Amici

**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

**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

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

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

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

**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