Amici

This release fixes two bugs:

* One bug introduced in v0.17.0, that causes an `ImportError`
on macOS (https://github.com/AMICI-dev/AMICI/issues/2075).
* An AttributeError in petab_import_pysb with petab>=0.2.0
https://github.com/AMICI-dev/AMICI/pull/2079

Features
* DAE support in SBML
by FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2017
* SBML import: flatten SBML-comp models
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2063
* Added sllh computation back to `petab_objective.simulate_petab`
by dilpath in https://github.com/AMICI-dev/AMICI/pull/1548
* CMake-based Python extension builds
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1992

Fixes
* Fixed CPU time tracking with multi-threading (partially)
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2023
* Fixed HDF5 ambiguous overload
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2031
* Fixed varying cmake libdir lib(64)/
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2033
* Fixed Equilibration cpu time computation
by plakrisenko in https://github.com/AMICI-dev/AMICI/pull/2035
* CMake: add header files to library sources for generated models
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2047
* CMake: Handle header-dependency of swig files
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2046
* Don't try to detect conservation laws for models with Species-AssignmentRules
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2056
* Smith benchmark and SBML initialization fix
by FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2034
* SBML import: Fixed check for required packages
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2064
* Nan observables
by FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2065
* Fixed check for discontinuities for conservation law computation
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2068
* Specify visualization dependencies
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2070
* Fixed sympy symbol name clashes during PEtab import
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2069
* Fixed ReturnData::{preeq_wrms,posteq_wrms} with FSA and check_sensi_steadystate_conv_=True
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2071

Extended / updated documentation, for example:
* Jax example notebook
by FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1996
* Updated Windows/MSVC installation instructions
by Podde1 in https://github.com/AMICI-dev/AMICI/pull/2053

New Contributors
* Podde1 made their first contribution in https://github.com/AMICI-dev/AMICI/pull/2053

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.16.1...v0.17.0

Fixes:
* Additional package names for finding blas via pkg-config
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1959
* Changed default interpolation type from hermite to polynomial
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1960
* PySB import: Change default simplify to work with multiprocessing
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1961
* Add --no-validate to amici_import_petab
dweindl in https://github.com/AMICI-dev/AMICI/pull/1963
* Fix get_model for direct import of swig interface
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1969
* Fix PytestReturnNotNoneWarning in test_conserved_quantities_demartino.py
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1968
* Fix MSVC builds / remove -W* flags
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1972
* Add option to use IDs when plotting trajectories
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1974
* Fix assignmentRules2observables - skip non-assignment-rule targets
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1973
* Use std::clock for measuring solver time
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1982
(*Note that this uses cpu-time consumed by all threads*)
* Fix narrowing-conversion-warning
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1983
* PEtab import: allow specifying default values for output parameters
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1987
* Print stacktraces only with debug logging level
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1985
* Change default ReturnData::status to AMICI_NOT_RUN
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1984
* Reduce time-tracking overhead
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1988
* Fix equilibraton status discrepancy
by plakrisenko in https://github.com/AMICI-dev/AMICI/pull/1991
* Pass model_name to _create_model_output_dir_name
by FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1994
* CMake: Build with OpenMP support if available
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2000
* Fix SuiteSparse Makefiles for compiler-paths
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2003
* CMake: Build with HDF5 support if available
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1999
* CMake: Fix reading version file on Windows
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2001
* CMake: raise minimum required version to 3.15
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2002
* Fix/extend runtime logging
by FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2005
* Fix error logging in steadystate solver
by FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2008
* Don't pass `-py3` to swig after 4.1.0
by FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2010
* SWIG __repr__s for different templated vector classes
by FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2009
* Matlab: If mex fails, print mex arguments
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2013
* Simplify OpenBLAS installation on Windows
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2016
* Remove model name prefix in generated model files
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2015
* ...

Documentation:
* Restructure sphinx doc
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1978
* Instructions for AMICI with singularity
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1964
* Illustrate options for potentially speeding up model import/simulation
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1965
* ...

