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

libpetab-python v0.2.5

• Fix accessing preequilibrationConditionId without checking for presence
  by @dweindl in #228
• Startpoint sampling for a subset of parameters
  by @dweindl in #230
• Treat observableParameter overrides as placeholders in noise formulae
  by @dilpath in #231

Full Changelog: v0.2.4...v0.2.5

libpetab-python v0.2.4

• Made figure sizes for visualization functions customizable via petab.visualize.plotting.DEFAULT_FIGSIZE
  by @dweindl in #222
• Fixed Handling missing nominalValue in Problem.get_x_nominal
  by @dweindl in #223
• Fixed pandas 2.1.0 FutureWarnings
  by @dweindl in #226
• Added pre-commit-config, ran black, isort, ...
  by @dweindl in #225

Full Changelog: v0.2.3...v0.2.4

libpetab-python v0.2.3

• Fixed validation failures in case of missing optional fields in visualization tables
  by @dweindl in #214
• Make validate_visualization_df work without matplotlib installation
  by @dweindl @dilpath in #215

Full Changelog: v0.2.2...v0.2.3