Merge pull request AMICI-dev#2019 from AMICI-dev/release_0.16.1

Release 0.16.1

Merge pull request AMICI-dev#1956 from AMICI-dev/release_0.16.0

Release 0.16.0

Release 0.15.0

Merge pull request AMICI-dev#1927 from AMICI-dev/release_0.15.0

Release 0.14.0 (AMICI-dev#1898)

* Fix pandas groupby deprecation warning (AMICI-dev#1873)

Fixes AMICI-dev#1872

* Update reference list (AMICI-dev#1874)

* Code printing: Use SymPy C99 math optimizations (AMICI-dev#1377)

for SBML import. Does not currently work with PySB import. Also fixes some argument type issues.

Co-authored-by: Daniel Weindl <daniel.weindl@helmholtz-muenchen.de>

* PEtab import: Add option for treating fixed parameters as constants (AMICI-dev#1877)

Makes the changes from AMICI-dev#1810 optional, as sometimes users prefer more flexible models.
The default remains to treat non-estimated parameters in PEtab as constants in AMICI.

Also adds a basic check for loading existing models during PEtab, to see if they are compatible to what was supposed to be imported. Only checks non-constant parameter IDs so far.

* Make sympy code optimizations optional (AMICI-dev#1878)

Turns out that applying sympy optimizations as introduced
in AMICI-dev#1377 is
potentially very costly. Therefore, they are disabled by
default. They can be enabled by setting
`AmiciCxxCodePrinter.optimizations` as shown in the test
case.

* Update reference list (AMICI-dev#1884)

* GHA: update actions (AMICI-dev#1885)

Fixes some GHA warnings.

* Add macos hdf5 header/library paths (AMICI-dev#1894)

* Doxygen 1.9.5 on RTD (AMICI-dev#1889)

Older binaries are no longer available.

* Code-gen: Fix missing `return` in non-void-returning functions (AMICI-dev#1892)

... and set `-Werror` for compiling models in debug mode.

* Add operator== for ExpData (AMICI-dev#1881)

Adds `operator==` for `amici::ExpData` and fixes issues for other  `operator==` in case of NaNs in arrays.


Closes AMICI-dev#1880

* Fix SetuptoolsDeprecationWarning (AMICI-dev#1893)

Setuptools meanwhile requires listing data directories as subpackages. Fixes AMICI-dev#1888.

* Dockerfile: Update base image to Ubuntu 22.04 (AMICI-dev#1896)

* GHA: Pin python version for osx tests (AMICI-dev#1891)

Fixes AMICI-dev#1890.

Also: 
* use homebrew boost version
* fix CMake logic for selecting a specific Python version.

* Fix `petab_import.import_model(..., compile=False)` failure (AMICI-dev#1897)

Fixes a bug where amici would fail importing an extension that was never built.

* bump version, update changelog

* fix changelog

* -Wno-error=deprecated-declarations

Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>
Co-authored-by: Lorenzo Contento <lcontento@users.noreply.github.com>
Co-authored-by: Daniel Weindl <daniel.weindl@helmholtz-muenchen.de>
Co-authored-by: Doresic <85789271+Doresic@users.noreply.github.com>

Merge pull request AMICI-dev#1870 from AMICI-dev/release_0.13.0

Release 0.13.0

Release 0.12.0

Merge pull request AMICI-dev#1849

Merge pull request AMICI-dev#1831 from AMICI-dev/release_0.11.32

Release 0.11.32

Merge pull request AMICI-dev#1827 from AMICI-dev/release_0.11.31

Release 0.11.31

Merge pull request AMICI-dev#1823 from AMICI-dev/release_0.11.30

Release 0.11.30

Release 0.11.29

Merge pull request AMICI-dev#1793 from AMICI-dev/release_0.11.29