Dependencies:
* Updated SuiteSparse to v7.0.1
by dweindl in https://github.com/AMICI-dev/AMICI/pull/2018

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.16.0...v0.16.1

Features
* Python 3.11 compatibility
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1876
* AMICI now runs on binder (https://mybinder.org/v2/gh/AMICI-dev/AMICI/develop?labpath=binder%2Foverview.ipynb)
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1935,
https://github.com/AMICI-dev/AMICI/pull/1937,
https://github.com/AMICI-dev/AMICI/pull/1939
* More informative `Solver.__repr__` and `ExpData.__repr__`
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1928
and FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1948
* `simulate_petab` returns the generated/used `ExpData`s
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1933
* Model module is now accessible from model instance
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1932
* Added `plot_jacobian`
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1930
* Now logs all nested execution times as debug
by FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1947
* Always check for finite initial states, not only with
`Model.setAlwaysCheckFinite(True)`
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1955

Fixes
* `ReturnDataView.status` now returns `int` instead of `float`
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1929
* Updated simulation status codes
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1931
* Skip irrelevant frames in stacktraces
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1934
* Fixed compiler warning (matlab)
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1954

Documentation:
* Added a notebook demonstrating common simulation failures and show how to
analyze / fix them
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1946
* various minor fixes / updates

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.15.0...v0.16.0

Features
* Improved logging by dweindl in https://github.com/AMICI-dev/AMICI/pull/1907

For Python: Don't print messages to stdout, but collect them in ReturnData
and forward them to python logging, making it easier to filter specific
messages or to disable output completely. Messages are also available via
`ReturnData.messages`.

**breaking change for C++ interface**:
Messages aren't printed to stdout by default, but are collected in
`ReturnData`. The user has to decide what to do with them.

* MultiArch docker build by FFroehlich
in https://github.com/AMICI-dev/AMICI/pull/1903
* Added cmake target for cmake-format
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1909
* Updated clang-format style, fixed clang-format target
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1908
* Subsetting `ReturnData` fields by ID via `ReturnDataView.by_id`
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1911 https://github.com/AMICI-dev/AMICI/pull/1916

Fixes
* PEtab import: fixed handling of fixed parameters for rule targets
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1915
* Fixed compiler warnings for matlab interface
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1919
* Fixed pandas DeprecationWarning for Series.iteritems()
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1921
* Fixed circular import in amici.petab_import_pysb
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1922
* Fixed 'operator ==' swig warning
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1923
* Prevent swig4.0.1 segfault
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1924

**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.14.0...v0.15.0

Features:

* Added optional functionality to apply C99 math optimization to generated C++ code
by dweindl and lcontento in https://github.com/AMICI-dev/AMICI/pull/1377, https://github.com/AMICI-dev/AMICI/pull/1878

* Added option to treat fixed parameters as constants in PEtab import

by dweindl in https://github.com/AMICI-dev/AMICI/pull/1877

* Added equality operator for ExpData

by dweindl in https://github.com/AMICI-dev/AMICI/pull/1881

* Updated base image for Dockerfile to Ubuntu 22.04/Python 3.10

by dweindl in https://github.com/AMICI-dev/AMICI/pull/1896


Fixes:

* Fixed deprecation warnings
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1873, https://github.com/AMICI-dev/AMICI/pull/1893

* Fixes/updates to GitHub actions
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1885, https://github.com/AMICI-dev/AMICI/pull/1893, https://github.com/AMICI-dev/AMICI/pull/1889, https://github.com/AMICI-dev/AMICI/pull/1891

* Added hdf5 search directories for arm64 architecture (M1/M2 macs)

by Doresic in https://github.com/AMICI-dev/AMICI/pull/1894

* Fixed missing return in generated non-void functions

by dweindl in https://github.com/AMICI-dev/AMICI/pull/1892

* Fixed import failure for pre-compiled models

by dweindl in https://github.com/AMICI-dev/AMICI/pull/1897

Documentation:

* Update reference list
by dweindl in https://github.com/AMICI-dev/AMICI/pull/1874, https://github.com/AMICI-dev/AMICI/pull/1884

**Full Changelog**:
https://github.com/AMICI-dev/AMICI/compare/v0.13.0...v0.14.0