Pep8fixes

Make version [1.5](https://github.com/jcrocholl/pep8/blob/master/CHANGES.txt) of the pep8 tool stop complaining (issue #243).

Changes:
- Comments must be followed by a space: `# foo bar`, not `#foo bar`.
- To test if an element is not in a container, use the idiom `x not in data` instead of `not x in data`. :+1:

So far I've only made "safe" changes. There are two things I've not edited yet:
- Sometimes we like to structure code using comments like `### Start blabla ###` but pep8 doesn't like it... When we ran autopep8 in a different project we also lost this option, but I'd like to get your thoughts on this.
- Comments like
```
tol = 1e-9  # A tolerance
            # value for sth.
```
now raise an error (ugh): either ` E111 indentation is not a multiple of four` or `E113 unexpected indentation`.

A safe solution is to set the pep8 version to 1.4 for now and apply the current changes while we discuss everything else.