Amici

Features:
* Introduced environment variable `AMICI_DLL_DIRS` to control DLL directories
on Windows (useful for setting BLAS library directory, as required by
Python>=3.8) by dweindl in https://github.com/AMICI-dev/AMICI/pull/1637
* Dropped Python3.7 support by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1635
* Include header files in CMake targets for better IDE integration by dweindl
in https://github.com/AMICI-dev/AMICI/pull/1639

Fixes:
* Fixed an issue in PEtab import where all-integer parameters would previously
result in a TypeError by stephanmg in
https://github.com/AMICI-dev/AMICI/pull/1634
* Fixed tempdir deletion issues for test suite on Windows by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1636
* Added functions to provide state IDs/names for x_solver by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1638
* Fixed docs on RTD by dweindl in https://github.com/AMICI-dev/AMICI/pull/1643

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.11.23...v0.11.24

Features:
* Added overload for Model::setParameterScale with vector<int> by dilpath in
https://github.com/AMICI-dev/AMICI/pull/1614
* Removed assert_fun argument from gradient checking, improve output
by dweindl, FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1609
* Added get_expressions_as_dataframe by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1621
* Added `id` field to ExpData and ReturnData by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1622
* Included condition id in dataframes by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1623

Fixes:
* C++: Fixed SUNMatrixWrapper ctor for size 0 matrices by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1608
* Python: Handle TemporaryDirectory cleanup failures on Windows by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1617
* Python: pysb.Model.initial_conditions throws a DeprecationWarning by
PaulJonasJost in https://github.com/AMICI-dev/AMICI/pull/1620
* Fixed wrong array size in warnings by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1624

NOTE: AMICI 0.11.23 requires numpy<1.22.0

**Full Changelog**:
https://github.com/AMICI-dev/AMICI/compare/v0.11.22...v0.11.23

* **Require sympy>=1.9,pysb>=1.13.1* by FFroehlich, dweindl
in https://github.com/AMICI-dev/AMICI/pull/1599
* Fixed sympy deprecation warning by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1600
* Updated Windows installation instructions for Python>=3.8 by dweindl
in https://github.com/AMICI-dev/AMICI/pull/1597
* Fixed plot labels by dweindl in https://github.com/AMICI-dev/AMICI/pull/1598

**Full Changelog**:
https://github.com/AMICI-dev/AMICI/compare/v0.11.21...v0.11.22

Fixes:
* Fixed a bug in recursion depth computation for model expressions. This may
have resulted in incorrect sensitivities for models with expressions nested
more than 2 levels. (1595)
* Fixed improper handling of Piecewise functions in PySB import which may have
produced incorrect simulation results. (1594)
* Fixed changed googletest reference which broke the CMake-based build if
tests were enabled (1592)

New:
* It's now possible to build AMICI using Ninja (1593)

New:
* Changed parameter mappings such that unassigned values have non-nan default values. This fixes erroneous evaluation of `llh` as `NaN` in some situations (1574)
* Added support for Python 3.10 (1555)

Fixes:
* Fixed a bug when simulation start time was not transferred when copying a solver instance (1573)
* Fixed a bug which led to incorrect sensitivies for models with multiple assignment rules or rate rules (1584)

Other:
* Update CI and documentation settings (1569, 1527, 1572, 1575, 1579, 1580, 1589, 1581)
* Extend set of validated benchmark models that is checked during CI (1571, 1577)
* Fixed string formatting in derivative checks (1585)
* Added helper methods to save and restore model instance-only settings (1576)

New:
* Added support for observable transformations (lin/log/log10) (1567). Thereby supporting additional noise distributions in combination with least squares solvers.

Fixes:
* Fixed a bug when Newton sensitivity computation was activated despite specifying newton_steps == 0. The error occurs when simulation converges to a steadystate but simulation sensitivities are not converged according to convergence criteria. In that case simulation returned failure, but the newton rootfinding "finds" a steadystate even before the iteration check, leading to the erroneous computation of sensitivities via Newton/IFT. For singular jacobians this means the overall simulation still fails, but a different, more informative error message is displayed. (1541)
* Fixed a bug where argument "outdir" in ODEExporter.__init__ would not be used (1543)

Other:
* Improve checking support for SBML extensions (1546)
* SBML import: Use more descriptive IDs for flux expressions (1551)
* Optimized SUNMatrixWrapper functions (1538)
* C++: Changed test suite from CppUTest to gtest (1532)
* Add CITATION.cff (1559)
* Updated documentation (1563, 1554, 1536)
* Removed distutils dependency (1557)
* Require sympy<1.9