How does PyCharm handle relative imports of modules?

You have to make sure work_dir is added in to sys.path or PYTHONPATH.

Python will add the parent folder of the script file into sys.path automatically. So if you run app.py in your shell, only FlaskControlPanel will be inserted into sys.path and python cannot find where models is (work_dir is not in sys.path).

But in pycharm, it will always add work_dir in sys.path. That's why you can run app.py without any problem.

For your problem, you can change directory to work_dir and run PYTHONPATH=. python FlaskControlPanel/app.py

https://docs.python.org/2/using/cmdline.html#interface-options

Execute the Python code contained in script, which must be a filesystem path (absolute or relative) referring to either a Python file, a directory containing a __main__.py file, or a zipfile containing a __main__.py file.

If this option is given, the first element of sys.argv will be the script name as given on the command line.

If the script name refers directly to a Python file, the directory containing that file is added to the start of sys.path, and the file is executed as the __main__ module.

If the script name refers to a directory or zipfile, the script name is added to the start of sys.path and the __main__.py file in that location is executed as the __main__ module.