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It’s easier to just update the package and not have to worry.

https://bandit.readthedocs.io/en/latest/ can do that for python.

but then if you could assert the call graph (easily, or even provably correctly), then why not just cull the unused code that led to vulnerability in the first place?

With a statically compiled language it is usually culled through dead-code elimination (DCE), and with static linking you don’t ship entire libraries.

The technology to cull code can work for dynamic languages too, even tho it does get difficult sometimes (google closure compiler[1] does dead code elimination for js, for example). It's just that most dynamic language users don't make the attempt (and you end up with this dependabot giving you thousands of false positives due to the deep dependency tree).

[1]https://github.com/google/closure-compiler