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

libpetab-python v0.1.27

Features:

• Added method to check if measurement time is at steady-state by @dilpath in #124
• Create dummy simulation conditions dataframe for empty measurements by @dilpath in #127
• Validator: Report empty noiseFormula by @dweindl in #134
• Speedup visspec assembly / fix deprecation warning by @dweindl in #135
• Handle incomplete PEtab problems in petab.Problem.from_yaml by @dweindl in #138
• Argument forwarding for Problem.get_optimization_to_simulation_parameter_mapping by @dweindl in #159
• Added candidate schema for version 2 by @dweindl in #142
• get_parameter_df: Allow any collection of parameter tables by @dweindl in #153, @m-philipps in #156, @dilpath in #157
• Updated visualization example notebooks by @dweindl in #137, by @plakrisenko in #146, by @plakrisenko in #147
• Added support for PEtab problems with multiple condition files by @dweindl in #152
• Added abstraction for (SBML) models by @dweindl in #133

Fixes:

• Apply get table method before write table method to ensure correct index by @dilpath in #126
• petablint: Fix incorrect noise-parameter-mismatch error message by @dweindl in #129
• Fixed handling of NaN values for parameters in condition table by @dweindl in #150
• More informative petab.calculate errors by @dweindl in #151

Removals:

• Removed ancient/deprecated default file naming scheme by @dweindl in #132
• Removed ancient deprecated functions related to specifying observables/noise models inside SBML
  by @dweindl in #140 #131
• Removed deprecated visualization functions by @dweindl in #130

New Contributors

• @m-philipps made their first contribution in #156

Full Changelog: v0.1.26...v0.1.27

libpetab-python v0.1.27.dev1

Features:

• Added method to check if measurement time is at steady-state by @dilpath in #124
• Create dummy simulation conditions dataframe for empty measurements by @dilpath in #127
• Validator: Report empty noiseFormula by @dweindl in #134
• Speedup visspec assembly / fix deprecation warning by @dweindl in #135
• Handle incomplete PEtab problems in petab.Problem.from_yaml by @dweindl in #138
• Argument forwarding for Problem.get_optimization_to_simulation_parameter_mapping by @dweindl in #159
• Added candidate schema for version 2 by @dweindl in #142
• get_parameter_df: Allow any collection of parameter tables by @dweindl in #153, @m-philipps in #156, @dilpath in #157
• Updated visualization example notebooks by @dweindl in #137, by @plakrisenko in #146, by @plakrisenko in #147
• Added support for PEtab problems with multiple condition files by @dweindl in #152
• Added abstraction for (SBML) models by @dweindl in #133

Fixes:

• Apply get table method before write table method to ensure correct index by @dilpath in #126
• petablint: Fix incorrect noise-parameter-mismatch error message by @dweindl in #129
• Fixed handling of NaN values for parameters in condition table by @dweindl in #150
• More informative petab.calculate errors by @dweindl in #151

Removals:

• Removed ancient/deprecated default file naming scheme by @dweindl in #132
• Removed ancient deprecated functions related to specifying observables/noise models inside SBML
  by @dweindl in #140 #131
• Removed deprecated visualization functions by @dweindl in #130

New Contributors

• @m-philipps made their first contribution in #156

Full Changelog: v0.1.26...v0.1.27

libpetab-python v0.1.26

What's Changed

• Fix SBML Rule handling logic by @dweindl in #120