libpetab-python v0.6.0

Fixes

• Implement proper truncation for prior distributions (parameter bounds now truncate the prior distribution instead of putting
  extra probability mass on the bounds)
  (by @dweindl in #335)
• Fixed get_required_parameters_for_parameter_table
  (by @dweindl in #340)
• Fixed Prior.from_par_dict for missing priorParameters columns
  (by @dweindl in #341)
• Fixed petablint v2 warning
  (by @dweindl in #342)
• Fixed linter failing on missing noiseFormula
  (by @dweindl in #367)
• Fixed v2 import Deprecation warning
  (by @dweindl in #346)
• petab.calculate: compare all common columns
  (by @dweindl in #347)
• Fixed version checks
  (by @dweindl in #350)
• Create output directories in write_*_df
  (by @dweindl in #352)
• Handle observableTransformation in petab.v1.simulate.sample_noise
  (by @dweindl in #383)
• Fixed residual calculation in v1.calculate
  (by @dweindl in #395)
• Allow empty string "" in columns to be overridden with default values in priors
  (by @PaulJonasJost in #384)
• Fixed goodness_of_fit plot and add color parameter
  (by @plakrisenko in #402
  & #437,
  by @dweindl in #440)
• Plot without vis spec without ids_per_plot
  (by @PaulJonasJost in #386)

Deprecations

• Using any PEtab-v2-related functionality currently in petab.v1 is deprecated and will be removed in a subsequent release.
  Use petab.v2 instead.

  This affects, for example, PEtab-v2-specific constants petab.v1.C (use petab.v2.C instead), petab.v1.mapping, or anything mapping-table-related in petab.v1.Problem.

Features

• Substantially extended and updated petab.v2 for working with PEtab v2 problems.

  PEtab v2 is still in draft stage -- feedback is welcome!

  • PEtab v2 support for petablint
  • The library uses pydantic-based objects for most PEtab entities instead of plain DataFrames
  • Functionality for converting PEtab v1 problems to (the current state of) PEtab v2

  At least until PEtab v2 is finalized, the petab.v2 API may change rapidly, and should not be considered stable.

• SbmlModel enhancements
  (by @fbergmann in #333)

• Added SbmlModel.from_antimony (by @dweindl in #331)

• Added SbmlModel.{to_antimony,to_sbml_str} (by @dweindl in #371)

• Enable passing the base path to Problem.from_yaml (by @dweindl in #327)

• Functions for adding conditions/observables/parameter to Problem (by @dweindl in #328)

• Added evaluate: bool argument to math parser (by @dweindl in #365)

• Added petab-compatible sympy string-printer (PetabStrPrinter/petab_math_str) (by @dweindl in #364)

• Prettified linter output (by @dweindl in #401)

• Store problem configuration in Problem (by @dweindl in #326)

• Store path info in *Table objects (by @dweindl in #416)

Full Changelog: v0.5.0...v0.6.0