Amici

* 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

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

*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

**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

**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