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AMICI v0.10.14
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@dweindl dweindl released this 02 Dec 23:35
· 1316 commits to master since this release
v0.10.14
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Learn about vigilant mode.

NOTE: For Python-imported SBML-models this release may compute incorrect sensitivities w.r.t. sigma. Bug introduced in 0.10.14, fixed in 0.10.15.

Python:

  • Don't require use of ModelPtr.get to call ExpData(Model)
  • Fix import in generated model Python package
  • Setup AMICI standalone scripts as setuptools entrypoints
  • Simplify symbolic sensitivity expressions during Python SBML import
    Fixes Infs in the Jacobian when using Hill-functions with states of 0.0.
  • Extended Newton solver #848
    The changes that allow performing Newton tests from the paper:
    G. T. Lines, Ł. Paszkowski, L. Schmiester, D. Weindl, P. Stapor, and J. Hasenauer. Efficient computation of steady states in large-scale ODE models of biochemical reaction networks. accepted for Proceedings of the 8th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE), Valencia, Spain, October 2019.
  • Use SWIG>=4.0 on travis to include PyDoc in sdist / pypi package (#841)
  • Fix choice of likelihood formula; failed if observable names were not equal to observable IDs
  • Fix(sbml-import) Compartment IDs in right-hand side of Rules are not replaced and lead to undefined identifiers in c++ files
  • Fix invalid logging level
  • Speed up sympy simplification (#871)

C++:

  • Performance: Avoid unnecessary repeated function calls for SUNMatrixWrapper dimensions
  • Add AmiciApplication class as context for handling so far global settings.
    This allows for example setting custom logging functions for concurrent AMICI
    runs, e.g. in multi-thread applications (Closes #576).

Misc:

  • Setup performance test on github actions (#853)
  • Update documentation and FAQ for CBLAS requirement and others
  • Update reference list
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