First of all, thank you in advance for taking the time to contribute with your answers. Even though the message is still warning Import "custom_modules" could not be resolved , this is how I did it.

I added the following configuration to the __init__.py script.

# Import the os modules to get access to the os system functions.

import os

# Package level setup

# Package name

__name__="custom_packages"

# Define the import all.
__all__=["custom_modules"]

# Optional define the version of the code.
version="0.0.1"

# Module level configuration

# Importing the module to be configured
from . import custom_modules as cm
# Package setup
cm.__package__="custom_packages"
# Setting up the name of the module
cm.__name__="custom_modules"
# Setting up the path of the module,
cm.__package__.__path__=os.getcwd()

# The os.getcwd() retrieves the current working directory
# allowing us to se the real path instead of the relative one.

# NOTE: this is a very basic setup, that works fine for this sample.
# For a more complete implementation review the python3 docs https://docs.python.org/3/library/

My tree directory is pretty similar to the suggested by you.

./custom_packages/
├── custom_modules.py
├── __init__.py

You can have more detials here.