Why is alembic not autogenerating?

When you run the alembic command, your app package is not in Python's module path. So it can't be imported. The easiest way to solve this is to use an extension such as Flask-Migrate or Flask-Alembic to handle setting up the migration environment for you. Both these extensions require you to use Flask-SQLAlchemy as well.

If you don't want to use an extension, the quick and dirty way is to just force the directory containing your app package to be on the path. In env.py, before importing Base, add

import os, sys
sys.path.insert(0, os.path.realpath(os.path.join(os.path.dirname(__file__), '..')))

A better solution would be to properly set up your project with a setup.py file and install your package in editable mode: pip install -e .. Then your package would be on the path the "right" way, as if it were actually installed.

You should use export PYTHONPATH='.'