (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2910)
  * Fixed check for sign change, fix Heaviside update (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2927)
* Fixed sign of residuals (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2896)
* Updated the steady state notebook to match the current implementation
  (by @plakrisenko & @dweindl in https://github.com/AMICI-dev/AMICI/pull/2891)
* Improved sigma<=0 error reporting (by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2829)
* Fixed sensitivities for the total abundances of conservation laws
  (only relevant if `AMICI_EXPERIMENTAL_SBML_NONCONST_CLS` is enabled)
  (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2782)
* Fix sensitivities w.r.t. unused log-scaled NaN parameters (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2903)

**Features**

* AMICI should now be pip-installable without pre-installing SWIG or BLAS
  (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2774,
  https://github.com/AMICI-dev/AMICI/pull/2772)
* Event/discontinuity handling for JAX models
  * Track discontinuities in JAX & fix gradient for models with parameter
    dependent roots (by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2815)
  * Improve JAX event integration (by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2841)
  * mask event functions in jax (by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2863)
* Handle state-independent, parameter-dependent event triggers without root-finding
  (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2913)
* Presimulation is now also supported in combination with adjoint sensitivities
  (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2786)
* It is now possible to set a separate $t_0$ for pre-equilibration and main
  simulation (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2793)
* Sensitivity analysis for `AlgebraicRule` / DAE models is now also supported
  for Python-imported models
  (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2101)
* An optional random generator seed can now be passed to
  `ExpData::ExpData(ReturnData const&, ...)` when generating synthetic
  measurements (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2802)
* Added `ReturnData::plist` (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2874)

... and extended tests, documentation, and many changes under the hood.

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.33.0...v0.34.0


### v0.33.0 (2025-06-11)

Note that this release requires Python >= 3.11.

**Fixes**

* Fixed an issue in SBML AlgebraicRule processing leading to import failure if
  a species occurred in multiple AlgebraicRules

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2744

* Fixed a potential segfault when running forward sensitivity analysis for
  models without state variables

  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2749

* Fixed a dimension bug for presimulation parameters in ExpDataView

  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2746

* Fixed incorrect initialization for initial assignments with explicit time
  dependence

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2779

**Features**

* AMICI now supports SBML events with `use_values_from_trigger_time=true`

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2741

* AMICI now supports SBML events with constant priorities

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2730

**Other changes**

* doc: Added a caveats section listing some known issues and potentially
  unexpected behavior in AMICI

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2735

* Added warnings for presimulation and steady state simulation with events.
  So far, events were not fully supported in these modes. This is subject to
  change.

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2755

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.32.0...v0.33.0

### v0.32.0 (2025-05-15)

**Breaking changes**

* Removed deprecated `amici.petab_*` modules (now under `amici.petab.*`)

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2658

* Removed deprecated CLI options to `amici_import_petab`

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2671

**Changed requirements**

* AMICI now requires a C++20-compatible compiler

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2660

* AMICI now requires swig>=4.1

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2693

* AMICI now uses the [sbmlmath](https://github.com/dweindl/sbmlmath/) package
  for sympification of SBML math constructs

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2681

**Fixes**

* Fixed Heaviside functions for `<`, `>` `<=`, `>=` which could have lead to
  incorrect simulation results.

  Note that `>` and `>=`, as well as `<` and `<=` can't be distinguished in
  some cases (see https://github.com/AMICI-dev/AMICI/issues/2707).
  Avoid situations where this would matter.

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2701

* Prevent segfaults under pytest after swig4.3 wrapping

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2696

* Fixed `SetuptoolsDeprecationWarning: \`project.license\` as a TOML table is deprecated`

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2697

* Updated Dockerfile, use Ubuntu 24.04 LTS

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2698

* SBML import: Handle unsolvable event triggers

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2705

* Added RTFUNC_FAIL simulation status

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2702

* doc: Enable building docs with Python 3.13

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2704

* Fixed crash for models without state variables

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2703

* SBML import: avoid repeated xdot==0 checks

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2706

* Fixed Boolean to float conversion issues during SBML import

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2725

**Features**

* Support for XOR, `==` and `!=` operators in SBML models

  *Note that not all (combinations of) Boolean functions will work well with*
  *AMICI's root-finding. It's recommended to verify the results.*

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2699,
  https://github.com/AMICI-dev/AMICI/pull/2708,
  and https://github.com/AMICI-dev/AMICI/pull/2716

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.31.2...v0.32.0

### v0.31.2 (2025-04-23)

Bugfix-only release.

* SBML import: Handle unsolvable event triggers
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2686
* Fixed a clang compiler warning related to variable length arrays
  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2688
* Temporarily require interpax<=0.3.6
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2678
* Update OpenBLAS installation script to work with CMake>=4
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2679
* GHA: Don't run cron jobs on forks by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2669
* Fixed Matlab documentation build with CMake 4.0
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2676

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.31.1...v0.31.2

### v0.31.1 (2025-03-21)

Bugfix-only release.

* Handle relational operators in SBML import
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2652

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.31.0...v0.31.1

### v0.31.0 (2025-02-18)

* Added `RDataReporting::observables_likelihood` for computing observables,
  likelihood and the respective sensitivities
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2627,
  https://github.com/AMICI-dev/AMICI/pull/2633
* JAX:
  * Updated diffrax & jaxlib
    by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2632
  * Avoid silent preequilibration failure in JAX
    by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2631
  * jax vectorisation
    by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2636
  * No flattening of timepoint specific overrides in jax
    by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2641
* Faster PEtab parameter mapping
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2638,
  https://github.com/AMICI-dev/AMICI/pull/2640

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.30.1...v0.31.0

### v0.30.1 (2025-02-18)

Bugfix-only release.

* Removed `eqx.debug.nan`, fixes #2629
  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2630
* Fixes an SBML import issue that led to incorrect results for models with
  species-dependent initial assignments (fixes #2642)
  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2643
* Fixed `CVodeGetSensDky` error message
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2644
* Disabled `CvodeF` checkpointing to prevent certain rare crashes when forward
  integration takes exactly `maxsteps` integration steps, plus some additional
  yet unclear condition.
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2645
* Fixed rare crashes due to uncaught exceptions in `~FinalStateStorer`
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2647

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.30.0...v0.30.1


### v0.30.0 (2024-12-10)

*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 https://github.com/AMICI-dev/AMICI/pull/2608

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

  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2609

* Separate pre-equilibration and dynamic simulation in jax

  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2617

* State reinitialisation in JAX

  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2619

**Fixes**

* Fixed ModelStateDerived copy ctor (fixes potential segfaults)

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2612

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

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2613

* `nan`-safe log&divide for JAX models

  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2611


**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.29.0...v0.30.0


### v0.29.0 (2024-11-28)

**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 https://github.com/AMICI-dev/AMICI/pull/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 https://github.com/AMICI-dev/AMICI/pull/2587

* Added missing fields in ExpData HDF5 I/O

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2593

* Added missing fields in ReturnData HDF5 output

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2602


* **Features**

* Generate models in a JAX-compatible format
  ([example](https://amici.readthedocs.io/en/develop/ExampleJaxPEtab.html))

  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1861

* Faster `fill_in_parameters_for_condition`

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2586

* Added Python function `writeSimulationExpData` for writing ExpData to HDF5

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/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
  `import`s, it is strongly recommended to use `amici.import_model_module()`.

