Amici

* 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

**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

* 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

Fixed package configuration for PyPI upload. No further changes.

**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