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You can use Django with SQLAlchemy instead of the native ORM for models where you need composite primary keys.
You will not be able to use the admin app with SQLAlchemy models without a surrogate key (this is probably the case with most of the Django ecosystem). You will also need a ModelForm replacement like WTForms.
If you need composite primary keys, take a look at Flask instead, You will be able to leverage most of your Django skills. It is very well documented and has a sizeable ecosystem.
Source:stackexchange.com