This same issue applies to setuptools (https://bitbucket.org/pypa/setuptools/issues/442/setuptools-1832-cannot-access-pypi-if-pypi).

I've created a test that captures the failure, but I struggled to find a solution that doesn't break across Python versions.

Thomas suggested guiding the user to provide two percent signs instead of one, but that breaks on Python 2, which will interpret the value as two percent signs.

As suggested, using RawConfigParser does address the issue on both Python 2 and 3, but that of course could break compatibility if interpolation was expected.

I have found that if one uses SafeConfigParser on Python 2 and 3, and requires the user to use two percent signs to represent one, it does seem to work on both Python 2 and 3.