Amici

**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

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

**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

**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

**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

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