Feature validation in examples closes #51

[jvanhoefer]

• Section regarding validation in both Lotka Volterra notebooks
• Now there is no message (YAML file is valid ✅) any more, if the yaml validation is done inside yaml2sbml function, but only when the yaml validator is directly called.

[dilpath]

👍

In the "Lotka_Volterra_CLI.ipynb" notebook:

• In the introductory text, two instances of "python" -> "Python

In the "Lotka_Volterra.ipynb" notebook:

• Could switch from plotObservableTrajectories to plotStateTrajectories. Or use the plotting function with custom labels etc from your previous PR?
  • Currently, plotting the observables also plots some constant y_2 = 1 line. Where does this come from?
• The parameters plot has negative values (I guess log10-scaled). Might be fixed with

fig, ax = plt.subplots()
visualize.parameters(result, ax=ax)
ax.set_xlabel('Logarithmically-scaled (base 10) parameter value')

[dilpath]

Is there an option to suppress any messages? e.g. in PEtab, the linter returns nothing if validation was successful, unless the -v verbose flag is passed. This means if another program wants to determine whether a PEtab is valid, it can interpret the lack of a return message as success. Similarly, if a message by default is preferred in yaml2sbml, then an option to suppress success-related messages could provide the same convenience.

[dilpath]

But this would also mean that all messages like "Path to yaml..." and "Validating..." would need to be suppressed. In other programs, such messages are not displayed unless a verbose flag is passed.

[jvanhoefer]

This is true, would be nice to have something like this :) I will address this in another PR :)

[jvanhoefer]

Thank you @dilpath The first two points are easy to address, I changed them. The latter is a general unfortunate problem of pypesto. I hope, that this will be resolved in pypesto at some point this year... :)