Upgrade sqlalchemy

Adapt code to prevent new warnings and errors (as of SQLAlchemy 1.4):
- Overlapping foreign key columns could be set in a conflicting way
  => This is prevented by the application logic
  => Ignore the warning by setting a `overlaps` flag
- Transaction already rolled back
  => This only happens when tests cause an `IntegrityError` on purpose
  => Filter away the corresponding warning in the fixture
- Query returns `Row` objects and not scalars
  => Add genexpr to pull out `primary_id`

tests/conftest.py

@@ -5,6 +5,7 @@ in the CLI layer need access to the database.
 """
 
 import os
+import warnings
 
 import pytest
 import sqlalchemy as sa
@@ -94,7 +95,9 @@ def db_session(db_connection):
 
     finally:
         session.close()
-        transaction.rollback()
+
+        with warnings.catch_warnings(record=True):
+            transaction.rollback()
 
 
 # Import the fixtures from the `fake_data` sub-package.