PEtab-dev/libpetab-python: 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 https://github.com/PEtab-dev/libpetab-python/pull/335)
• Fixed get_required_parameters_for_parameter_table (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/340)
• Fixed Prior.from_par_dict for missing priorParameters columns (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/341)
• Fixed petablint v2 warning (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/342)
• Fixed linter failing on missing noiseFormula (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/367)
• Fixed v2 import Deprecation warning (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/346)
• petab.calculate: compare all common columns (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/347)
• Fixed version checks (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/350)
• Create output directories in write_*_df (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/352)
• Handle observableTransformation in petab.v1.simulate.sample_noise (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/383)
• Fixed residual calculation in v1.calculate (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/395)
• Allow empty string "" in columns to be overridden with default values in priors (by @PaulJonasJost in https://github.com/PEtab-dev/libpetab-python/pull/384)
• Fixed goodness_of_fit plot and add color parameter (by @plakrisenko in https://github.com/PEtab-dev/libpetab-python/pull/402 & https://github.com/PEtab-dev/libpetab-python/pull/437, by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/440)
• Plot without vis spec without ids_per_plot (by @PaulJonasJost in https://github.com/PEtab-dev/libpetab-python/pull/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 https://github.com/PEtab-dev/libpetab-python/pull/333)

• Added SbmlModel.from_antimony (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/331)

• Added SbmlModel.{to_antimony,to_sbml_str} (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/371)

• Enable passing the base path to Problem.from_yaml (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/327)

• Functions for adding conditions/observables/parameter to Problem (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/328)

• Added evaluate: bool argument to math parser (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/365)

• Added petab-compatible sympy string-printer (PetabStrPrinter/petab_math_str) (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/364)

• Prettified linter output (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/401)

• Store problem configuration in Problem (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/326)

• Store path info in *Table objects (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/416)

Full Changelog: https://github.com/PEtab-dev/libpetab-python/compare/v0.5.0...v0.6.0