This pull request implements 4 features/bug fixes:
The PySCeS TL can now fit datasets with multiple replicates
A function has been added to plot the experimental data together with the fitted model
Various cases where parameters with a zero value were not loaded/saved, have been fixed (if self.value: -> if self.value is not None).
The PySCeS loading of the model has been optimized, the conversion to PSC is only done if the EnzymeMLDoc is newer (this process takes time), and a bug with compartment volumes not equal to 1 has been fixed.
The new functionality is demonstrated with an example notebook that I am sharing with @JR-1991 via Google Colab. Any other reviewers, let me know and I'll be happy to share it. It takes the Model 3 from Scenario 4 from the Lauterbach 2022 paper and fits this with PySCeS. The fitted parameters are the same (within small errors) as obtained with direct fitting in the Jupyter notebook using lmfit and odeint.
This pull request implements 4 features/bug fixes:
if self.value:->if self.value is not None).The new functionality is demonstrated with an example notebook that I am sharing with @JR-1991 via Google Colab. Any other reviewers, let me know and I'll be happy to share it. It takes the Model 3 from Scenario 4 from the Lauterbach 2022 paper and fits this with PySCeS. The fitted parameters are the same (within small errors) as obtained with direct fitting in the Jupyter notebook using
lmfitandodeint.This change is