AMICI v0.21.0

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 #2205, #2211, #2252

Features

• Handle events occurring at fixed timepoints without root-finding.
  This avoids event-after-reinitialization errors in many cases brings a
  slight performance improvement.
  by @dweindl in #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 #2255
• code-gen: Simplified switch statements, leading to reduced file sizes and
  faster compilation for certain models.
  by @dweindl in #2240
• Made Model and ModelPtr deepcopyable
  by @dweindl in #2247
• Made Solver and SolverPtr deepcopyable
  by @dweindl in #2245
• Added a debugging helper get_model_for_preeq for debugging simulation
  issues during pre-equilibration.
  by @dweindl in #2250
• Added SwigPtrView fields to dir() outputs
  by @dweindl in #2244
• Use proper labels for in plotting functions if IDs are available in
  ReturnData.
  by @dweindl in #2249
• Added ExpData::clear_observations to set all measurements/sigmas to NaN
  by @dweindl in #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 #2243
• CMake: Fixed model debug builds
  by @dweindl in #2222
• Fixed CMake potentially using incorrect Python library for building model
  extension
  by @dweindl in #2220
• CMake: fixed cxx flag check
  by @dweindl in #2225
• Fixed potential out-of-bounds read in Model::checkFinite for
  matlab-imported models
  by @dweindl in #2232
• Fixed piecewise/Heaviside handling
  by @dweindl in #2234
• Deterministic order of event assignments
  by @dweindl in #2242
• Proper error message in case of unsupported state-dependent sigmas
  by @dweindl in #2239
• Fixed swig shadow warning + other linting issues
  by @dweindl in #2261
• Fixed SwigPtrView.__getattr__
  by @dweindl in #2259
• simulate_petab: Avoid warning when simulating with default parameters
  by @dweindl in #2265

Documentation

• Updated Python package installation instructions for Arch Linux
  by @willov in #2212
• Updated ExpData documentation
  by @dweindl in #2254
• Documented simulation starting time t0
  by @dweindl in #2263
• Updated PEtab example
  by @dweindl in #2255

...

Full Changelog: v0.20.0...v0.21.0

AMICI v0.20.0

Fixes

• Fixed CMake cmake_minimum_required deprecation warning
  by @dweindl in #2183
• Fixed misleading preequilibration failure messages
  by @dweindl in #2181
• Removed setuptools<64 restriction
  by @dweindl in #2180
• Fixed ExpData equality operator for Python
  by @dweindl in #2194
• Enabled deepcopy for ExpData(View)
  by @dweindl in #2196
• Allowed subsetting simulation conditions in simulate_petab
  by @dweindl in #2199
• Set CMake CMP0144 to prevent warning
  by @dweindl in #2209

Features

• Possibility to evaluate and plot symbolic expressions based on simulation results
  by @dweindl in #2152
• Easier access to timepoints via ExpDataView
  by @dweindl in #2193
• Nicer __repr__ for ReturnDataView
  by @dweindl in #2192

Documentation

• Added installation instructions for Arch Linux
  by @stephanmg in #2173
• Updated reference list
  by @dweindl in #2172
• Installation guide: optional requirements
  by @dweindl in #2207

Full Changelog: v0.19.0...v0.20.0

AMICI v0.19.0

Features

• SBML import now supports rateOf
  by @dweindl in #2120

• Added Model.{get,set}SteadyStateComputationMode (analogous to SteadyStateSensitivityMode)
  which allows to choose how steady state is computed.
  by @plakrisenko in #2074

  Note: The default SteadyStateSensitivityMode changed from newtonOnly to integrateIfNewtonFails.

• SBML import: Allow hardcoding of numerical values
  by @dweindl in #2134

• Added antimony2amici for more convenient antimony import
  (simplifies working with raw ODEs, see documentation)
  by @dweindl in #2142

• Added AMICI_TRY_ENABLE_HDF5 environment variable to control whether to search for HDF5 or not
  by @dweindl in #2148

Fixes

• Fixed SBML import for events with trigger functions depending on parameters that are initial
  assignment targets
  by @dweindl in #2145
• Fixed SBML import for event-assigned parameters with non-float initial assignments
  by @dweindl in #2156
• Fixed unistd.h dependency of hdf5.cpp that led to compilation
  failures on Windows
  by @dweindl in #2154
• Set CMake policies for cmake 3.27 by @dweindl in #2162
• Fixed a lib/ vs lib64/ issue, leading to SUNDIALSConfig.cmake-not-found issues
  on some systems
  by @dweindl in #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 #2163

Performance

• Combined code for sparse model functions and their index files for slightly faster
  compilation of small models
  by @dweindl in #2159

• Removed complex / complex long KLU functions for slightly faster amici package installation
  by @dweindl in #2160

Full Changelog: v0.18.1...v0.19.0

AMICI v0.18.1

Fixes:

• Fixed pysb pattern matching during PEtab import by @FFroehlich in #2118
• Fixed sp.Matrix errors with numpy==1.25 by @dweindl in #2124
• Readme: added info containers by @dweindl in #2125
• Fixed deprecation warnings by @dweindl in #2122 #2131
• Fixed logging typo in SBML import by @dilpath in #2126
• Added minimum version for pandas by @dilpath in #2129

Full Changelog: v0.18.0...v0.18.1

AMICI v0.18.0

Features

• More efficient handling of splines in SBML models
  by @paulstapor, @lcontento, @dweindl in #1515
• Partial support of current PEtab2.0 draft, including support for PySB models
  by @dweindl, @FFroehlich in #1800

Fixes

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

Full Changelog: v0.17.1...v0.18.0

AMICI v0.17.1

This release fixes two bugs:

• One bug introduced in v0.17.0, that causes an ImportError
  on macOS (#2075).
• An AttributeError in petab_import_pysb with petab>=0.2.0
  #2079

AMICI v0.17.0

AMICI v0.17.0 requires Python>=3.9 and a C++17 compatible compiler

Features

• DAE support in SBML
  by @FFroehlich in #2017
• SBML import: flatten SBML-comp models
  by @dweindl in #2063
• Added sllh computation back to petab_objective.simulate_petab
  by @dilpath in #1548
• CMake-based Python extension builds
  by @dweindl in #1992

Fixes

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

Extended / updated documentation, for example:

• Jax example notebook
  by @FFroehlich in #1996
• Updated Windows/MSVC installation instructions
  by @Podde1 in #2053

New Contributors

• @Podde1 made their first contribution in #2053

Full Changelog: v0.16.1...v0.17.0

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