Take a look at the following info from PEP 328:

Relative imports use a module's __name__ attribute to determine that module's position in the package hierarchy. If the module's name does not contain any package information (e.g. it is set to '__main__') then relative imports are resolved as if the module were a top level module, regardless of where the module is actually located on the file system.

When you run foo.py as a script, that module's __name__ is '__main__', so you cannot do relative imports. This would be true even if mypackage was on sys.path. Basically, you can only do relative imports from a module if that module was imported.

Here are a couple of options for working around this:

1) In foo.py, check if __name__ == '__main__' and conditionally add mypackage to sys.path:

if __name__ == '__main__':
    import os, sys
    # get an absolute path to the directory that contains mypackage
    foo_dir = os.path.dirname(os.path.join(os.getcwd(), __file__))
    sys.path.append(os.path.normpath(os.path.join(foo_dir, '..', '..')))
    from mypackage import bar
else:
    from .. import bar

2) Always import bar using from mypackage import bar, and execute foo.py in such a way that mypackage is visible automatically:

$ cd <path containing mypackage>
$ python -m mypackage.foo.foo

My solution looks a bit cleaner and can go at the top, with all the other imports:

try:
   from foo import FooClass
except ModuleNotFoundError:
   from .foo import FooClass