[bugFix] sdks/python: properly add Milvus as extra dependency

[mohamedawnallah]

Description

Cherry-picked from #35816.
Cherry-picked from #35954.

Motivation and Context

This PR properly adds milvus as extra dependency in addition to resolving the recent flakes of PostCommit Python Arm job (#30760 (comment)). Though the following PR #35900 patch was previously submitted to address this, It didn't resolve the root cause issue of milvus extra dependency issue

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[mohamedawnallah]

cc @Amar3tto, @damccorm

[gemini-code-assist]

Summary of Changes

Hello @mohamedawnallah, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request focuses on correctly integrating Milvus as an extra dependency for the Python SDK and resolving persistent flakiness in the PostCommit Python Arm job. The changes involve a significant update of various Python package versions across different Python environment requirement files, alongside a structural refinement in the setup.py file to better manage the Milvus dependency. The overall goal is to enhance the stability and maintainability of the Python SDK's build and test processes.

Highlights

• Milvus Dependency Management Refinement: The setup.py file has been updated to properly define pymilvus as a dedicated milvus_dependency list. This ensures pymilvus is correctly handled as an extra dependency and is no longer directly listed within the general io extra, streamlining dependency management.
• Comprehensive Python Dependency Version Bumps: Numerous Python package versions have been updated across base_image_requirements.txt and ml_image_requirements.txt files for Python 3.9, 3.10, 3.11, 3.12, and 3.13 environments. These updates include critical packages such as charset-normalizer, cloud-sql-python-connector, Cython, google-cloud-aiplatform, pymilvus, requests, SQLAlchemy, and transformers, among others, contributing to a more stable and up-to-date environment.
• CI Trigger for Validation: A minor, trivial change was made to .github/trigger_files/beam_PostCommit_Python.json to trigger the associated CI job, which is a standard practice to validate the impact of dependency changes on the build system.

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[mohamedawnallah]

Fixed linting and formatting issues proposed by CI

[github-actions]

Checks are failing. Will not request review until checks are succeeding. If you'd like to override that behavior, comment assign set of reviewers

[damccorm]

Waiting on checks to complete, but the change looks good to me

[damccorm]

Hm, I see the following error logs in the postcommit python:

<testcase classname="apache_beam.ml.rag.enrichment.milvus_search_it_test.TestMilvusSearchEnrichment" name="test_empty_input_chunks" time="26.780">
<error message="failed on setup with "pymilvus.exceptions.MilvusException: <MilvusException: (code=2, message=Fail connecting to server on 172.17.0.2:51635, illegal connection params or server unavailable)>"">cls = <class 'apache_beam.ml.rag.enrichment.milvus_search_it_test.TestMilvusSearchEnrichment'> @classmethod def setUpClass(cls): cls._db = MilvusEnrichmentTestHelper.start_db_container(cls._version) cls._connection_params = MilvusConnectionParameters( uri=cls._db.uri, user=cls._db.user, password=cls._db.password, db_id=cls._db.id, token=cls._db.token) cls._collection_load_params = MilvusCollectionLoadParameters() > cls._collection_name = MilvusEnrichmentTestHelper.initialize_db_with_data( cls._connection_params) apache_beam/ml/rag/enrichment/milvus_search_it_test.py:496: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ apache_beam/ml/rag/enrichment/milvus_search_it_test.py:365: in initialize_db_with_data client = MilvusClient(**connc_params.__dict__) target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/pymilvus/milvus_client/milvus_client.py:64: in __init__ self._using = create_connection( target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/pymilvus/milvus_client/_utils.py:49: in create_connection raise ex from ex target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/pymilvus/milvus_client/_utils.py:44: in create_connection connections.connect( target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/pymilvus/orm/connections.py:459: in connect connect_milvus(**kwargs, user=user, password=password, token=token, db_name=db_name) target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/pymilvus/orm/connections.py:420: in connect_milvus raise e from e target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/pymilvus/orm/connections.py:412: in connect_milvus gh._wait_for_channel_ready(timeout=timeout) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <pymilvus.client.grpc_handler.GrpcHandler object at 0x7cdbb04fed30> timeout = 10.0 def _wait_for_channel_ready(self, timeout: Union[float] = 10): if self._channel is None: raise MilvusException( code=Status.CONNECT_FAILED, message="No channel in handler, please setup grpc channel first", ) try: grpc.channel_ready_future(self._channel).result(timeout=timeout) self._setup_identifier_interceptor(self._user, timeout=timeout) except grpc.FutureTimeoutError as e: self.close() > raise MilvusException( code=Status.CONNECT_FAILED, message=f"Fail connecting to server on {self._address}, illegal connection params or server unavailable", ) from e E pymilvus.exceptions.MilvusException: <MilvusException: (code=2, message=Fail connecting to server on 172.17.0.2:51635, illegal connection params or server unavailable)> target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/pymilvus/client/grpc_handler.py:159: MilvusException</error>
</testcase>

Could you please take a look?

