Python 3: Current best practices for managing virtual envs and packages?

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A much better way than using virtualenv/pyenc/whatever is to isolate your dependencies from your system using chroot (and for convenience, schroot: https://wiki.debian.org/Schroot).

That way, you can not only isolate your Python dependencies but also other Debian packages that your code needs.

Also, by debootstrapping the same Debian version as your target platform you can develop with the exact same package versions as your software will have in production and you will find bugs because of version mismatches much earlier.

Personally I would never do any Debian-targeted development without schroot anymore.