Amici

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

**Fixes**

* Fixed CMake `cmake_minimum_required` deprecation warning
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2183
* Fixed misleading preequilibration failure messages
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2181
* Removed setuptools<64 restriction
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2180
* Fixed ExpData equality operator for Python
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2194
* Enabled deepcopy for ExpData(View)
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2196
* Allowed subsetting simulation conditions in simulate_petab
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2199
* Set CMake CMP0144 to prevent warning
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2209

**Features**

* Possibility to evaluate and plot symbolic expressions based on simulation results
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2152
* Easier access to timepoints via ExpDataView
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2193
* Nicer `__repr__` for ReturnDataView
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2192

**Documentation**

* Added installation instructions for Arch Linux
by stephanmg in https://github.com/AMICI-dev/AMICI/pull/2173
* Updated reference list
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2172
* Installation guide: optional requirements
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2207

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.19.0...v0.20.0

**Features**
* SBML import now supports `rateOf`
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2120
* Added `Model.{get,set}SteadyStateComputationMode` (analogous to `SteadyStateSensitivityMode`)
which allows to choose how steady state is computed.
by plakrisenko in https://github.com/AMICI-dev/AMICI/pull/2074

**Note: The default `SteadyStateSensitivityMode` changed from `newtonOnly` to `integrateIfNewtonFails`.**

* SBML import: Allow hardcoding of numerical values
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2134
* Added `antimony2amici` for more convenient antimony import
(simplifies working with raw ODEs, see documentation)
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2142
* Added `AMICI_TRY_ENABLE_HDF5` environment variable to control whether to search for HDF5 or not
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2148

**Fixes**

* Fixed SBML import for events with trigger functions depending on parameters that are initial
assignment targets
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2145
* Fixed SBML import for event-assigned parameters with non-float initial assignments
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2156
* Fixed `unistd.h` dependency of `hdf5.cpp` that led to compilation
failures on Windows
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2154
* Set CMake policies for cmake 3.27 by dweindl in https://github.com/AMICI-dev/AMICI/pull/2162
* Fixed a `lib/` vs `lib64/` issue, leading to `SUNDIALSConfig.cmake`-not-found issues
on some systems
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2165
* CMake: fixed scope of `-DHAS_BOOST_CHRONO` which may have lead to a mix of
`boost::chrono::thread_clock` and `std::clock` being used in programs using amici,
and potentially segmentation faults
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2163

Performance:
* Combined code for sparse model functions and their index files for slightly faster
compilation of small models
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2159

* Removed complex / complex long KLU functions for slightly faster amici package installation
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2160

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.18.1...v0.19.0

Fixes:
* Fixed pysb pattern matching during PEtab import
by FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2118
* Fixed `sp.Matrix` errors with `numpy==1.25`
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2124
* Readme: added info containers
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2125
* Fixed deprecation warnings
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2122
https://github.com/AMICI-dev/AMICI/pull/2131
* Fixed logging typo in SBML import
by dilpath in https://github.com/AMICI-dev/AMICI/pull/2126
* Added minimum version for `pandas`
by dilpath in https://github.com/AMICI-dev/AMICI/pull/2129

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.18.0...v0.18.1

Features:
* More efficient handling of splines in SBML models
by paulstapor, lcontento, dweindl
in https://github.com/AMICI-dev/AMICI/pull/1515
* Partial support of current PEtab2.0 draft, including support for PySB models
by dweindl, FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1800

Fixes:
* **Fixed incorrect forward sensitivities for models with events with**
**state-dependent trigger functions**
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2084
* Model import: Don't create spl.h and sspl.h for models without splines
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2088
* SBML import - faster processing of SpeciesReference IDs
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2094
* Update swig ignores
by FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2098
* CMake: Fixed choosing SWIG via `SWIG` env variable
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2100
* CMake: Try FindBLAS if no other information was provided
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2104
* Fixed cblas error for models without solver states in combination with
forward sensitivities
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2108
* Fixed compilation error for models with events and xdot=0
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2111
* Fixed import error for models with events and 0 states
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2112

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.17.1...v0.18.0