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2604, https://github.com/AMICI-dev/AMICI/pull/2603, https://github.com/AMICI-dev/AMICI/pull/2596

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.28.0...v0.29.0


### v0.28.0 (2024-11-11)

**Breaking changes**

* Changed the default steady-state method to `integrationOnly`
  (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/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:
  ```python
  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 `ValueError`s (https://github.com/AMICI-dev/AMICI/pull/2563).

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2562

* Fixed potentially incorrect disabling of Newton's method

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2576

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

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2583

* Added missing simulation status codes

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2560

* Check for unsupported observable IDs in sigma expressions

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2563


**Features**

* Optional warning in `fill_in_parameters`

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2578

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.27.0...v0.28.0

### v0.27.0 (2024-10-21)

This release comes with an **updated version of the SUNDIALS package (7.1.1)** (https://github.com/AMICI-dev/AMICI/pull/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 https://github.com/AMICI-dev/AMICI/pull/2555

* CMake: Fixes compilation errors for models named `model`

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/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 https://github.com/AMICI-dev/AMICI/pull/2540

* CMake: Set policies for CMake 3.31

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2539

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

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.26.3...v0.27.0


### v0.26.3 (2024-10-03)

**Fixes**

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

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2514
  and https://github.com/AMICI-dev/AMICI/pull/2519

* Got rid of petab `DeprecationWarnings` when using the `amici_import_petab`
  CLI

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2517

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

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2515

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.26.2...v0.26.3

### v0.26.2 (2024-09-25)

**Fixes**

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

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2499

* Fixed some warnings from recent CMake versions

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2492

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

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2493

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.26.1...v0.26.2


### v0.26.1 (2024-07-11)

**Fixes**

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

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2484

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

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2481

* Fixed CMP0167 warning with CMake 3.30

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2480


**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.26.0...v0.26.1

### v0.26.0 (2024-07-02)

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

**Policy changes**

* Updated AMICI's [versioning / deprecation policy](https://amici.readthedocs.io/en/develop/versioning_policy.html)

  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 https://github.com/AMICI-dev/AMICI/pull/2464

**Fixes**

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

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2468

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.25.2...v0.26.0


### v0.25.2 (2024-06-16)

**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**: https://github.com/AMICI-dev/AMICI/compare/v0.25.1...v0.25.2

### v0.25.1 (2024-05-16)

**Fixes**
* Avoid clashes with sympy-entities in `plot_expressions`
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/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 https://github.com/AMICI-dev/AMICI/pull/2449
* CMake: Fix Intel MKL detection when not using environment modules
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2443
* CMake: Fix some issues with multi-config generators
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2445

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.25.0...v0.25.1


### v0.25.0 (2024-05-08)

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 https://github.com/AMICI-dev/AMICI/pull/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 https://github.com/AMICI-dev/AMICI/pull/2429
* Faster code generation for models with events if they don't have
  state-dependent triggers
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2417
* Most warnings now come with a more informative code location
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2421
* `amici.ExpData` was changed so that `isinstance(edata, amici.ExpData)` works
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2396

**Features**
* Event-assignments to compartments are now supported. Previously, this only
  worked for compartments that were rate rule targets.
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2425
* Releases are now deployed to Docker Hub
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2413

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.24.0...v0.25.0

### v0.24.0 (2024-04-22)

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 https://github.com/AMICI-dev/AMICI/pull/2389
* Added status code `AMICI_CONSTR_FAIL`
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2379
* Fixed certain initial state issues with PEtab
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2382
* Fixed Solver `operator==` and copyctor
  (constraints were not copied correctly)
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2388
* Avoid confusing warnings about non-finite timepoints
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2395
* Fixed incorrect exception types / messages for `IDASolver`
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2398
* cmake: set SUNDIALS path hint for python package to help CMake find
  the correct SUNDIALS installation
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2397

**Features**

* Optionally include measurements in `plot_observable_trajectories`
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2381
* Improved type annotations in swig-wrappers
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2401
* Additional attributes are accessible directly via `ReturnDataView` and
  `ExpDataView`, e.g. `ReturnDataView.ny`, `ReturnDataView.nx`
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/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 https://github.com/AMICI-dev/AMICI/pull/2387

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.23.1...v0.24.0


### v0.23.1 (2024-03-11)

* Fixes installation issues related to building SuiteSparse on some systems
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2375

### v0.23.0 (2024-03-07)

**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 https://github.com/AMICI-dev/AMICI/pull/2304,
  https://github.com/AMICI-dev/AMICI/pull/2305,
  https://github.com/AMICI-dev/AMICI/pull/2345,
  https://github.com/AMICI-dev/AMICI/pull/2359
* Upgraded to SuiteSparse 7.6
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2316
* Model expressions `w` are now split into static and dynamic expressions,
  and only evaluated as needed
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/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 https://github.com/AMICI-dev/AMICI/pull/2335,
  https://github.com/AMICI-dev/AMICI/pull/2360,
  https://github.com/AMICI-dev/AMICI/pull/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 https://github.com/AMICI-dev/AMICI/pull/2349,
  https://github.com/AMICI-dev/AMICI/pull/2347,
  https://github.com/AMICI-dev/AMICI/pull/2366
* Updated dataframes import/export to include parameter values and scales
  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2351

**Fixes**

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

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.22.0...v0.23.0

### v0.22.0 (2024-02-23)

**Features**

* PEtab import: User option to fail if model needs to be compiled
  by @dilpath in https://github.com/AMICI-dev/AMICI/pull/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 https://github.com/AMICI-dev/AMICI/pull/2301

**Fixes**

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

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.21.2...v0.22.0

### v0.21.2 (2024-02-06)

* Fixed `Solver` copyctor issues with swig4.2 that resulted in installation
  errors
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2276
* Fixed error when calling `amici.ExpData()`
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2280
* Fixed invalid-type-error when loading an antimony model from file
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2281

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.21.1...v0.21.2

### v0.21.1 (2024-01-17)

Fixed package configuration for PyPI upload. No further changes.

### v0.21.0 (2024-01-16)

**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 https://github.com/AMICI-dev/AMICI/pull/2205,
  https://github.com/AMICI-dev/AMICI/pull/2211,
  https://github.com/AMICI-dev/AMICI/pull/2252

**Features**

* Handle events occurring at fixed timepoints without root-finding.
  This avoids event-after-reinitialization errors in many cases a brings a
  slight performance improvement.
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/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 https://github.com/AMICI-dev/AMICI/pull/2255
* code-gen: Simplified `switch` statements, leading to reduced file sizes and
  faster compilation for certain models.
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2240
* Made `Model` and `ModelPtr` deepcopyable
