Amici

Fixes:
* Fixed `ImportError`s during package installation with recent setuptools
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1830

Fixes:
* Fixed `ParameterMapping.__getitem__` to either return a
`ParameterMappingForCondition` or a new `ParameterMapping`, but not a list
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1826

Features:
* Allow overriding model name during PySB import by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1801
* Added __repr__ for parameter mapping classes by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1799
* More informative warning messages for NaNs/Infs by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1798
* Moved `sim_steps` increment by plakrisenko in
https://github.com/AMICI-dev/AMICI/pull/1806
* Re-arranged application of parameters from `ExpData` to avoid initial
sensitivities error by dilpath in
https://github.com/AMICI-dev/AMICI/pull/1805
* Checking for unused parameters in `simulate_petab` by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1816
* Add `create_parameter_mapping` kwarg forwarding by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1820

Other
* Remove `constant_species_to_parameters` by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1809

Fixes
* Fixed handling of SBML models given as `pathlib.Path` in
`petab_import.import_model_sbml by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1808
* Fixed missing CPU time reset by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1814
* Raise in `simulate_petab` with `scaled_parameters=True`
`problem_parameters=None` by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1819

...

**Full Changelog**:
https://github.com/AMICI-dev/AMICI/compare/v0.11.29...v0.11.30

What's Changed

Features:
* Performance: Limit newton step convergence check by FFroehlich in
https://github.com/AMICI-dev/AMICI/pull/1780
* More informative NaN/Inf warnings by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1640
* SBML import can now handle initial events by FFroehlich in
https://github.com/AMICI-dev/AMICI/pull/1789

Fixes:
* Avoid error if no measurements in PEtab problem; fixed type handling in
PEtab parameter mapping by dilpath in
https://github.com/AMICI-dev/AMICI/pull/1783
* Fixed substitution of expressions in root and stau by dilpath in
https://github.com/AMICI-dev/AMICI/pull/1784
* Workaround for PEtab problems with state-dependent noise models by dweindl
in https://github.com/AMICI-dev/AMICI/pull/1791

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.11.28...v0.11.29

New features:
* Added `Solver.setSteadyStateToleranceFactor` and
`Solver.setSteadyStateSensiToleranceFactor` to specify a steady state
tolerance factor by dilpath in https://github.com/AMICI-dev/AMICI/pull/1758

**NOTE: This also relaxed the default steady state (sensitivity)**
**tolerances by a factor of 100.**
* Added support for `pathlib.Path` by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1769
* Allow specifying initial timepoint with `ExpData` by dilpath in
https://github.com/AMICI-dev/AMICI/pull/1776

Performance:
* Speedup for models with conservation laws by FFroehlich in
https://github.com/AMICI-dev/AMICI/pull/1765
* Improved efficiency of newton step convergence check by FFroehlich in
https://github.com/AMICI-dev/AMICI/pull/1775

Fixes:
* Fixed deprecation warning for pandas.DataFrame.append in
`rdatas_to_measurement_df` by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1770
* Fixed Rule-target handling in PEtab import by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1753

Removed functionality:
* Removed long deprecated `sbml2amici` arguments `modelName`
and `constantParameters` by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1774

**Full Changelog**:
https://github.com/AMICI-dev/AMICI/compare/v0.11.27...v0.11.28

New features:
* Checking condition number when computing sensitivities via Newton
by FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1730
* Removed SPBCG solver by FFroehlich in
https://github.com/AMICI-dev/AMICI/pull/1729
* Added Newton step convergence checks to steadystate solver by FFroehlich in
https://github.com/AMICI-dev/AMICI/pull/1737
* Removed legacy options/members `amioption.newton_preeq` and `Solver::r… by
dweindl in https://github.com/AMICI-dev/AMICI/pull/1744
* Added `ReturnData::cpu_time_total` to track total time spent in
`runAmiciSimulation` by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1743
* SBML import: Alternative algorithm for identifying conservation laws by
dweindl in https://github.com/AMICI-dev/AMICI/pull/1748
* Use `amici.AmiciVersionError` to indicate version mismatch by dweindl in https://github.com/AMICI-dev/AMICI/pull/1764

Performance:
* Optional parallel computation of derivatives during model import by dweindl
in https://github.com/AMICI-dev/AMICI/pull/1740
* Sparsify jacobian by FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1766
* Speedup conservation law computation by FFroehlich in
https://github.com/AMICI-dev/AMICI/pull/1754
* Exploit stoichiometric matrix in pysb import by FFroehlich in
https://github.com/AMICI-dev/AMICI/pull/1761
* Speedup edata construction from petab problems by FFroehlich in
https://github.com/AMICI-dev/AMICI/pull/1746

Fixes:
* Fixed `get_model_settings` that would to setting incorrect initial states and
initial state sensitivities for models with parameter-dependent initial
states by dweindl in https://github.com/AMICI-dev/AMICI/pull/1751
* Use correct tolerances for convergence check in Newton solver by FFroehlich
in https://github.com/AMICI-dev/AMICI/pull/1728
* Harmonized convergence checks by FFroehlich in
https://github.com/AMICI-dev/AMICI/pull/1731
* Made sundials' KLU_INDEXTYPE match actual klu index type by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1733
* Fixed `Model::setStateIsNonNegative` logic that would raise exceptions in
cases where it shouldn't by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1736
* Fixed undefined reference to dladdr by kristianmeyerr in
https://github.com/AMICI-dev/AMICI/pull/1738
* Fixed HDF5 OSX intermediate group creation errors by dweindl in
https://github.com/AMICI-dev/AMICI/pull/1741
* Fixed recent cmake-based build issues due to changed sundials library
directory by dweindl in https://github.com/AMICI-dev/AMICI/pull/1756
* Updated Windows installation instructions by paulflang in
https://github.com/AMICI-dev/AMICI/pull/1763

... and other contributions by FFroehlich, dweindl

**Full Changelog**:
https://github.com/AMICI-dev/AMICI/compare/v0.11.26...v0.11.27