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Bump version; update changelog
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dweindl committed Mar 7, 2024
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70 changes: 70 additions & 0 deletions CHANGELOG.md
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## v0.X Series

### 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**
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0.22.0
0.23.0

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