AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models

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 by @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 reprs 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