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I'm a beginner at this, but based on the flask, nginx, and uwsgi documentation and tutorials I've found, the standard seems to be to use nginx to pass configuration variables to uwsgi.

Why is this preferable to setting the configuration variables in an ini file in /etc/uwsgi/myapp.ini ? It seems weird to me to tie in uwsgi to nginx when there is a pretty simple way to separate everything.

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I think what you are referring to are CGI/WSGI vars. They are the only thing required from the nginx side. All of the other setup go in uWSGI specific configuration. There is the possibility to load WSGI apps passing their name from nginx, but it is far from being "the standard" (and i strongly discourage such kind of setup)

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