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2247
* Made `Solver` and `SolverPtr` deepcopyable
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2245
* Added a debugging helper `get_model_for_preeq` for debugging simulation
  issues during pre-equilibration.
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2250
* Added `SwigPtrView` fields to `dir()` outputs
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2244
* Use proper labels for in plotting functions if IDs are available in
  `ReturnData`.
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2249
* Added `ExpData::clear_observations` to set all measurements/sigmas to NaN
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/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 https://github.com/AMICI-dev/AMICI/pull/2243
* CMake: Fixed model debug builds
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2222
* Fixed CMake potentially using incorrect Python library for building model
  extension
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2220
* CMake: fixed cxx flag check
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2225
* Fixed potential out-of-bounds read in `Model::checkFinite` for
  matlab-imported models
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2232
* Fixed piecewise/Heaviside handling
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2234
* Deterministic order of event assignments
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2242
* Proper error message in case of unsupported state-dependent sigmas
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2239
* Fixed swig shadow warning + other linting issues
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2261
* Fixed `SwigPtrView.__getattr__`
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2259
* `simulate_petab`: Avoid warning when simulating with default parameters
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2265

**Documentation**

* Updated Python package installation instructions for Arch Linux
  by @willov in https://github.com/AMICI-dev/AMICI/pull/2212
* Updated `ExpData` documentation
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2254
* Documented simulation starting time `t0`
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2263
* Updated PEtab example
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2255

...

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.20.0...v0.21.0

### v0.20.0 (2023-11-23)

**Fixes**

* Fixed CMake `cmake_minimum_required` deprecation warning
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2183
* Fixed misleading preequilibration failure messages
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2181
* Removed setuptools<64 restriction
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2180
* Fixed ExpData equality operator for Python
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2194
* Enabled deepcopy for ExpData(View)
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2196
* Allowed subsetting simulation conditions in simulate_petab
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2199
* Set CMake CMP0144 to prevent warning
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2209

**Features**

* Possibility to evaluate and plot symbolic expressions based on simulation results
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2152
* Easier access to timepoints via ExpDataView
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2193
* Nicer `__repr__` for ReturnDataView
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2192

**Documentation**

* Added installation instructions for Arch Linux
  by @stephanmg in https://github.com/AMICI-dev/AMICI/pull/2173
* Updated reference list
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2172
* Installation guide: optional requirements
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2207

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.19.0...v0.20.0


### v0.19.0 (2023-08-26)

**Features**
* SBML import now supports `rateOf`
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2120
* Added `Model.{get,set}SteadyStateComputationMode` (analogous to `SteadyStateSensitivityMode`)
  which allows to choose how steady state is computed.
  by @plakrisenko in https://github.com/AMICI-dev/AMICI/pull/2074

  **Note: The default `SteadyStateSensitivityMode` changed from `newtonOnly` to `integrateIfNewtonFails`.**

* SBML import: Allow hardcoding of numerical values
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2134
* Added `antimony2amici` for more convenient antimony import
  (simplifies working with raw ODEs, see documentation)
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2142
* Added `AMICI_TRY_ENABLE_HDF5` environment variable to control whether to search for HDF5 or not
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2148

**Fixes**

* Fixed SBML import for events with trigger functions depending on parameters that are initial
  assignment targets
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2145
* Fixed SBML import for event-assigned parameters with non-float initial assignments
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2156
* Fixed `unistd.h` dependency of `hdf5.cpp` that led to compilation
  failures on Windows
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2154
* Set CMake policies for cmake 3.27 by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2162
* Fixed a `lib/` vs `lib64/` issue, leading to `SUNDIALSConfig.cmake`-not-found issues
  on some systems
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/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 https://github.com/AMICI-dev/AMICI/pull/2163

Performance:
* Combined code for sparse model functions and their index files for slightly faster
  compilation of small models
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2159

* Removed complex / complex long KLU functions for slightly faster amici package installation
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2160

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.18.1...v0.19.0


### v0.18.1 (2023-06-26)

Fixes:
* Fixed pysb pattern matching during PEtab import
  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2118
* Fixed `sp.Matrix` errors with `numpy==1.25`
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2124
* Readme: added info containers
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2125
* Fixed deprecation warnings
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2122
  https://github.com/AMICI-dev/AMICI/pull/2131
* Fixed logging typo in SBML import
  by @dilpath in https://github.com/AMICI-dev/AMICI/pull/2126
* Added minimum version for `pandas`
  by @dilpath in https://github.com/AMICI-dev/AMICI/pull/2129

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.18.0...v0.18.1

### v0.18.0 (2023-05-26)

Features:
* More efficient handling of splines in SBML models
  by @paulstapor, @lcontento, @dweindl
  in https://github.com/AMICI-dev/AMICI/pull/1515
* Partial support of current PEtab2.0 draft, including support for PySB models
  by @dweindl, @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1800

Fixes:
* **Fixed incorrect forward sensitivities for models with events with**
  **state-dependent trigger functions**
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2084
* Model import: Don't create spl.h and sspl.h for models without splines
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2088
* SBML import - faster processing of SpeciesReference IDs
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2094
* Update swig ignores
  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2098
* CMake: Fixed choosing SWIG via `SWIG` env variable
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2100
* CMake: Try FindBLAS if no other information was provided
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2104
* Fixed cblas error for models without solver states in combination with
  forward sensitivities
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2108
* Fixed compilation error for models with events and xdot=0
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2111
* Fixed import error for models with events and 0 states
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2112

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.17.1...v0.18.0

### v0.17.1 (2023-05-10)

This release fixes two bugs:

* One bug introduced in v0.17.0, that causes an `ImportError`
  on macOS (https://github.com/AMICI-dev/AMICI/issues/2075).
* An AttributeError in petab_import_pysb with petab>=0.2.0
  https://github.com/AMICI-dev/AMICI/pull/2079

### v0.17.0 (2023-05-09)

AMICI v0.17.0 requires Python>=3.9 and a C++17 compatible compiler

Features
* DAE support in SBML
  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2017
* SBML import: flatten SBML-comp models
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2063
* Added sllh computation back to `petab_objective.simulate_petab`
  by @dilpath in https://github.com/AMICI-dev/AMICI/pull/1548
* CMake-based Python extension builds
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1992

Fixes
* Fixed CPU time tracking with multi-threading (partially)
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2023
* Fixed HDF5 ambiguous overload
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2031
* Fixed varying cmake libdir lib(64)/
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2033
* Fixed Equilibration cpu time computation
  by @plakrisenko in https://github.com/AMICI-dev/AMICI/pull/2035
* CMake: add header files to library sources for generated models
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2047
* CMake: Handle header-dependency of swig files
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2046
* Don't try to detect conservation laws for models with Species-AssignmentRules
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2056
* Smith benchmark and SBML initialization fix
  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2034
* SBML import: Fixed check for required packages
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2064
