A few bugfixes and cleanups for the Jupyter widgets

[ceriottm]

Stumbled on a bunch of bugs and deprecation warnings in the widgets and decided to fix them. Mainly:

• handle the case of partial environments definitions also for StructureWidget
• solve a deprecation warning and handles better the resizing of the plotly panel

[Luthaf]

I cleaned up the commits history, since they are unrelated I would prefer not to squash all of them in a single one.