app.py

import os
from flask import Flask


def create_app(config_file=None, config_object=None):
    """
    Bootstrap the flask application, registering blueprints, modules and other fun things.
    :param config_file: a python file containing key/values variables
    :param config_object: a python object (can be a dict) containing key/values variables
    :return: the app object
    """
    app = Flask(__name__, static_folder='public')

    # Configuration
    app.config.from_object('my_app.settings.BaseConfig')
    app.environment = os.getenv('MY_APP_ENV', 'dev')

    if config_file:
        app.config.from_pyfile(config_file)
    if config_object:
        app.config.update(**config_object)
        
    from custom_class import custom_class
    custom_class.init_app(app)
   
    return app

custom_class.py

class CustomClass(object):

    app = None
    config = None
    
    def __init__(self, app=None):
        if app:
            self.init_app(app)
            
    def init_app(self, app):
        self.app = app
        self.config = self.app.config['CUSTOM_CLASS']
        # Init anything else
        
custom_class = CustomClass()