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There are lot of ways to manage code reloads in uWSGI, the vast majority of them is described in this article: http://uwsgi-docs.readthedocs.org/en/latest/articles/TheArtOfGracefulReloading.html
Try to adapt the concepts described there with your specific situation
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Two options come to mind.
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Stop uwsgi and restart when finished.
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Deploy to a second directory. For example, assuming the app is pointed at /opt/app, then deploy the code to ~/app, and rm -rf /opt/app/* && cp -r ~/app/ /opt/app; You still may need to restart uwsgi in case it’s hanging on to any FDs.
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