The new version of SQLite has the ability to enforce Foreign Key constraints, but for the sake of backwards-compatibility, you have to turn it on for each database connection separately!

sqlite> PRAGMA foreign_keys = ON;

I am using SQLAlchemy -- how can I make sure this always gets turned on? What I have tried is this:

engine = sqlalchemy.create_engine('sqlite:///:memory:', echo=True)
engine.execute('pragma foreign_keys=on')

...but it is not working!...What am I missing?

EDIT: I think my real problem is that I have more than one version of SQLite installed, and Python is not using the latest one!

>>> import sqlite3
>>> print sqlite3.sqlite_version
3.3.4

But I just downloaded 3.6.23 and put the exe in my project directory! How can I figure out which .exe it's using, and change it?

I now have this working:

Download the latest sqlite and pysqlite2 builds as described above: make sure correct versions are being used at runtime by python.

import sqlite3   
import pysqlite2 
print sqlite3.sqlite_version   # should be 3.6.23.1
print pysqlite2.__path__       # eg C:\\Python26\\lib\\site-packages\\pysqlite2

Next add a PoolListener:

from sqlalchemy.interfaces import PoolListener
class ForeignKeysListener(PoolListener):
    def connect(self, dbapi_con, con_record):
        db_cursor = dbapi_con.execute('pragma foreign_keys=ON')

engine = create_engine(database_url, listeners=[ForeignKeysListener()])

Then be careful how you test if foreign keys are working: I had some confusion here. When using sqlalchemy ORM to add() things my import code was implicitly handling the relation hookups so could never fail. Adding nullable=False to some ForeignKey() statements helped me here.

The way I test sqlalchemy sqlite foreign key support is enabled is to do a manual insert from a declarative ORM class:

# example
ins = Coverage.__table__.insert().values(id = 99,
                                    description = 'Wrong',
                                    area = 42.0,
                                    wall_id = 99,  # invalid fkey id
                                    type_id = 99)  # invalid fkey_id
session.execute(ins) 

Here wall_id and type_id are both ForeignKey()'s and sqlite throws an exception correctly now if trying to hookup invalid fkeys. So it works! If you remove the listener then sqlalchemy will happily add invalid entries.

I believe the main problem may be multiple sqlite3.dll's (or .so) lying around.