[python] Cannot find reference 'xxx' in __init__.py - Python / Pycharm

I have a project in Pycharm organized as follows:

-- Sources
   |--__init__.py
   |--Calculators
      |--__init__.py
      |--Filters.py
   |--Controllers
      |--__init__.py
      |--FiltersController.py
   |--Viewers
      |--__init__.py
      |--DataVisualization.py
   |--Models
      |--__init__.py
      |--Data

All of my __init__.py, except for the one right above Sources are blank files. I am receiving a lot of warnings of the kind:

Cannot find reference 'xxx' in __init__.py

For example, my FiltersController.py has this piece of code:

import numpy.random as npr

bootstrap = npr.choice(image_base.data[max(0, x-2):x+3, max(0, y-2):y+3].flatten(), size=(3, 3), replace=True)

And I get this warning:

Cannot find reference 'choice' in __init__.py

I'm googling wondering what does this mean and what should I do to code properly in Python.

Thank you in advance.

Did you forget to add the init.py in your package?

You should first take a look at this. This explains what happens when you import a package. For convenience:

The import statement uses the following convention: if a package’s __init__.py code defines a list named __all__, it is taken to be the list of module names that should be imported when from package import * is encountered. It is up to the package author to keep this list up-to-date when a new version of the package is released. Package authors may also decide not to support it, if they don’t see a use for importing * from their package.

So PyCharm respects this by showing a warning message, so that the author can decide which of the modules get imported when * from the package is imported. Thus this seems to be useful feature of PyCharm (and in no way can it be called a bug, I presume). You can easily remove this warning by adding the names of the modules to be imported when your package is imported in the __all__ variable which is list, like this

__init__.py

from . import MyModule1, MyModule2, MyModule3
__all__ = [MyModule1, MyModule2, MyModule3]

After you add this, you can ctrl+click on these module names used in any other part of your project to directly jump to the declaration, which I often find very useful.

I have solved this problem in my pycharm in a bit different way.

Go to settings -> Project Interpreter and then click on the base package there.

You will see a page like this

After that when your package is installed then you should see the package is colored blue rather than white.

And the unresolved reference is also gone too.

I know this is old, but Google sent me here so I guess others will come too like me.

The answer on 2018 is the selected one here: Pycharm: "unresolved reference" error on the IDE when opening a working project

Just be aware that you can only add one Content Root but you can add several Source Folders. No need to touch __init__.py files.

You can mark source directory as a source root like so:

• Right-click on source directory
• Mark Directory As --> Source Root
• File --> Invalidate Caches / Restart... -> Invalidate and Restart

Make sure you didn't by mistake changed the file type of __init__.py files. If, for example, you changed their type to "Text" (instead of "Python"), PyCharm won't analyze the file for Python code. In that case, you may notice that the file icon for __init__.py files is different from other Python files.

To fix, in Settings > Editor > File Types, in the "Recognized File Types" list click on "Text" and in the "File name patterns" list remove __init__.py.