libpetab-python v0.7.0

Fixes

• Misc minor petab.v2
  (by @dweindl in #445
  and #450)
• Fixed serialization of priorParameters
  (by @dweindl in #449)

Features

• Added PySBModel.to_str
  (by @dweindl in #451)
• Added id field to v2.ProblemConfig
  (by @dweindl in #442)
• Updated ExperimentsToEventsConverter to changed initialization semantics
  (by @dweindl in #443)
• Added v2.Problem.{get_output_parameters,get_x_nominal_dict}
  (by @dweindl in #447)
• Extended PEtab v2 mapping table validation
  (by @dweindl in #452)

Full Changelog: v0.6.0...v0.7.0

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

libpetab-python v0.5.0

Fixes

• Circumvent SettingWithCopyWarning

  by @m-philipps in #306

• If flatten_timepoint_specific_output_overrides makes the visualization table invalid, remove it from Problem

  by @m-philipps in #316

Features

• Added petab.v2.models by @dweindl in #302

• Added petab.v1.priors.priors_to_measurements(...) for replacing objectivePrior* by observables/measurements

  by @dweindl in #309, #315, #317

• Made model id optional for PySBModel

  by @dweindl in #318

• Implemented Model.__repr__

  by @dweindl in #319

Full Changelog: v0.4.1...v0.5.0

libpetab-python v0.4.1

This series contains many changes related to the new petab.v2 subpackage. petab.v2 should not be considered stable; the petab.v2 API may change rapidly until we release libpetab-python v1.0.0.

• Fix: keep previously-optional dependencies optional by @dweindl in #298
• Add petab.v2.C by @dweindl in #299

Full Changelog: v0.4.0...v0.4.1

libpetab-python v0.4.0

Prepare for PEtab v2

To enable ongoing support for PEtab v1, while "forking" the v1 code for PEtab v2, the old code base is now available at petab.v1, and the new code base will be at petab.v2. For now, old import petab.* statements still work, but are marked as deprecated, and import petab.v1.* should be used instead. petablint will be designed for use with only full PEtab problems in future too, rather than individual tables -- partial problems will be supported to validate individual tables.

• Add PEtab math parser and sympy converter by @dweindl in #260
• Deprecate petablint with individual tables by @dweindl in #274
• Introduce petab.v1 package by @dweindl in #282
• Separate v1 and v2 tests by @dweindl in #284
• Add petab.v2.Problem by @dweindl in #285
• PEtab v1 to v2 converter by @dweindl in #281
• Fix imports related to v1 subpackage by @dweindl in #293

Validation

Validation will become increasingly atomic and OOP, to support extension-specific validation in PEtab v2.

• Validator: check for positive bounds for log-scaled parameter by @dweindl in #278
• Validator: check prior parameters by @dweindl in #279
• Fix validation for remote files by @dweindl in #287
• New validation API by @dweindl in #288

Documentation

• Fixed formatting / missing type annotations by @dweindl in #292
• Added versioning and deprecation policy by @dweindl in #277

Other changes

• Simplify yaml schema by @dweindl in #264
• Handle numpy types in sympify_petab by @dweindl in #294
• New get_path_prefix method to get the base path for relative paths in PEtab problem YAML by @dweindl in #280

New Contributors

• @dependabot made their first contribution in #267

Full Changelog: v0.3.0...v0.4.0

libpetab-python v0.3.0

This release requires python>=3.10

Features

• Visualization: Make line plot lines configurable via
  petab.visualize.plotter.measurement_line_kwargs and petab.visualize.plotter.simulation_line_kwargs`
  by @dweindl in #254
• Validator: check that datasetIds referenced in visualization tables exists
  in measurement tables
  by @dweindl in #255

Fixes

• Drop an index if it's reset
  by @dilpath in #262

New Contributors

• @PaulJonasJost made their first contribution in #250

Full Changelog: v0.2.9...v0.3.0

libpetab-python v0.2.9

• Fixed a bug in SbmlModel.get_free_parameter_ids_with_values that led to
  potentially wrong initial values in the parameter mapping for parameters that
  are targets of initialAssignments (the value from their value was taken
  instead of the initial assignment)
  by @dweindl in #248

libpetab-python v0.2.8

• Fixed pandas FutureWarning in petab/visualize/lint.py
  by @dweindl in #242
• Added petab.Problem.n_{estimated,measurements,priors}
  by @dweindl in #243
• Require pyarrow
  by @dweindl in #244

Full Changelog: v0.2.7...v0.2.8

libpetab-python v0.2.7

• Fixed a bug in flatten_timepoint_specific_output_overrides, which
  did not handle numeric values correctly

Full Changelog: v0.2.6...v0.2.7

libpetab-python v0.2.6

• Fixed flatten_timepoint_specific_output_overrides not supporting
  observableParameter overrides as placeholders in noise formulae
  by @dweindl in #235
• Visualization: fixed replicate sorting
  by @plakrisenko in #232
• Doc: Revised visualization examples
  by @dweindl in #236

Full Changelog: v0.2.5...v0.2.6