AMICI v0.16.1

Fixes:

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

Documentation:

• Restructure sphinx doc
  by @dweindl in #1978
• Instructions for AMICI with singularity
  by @dweindl in #1964
• Illustrate options for potentially speeding up model import/simulation
  by @dweindl in #1965
• ...

Dependencies:

• Updated SuiteSparse to v7.0.1
  by @dweindl in #2018

Full Changelog: v0.16.0...v0.16.1

AMICI v0.16.0

Features

• Python 3.11 compatibility by @dweindl in #1876
• AMICI now runs on binder (example) by @dweindl in #1935, #1937, #1939
• More informative Solver.__repr__ and ExpData.__repr__ by @dweindl in #1928 and @FFroehlich in #1948
• simulate_petab returns the generated/used ExpDatas by @dweindl in #1933
• Model module is now accessible from model instance by @dweindl in #1932
• Added plot_jacobian by @dweindl in #1930
• Now logs all nested execution times as debug by @FFroehlich in #1947
• Always check for finite initial states, not only with Model.setAlwaysCheckFinite(True)
  by @dweindl in #1955

Fixes

• ReturnDataView.status now returns int instead of float by @dweindl in #1929
• Updated simulation status codes by @dweindl in #1931
• Skip irrelevant frames in stacktraces by @dweindl in #1934
• Fixed compiler warning (matlab) by @dweindl in #1954

Documentation:

• Added a notebook demonstrating common simulation failures and show how to analyze / fix them by @dweindl in #1946
• various minor fixes / updates

Full Changelog: v0.15.0...v0.16.0

AMICI v0.15.0

Features

• Improved logging by @dweindl in #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 #1903

• Added cmake target for cmake-format by @dweindl in #1909

• Updated clang-format style, fixed clang-format target by @dweindl in #1908

• Subsetting ReturnData fields by ID via ReturnDataView.by_id by @dweindl in #1911 #1916

Fixes

• PEtab import: fixed handling of fixed parameters for rule targets by @dweindl in #1915
• Fixed compiler warnings for matlab interface by @dweindl in #1919
• Fixed pandas DeprecationWarning for Series.iteritems() by @dweindl in #1921
• Fixed circular import in amici.petab_import_pysb by @dweindl in #1922
• Fixed 'operator ==' swig warning by @dweindl in #1923
• Prevent swig4.0.1 segfault by @dweindl in #1924

Full Changelog: v0.14.0...v0.15.0

AMICI v0.14.0

Features:

• Added optional functionality to apply C99 math optimization to generated C++ code
  by @dweindl and @lcontento in #1377, #1878

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

  by @dweindl in #1877

• Added equality operator for ExpData

  by @dweindl in #1881

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

  by @dweindl in #1896

Fixes:

• Fixed deprecation warnings
  by @dweindl in #1873, #1893

• Fixes/updates to GitHub actions
  by @dweindl in #1885, #1893, #1889, #1891

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

  by @Doresic in #1894

• Fixed missing return in generated non-void functions

  by @dweindl in #1892

• Fixed import failure for pre-compiled models

  by @dweindl in #1897

Documentation:

• Update reference list
  by @dweindl in #1874, #1884

Full Changelog:
v0.13.0...v0.14.0

AMICI v0.13.0

• Fixed extraction of common subexpressions by @dweindl in #1865
• Added function to convert ReturnData::status flags to string by @dweindl in #1864

And further contributions by @dweindl, @FFroehlich

Full Changelog: v0.12.0...v0.13.0

AMICI v0.12.0

Features:

• Support for event observables via the Python interface by @FFroehlich in #1845
• Treat non-estimated parameters as constants during SBML-PEtab import by @dweindl in #1810
• Updated SUNDIALS to v5.8.0 by @dweindl in #1836
• Option to extract common subexpressions by @dweindl in #1852, #1856
• Parallelize matrix simplification by @dweindl in #1778
• Validate PEtab problems before attempting import by @dweindl in #1842
• Improved type annotations for the swig interface by @dweindl in #1860

Fixes:

• Fixed an issue with potentially infinite loops during conservation law processing by @FFroehlich in #1833
• Fixed potential deadlocks during parallel simplification by @dweindl in #1844
• Fix resetting ReturnData::numstepsB when re-using Solver by @dweindl in #1841

And further contributions by @dilpath, @dweindl, @FFroehlich

Full Changelog: v0.11.32...v0.12.0

AMICI v0.11.32

Fixes:

• Fixed ImportErrors during package installation with recent setuptools by @dweindl in #1830

AMICI v0.11.31

Fixes:

• Fixed ParameterMapping.__getitem__ to either return a ParameterMappingForCondition or a new ParameterMapping, but not a list by @dweindl in #1826

Full Changelog: v0.11.30...v0.11.31

AMICI v0.11.30

Features:

• Allow overriding model name during PySB import by @dweindl in #1801
• Added repr for parameter mapping classes by @dweindl in #1799
• More informative warning messages for NaNs/Infs by @dweindl in #1798
• Moved sim_steps increment by @plakrisenko in #1806
• Re-arranged application of parameters from ExpData to avoid initial sensitivities error by @dilpath in #1805
• Checking for unused parameters in simulate_petab by @dweindl in #1816
• Add create_parameter_mapping kwarg forwarding by @dweindl in #1820

Other

• Remove constant_species_to_parameters by @dweindl in #1809

Fixes

• Fixed handling of SBML models given as pathlib.Path in `petab_import.import_model_sbml by @dweindl in
  #1808
• Fixed missing CPU time reset by @dweindl in #1814
• Raise in simulate_petab with scaled_parameters=True problem_parameters=None by @dweindl in #1819

...

Full Changelog:
v0.11.29...v0.11.30

AMICI v0.11.29

Features:

• Performance: Limit newton step convergence check by @FFroehlich in #1780
• More informative NaN/Inf warnings by @dweindl in #1640
• SBML import can now handle initial events by @FFroehlich in #1789

Fixes:

• Avoid error if no measurements in PEtab problem; fixed type handling in PEtab parameter mapping by @dilpath in #1783
• Fixed substitution of expressions in root and stau by @dilpath in #1784
• Workaround for PEtab problems with state-dependent noise models by @dweindl in #1791