* Nan observables
  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2065
* Fixed check for discontinuities for conservation law computation
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2068
* Specify visualization dependencies
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2070
* Fixed sympy symbol name clashes during PEtab import
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2069
* Fixed ReturnData::{preeq_wrms,posteq_wrms} with FSA and check_sensi_steadystate_conv_=True
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2071

Extended / updated documentation, for example:
* Jax example notebook
  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1996
* Updated Windows/MSVC installation instructions
  by @Podde1 in https://github.com/AMICI-dev/AMICI/pull/2053

New Contributors
* @Podde1 made their first contribution in https://github.com/AMICI-dev/AMICI/pull/2053

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.16.1...v0.17.0


### v0.16.1 (2023-02-24)

Fixes:
* Additional package names for finding blas via pkg-config
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1959
* Changed default interpolation type from hermite to polynomial
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1960
* PySB import: Change default simplify to work with multiprocessing
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1961
* Add --no-validate to amici_import_petab
  @dweindl in https://github.com/AMICI-dev/AMICI/pull/1963
* Fix get_model for direct import of swig interface
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1969
* Fix PytestReturnNotNoneWarning in test_conserved_quantities_demartino.py
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1968
* Fix MSVC builds / remove -W* flags
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1972
* Add option to use IDs when plotting trajectories
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1974
* Fix assignmentRules2observables - skip non-assignment-rule targets
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1973
* Use std::clock for measuring solver time
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1982
  (*Note that this uses cpu-time consumed by all threads*)
* Fix narrowing-conversion-warning
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1983
* PEtab import: allow specifying default values for output parameters
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1987
* Print stacktraces only with debug logging level
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1985
* Change default ReturnData::status to AMICI_NOT_RUN
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1984
* Reduce time-tracking overhead
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1988
* Fix equilibraton status discrepancy
  by @plakrisenko in https://github.com/AMICI-dev/AMICI/pull/1991
* Pass model_name to _create_model_output_dir_name
  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1994
* CMake: Build with OpenMP support if available
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2000
* Fix SuiteSparse Makefiles for compiler-paths
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2003
* CMake: Build with HDF5 support if available
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1999
* CMake: Fix reading version file on Windows
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2001
* CMake: raise minimum required version to 3.15
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2002
* Fix/extend runtime logging
  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2005
* Fix error logging in steadystate solver
  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2008
* Don't pass `-py3` to swig after 4.1.0
  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2010
* SWIG __repr__s for different templated vector classes
  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2009
* Matlab: If mex fails, print mex arguments
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2013
* Simplify OpenBLAS installation on Windows
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2016
* Remove model name prefix in generated model files
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2015
* ...

Documentation:
* Restructure sphinx doc
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1978
* Instructions for AMICI with singularity
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1964
* Illustrate options for potentially speeding up model import/simulation
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1965
* ...

Dependencies:
* Updated SuiteSparse to v7.0.1
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2018

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.16.0...v0.16.1


### v0.16.0 (2023-01-25)

Features
* Python 3.11 compatibility
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1876
* AMICI now runs on binder (https://mybinder.org/v2/gh/AMICI-dev/AMICI/develop?labpath=binder%2Foverview.ipynb)
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1935,
  https://github.com/AMICI-dev/AMICI/pull/1937,
  https://github.com/AMICI-dev/AMICI/pull/1939
* More informative `Solver.__repr__` and `ExpData.__repr__`
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1928
  and @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1948
* `simulate_petab` returns the generated/used `ExpData`s
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1933
* Model module is now accessible from model instance
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1932
* Added `plot_jacobian`
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1930
* Now logs all nested execution times as debug
  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1947
* Always check for finite initial states, not only with
  `Model.setAlwaysCheckFinite(True)`
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1955

Fixes
* `ReturnDataView.status` now returns `int` instead of `float`
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1929
* Updated simulation status codes
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1931
* Skip irrelevant frames in stacktraces
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1934
* Fixed compiler warning (matlab)
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1954

Documentation:
* Added a notebook demonstrating common simulation failures and show how to
  analyze / fix them
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1946
* various minor fixes / updates

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.15.0...v0.16.0


### v0.15.0 (2023-01-11)

Features
* Improved logging by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1907

  For Python: Don't print messages to stdout, but collect them in ReturnData
  and forward them to python logging, making it easier to filter specific
  messages or to disable output completely. Messages are also available via
  `ReturnData.messages`.

  **breaking change for C++ interface**:
  Messages aren't printed to stdout by default, but are collected in
  `ReturnData`. The user has to decide what to do with them.

* MultiArch docker build by @FFroehlich
  in https://github.com/AMICI-dev/AMICI/pull/1903
* Added cmake target for cmake-format
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1909
* Updated clang-format style, fixed clang-format target
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1908
* Subsetting `ReturnData` fields by ID via `ReturnDataView.by_id`
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1911  https://github.com/AMICI-dev/AMICI/pull/1916

Fixes
* PEtab import: fixed handling of fixed parameters for rule targets
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1915
* Fixed compiler warnings for matlab interface
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1919
* Fixed pandas DeprecationWarning for Series.iteritems()
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1921
* Fixed circular import in amici.petab_import_pysb
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1922
* Fixed 'operator ==' swig warning
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1923
* Prevent swig4.0.1 segfault
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1924

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.14.0...v0.15.0


### v0.14.0 (2022-11-23)

#### Features:

* Added optional functionality to apply C99 math optimization to generated C++ code
  by @dweindl and @lcontento in https://github.com/AMICI-dev/AMICI/pull/1377, https://github.com/AMICI-dev/AMICI/pull/1878

* Added option to treat fixed parameters as constants in PEtab import

  by @dweindl in  https://github.com/AMICI-dev/AMICI/pull/1877

* Added equality operator for ExpData

  by @dweindl in  https://github.com/AMICI-dev/AMICI/pull/1881

* Updated base image for Dockerfile to Ubuntu 22.04/Python 3.10

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1896


#### Fixes:

* Fixed deprecation warnings
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1873, https://github.com/AMICI-dev/AMICI/pull/1893

* Fixes/updates to GitHub actions
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1885, https://github.com/AMICI-dev/AMICI/pull/1893, https://github.com/AMICI-dev/AMICI/pull/1889, https://github.com/AMICI-dev/AMICI/pull/1891

* Added hdf5 search directories for arm64 architecture (M1/M2 macs)

  by @Doresic in https://github.com/AMICI-dev/AMICI/pull/1894

* Fixed missing return in generated non-void functions

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1892

* Fixed import failure for pre-compiled models

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1897

#### Documentation:

* Update reference list
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1874, https://github.com/AMICI-dev/AMICI/pull/1884

**Full Changelog**:
https://github.com/AMICI-dev/AMICI/compare/v0.13.0...v0.14.0

### v0.13.0 (2022-10-04)

* Fixed extraction of common subexpressions
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1865
* Added function to convert `ReturnData::status` flags to string
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1864

And further contributions by @dweindl, @FFroehlich

