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AMICI v0.16.1

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@dweindl dweindl released this 24 Feb 12:34
· 478 commits to master since this release
1a99308

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:

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