NamedStream cleanup

[orbeckst]

As discussed in #649 and PR #652, NamedStream is a bit of a hack... not necessarily in the best sense of the word. This PR builds on #652 (towards Py3 compatibility) and tries to make NamedStream work as seamlessly as advertised or at least document its failures.

I added tests that explore the limitations of using a NamedStream instance as a filename under the new scheme where the class is not derived from either basestring or str. I apply most of the filename-related tests in os.path.

The tests partially fail on those that have to do a string concatenation with NamedString as the argument, i.e.

  str + NamedStream

which is

 str.__add__(NamedStream)

That seems to be a problem that can only be resolved by properly inheriting from something that str.__add__ is willing to consume.

UPDATE: Below @richardjgowers rightly points out that NamedStream.__radd__ will solve the problem.

[richardjgowers]

This should fix the last problem

    def __radd__(self, other):
        return other + self.name

It overrides the radd of NamedStream, so when str.__add__ fails it looks for NamedStream.__radd__

[richardjgowers]

Oh wait, I've just seen you've added radd, which is weird because I got:

In [2]: s = mda.lib.util.NamedStream(open('./two_water_gro.gro'), 'magicgro')

In [3]: 'this' + s
Out[3]: 'thismagicgro'

[orbeckst]

__radd__ works! I had not included it because I did not see it in a native string via introspection.

I am just doing an amend... incoming.

[orbeckst]

Most of the os.path functions work except

• expandvars just returns NamedStream without doing anything
• expanduser works in that it does return a string with ~ expanded but if it does no expansions it returns the NamedStream. In principle this is acceptable behavior but unexpected; it should work (tm) because downstream string processing should be dealt with correctly with the NamedStream.

Unfortunately, my tests segmentation faulted for expandvars and non-expanding expanduser so I skip them at the moment...

[richardjgowers]

Another py3 enemy bites the dust, awesome