**Full Changelog**:
https://github.com/AMICI-dev/AMICI/compare/v0.12.0...v0.13.0

### v0.12.0 (2022-08-26)

Features:
* Support for event observables via the Python interface
  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1845
* Treat non-estimated parameters as constants during SBML-PEtab import
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1810
* Updated SUNDIALS to v5.8.0
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1836
* Option to extract common subexpressions
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1852,
  https://github.com/AMICI-dev/AMICI/pull/1856
  **not available in this release, use v0.13.0**
* Parallelize matrix simplification
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1778
* Validate PEtab problems before attempting import
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1842
* Improved type annotations for the swig interface
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1860

Fixes:
* Fixed an issue with potentially infinite loops during conservation law
  processing by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1833
* Fixed potential deadlocks during parallel simplification
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1844
* Fix resetting `ReturnData::numstepsB` when re-using Solver
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1841

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

**Full Changelog**:
https://github.com/AMICI-dev/AMICI/compare/v0.11.32...v0.12.0

### v0.11.32 (2022-07-15)

Fixes:
* Fixed `ImportError`s during package installation with recent setuptools
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1830

### v0.11.31 (2022-07-12)

Fixes:
* Fixed `ParameterMapping.__getitem__` to either return a
  `ParameterMappingForCondition` or a new `ParameterMapping`, but not a list
  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1826

### v0.11.30 (2022-07-07)

Features:
* Allow overriding model name during PySB import by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1801
* Added __repr__ for parameter mapping classes by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1799
* More informative warning messages for NaNs/Infs by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1798
* Moved `sim_steps` increment by @plakrisenko in
  https://github.com/AMICI-dev/AMICI/pull/1806
* Re-arranged application of parameters from `ExpData` to avoid initial
  sensitivities error by @dilpath in
  https://github.com/AMICI-dev/AMICI/pull/1805
* Checking for unused parameters in `simulate_petab` by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1816
* Add `create_parameter_mapping` kwarg forwarding by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1820

Other
* Remove `constant_species_to_parameters` by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1809

Fixes
* Fixed handling of SBML models given as `pathlib.Path` in
  `petab_import.import_model_sbml by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1808
* Fixed missing CPU time reset by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1814
* Raise in `simulate_petab` with `scaled_parameters=True`
  `problem_parameters=None` by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1819

...

**Full Changelog**:
https://github.com/AMICI-dev/AMICI/compare/v0.11.29...v0.11.30

### v0.11.29 (2022-05-06)

## What's Changed

Features:
* Performance: Limit newton step convergence check by @FFroehlich in
  https://github.com/AMICI-dev/AMICI/pull/1780
* More informative NaN/Inf warnings by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1640
* SBML import can now handle initial events by @FFroehlich in
  https://github.com/AMICI-dev/AMICI/pull/1789

Fixes:
* Avoid error if no measurements in PEtab problem; fixed type handling in
  PEtab parameter mapping by @dilpath in
  https://github.com/AMICI-dev/AMICI/pull/1783
* Fixed substitution of expressions in root and stau by @dilpath in
  https://github.com/AMICI-dev/AMICI/pull/1784
* Workaround for PEtab problems with state-dependent noise models by @dweindl
  in https://github.com/AMICI-dev/AMICI/pull/1791

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.11.28...v0.11.29


### v0.11.28 (2022-04-08)

New features:
* Added `Solver.setSteadyStateToleranceFactor` and
  `Solver.setSteadyStateSensiToleranceFactor` to specify a steady state
  tolerance factor by @dilpath in https://github.com/AMICI-dev/AMICI/pull/1758

  **NOTE: This also relaxed the default steady state (sensitivity)**
  **tolerances by a factor of 100.**
* Added support for `pathlib.Path` by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1769
* Allow specifying initial timepoint with `ExpData` by @dilpath in
  https://github.com/AMICI-dev/AMICI/pull/1776

Performance:
* Speedup for models with conservation laws by @FFroehlich in
  https://github.com/AMICI-dev/AMICI/pull/1765
* Improved efficiency of newton step convergence check by @FFroehlich in
  https://github.com/AMICI-dev/AMICI/pull/1775

Fixes:
* Fixed deprecation warning for pandas.DataFrame.append in
  `rdatas_to_measurement_df` by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1770
* Fixed Rule-target handling in PEtab import by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1753

Removed functionality:
* Removed long deprecated `sbml2amici` arguments `modelName`
  and `constantParameters` by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1774

**Full Changelog**:
https://github.com/AMICI-dev/AMICI/compare/v0.11.27...v0.11.28

### v0.11.27 (2022-04-04)

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

Performance:
* Optional parallel computation of derivatives during model import by @dweindl
  in https://github.com/AMICI-dev/AMICI/pull/1740
* Sparsify jacobian by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1766
* Speedup conservation law computation by @FFroehlich in
  https://github.com/AMICI-dev/AMICI/pull/1754
* Exploit stoichiometric matrix in pysb import by @FFroehlich in
  https://github.com/AMICI-dev/AMICI/pull/1761
* Speedup edata construction from petab problems by @FFroehlich in
  https://github.com/AMICI-dev/AMICI/pull/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 https://github.com/AMICI-dev/AMICI/pull/1751
* Use correct tolerances for convergence check in Newton solver by @FFroehlich
  in https://github.com/AMICI-dev/AMICI/pull/1728
* Harmonized convergence checks by @FFroehlich in
  https://github.com/AMICI-dev/AMICI/pull/1731
* Made sundials' KLU_INDEXTYPE match actual klu index type by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1733
* Fixed `Model::setStateIsNonNegative` logic that would raise exceptions in
  cases where it shouldn't by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1736
* Fixed undefined reference to dladdr by @kristianmeyerr in
  https://github.com/AMICI-dev/AMICI/pull/1738
* Fixed HDF5 OSX intermediate group creation errors by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1741
* Fixed recent cmake-based build issues due to changed sundials library
  directory by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1756
* Updated Windows installation instructions by @paulflang in
  https://github.com/AMICI-dev/AMICI/pull/1763

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

**Full Changelog**:
https://github.com/AMICI-dev/AMICI/compare/v0.11.26...v0.11.27

### v0.11.26 (2022-03-14)

New features:
* Import of BioNetGenLanguage (BNGL) models by @FFroehlich in
  https://github.com/AMICI-dev/AMICI/pull/1709
* Added support for observable-dependent sigmas by @dweindl, @FFroehlich in
  https://github.com/AMICI-dev/AMICI/pull/1692
* Added support for pysb local functions by @FFroehlich in
  https://github.com/AMICI-dev/AMICI/pull/1666
* Added experimental support for conservation laws for non-constant species to
  SBML import: conservation laws for non-constant species
  by @stephanmg, @dweindl in https://github.com/AMICI-dev/AMICI/pull/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 https://github.com/AMICI-dev/AMICI/pull/1677
  * Added support for parameter-dependent conservation laws by @dweindl,
    @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1678
* Added optional caching for symbolic simplifications in ODE export by @dilpath
  in https://github.com/AMICI-dev/AMICI/pull/1672
* Added CLI option `--no-sensitivities` to `amici_import_petab` by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1688

Fixes:
* SBML import: Raise in case of nested observables by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1690
* Sympy 1.10 compatibility by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1694

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.11.25...v0.11.26

### v0.11.25 (2022-02-09)

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

**Full Changelog**:
https://github.com/AMICI-dev/AMICI/compare/v0.11.24...v0.11.25

### v0.11.24 (2022-02-01)

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 https://github.com/AMICI-dev/AMICI/pull/1637
* Dropped Python3.7 support by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1635
* Include header files in CMake targets for better IDE integration by @dweindl
  in https://github.com/AMICI-dev/AMICI/pull/1639

Fixes:
* Fixed an issue in PEtab import where all-integer parameters would previously
  result in a TypeError by @stephanmg in
  https://github.com/AMICI-dev/AMICI/pull/1634
* Fixed tempdir deletion issues for test suite on Windows by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1636
* Added functions to provide state IDs/names for x_solver by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1638
* Fixed docs on RTD by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1643

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.11.23...v0.11.24

### v0.11.23 (2022-01-11)

Features:
* Added overload for Model::setParameterScale with vector<int> by @dilpath in
  https://github.com/AMICI-dev/AMICI/pull/1614
* Removed assert_fun argument from gradient checking, improve output
  by @dweindl, @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1609
* Added get_expressions_as_dataframe by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1621
