Use Engine.begin() instead of Engine.connect() to ensure DML/DDL stat…

…ements are committed in migration code (#1129)

# Description
One of the changes in SQLAlchemy from 1.4.X -> 2.X is that they've
removed automatic commits for DDL/DML statements fed into `Connection`s
created from `Engine.connect()`. This leads to a few minor bugs in the
DB migration code post `0.39.0` release (and the SQLAlchemy 2.X
migration in #1127).

## This PR
This PR fixes those bugs by using `Connection`s created by
`Engine.begin()` instead

### Testing
```bash
$ bazel run sematic/db/tests:test_migrate
```
+ manual testing in a repo that's using Sematic as a dependency

sematic/db/migrate.py

@@ -51,7 +51,7 @@ def _is_migration_file(file_name: str) -> bool:
 
 
 def _get_current_versions() -> List[str]:
-    with db().get_engine().connect() as conn:
+    with db().get_engine().begin() as conn:
         conn.execute(
             text(
                 "CREATE TABLE IF NOT EXISTS "

sematic/db/migrations/20220930014400_migrate_exception_data.py

@@ -30,7 +30,7 @@ def up():
 
 
 def down():
-    with db().get_engine().connect() as conn:
+    with db().get_engine().begin() as conn:
         # TODO #303: standardize NULL vs 'null'
         run_id_exception_json_pairs = conn.execute(
             text(

sematic/db/tests/test_migrate.py

@@ -83,7 +83,7 @@ def test_invalid_sql(_, test_db_empty):  # noqa: F811
 def test_migrate(_, test_db_empty):  # noqa: F811
 
     with pytest.raises(OperationalError):
-        with db().get_engine().connect() as conn:
+        with db().get_engine().begin() as conn:
             conn.execute(text("SELECT version FROM schema_migrations;"))
 
     migrate_up()
@@ -93,7 +93,7 @@ def test_migrate(_, test_db_empty):  # noqa: F811
     assert len(current_versions) > 0
 
     # Test tables were created
-    with db().get_engine().connect() as conn:
+    with db().get_engine().begin() as conn:
         run_count = conn.execute(text("SELECT COUNT(*) from runs;"))
 
     assert list(run_count)[0][0] == 0