Hide external modules when importing a module (e.g. regarding code-completion)

I had the same problem, and solved it by adding a leading underscore to all my imports. It doesn't look brilliant, but it achieves what you're after.

from __future__ import division as _division
import numpy as _np
import pandas as _pd

Only the stuff that starts without an underscore is imported when you import the module using from .. import *. or when you use tab-completion in IPython or spyder.

I've come to like and use this approach. Starting with your project structure, we will hide all the content of matrix_kit that you don't want to show.

the_toolkit:
    __init__.py
    basic_io.py
    simple_math.py
    matrix_kit.py
    ...

Move matrix_kit.py into a package with the same name, and place one underscore in the beginning of the module's name:

the_toolkit:
    __init__.py
    basic_io.py
    simple_math.py
    matrix_kit:
        __init__.py
        _matrix_kit.py
    ...

Now in _matrix_kit.py add a global variable __all__ = [...] listing the names of all functions/classes/variables you want to be visible. Then, add the following line to matrix_kit/__init__.py:

from ._matrix_kit import *

It will only import the stuff listed in the __all__ attribute of the module. Then, while importing matrix_kit like you've done before, you will actually import the __init__.py and its content.