* Added `id` field to ExpData and ReturnData by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1622
* Included condition id in dataframes by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1623

Fixes:
* C++: Fixed SUNMatrixWrapper ctor for size 0 matrices by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1608
* Python: Handle TemporaryDirectory cleanup failures on Windows by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1617
* Python: pysb.Model.initial_conditions throws a DeprecationWarning by
  @PaulJonasJost in https://github.com/AMICI-dev/AMICI/pull/1620
* Fixed wrong array size in warnings by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1624

NOTE: AMICI 0.11.23 requires numpy<1.22.0

**Full Changelog**:
https://github.com/AMICI-dev/AMICI/compare/v0.11.22...v0.11.23

### v0.11.22 (2021-12-02)

* **Require sympy>=1.9,pysb>=1.13.1*  by @FFroehlich, @dweindl
  in https://github.com/AMICI-dev/AMICI/pull/1599
* Fixed sympy deprecation warning by @dweindl in
  https://github.com/AMICI-dev/AMICI/pull/1600
* Updated Windows installation instructions for Python>=3.8 by @dweindl
  in https://github.com/AMICI-dev/AMICI/pull/1597
* Fixed plot labels by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1598

**Full Changelog**:
https://github.com/AMICI-dev/AMICI/compare/v0.11.21...v0.11.22

### v0.11.21 (2021-11-21)

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)


### v0.11.20 (2021-11-12)

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)


### v0.11.19 (2021-10-13)

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


### v0.11.18 (2021-07-12)

New:
* Allow specifying maximum integration time via
  `amici::Solver::setMaxTime()` (#1530)
* Py: Add `failfast` and `num_threads` argument to `simulate_petab`
  (#1528, #1524)
* Enable typehints / static type checking for AMICI-generated model modules
  (#1514) (`amici.ModelModule`, available with Python>=3.8)

Fixes:
* Python: Fix unused argument `generate_sensitivity_code` in `pysb2amici`
  (#1526)
* Python: Fix C(++) stdout redirection which could have let to deadlocks in
  exotic situations (#1529)
* Py: Fixed deprecation warning (#1525)
* Py: Proper typehints for SWIG interface (#1523), enabling better static type
  checking and IDE integration (available with Python>=3.9)
* C++: Fixed clang compiler warning (#1521)
* C++: Fix inherited variadic ctor in exception class (#1520)
* PEtab: More informative output for unhandled species overrides (#1519)
* Return SbmlImporter from PEtab model import (#1517)


### v0.11.17 (2021-05-30)

Fixes:
* Fix "maybe-uninitialized" compiler warning (#1495)
* Fix substitution of expressions in `drootdt_total (#1512)
* C++: Fix serialization and == operator (#1493)
* C++: Avoid `w` in `root` and `stau` headers (refactor) (#1503)

Documentation:
* Updated OpenBLAS Windows installation instructions (#1496)
* Updated how-to-cite to Bioinformatics paper (#1499)
* Updated list of papers using AMICI (#1509)

Other:
* Remove sllh computation from `petab_objective.simulate_petab` (#1498)
* Add __main__.py to Python package to provide info on AMICI installation
  via `python -m amici` (#1500)

### v0.11.16 (2021-04-13)

Fixes:
* Fixed serialization bug  (#1490)

New:
* Construction of condition specific plist for parameter mappings (#1487, #1488)
* **Add support for error residuals** (#1489)

### v0.11.15 (2021-03-31)

Fixes:
* Fixed initial state sensitivities in adjoint preequilibration (#1468)
* Fixed various model import / parameter mapping issues (#1469, #1473, #1475)

New:
* New AMICI releases will automatically trigger releases at
  https://biosimulators.org/simulators/amici/latest
* Transparent logo

### v0.11.14 (2021-03-16)

New features:
* **Python import now supports SBML Events** (#1443)
* Implement support for compilation without sensitivities (#1454)

Fixes:
  * Issue #1446: Check whether constant parameters are valid targets (#1450)
  * Issue #1422: Fix Steadystate solver failing if preequilibration starts in
    steadystate (#1461)
  * Issue #1401: Ensure diagnostics variables in ReturnData are always of
    expected length (#1438, #1447)
  * Fix FIM approximation for parameter dependent sigma (#1441)
  * Fix invalid SBML in PEtab/PySB import (#1433)
  * Fix: No context for inspect.getouterframes (#1432)

Documentation:
* Added this CHANGELOG
* Added feature request issue template (#1437)
* Updated reference list (#1430)
* Overhauled experimental conditions notebook (#1460)

CI:
* Test Matlab interface on GHA  (#1451)
* Include componentTags in SBML test suite output (#1462)
* Split SBML semantic test suite into multiple jobs (#1452)
* Fix Crauste ref val, fixes #1458 (#1459)

Misc:
* Various cleanup (#1465, #1448, #1455)
* Micro-optimize SUNMatrixWrapper::transpose (#1439)
* Remove constant triggers from roots in Heaviside (#1440)

### v0.11.13 (2021-02-20)

Breaking changes:
* AMICI requires Python>=3.7
* Updated package installation (PEP517/518):
  Creating source distributions requires https://github.com/pypa/build (#1384)
  (but now handles all package building dependencies properly)

Features:
* More flexible state reinitialization (#1417)

Updated dependencies:
* Upgrade to sundials 5.7.0 (#1392)

Fixes:
* Python: account for heaviside functions in expressions (#1382)
* Python: allow loading of existing models in import_petab_problem (#1383)
* Python: Don't override user-provided compiler/linker flags (#1389)
* Python: PEtab import reinitialization fixes (#1417)
* Python: Fix PEtab observables for pysb models (#1390)
* Python: Substitute expressions in event condition expressions (#1404)
* Python: Unspecified initial states in PEtab conditions table default to SBML initial value (#1397)
* C++: Fix timepoint out of bounds access (#1402)
* C++: Fix exported CMake config (#1388)
* Fixed Dockerfile: add python3-venv (#1398, #1408)

Other:
* Slim exported swig interface (#1425)
* Updated documentation
    * Getting started tutorial (#1423)
    * List supported SBML test tags (#1428)
    * Add AMICI C++/Python/Matlab feature comparison (#1409)
    * ...
* Various minor CI improvements
* ...

### v0.11.12 (2021-01-26)

Features:
* Add expression IDs and names to generated models (#1374)

Fixes:
* Raise minimum sympy version to 1.7.1 (Closes #1367)
* Fix species assignment rules in reactions (#1372)
* Fix id vector for DAEs (#1376)

Docs:
* Update how-to-cite (#1378)


### v0.11.11 (2020-12-15)

#### Python
* Restore support for species references (#1358)
* Add support for noise models in pysb (#1360)
* Proper handling of discontinuities in the ODE rhs (#1352)
* Fix directly calling AMICI from snakemake (#1348 )
* Extend mathml function support, particularly for numerical arguments (#1357)
* Restore support for sympy 1.6 (#1356)

#### C++
* Fix some compiler related warnings (#1349, #1362 )
* Fix a rare segfault for adjoint sensitivities (#1351)

#### CI
* Move windows tests to GHA (#1354)
* Pin breathe to 4.24.1

#### Docker
* Update ubuntu to 20.04

### v0.11.10 (2020-11-30)

Bugfix release that restores compatibility with sympy 1.7

### v0.11.9 (2020-11-29)

#### Python
* General improvements to SBML import (#1312, #1316, #1315, #1322 , #1324 #1333, #1329)
* Small bugfixes and improvements (#1321 )
* Improve derivative computation for instances of `power` (#1320 )

#### C++
* Fix FIM and residual computation for models with parameter dependent sigma. (#1338)
* Disable chi2/residual/FIM computation for non-gaussian objective functions. (#1338)
* Bugfix for integration failure during adjoint solve (#1327)

#### Doc
* Update references (#1331, #1336)

#### CI
* Update OpenBLAS for windows (#1334)

### v0.11.8 (2020-10-21)

#### Python
* Fix pysb-petab support (#1288)
* Fix ExpData constructor overloading (#1299)
* Fix support for positivity enforcement (#1306)
* **Refactor SBML import, adds support for parameter rate rules and initial assignments** (#1284, #1296, #1304)
* Improve model generation for models with many parameters (#1300)
* Add support for PEtab based synthetic data generation (#1283)

#### C++
* Make HDF5 an optional dependency (#1285)

#### Doc
* General Improvements to Documentation (#1289, #1291, #1292, #1293, #1294, #1286, #1277, #1281)

#### CI
* Add python 3.9 support test (#1282)
* Allow manual triggering of GitHub actions (#1287)
* Remove appveyor config (#1295)
* Update GHA env and path management (#1302)

### v0.11.7 (2020-09-22)

#### Python
* Improve and extend available objective functions (#1235)
* Fix processing of compartment definitions (#1223)
* Fix replacement of reserved symbols (#1265)
* Use Hierarchical Derivatives for Expressions (#1224, #1246)
* Fix duplicate running of swig (#1216)
* Overload python interface functions for amici.{Model,Solver,ExpData} and amici.{Model,Solver,ExpData}Ptr (#1271)

#### C++
* Fix and extend use of sparse matrix operations (#1230, #1240, #1244, #1247, #1271)
* **Fix application of maximal number of steps**, MaxNumStep parameter now limit total number of steps, not number of steps between output times. (#1267)

#### Doc
* Move all Documentation to RTD (#1229, #1241)
* General Improvements to Documentation (#1225, #1227, #1219, #1228, #1232, #1233, #1234, #1237,  #1238, #1239, #1243, #1253, #1255, #1262)

#### CI
* Better check for doc building (#1226)
* Add more gradient checks (#1213)
* Update GHA to Ubuntu 20.04 (#1268)

### v0.11.6 (2020-08-20)

#### Python
* Bugfix for piecewise functions (#1199)
* Refactor swigging - generate one single wrapper (#1213)

#### C++
* Fix warnings: account for zero indexing in nan/inf error (#1112)

#### Doc
* Update Windows build instructions (#1200, #1202)
* Update README: Projects using AMICI (#1209)
* Add CODE_OF_CONDUCT.md (#1210)
* Update documentation for Python interface (#1208)

#### CI
* Create sdist on GHA using swig4.0.1 (#1204)  (Fixing broken pypi package)
* Fix links after repository move
* Speed-up swig build: disable all languages except python (#1211)
* Fix doc generation on readthedocs (#1196)


### v0.11.5 (2020-08-07)

#### General
* Move repo to new organization (#1193)
* Update Bibliography

