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I have been using Heroku, which does not support a persistent file system; i.e. I cannot be sure that a file I have written will be available at a later time. How does that work in pythonanywhere? Can I be sure of the persistence of files, or do I need to store files in a separate service like S3?

yup we do offer a persistent file system. think of it as having your own linux box instead of heroku.

you can be sure of persistence (we also take backups for ourselves in case of hardware failure etc).