Conveniently create tables on first use for in-memory SQLite

mutalyzer/db/__init__.py

@@ -42,6 +42,13 @@ def create_engine():
             connect_args={'check_same_thread': False},
             poolclass=StaticPool)
 
+        engine = sqlalchemy.create_engine(url, **options)
+
+        # For convenience, we also create tables if we're using an SQLite
+        # in-memory database. By definition they won't yet exist
+        Base.metadata.create_all(engine)
+        return engine
+
     return sqlalchemy.create_engine(url, **options)
 
 

mutalyzer/entrypoints/admin.py

@@ -161,9 +161,7 @@ def setup_database(alembic_config_path=None, destructive=False):
 
     if destructive:
         db.Base.metadata.drop_all(db.session.get_bind())
-
     db.Base.metadata.create_all(db.session.get_bind())
-    db.session.commit()
 
     if alembic_config_path:
         context = MigrationContext.configure(db.session.connection())

tests/fixtures.py

@@ -162,7 +162,6 @@ def database():
     Fixture for database table definitions.
     """
     Base.metadata.create_all(session.get_bind())
-    session.commit()
 
 
 def hg19():