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libpetab-python v0.9.0

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@dweindl dweindl released this 07 Sep 13:26

This release will require Python>=3.12 and numpy>=2.1.

Fixes

  • Fixed the mean of residuals and added an option to choose between
    normalized and unnormalized errors in plot_goodness_of_fit
    (by @plakrisenko in #473)
  • Made scipy a lazy import, so it is no longer required unless
    probability distributions are actually used
    (by @dweindl in #486)
  • Fixed PetabStrPrinter for non-integer rational exponents
    (by @wshlavacek in #489)
  • Fixed spurious nan-related warnings in Subplot.from_df
    (by @dweindl in #496)
  • Fixed a missing return in the noise distribution merge of
    petab1to2, which caused noiseDistribution to always be NaN after
    conversion
    (by @dweindl in #502)
  • Fixed the PEtab v2 extension config model
    (by @dweindl in #506)
  • Fixed SBML math parsing by using sbmlmath instead of
    sympy.sympify
    (by @dweindl in #509)

Features

  • Added support for PEtab SciML problems, including a dedicated linter
    (by @BSnelling, @m-philipps and @dilpath in #482,
    #505, #499, #498, #511, #513, and #516)
  • Added support for BNGL models (by @wshlavacek in #508)
  • Added linting of the mapping table, and allowed pure annotation-only
    mapping entries (by @m-philipps and @BSnelling in #480 and #500)
  • Minor improvements to the v1-to-v2 converter: warn when dropping
    parameterScale/initializationPriorType/initializationPriorParameters,
    and use the experiments table column order suggested by the PEtab format
    (by @m-philipps in #479)