PEP 8 fixes, assisted by Syntastic and flake8.

Remove obsolete :api: role, and replace refs.

Also removes now unused scripts.

Better exceptions

This error was previously caught as a MissingInputException.

Use sys.executable instead of 'python'

This way, the same executable will be used.

Add err

Minor stuff

Also fixed some small typos and replaced a zip by izip.

Also fixed a few more typos in surrounding code.

Also better formatting of this line.

Debugprint id2

Detect unused inputs to theano.function