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My point is adding stuff to an existing version doesn’t make it immutable like it should
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I'm learning here, but for option 2, besides the security risk, doesn't this create the possibility that users could get a broken/unfinished package any time they're updating to a recently "published" release? The property of releases being atomic seems very important.
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Generally each artifact in the release is atomic, as is (and was) the case here.

You’ll never get served a partially uploaded wheel for amd64 Linux, but somebody could come back a year later and add a 2nd wheel to that release for a different architecture.

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