Working on v3.19.0, I used the following declarative class to generate two migrations. The first creates the 'test' table with only the 'id' column, the second adds the 'name column.

engine = create_engine(settings.SPANNER_URL)
metadata = MetaData(bind=engine)
Base = declarative_base(metadata=metadata)

class Test(Base):
    __tablename__ = 'test'

    id = Column(String(3), primary_key=True)
    name = Column(String(3))

Running the first migration works fine. But running the second migration gives :

root ➜ /workspaces/hydra-monorepo/migrations (google_sqlalchemy ✗) $ ./alembic-google upgrade head
INFO  [alembic.runtime.migration] Context impl SpannerImpl.
INFO  [alembic.runtime.migration] Will assume non-transactional DDL.
INFO  [alembic.runtime.migration] Running upgrade 16cbbcf75d48 -> b1c6f829e41b, add column
Traceback (most recent call last):
  File "/root/.local/lib/python3.9/site-packages/google/api_core/grpc_helpers.py", line 140, in error_remapped_callable
    return _StreamingResponseIterator(
  File "/root/.local/lib/python3.9/site-packages/google/api_core/grpc_helpers.py", line 66, in __init__
    self._stored_first_result = next(self._wrapped)
  File "/root/.local/lib/python3.9/site-packages/grpc/_channel.py", line 426, in __next__
    return self._next()
  File "/root/.local/lib/python3.9/site-packages/grpc/_channel.py", line 826, in _next
    raise self
grpc._channel._MultiThreadedRendezvous: <_MultiThreadedRendezvous of RPC that terminated with:
        status = StatusCode.ABORTED
        details = "Transaction aborted. Database schema probably changed during transaction, retry may succeed."
        debug_error_string = "{"created":"@1661283549.074681776","description":"Error received from peer ipv4:172.217.13.170:443","file":"src/core/lib/surface/call.cc","file_line":966,"grpc_message":"Transaction aborted. Database schema probably changed during transaction, retry may succeed.","grpc_status":10}"
>

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/root/.local/lib/python3.9/site-packages/google/cloud/spanner_dbapi/cursor.py", line 269, in execute
    self._itr = PeekIterator(self._result_set)
  File "/root/.local/lib/python3.9/site-packages/google/cloud/spanner_dbapi/utils.py", line 38, in __init__
    head = next(itr_src)
  File "/root/.local/lib/python3.9/site-packages/google/cloud/spanner_v1/streamed.py", line 145, in __iter__
    self._consume_next()
  File "/root/.local/lib/python3.9/site-packages/google/cloud/spanner_v1/streamed.py", line 117, in _consume_next
    response = next(self._response_iterator)
  File "/root/.local/lib/python3.9/site-packages/google/cloud/spanner_v1/snapshot.py", line 59, in _restart_on_unavailable
    iterator = method(request=request)
  File "/root/.local/lib/python3.9/site-packages/google/cloud/spanner_v1/services/spanner/client.py", line 1138, in execute_streaming_sql
    response = rpc(
  File "/root/.local/lib/python3.9/site-packages/google/api_core/gapic_v1/method.py", line 154, in __call__
    return wrapped_func(*args, **kwargs)
  File "/root/.local/lib/python3.9/site-packages/google/api_core/timeout.py", line 99, in func_with_timeout
    return func(*args, **kwargs)
  File "/root/.local/lib/python3.9/site-packages/google/api_core/grpc_helpers.py", line 144, in error_remapped_callable
    raise exceptions.from_grpc_error(exc) from exc
google.api_core.exceptions.Aborted: 409 Transaction aborted. Database schema probably changed during transaction, retry may succeed. [retry_delay {
  nanos: 10589511
}
]