[mohamedawnallah]

Hm, I see the following error logs in the postcommit python:

<testcase classname="apache_beam.ml.rag.enrichment.milvus_search_it_test.TestMilvusSearchEnrichment" name="test_empty_input_chunks" time="26.780">
<error message="failed on setup with "pymilvus.exceptions.MilvusException: <MilvusException: (code=2, message=Fail connecting to server on 172.17.0.2:51635, illegal connection params or server unavailable)>"">cls = <class 'apache_beam.ml.rag.enrichment.milvus_search_it_test.TestMilvusSearchEnrichment'> @classmethod def setUpClass(cls): cls._db = MilvusEnrichmentTestHelper.start_db_container(cls._version) cls._connection_params = MilvusConnectionParameters( uri=cls._db.uri, user=cls._db.user, password=cls._db.password, db_id=cls._db.id, token=cls._db.token) cls._collection_load_params = MilvusCollectionLoadParameters() > cls._collection_name = MilvusEnrichmentTestHelper.initialize_db_with_data( cls._connection_params) apache_beam/ml/rag/enrichment/milvus_search_it_test.py:496: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ apache_beam/ml/rag/enrichment/milvus_search_it_test.py:365: in initialize_db_with_data client = MilvusClient(**connc_params.__dict__) target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/pymilvus/milvus_client/milvus_client.py:64: in __init__ self._using = create_connection( target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/pymilvus/milvus_client/_utils.py:49: in create_connection raise ex from ex target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/pymilvus/milvus_client/_utils.py:44: in create_connection connections.connect( target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/pymilvus/orm/connections.py:459: in connect connect_milvus(**kwargs, user=user, password=password, token=token, db_name=db_name) target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/pymilvus/orm/connections.py:420: in connect_milvus raise e from e target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/pymilvus/orm/connections.py:412: in connect_milvus gh._wait_for_channel_ready(timeout=timeout) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <pymilvus.client.grpc_handler.GrpcHandler object at 0x7cdbb04fed30> timeout = 10.0 def _wait_for_channel_ready(self, timeout: Union[float] = 10): if self._channel is None: raise MilvusException( code=Status.CONNECT_FAILED, message="No channel in handler, please setup grpc channel first", ) try: grpc.channel_ready_future(self._channel).result(timeout=timeout) self._setup_identifier_interceptor(self._user, timeout=timeout) except grpc.FutureTimeoutError as e: self.close() > raise MilvusException( code=Status.CONNECT_FAILED, message=f"Fail connecting to server on {self._address}, illegal connection params or server unavailable", ) from e E pymilvus.exceptions.MilvusException: <MilvusException: (code=2, message=Fail connecting to server on 172.17.0.2:51635, illegal connection params or server unavailable)> target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/pymilvus/client/grpc_handler.py:159: MilvusException</error>
</testcase>

Could you please take a look?

@damccorm - The root cause of this because of changing milvus server version in the integration tests from v2.5.10to v2.3.9 in that PR #35889. This is not aligned with our pymilvus dependency in sdk/python/setup.py: 'pymilvus>=2.5.10,<3.0.0'

@A1K28 Could please elaborate more about the rational behind this change? I see the note there in PR description Downgrades milvus version to account for CPU instability and I am not sure I am able to get this

With a note as well if we decided to downgrade that we will lose nice features like BM25 Metric Type. Seeing:
milvus-io/milvus#39652 (comment)

[A1K28]

@A1K28 Could please elaborate more about the rational behind this change? I see the note there in PR description Downgrades milvus version to account for CPU instability and I am not sure I am able to get this

Yes, feel free to revert that specific change. The reason for it was:

"Your CPU must support one of the following instruction sets to run Milvus: SSE4. 2, AVX, AVX2, AVX512.". Retrieved from https://milvus.io/docs/v2.4.x/product_faq.md. Some of my self hosted runners were screaming about that.

[damccorm]

I'm still seeing the precommit coverage workflow failing with similar errors unfortunately:

