Update dependencies to be compatible with JupyterLab 4.x

[lresende]

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[karlaspuldaro]

We need a detailed issue for migration to JupyterLab 4, to keep track of all required steps, this PR could be step one.
In my opinion, it would be best to plan the steps more carefully, so they're better isolated. Changing all dependencies at once can affect everything, and the changes become complex too quickly.