PEtab-dev / libpetab-python

Python package for working with PEtab files

https://libpetab-python.readthedocs.io

PEtab-dev/libpetab-python Issues

Validator: check `datasetId` in visualizations table exists in measurements table
Updated 2 months ago
Wrong plot_goodness_of_fit if different order of rows in measurement_df and simulation_df
Updated 2 months ago
petab/visualize/lint.py pandas FutureWarning
Closed 5 months ago
`flatten_timepoint_specific_output_overrides` does not support observableParameter overrides as placeholders in noise formulae
Closed 6 months ago
pandas FutureWarning: Setting an item of incompatible dtype is deprecated
Closed 9 months ago
Validator does not check for required column `noiseFormula` in observables table
Updated 10 months ago
API for creating petab problems from scratch
Updated 10 months ago
Improve error handling in Problem.from_yaml - format_version
Updated 10 months ago
Improve error handling in Problem.from_yaml - parameter_file
Updated 10 months ago
PEtab validation should not require matplotlib
Closed a year ago
Handle default for `plotTypeData` in validation of visualization tables
Closed a year ago
test_visualization_with__t_inf fails
Closed a year ago
Calculation of LLH in `calculate_llh` / `calculate_single_llh`
Closed a year ago2
petab.get_model_for_condition may remove rateRules where it shouldn't
Updated a year ago
Update visualization notebooks
Closed 2 years ago5
Incorrect check in linter on transformed parameter bounds
Closed 2 years ago8
Drop Python 3.7 support?
Closed 2 years ago3
`log_sbml_errors` ignores error severity
Closed 2 years ago
incorrect deprecation warning
Closed 2 years ago
model.is_valid logs sbml errors twice
Closed 2 years ago
observables but not species supported in `noiseFormula`
Closed 2 years ago4
empty `noiseFormula` is invalid but passes linting
Closed 2 years ago
Reduce tests to min+max python?
Closed 2 years ago
Parameters dropped when using subset parameter files
Closed 2 years ago
Unclear how to encode noise model: `Mismatch of noise parameter overrides`
Closed 2 years ago2
Unclear what is wrong with PEtab problem after running linter
Closed 2 years ago14
Missing validity check for simulationConditionId.
Closed 2 years ago3
Validator: Add option to warn about unused / non-standard columns
Updated 2 years ago
How to run validation programmatically?
Closed 2 years ago2
recommonmark is deprecated since may
Closed 2 years ago3
Visualization: cropped error bars
Closed 2 years ago
petab.visualize.* changes matplotlib rcParams
Closed 3 years ago1
Add consistent support for pathlib.Path
Closed 3 years ago
GHA: Add Windows
Closed 3 years ago1
no lint error for non-unique condition ids
Closed 3 years ago
encoding issue while writing out experiment
Closed 3 years ago6
pandas 1.2.x requirement?
Closed 3 years ago3
lint doesnt check for `;` at the end of observable parameter definitions
Closed 3 years ago
Simulation is not plotted correctly using visualization specification
Closed 3 years ago1
Errorbars not directly plotted
Closed 3 years ago1
Visualization: plotTypeData ' replicate ' not working
Closed 3 years ago3
Logic of petab.visualize.helper_functions.get_vis_spec_dependent_columns_dict
Closed 3 years ago8
plotting petab problem with simulations by observables does not work
Closed 3 years ago7
visu-error if dataset_id not given, but yValues, yValues need to be sorted alphabetically
Closed 3 years ago1
datasetId not optional for visualization table
Closed 3 years ago1
Unreachable TypeError in `petab.parameter_mapping.apply_overrides_for_observable`
Closed 3 years ago2
Petablint doesn't check for noise in measurement table
Closed 3 years ago1
wrong legends when visu_specification file without datasetId & yValues
Closed 3 years ago
Python API for linter
Updated 3 years ago2
Cleanup repository after splitting off PEtab library
Closed 3 years ago