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AMICI v0.11.19
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@dweindl dweindl released this 13 Oct 16:13
· 855 commits to master since this release
v0.11.19
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Learn about vigilant mode.

New:

  • Added support for observable transformations (lin/log/log10) (#1567). Thereby supporting additional noise distributions in combination with least squares solvers.

Fixes:

  • Fixed a bug when Newton sensitivity computation was activated despite specifying newton_steps == 0. The error occurs when simulation converges to a steadystate but simulation sensitivities are not converged according to convergence criteria. In that case simulation returned failure, but the newton rootfinding "finds" a steadystate even before the iteration check, leading to the erroneous computation of sensitivities via Newton/IFT. For singular jacobians this means the overall simulation still fails, but a different, more informative error message is displayed. (#1541)
  • Fixed a bug where argument outdir in ODEExporter.__init__ would not be used (#1543)

Other:

  • Improve checking support for SBML extensions (#1546)
  • SBML import: Use more descriptive IDs for flux expressions (#1551)
  • Optimized SUNMatrixWrapper functions (#1538)
  • C++: Changed test suite from CppUTest to gtest (#1532)
  • Add CITATION.cff (#1559)
  • Updated documentation (#1563, #1554, #1536)
  • Removed distutils dependency (#1557)
  • Require sympy<1.9
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