<testcase classname="apache_beam.ml.rag.enrichment.milvus_search_it_test.TestMilvusSearchEnrichment" name="test_keyword_search_with_inner_product_sparse_embedding" time="0.001">
<error message="failed on setup with "Failed: Timeout (>600.0s) from pytest-timeout."">wrapped = <bound method DockerContainer.get_exposed_port of <apache_beam.ml.rag.enrichment.milvus_search_it_test.CustomMilvusContainer object at 0x79a1ec603cd0>> instance = <apache_beam.ml.rag.enrichment.milvus_search_it_test.CustomMilvusContainer object at 0x79a1ec603cd0> args = (36185,), kwargs = {} @wrapt.decorator # type: ignore[misc] def wrapper(wrapped: Callable[..., Any], instance: Any, args: list[Any], kwargs: dict[str, Any]) -> Any: from testcontainers.core.container import DockerContainer if isinstance(instance, DockerContainer): logger.info("Waiting for container %s with image %s to be ready ...", instance._container, instance.image) else: logger.info("Waiting for %s to be ready ...", instance) exception = None for attempt_no in range(config.max_tries): try: > return wrapped(*args, **kwargs) target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/testcontainers/core/waiting_utils.py:59: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/testcontainers/core/container.py:237: in get_exposed_port return int(self.get_docker_client().port(c.id, port)) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <testcontainers.core.docker_client.DockerClient object at 0x79a1ec603d30> container_id = 'feced16dceea3235bfbdda7d020425c9513b4cb37360ab33254292421da7c97d' port = 36185 def port(self, container_id: str, port: int) -> str: """ Lookup the public-facing port that is NAT-ed to :code:`port`. """ port_mappings = self.client.api.port(container_id, port) if not port_mappings: > raise ConnectionError(f"Port mapping for container {container_id} and port {port} is not available") E ConnectionError: Port mapping for container feced16dceea3235bfbdda7d020425c9513b4cb37360ab33254292421da7c97d and port 36185 is not available target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/testcontainers/core/docker_client.py:170: ConnectionError During handling of the above exception, another exception occurred: cls = <class 'apache_beam.ml.rag.enrichment.milvus_search_it_test.TestMilvusSearchEnrichment'> @classmethod def setUpClass(cls): > cls._db = MilvusEnrichmentTestHelper.start_db_container(cls._version) apache_beam/ml/rag/enrichment/milvus_search_it_test.py:488: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ apache_beam/ml/rag/enrichment/milvus_search_it_test.py:318: in start_db_container vector_db_container.start() target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/testcontainers/milvus/__init__.py:83: in start self._connect() target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/testcontainers/core/waiting_utils.py:59: in wrapper return wrapped(*args, **kwargs) target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/testcontainers/milvus/__init__.py:65: in _connect self._healthcheck() target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/testcontainers/core/waiting_utils.py:59: in wrapper return wrapped(*args, **kwargs) target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/testcontainers/milvus/__init__.py:74: in _healthcheck healthcheck_url = self._get_healthcheck_url() target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/testcontainers/milvus/__init__.py:69: in _get_healthcheck_url port = self.get_exposed_port(self.healthcheck_port) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ wrapped = <bound method DockerContainer.get_exposed_port of <apache_beam.ml.rag.enrichment.milvus_search_it_test.CustomMilvusContainer object at 0x79a1ec603cd0>> instance = <apache_beam.ml.rag.enrichment.milvus_search_it_test.CustomMilvusContainer object at 0x79a1ec603cd0> args = (36185,), kwargs = {} @wrapt.decorator # type: ignore[misc] def wrapper(wrapped: Callable[..., Any], instance: Any, args: list[Any], kwargs: dict[str, Any]) -> Any: from testcontainers.core.container import DockerContainer if isinstance(instance, DockerContainer): logger.info("Waiting for container %s with image %s to be ready ...", instance._container, instance.image) else: logger.info("Waiting for %s to be ready ...", instance) exception = None for attempt_no in range(config.max_tries): try: return wrapped(*args, **kwargs) except transient_exceptions as e: logger.debug( f"Connection attempt '{attempt_no + 1}' of '{config.max_tries + 1}' " f"failed: {traceback.format_exc()}" ) > time.sleep(config.sleep_time) E Failed: Timeout (>600.0s) from pytest-timeout. target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/testcontainers/core/waiting_utils.py:65: Failed</error>

[mohamedawnallah]

5,), kwargs = {} @wrapt.decorator # type: ignore[misc] def wrapper(wrapped: Callable[..., Any], instance: Any, args: list[Any], kwargs: dict[str, Any]) -> Any: from testcontainers.core.container import DockerContainer if isinstance(instance, DockerContainer): logger.info("Waiting for container %s with image %s to be ready ...", instance._container, instance.image) else: logger.info("Waiting for %s to be ready ...", instance) exception = None for attempt_no in range(config.max_tries): try: return wrapped(*args, **kwargs) except transient_exceptions as e: logger.debug( f"Connection attempt '{attempt_no + 1}' of '{config.max_tries + 1}' " f"failed: {traceback.format_exc()}" ) > time.sleep(config.sleep_time) E Failed: Timeout (>600.0s) from pytest-timeout. target/.tox-py39-cloudcoverage/py39-cloudcoverage/lib/python3.9/site-packages/testcontainers/core/waiting_utils.py:65: Failed

Thanks 🙏. Given we haven't integrated the ubuntu-latest yet to run those tests with require_docker_in_docker pytest marker, Curious why they are currently even running. Let me check this out and report back here

[damccorm]

Merged into my test branch here - https://github.com/apache/beam/actions/runs/17278672942

And running checks here - https://github.com/apache/beam/actions/runs/17278672942

[damccorm]

This LGTM, thanks for being patient through the review process!