#### Python
* Fix bug for energyPySB models (#1191)

#### CI
* Fix release deployment (#1189)

### v0.11.4 (2020-08-06)

#### Python
* Skip unnecessary expressions in pysb models (#1185)
* MSVC compiler support (this time for real... #1152)

#### CI
* Implement MSVC tests (#1152)
* Rename and group GitHub actions (#1186)
* Fix release deployment (#1186)

### v0.11.3 (2020-08-06)

#### Python
* Fix simplification for pysb models (#1168)
* Pass verbosity flags to pysb network generation (#1173)
* Enable experimental pysb-petab support (#1175)
* Add installation instructions for Fedora (#1177)
* Implement support for SBML rate-references (#1180)

#### C++
* Refactoring (#1162, #1163)

#### CI
* Move majority of tests to Github Actions (#1166, #1160)
* Improve reporting of skipped tests in SBML testsuite (#1183)

### v0.11.2 (2020-07-17)

#### 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)

### v0.11.1 (2020-06-05)

#### 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)


### v0.11.0 (2020-05-10)

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)

### v0.10.21 (2020-04-04)

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)


### v0.10.20 (2020-03-18)

* 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)

### v0.10.19 (2020-02-13)

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

### v0.10.18 (2020-02-11)

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

### v0.10.17 (2020-01-15)

- **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)

### v0.10.16 (2019-12-11)

* **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)


### v0.10.15 (2019-12-03)

Bugfix release due to incorrect sensitivities w.r.t. sigmas introduced in 0.10.14.

No other changes.

### v0.10.14 (2019-12-02)

**NOTE: For Python-imported SBML-models this release may compute incorrect sensitivities w.r.t. sigma. Bug introduced in 0.10.14, fixed in 0.10.15.**

Python:

* Don't require use of ModelPtr.get to call ExpData(Model)
* Fix import in generated model Python package
* Setup AMICI standalone scripts as setuptools entrypoints
* Simplify symbolic sensitivity expressions during Python SBML import
        Fixes Infs in the Jacobian when using Hill-functions with states of 0.0.
* Extended Newton solver #848
    The changes that allow performing Newton tests from the paper:
    G. T. Lines, Ł. Paszkowski, L. Schmiester, D. Weindl, P. Stapor, and J. Hasenauer. Efficient computation of steady states in large-scale ODE models of biochemical reaction networks. accepted for Proceedings of the 8th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE), Valencia, Spain, October 2019.
* Use SWIG>=4.0 on travis to include PyDoc in sdist / pypi package (#841)
* **Fix choice of likelihood formula; failed if observable names were not equal to observable IDs**
* Fix(sbml-import) Compartment IDs in right-hand side of Rules are not replaced and lead to undefined identifiers in c++ files
* Fix invalid logging level
* Speed up sympy simplification (#871)

C++:

* Performance: Avoid unnecessary repeated function calls for SUNMatrixWrapper dimensions
*   Add AmiciApplication class as context for handling so far global settings.
    This allows for example setting custom logging functions for concurrent AMICI
    runs, e.g. in multi-thread applications (Closes #576).

Misc:

* Setup performance test on github actions (#853)
* Update documentation and FAQ for CBLAS requirement and others
* Update reference list

### v0.10.13 (2019-10-09)

* BREAKING CHANGE: Renaming {get|set}tNewtonPreequilibration to {get|set}Preequilibration (Closes #720)
* Make wurlitzer non-optional requirement for AMICI python package (Fixes missing AMICI errors when running from jupyter notebooks)
* Compute initial state for Model::getInitialStates if not already set (Fixes #818)
* Make swig generate pydoc comments from doxygen comments #830 (Closes #745) to provide Python docstrings for C++ wrapper functions
* feature(cmake) Add option to disable compiler optimizations for wrapfunctions.cpp (Fixes #828) (#829)
* Change SBML test suite to pytest to allow for parallel test execution… (#824)
* Fix(cmake): -E option is not available in all sed versions. Neither is the equivalent -r. Use --regexp-extended instead (Closes #826)
* Refactor(python) Move PEtab import code from command line script… (#825)
* Fix(core) Fix regular expressions for intel compiler (Closes #754) (#822)
* Update workflow figure to include PySB (Closes #799)
* Fix compiler warnings

### v0.10.12 (2019-09-28)

* Fix handling of species specified in PEtab condition table (#813)
* Fix some Visual C++ issues, update cppcheck handling, cleanup (VisualC++ still not fully supported)
* Minor fixups (#801)
* Create SBML test suite result files for upload to http://sbml.org/Facilities/Database/ (#798)


### v0.10.11 (2019-08-31)

* Fixed setting initial conditions for preequilibration (#784)
* Fixed species->parameter conversion during PEtab import (#782)
* Set correct Matlab include directories in CMake (#793)
* Extended and updated documentation (#785, #787)
* Fix various SBML import issues
* Run SBML test suite using github actions instead of travisCI (#789)

### v0.10.10 (2019-08-07)

* Simplify/fix AMICI installation
   * If available use environment modules to detect dependencies

  * Add SWIG installation script

* Update list of publication
* Update documentation
    * Update doc for SWIG build and custom SWIG location.
    * Add AMICI interface overview / workflow figure and show in README
    * Document environment variables for model/core compilation (Closes #737)

* Added handling of abs function, since there seem to be problems with case sensitivity (#713) Closes #770

Detaills:
    * cmake: Use package_ROOT environment variables
    * fix(cmake) Fix finding version.txt
    * cmake: Auto-detect loaded MKL environment module
    * cmake: Use new FindPython3 modules where possible
    * fix(python) Restore python3.6 compatibility
    * Inside venv, use pip instead of pip3 which should point to the correct version
    * fix(python) Workaround for missing ensurepip during venv creation [ci skip]
    * feature(python) Use MKL from environment modules to provide cblas
    * fix(python) Fix define_macros not being passed to setuptools for Extension
    * fix(python) Fix define_macros not being passed to setuptools for clibs
    * Do not always add 'cblas' library since users may want to override that by a cblas-compatible library with a different name (closes #736)
    * Update HDF5 path hints; use shared library if static is not available.
    * Check for HDF5_BASE from environment module
    * Fix system-dependent sundials library directory (Fixes #749) (#750)
    * Handle OSTYPE==linux in scripts/buildBNGL.sh (Fixes #751)
    * Add SWIG download and build script
    * Improve finding swig executable and allow user override via SWIG environment variable
    * Provide installation hints if no SWIG found (Closes #724)
    * Allow overriding cmake executable with environment variables in build scripts (Closes #738)


### v0.10.9 (2019-07-24)

Fixup for missing version bump in v0.10.8 release. No code changes compared to v0.10.8.

### v0.10.8 (2019-07-24)

Changes in this release:

All:
- Updated / extended documentation
- Fix reuse of  `Solver` instances (#541)

C++:
-  Check for correct AMICI version for model in CMake
- Add reporting of computation times (#699)

Python:
- Fix manifest file (#698)
- Fix initial amounts/concentrations in SBML import

... and various other minor fixes/improvements

### v0.10.7 (2019-05-01)

Python
* fix unset noise distribution when automatically generating observables in case None are passed (#691)

### v0.10.6 (2019-04-19)

C++
- Add SuperLUMT support (#681)
- Sparsified dJydy (#686)
- Enabled support of impulse-free events for DAE models (#687) - thanks to Sebastien Sten for providing a testcase for this

Python
- Enabled support for piecewise functions in SBML import (#662)
- Fix numeric type when constructing ExpData from Dataframes (#690)
- Fix dynamic override in PETab


### v0.10.5 (2019-04-08)

Bugfix release

Doc
- Update documentation of Windows installation

C++
- Fix missing source files in CMakeLists.txt (#658)
- Set CMake policies to prevent warnings (Closes #676) (#677)
- Start using gsl::span instead of raw pointers (#393) (#678)

Python
- PySB parsing fix (#669)
- Fix failure to propagate BLAS_LIBS contents (#665)
- Require setuptools at setup (#673)
- Updated PEtab import to allow for different noise models


### v0.10.4 (2019-03-21)

Features / improvements:

* Implement ReturnData and ExpData wrappers as more efficient views (#657)
* Add list of references using AMICI (#659)
* Custom llh (normal/laplace, lin/log/log10) (#656)

Bugfixes:

+ Speedup and fix travis build

### v0.10.3 (2019-03-13)

Features / improvements:

- adds the option for early termination on integration failures for runAmiciSimulations
- improve runtime of `SUNMatrixWrapper::mutliply`
- expose finite difference routines in public API
- enable parallel compilation of clib source files

Bugfixes:

- fixed symbolic processing for unreleased pysb features

### v0.10.2 (2019-03-07)

Features / improvements:

- extended `ExpData` interface to allow for condition specific parameters, parameter scales, parameter lists, initial conditions and initial condition sensitivities.

Bugfixes:

- fixed output values of `ReturnData::x_ss` and `ReturnData::sx_ss`

### v0.10.1 (2019-03-04)

* travis-ci.com migration
* fix problem with has{variable} functions
* allow to import sbml model from string, not only file

### v0.10.0 (2019-03-01)

Features / improvements:

- updated sundials to 4.1.0
- updated SuiteSparse to 5.4.0
- added generic implementations for symbolic expressions that were sparse matrix vector products

Bugfixes:

- fixed return value of `rz` when no data is provided.

### v0.9.5 (2019-02-26)

Features / improvements:

- allow python installations without compilation of c++ extension
- improvements to ExpData <-> pandas.DataFrame interface
- allow generation of matlab models from python
- implement CLI interface for PEtab
