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

libpetab-python v0.2.2

Fixes:

• Fixed IndexError with numpy 1.25.0 by @dweindl in #209
• Made SbmlModel.from_file(..., model_id) optional by @dilpath in #207

Full Changelog: v0.2.1...v0.2.2

libpetab-python v0.2.1

Fixes two issues introduced in v0.2.0:

• Fix PySBModel.get_parameter_value by @dweindl in #203
• Fix Problem.to_files(model_file=...) by @dweindl in #204

Full Changelog: v0.2.0...v0.2.1

libpetab-python v0.2.0

Note: petab 0.2.0 requires Python>=3.9

Features:

• Plot measurements for t = 'inf' by @plakrisenko in #149
• Added validation for visualization files by @dweindl in #184 #189
• Startpoints as dict by @dweindl in #188
• Residuals plot by @plakrisenko in #187 #191
• add goodness of fit plot by @plakrisenko in #192
• Add PySBModel for handling of PySB models by @dweindl in #145

Fixes

• Vis: Don't fail on missing simulations by @dweindl in #185
• prevent strings being parsed as nan in get_visualization_df by @plakrisenko in #193
• Fix get_model_for_condition by @dweindl in #194
• Simulator: rename measurement column to simulation by @dilpath in #199
• Fix sympy symbol name clashes by @dweindl in #202

Full Changelog: v0.1.30...v0.2.0

libpetab-python v0.1.30

Various smaller fixes:

• Vis: Handle missing data more gracefully by @dweindl in #175
• Fix test dependencies: scipy by @dweindl in #177
• Add petab.Problem.str by @dweindl in #178
• Fix deprecated tight layout matplotlib by @yannikschaelte in #180
• Move tests to tox by @yannikschaelte in #182
• Update deprecated functions in tests by @yannikschaelte in #181
• Use petab identifier for combine archives by @fbergmann in #179

New Contributors

• @fbergmann made their first contribution in #179

Full Changelog: v0.1.29...v0.1.30

libpetab-python v0.1.29

Features:

• Method to unflatten simulation dataframe produced by flattened PEtab problem by @dilpath in #171
• Methods to simplify PEtab problems by @dweindl in #172

Fixes:

• Fix relative paths for model files by @dilpath in #173

Full Changelog: v0.1.28...v0.1.29

libpetab-python v0.1.28

• Fixed validation for output parameters columns in the condition table by @dweindl in #161
• Added Python support policy by @dweindl in #162
• Fixed typehints and deprecation warning by @dweindl in #165
• Fixed SBML validation by @dweindl in #168
• Fixed deprecation warning from get_model_for_condition by @dweindl in #169

Full Changelog: v0.1.27...v0.1.28