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There's a bunch of discussion and links in this[1] SO question. It looks like numpy's size becomes an issue.

It appears that some people do use the two projects together, though.

Even if it the end it spits out an exe, it's 100s of MB. This makes it a non-starter for short lived numerical programs.

Are you using --standalone flag? Nuitka scans for dependencies recursively, that's why output bundle's so big.

I don't understand why you've that large .exe, a bunch of DLLs is what should be heavy.