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General improvements

Marcus Oskarsson requested to merge gh-0e51e4d5/617/mxcube/general_improvements into master

Created by: mguijarr

Most notably, this increases Python libraries versions - so, when testing this do not forget to do a pip install upgrade beforehand otherwise it won't work as some code is now specific to Flask-Socketio 2.9.

Otherwise look at commit messages for details.

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