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After using jupyter_conf_search to track down config files calling server_extensions (instead of the new nbserver_extensions), I'm still getting the warning:
[W 15:42:43.327 NotebookApp] server_extensions is deprecated, use nbserver_extensions
Every mention of server_extensions was deleted or has been commented out e.g.:

199: #c.NotebookApp.nbserver_extensions = {}

242: ## DEPRECATED use the nbserver_extensions dict instead

243: #c.NotebookApp.server_extensions = []

Since you asked about this in the meeting, here are some options for building command line interfaces.

• argparse is the default option because it's part of the standard library. It's quite lengthy and the kind of thing I always have to look up, but it's powerful and non-magical.
• docopt is quite popular, but too magical for my taste.
• click is a newer option by Armin Ronacher (Flask, Jinja, etc.). I haven't used it, but it seems to use decorators heavily.
• For historical interest, getopt is the old-school way of doing it. It's not recommended now, though, because the other options above give you things like help info for free.

There are of course plenty of other tools on PyPI doing similar things.