M.-A. Lemburg writes:

 > Hmm, setuptools doesn't support the notion of base packages, ie.
 > packages that provide their own __init__.py module, so I fail
 > to see how your list or any other list of setuptools-depend
 > packages can be taken as indicator for anything related to
 > base packages.

AFAICS the only things PJE has said about base packages is that

  (a) they aren't a universal use case for namespace packages, and
  (b) he'd like to be able to support them in setuptools, but admits
      that at present they aren't.

Your arguments against the PEP supporting namespace packages as
currently supported by setuptools seem purely theoretical to me, while
he's defending an actual and common use case.  "Although practicality
beats purity."  I think that for this PEP it's more important to unify
the various use cases for namespace packages than it is to get rid of
the .pth files.
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