The toughest part of it will be to ensure that the dependencies of a module matches another
module in PyPI.

I don't see it this way. As far as I'm concerned, you just have to say "The dependencies are X, Y and Z. I can download and install X and Z but you'll have to find Y for yourself." Enough irate (or motivated) users later, and someone will upload Y to PyPI :)
From a viewpoint of a human user, yes, that can be expected. We will in fact expect the person to google for it if it is not in PyPI. From a viewpoint of a tool, that may be too tricky.

Another thing in my radar is that package names may change. I was reading an article on O'Reilly ONLamp.com, "Using PySOAP" by Cameron Laird, written on 06/14/2001 (www.onlamp.com/pub/a/python/2001/06/14/pysoap.html). When reading it, I realise that instead of PySOAP, it should be SOAPpy. Of course, I do not know if SOAPpy was named as PySOAP back then, but you see my point......

We can't hold things up just because PyPI isn't complete - that's going to take quite a while to happen. For now we just have to assume that we can't satisfy all dependencies by downloading and installing automatically.

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