- improve computation time for conservation laws from pysb import

Bugfixes:

- Fix sign in undamped Newton step.

Maintenance:

- use newer CI images

### v0.9.4 (2019-02-11)

Minor fixes only:
- fix(core) Get solver diagnostics for first(last) timepoint (#588) (Closes #586)
- fix(ci) Fix autodeploy (Closes #589)

### v0.9.3 (2019-02-07)

**CRITICAL FIXES**
- **fix(python) fix symbolic computations for adjoint (#583)**

**Features**
- feature(python) Check for matching AMICI versions when importing model (Closes #556). Set exact AMICI version as model package requirement.
- feature(core) Add option to rethrow AMICI exception (Closes #552)
- feature(python) Redirect C/C++ output in stdout is redirected (e.g. in ipython notebooks) (Closes #456)

**Minor fixes**
- fix(python) Fix doc and rename sys_pipes to something more meaningful
- fix(ci) Fix premature exit of scripts/runNotebook.sh
- fix(deploy) Update pyenv shims to find twine



### v0.9.2 (2019-01-30)

Bugfixes:

- fixes a critical bug in the newton solver
- fixes multiple bugs in sbml import for degenerate models, empty stoichiometry assignments and conversion factors
- improved error messages for sbml import
- #560
- #557
- #559


### v0.9.1 (2019-01-21)

Features / improvements:

- make pure steadystate results available as `rdata['x_ss']` and `rdata['sx_ss'] `
- add option to specify integration tolerances for the adjoint problem via `atolB` and `rtolB`

Bugfixes:

- improved conservation law identification to also account for constant species.
- fixed a bug where simulation results were written into results of the second newton solver attempt
- fixed an openMP related warning

Maintenance:

- attempt to fix automatic deploy to pypi via travis

### v0.9.0 (2019-01-18)

Features / improvements:

- Allow computation and application of conservation laws for pysb importet models. This enables use of NewtonSolver for preequilibration for models where it was previously not possible.
- Use `klu_refactor` in the sparse Newton solver instead of always using `klu_factor` and only perform symbolic factorization once (#421)
- Allow more detailed finiteness checks (#514)

Bugfixes:
 - #491

Maintenance:
- Several improvements to travis log sizes and folding
- Use default copy constructor for Model by implementing class wrappers for sundials matrix types (#516)
- Reenable run of SBML testsuite


### v0.8.2 (2019-01-07)

Features / improvements:
* Speedup symbolic processing for ODE generation in python

Bugfixes:
* Fix(python) Add missing deepcopy (introduced in 6847ba675f2088854db583199b8754aaa6e01576)
* Fix(core) Prevent parameter scaling length mismatch (#488)
* Fix(python) Set distutils dependency to current version to fix </usr/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'long_description_content_type'>
* fix(python) add symlink to version.txt to be included in package

Backwards-compatibility:
* Replace 'newline' by literal to restore <R2016b compatibility (Fixes #493)

Maintenance:
* Remove obsolete swig library build via cmake and related file copying
* Provide issue template for bug reports
* Providing valid SBML document to import is not optional anymore
* Update documentation and tests
* Add python version check and raise required version to 3.6 to prevent cryptic error messages when encountering f-strings

### v0.8.1 (2018-11-25)

- [all] **critical** Fix long standing bugs in solving steadystate problems (including preequilibration) (#471)
- [all] Fix AmiVector constructor from std::vector (#471)
- [python] Reenable Solver and Model copy constructors
- Update documentation


### v0.8.0 (2018-11-25)

- replaced symengine by sympy for symbolic processing in python *which fixes several critical bugs* that were due to bugs in symengine (#467)


### v0.7.13 (2018-11-18)

- fixes a critical bug in objective function computation for models compiled using `sbml2amici` and `pysb2amici` that was introduced in v0.7.12
- fixes a critical bug in sensitivity computation when`model.reinitializeFixedParameterInitialStates` was set to true
- readds the python interface to the ExpData copy constructor that was inadvertently removed in 0.7.12 and streamlines the respective convenience wrapper to provide access to the full range of constructors.

### v0.7.12 (2018-11-17)

- fixed a critical bug in `amici.constructEdataFromDataFrame`
- enabled multithreaded simulation of multiple experiments (requires compilation with openMP)
- modularized sbml import and added pysb import

### v0.7.11 (2018-10-15)

- [python] Added numpy and python wrappers that provide a more user friendly python API
- [python] Enable import of SBML models with non-float assignment rules
- [python] Enable handling of exceptions in python
- [python] Enable nativ python access to std::vector data-structures
- [core] Provide an API for more fine-grained control over sensitivity tolerances and steady-state tolerances
- [core] Provide an API to specify non-negative state variables (this feature is still preliminary)

### v0.7.10 (2018-08-29)

- Fixed python SBML import `log()` issues (#412)

### v0.7.9 (2018-08-24)

- fixes MATLAB compilation of models
- adds option to perform steady state sensitivity analysis via FSA
- condition dependent intitial conditions are now newly set after preequilibration is done

### v0.7.8 (2018-08-19)

- bugfixes for the ExpData interface
- created build configuration that enables debugging of c++ extensions on os x
- fixed python sbml import when stoichiometry is empty

### v0.7.7 (2018-08-17)

Fixes a couple of bugs just introduced in v0.7.6

### v0.7.6 (2018-08-13)

Important: **Use AMICI v0.7.7 due to https://github.com/ICB-DCM/AMICI/pull/403/commits/3a495d3db2fdbba70c2b0d52a3d4655c33c817a2**

Bug fixes:
- Python import: Fix log10 issues in observables (#382)
- Matlab: Fix broken model compilation (#392)
- Fixed simulation for models without observables (#390)
- Fixed potential matlab memory leaks (#392)

Breaking C++ API changes:
- Revised ExpData interface (#388)

### v0.7.5 (2018-07-30)

Features/enhancements:
- Add computation of residuals, residuals sensitivity, Fisher information matrix (#223)
- More efficient conversion of std::vector to numpy ndarray (#375)
- Allow specifying timepoints in ExpData (#370)

Minor fixes:
- Condition parameters in ExpData now only temporarily override Model parameters (#371)
- Ensure non-negative states for Newton solver (#378)

### v0.7.4 (2018-07-27)

Features/enhancements:
- Check SBML model validity (#343)
- Allow per-parameter setting of amioptions::pscale from matlab interface (#350)
- Documentation

Major fixes:
- Don't compile main.cpp into python model module which broke modules if amici was compiled without libhdf5 (#363)

Minor fixes:
- Fix compiler warnings (#353)
- Plotting, SBML example mode, ...

### v0.7.3 (2018-07-13)

Features:
- Added symbol names to python-wrapped models and make available via Model.getParameterNames(), model.getStateNames(), ...
- Extended Python interface example

Python package available via pypi: https://pypi.org/project/amici/0.7.3/

### v0.7.2 (2018-07-03)

Features:
- Python package: more flexible HDF5 library localization
- Extended CI: python tests, preequilibration tests, run in venv

Major bugfixes:
- Fix python sbml model import / compilation error (undefined function)
- Fix model preequilibration

Minor fixes:
- Various fixes for mingw compilation of python source distribution
- Cmake compatibility with < 3.8 restored

### v0.7.1 (2018-06-12)

Features:
- Allow specifying sigma-parameters from Python interface

Major bugfixes:
- Fix dsigma_y/dp and downstream sensitivity errors

### v0.7.0 (2018-06-09)

- Major revision of documentation
- Improved Python interface
- More comprehensive Python interface example
- Fixed sensitivity computation in Python-generated models
- Various other bug fixes

WARNING:
- For models with sigma-parameters and dsigma_y/dp != 0, dsigma_y/dp was computed incorrectly. This propagates to all dependent sensitivities. This applies also to some older releases and has been fixed in v0.7.1.

### v0.6.0 (2018-05-22)

Implement experimental support for python via swig.
Python interface is now usable, but API will still receive some updates in the future.

WARNING:
- There is a bug in sensitivity computation for  Python-generated models
- Matlab C++ compilation will fail due to undefined M_PI
-> Please use v0.7.0

### v0.5.0 (2018-03-15)

Main new features are:

- Reimplemented support for DAE equations
- Added newton solver for steady state calculation and preequilibration
- Better caching for recompilation of models
- Blas support to  allow compilation of large models with many observables
- Improved SBML support
- Added c++ interface
- Added support for second order adjoint computation

- Rewrote large parts of the code as proper c++11 code to allow easier code maintanance
- Substantially extended testing in continuous integration to assure code quality

### v0.4.0 (2017-05-15)

* First citable version of AMICI (via zenodo integration).
* Better support for standalone compilation
* Improved SBML import scripts
* General Code Cleanup

### v0.3.0 (2016-09-05)

This update comes with many improvements, bug fixes and several new features. Most notably:

1) AMICI should now run on older versions of MATLAB (back to R2014a)
2) AMICI now compiles using older versions of Visual Studio
3) AMICI now also supports second order adjoint sensitivities (full (via the o2flag = 1 and as a vector product via o2flag = 2)
4) AMICI now supports more SBML, SBML v2 and rate rules


### 0.2.1 (2016-05-09)

Bugfix release. This release also includes some changes that should improve the performance on the new R2016a release of MATLAB.


### v0.2 (2016-03-17)

This update comes with many improvements to the computation time for both compilation and simulation. Moreover several new features were included:

1) Hessian Vector products for second order forward sensitivities
2) Correct treatment of parameter/state dependent discontinuities for both forward and adjoint sensitivities


### v0.1 (2015-11-05)

This is the initial release of the toolbox