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The sad part is you're right that we can't assume secure operation of components anymore, but the tooling hasn't caught up to that reality. Chroot jails help with runtime isolation but the attack here happened at build time, the malicious code was already in the package before any test could run. And the supply chain is deep. Trivy gets compromised, which gives CI access, which gives PyPI access. Even if you jail your own builds you're trusting that every tool in your pipeline wasn't the entry point. 97 million monthly downloads means a lot of people's "secure" pipelines just ran attacker code with full access.
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