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/root/.local/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1900, in _execute_context
    self.dialect.do_execute(
  File "/root/.local/lib/python3.9/site-packages/google/cloud/sqlalchemy_spanner/sqlalchemy_spanner.py", line 1006, in do_execute
    cursor.execute(statement, parameters)
  File "/root/.local/lib/python3.9/site-packages/google/cloud/spanner_dbapi/cursor.py", line 70, in wrapper
    return function(cursor, *args, **kwargs)
  File "/root/.local/lib/python3.9/site-packages/google/cloud/spanner_dbapi/cursor.py", line 272, in execute
    self.connection.retry_transaction()
  File "/root/.local/lib/python3.9/site-packages/google/cloud/spanner_dbapi/connection.py", line 263, in retry_transaction
    self._rerun_previous_statements()
  File "/root/.local/lib/python3.9/site-packages/google/cloud/spanner_dbapi/connection.py", line 298, in _rerun_previous_statements
    _compare_checksums(statement.checksum, retried_checksum)
  File "/root/.local/lib/python3.9/site-packages/google/cloud/spanner_dbapi/checksum.py", line 78, in _compare_checksums
    raise RetryAborted(
google.cloud.spanner_dbapi.exceptions.RetryAborted: The transaction was aborted and could not be retried due to a concurrent modification.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/root/.local/bin/alembic", line 8, in <module>
    sys.exit(main())
  File "/root/.local/lib/python3.9/site-packages/alembic/config.py", line 590, in main
    CommandLine(prog=prog).main(argv=argv)
  File "/root/.local/lib/python3.9/site-packages/alembic/config.py", line 584, in main
    self.run_cmd(cfg, options)
  File "/root/.local/lib/python3.9/site-packages/alembic/config.py", line 561, in run_cmd
    fn(
  File "/root/.local/lib/python3.9/site-packages/alembic/command.py", line 322, in upgrade
    script.run_env()
  File "/root/.local/lib/python3.9/site-packages/alembic/script/base.py", line 569, in run_env
    util.load_python_file(self.dir, "env.py")
  File "/root/.local/lib/python3.9/site-packages/alembic/util/pyfiles.py", line 94, in load_python_file
    module = load_module_py(module_id, path)
  File "/root/.local/lib/python3.9/site-packages/alembic/util/pyfiles.py", line 110, in load_module_py
    spec.loader.exec_module(module)  # type: ignore
  File "<frozen importlib._bootstrap_external>", line 850, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "google_error_reporting/env.py", line 83, in <module>
    run_migrations_online()
  File "google_error_reporting/env.py", line 77, in run_migrations_online
    context.run_migrations()
  File "<string>", line 8, in run_migrations
  File "/root/.local/lib/python3.9/site-packages/alembic/runtime/environment.py", line 853, in run_migrations
    self.get_context().run_migrations(**kw)
  File "/root/.local/lib/python3.9/site-packages/alembic/runtime/migration.py", line 630, in run_migrations
    head_maintainer.update_to_step(step)
  File "/root/.local/lib/python3.9/site-packages/alembic/runtime/migration.py", line 854, in update_to_step
    self._update_version(from_, to_)
  File "/root/.local/lib/python3.9/site-packages/alembic/runtime/migration.py", line 791, in _update_version
    ret = self.context.impl._exec(
  File "/root/.local/lib/python3.9/site-packages/alembic/ddl/impl.py", line 195, in _exec
    return conn.execute(construct, multiparams)
  File "/root/.local/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1380, in execute
    return meth(self, multiparams, params, _EMPTY_EXECUTION_OPTS)
  File "/root/.local/lib/python3.9/site-packages/sqlalchemy/sql/elements.py", line 333, in _execute_on_connection
    return connection._execute_clauseelement(
  File "/root/.local/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1572, in _execute_clauseelement
    ret = self._execute_context(
  File "/root/.local/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1943, in _execute_context
    self._handle_dbapi_exception(
  File "/root/.local/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 2124, in _handle_dbapi_exception
    util.raise_(
  File "/root/.local/lib/python3.9/site-packages/sqlalchemy/util/compat.py", line 208, in raise_
    raise exception
  File "/root/.local/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1900, in _execute_context
    self.dialect.do_execute(
  File "/root/.local/lib/python3.9/site-packages/google/cloud/sqlalchemy_spanner/sqlalchemy_spanner.py", line 1006, in do_execute
    cursor.execute(statement, parameters)
  File "/root/.local/lib/python3.9/site-packages/google/cloud/spanner_dbapi/cursor.py", line 70, in wrapper
    return function(cursor, *args, **kwargs)
  File "/root/.local/lib/python3.9/site-packages/google/cloud/spanner_dbapi/cursor.py", line 272, in execute
    self.connection.retry_transaction()
  File "/root/.local/lib/python3.9/site-packages/google/cloud/spanner_dbapi/connection.py", line 263, in retry_transaction
    self._rerun_previous_statements()
  File "/root/.local/lib/python3.9/site-packages/google/cloud/spanner_dbapi/connection.py", line 298, in _rerun_previous_statements
    _compare_checksums(statement.checksum, retried_checksum)
  File "/root/.local/lib/python3.9/site-packages/google/cloud/spanner_dbapi/checksum.py", line 78, in _compare_checksums
    raise RetryAborted(
sqlalchemy.exc.OperationalError: (google.cloud.spanner_dbapi.exceptions.RetryAborted) The transaction was aborted and could not be retried due to a concurrent modification.
[SQL: UPDATE alembic_version SET version_num='b1c6f829e41b' WHERE alembic_version.version_num = '16cbbcf75d48']
(Background on this error at: https://sqlalche.me/e/14/e3q8)

Note that examining the equivalent DDL for the alembic_version table in the database gives this:

So it would seem that the version_num column is tagged as the primary key even though we specify version_table_pk=False in our env.py as prescribed.

Alembic generated migrations support #229

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