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pyPESTO v0.5.5

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@PaulJonasJost PaulJonasJost released this 13 Jan 14:46
b628397
  • Breaking Changes
    • PETab select: There are some deprecated features that will show up as warnings. In addition:

      • The plotting methods ignore some arguments. You will need to reimplement these with the newer approach, which uses
        plotting methods from the PEtab Select library instead. See the model selection notebook for examples.

      • All objects containing multiple models (e.g., dictionaries or lists) are now replaced by petab_select.Models,
        which supports dictionary and list methods.

        To convert your old list of models:

        petab_select.Models(list_of_Model)
  • General
  • Hierarchical
    • Fix no error if inner observable parameter in noise formula & viceversa (#1504)
    • Remove inner datas from relative calculator (#1505)
    • Fix not scaling inner pars when applying to rdatas (#1534)
  • Optimization
    • ESSOptimizer: Fix priority for local search startpoints (#1503)
    • Fix NLoptOptimizer.repr (#1518)
    • Improve exception-handling in SacessOptimizer (#1517)
    • Fix ESSOptimizer min of empty sequence (#1510)
    • Don't modify sys.path for amici model imports (#1522)
    • Set OptimizerResult.optimizer in Optimizer.minimize (#1525)
    • SacessOptimizer: More efficient saving of intermediate results (#1529)
  • Objective
    • AmiciObjective/PEtab import: Fix plist (#1493)
    • PEtab: Fix warning from fill_in_parameters with fixed parameters (#1509)
    • Amici: Fix handling of PEtab fixed parameters (#1514)
    • Fix get_parameter_prior_dict docstring (#1537)
  • Select
    • Support user-provided calibration results (#1338)
    • Problem-specific minimize method for SaCeSS (#1339)
    • Update for the latest PEtab Select version; see example notebook or the PEtab Select repo (#1530)
  • Storage
    • Enable writing Optimize(r)Result directly in Writer (#1528)
    • Update parameter scale storage (#1542
  • Visualize
    • Fix flatten of observable mapping with one observable (#1515)