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When you download locally a file in iCloud Drive, it will stay on your iDevice until IOS needs some disk space for other things (new apps, new files, ...).
Is that the same for Pythonista 3 iCloud Drive? I've put a lot of big files in Pythonista/iCloud and the remaining disk space seems to decrease with the same size. It should not, I think.

Pythonista downloads all files in its iCloud folder, so that they're available when you're offline (and also because there isn't a good way to trigger iCloud downloads from scripts that might need the files). There's currently no way to disable this, sorry.