diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 64ad3f6ab..06f1accda 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -36,7 +36,7 @@ pytest tests/ ## Running Tests -Tests use [testcontainers](https://testcontainers.com/) to automatically manage MySQL, PostgreSQL, and MinIO containers. No manual `docker-compose up` required. +Tests use [testcontainers](https://testcontainers.com/) to automatically manage MySQL, PostgreSQL, and S3 ([SeaweedFS](https://github.com/seaweedfs/seaweedfs)) containers. No manual `docker-compose up` required. Integration tests are **backend-parameterized** — tests using the `backend` fixture run automatically against both MySQL and PostgreSQL. @@ -67,13 +67,13 @@ Tests automatically spin up both MySQL and PostgreSQL containers via testcontain ### External Containers (for debugging) ```bash -# MySQL + MinIO -docker compose up -d db minio +# MySQL + S3 +docker compose up -d db s3 DJ_USE_EXTERNAL_CONTAINERS=1 pixi run -e test test docker compose down -# MySQL + PostgreSQL + MinIO -docker compose up -d db postgres minio +# MySQL + PostgreSQL + S3 +docker compose up -d db postgres s3 DJ_USE_EXTERNAL_CONTAINERS=1 pixi run -e test test docker compose down ``` @@ -133,7 +133,7 @@ For `DJ_USE_EXTERNAL_CONTAINERS=1`: | Variable | Default | Description | |----------|---------|-------------| -| `S3_ENDPOINT` | `localhost:9000` | MinIO endpoint | +| `S3_ENDPOINT` | `localhost:8333` | S3 endpoint | --- diff --git a/docker-compose.yaml b/docker-compose.yaml index 23fd773c1..fb7e4079e 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -1,4 +1,4 @@ -# Development environment with MySQL and MinIO services +# Development environment with MySQL, PostgreSQL, and S3 (SeaweedFS) services # # NOTE: docker-compose is OPTIONAL for running tests. # Tests use testcontainers to automatically manage containers. @@ -6,7 +6,7 @@ # # Use docker-compose for development/debugging when you want # persistent containers that survive test runs: -# docker compose up -d db minio # Start services manually +# docker compose up -d db s3 # Start services manually # pytest tests/ # Tests will use these containers # # Full Docker testing (CI): @@ -37,20 +37,17 @@ services: timeout: 30s retries: 5 interval: 15s - 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"testcontainers[mysql,minio,postgres]>=4.0", + "testcontainers[mysql,postgres]>=4.0", "polars>=0.20.0", "pyarrow>=14.0.0", ] @@ -117,7 +117,7 @@ test = [ "matplotlib", "ipython", "s3fs>=2023.1.0", - "testcontainers[mysql,minio,postgres]>=4.0", + "testcontainers[mysql,postgres]>=4.0", "psycopg2-binary>=2.9.0", "polars>=0.20.0", "pyarrow>=14.0.0", @@ -245,7 +245,7 @@ ignore-words-list = "rever,numer,astroid" [tool.pytest.ini_options] markers = [ "requires_mysql: marks tests as requiring MySQL database (deselect with '-m \"not requires_mysql\"')", - "requires_minio: marks tests as requiring MinIO object storage (deselect with '-m \"not requires_minio\"')", + "requires_s3: marks tests as requiring S3-compatible object storage (deselect with '-m \"not requires_s3\"')", "mysql: marks tests that run on MySQL backend (select with '-m mysql')", "postgresql: marks tests that run on PostgreSQL backend (select with '-m postgresql')", "backend_agnostic: marks tests that should pass on all backends (auto-marked for parameterized tests)", @@ -293,7 +293,7 @@ test-py315 = { features = ["test", "py315"] } test = "pytest tests/" test-cov = "pytest --cov-report term-missing --cov=datajoint tests/" # Optional: use external containers (docker-compose) instead of testcontainers -services-up = "docker compose up -d db minio" +services-up = "docker compose up -d db s3" services-down = "docker compose down" test-external = { cmd = "DJ_USE_EXTERNAL_CONTAINERS=1 pytest tests/", depends-on = ["services-up"] } diff --git a/tests/conftest.py b/tests/conftest.py index bfbbc293d..6173f6623 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -3,7 +3,7 @@ Tests are organized by their dependencies: - Unit tests: No external dependencies, run with `pytest -m "not requires_mysql"` -- Integration tests: Require MySQL/MinIO, marked with @pytest.mark.requires_mysql +- Integration tests: Require MySQL/S3, marked with @pytest.mark.requires_mysql Containers are automatically started via testcontainers when needed. Just run: pytest tests/ @@ -58,9 +58,9 @@ def pytest_collection_modifyitems(config, items): "db_creds_root", "db_creds_test", } - # Tests that use these fixtures require MinIO - minio_fixtures = { - "minio_client", + # Tests that use these fixtures require S3 object storage + s3_fixtures = { + "s3_client", "s3fs_client", "s3_creds", "stores_config", @@ -83,8 +83,8 @@ def pytest_collection_modifyitems(config, items): # Auto-add marks based on fixture usage if fixturenames & mysql_fixtures: item.add_marker(pytest.mark.requires_mysql) - if fixturenames & minio_fixtures: - item.add_marker(pytest.mark.requires_minio) + if fixturenames & s3_fixtures: + item.add_marker(pytest.mark.requires_s3) # Auto-mark backend-parameterized tests if fixturenames & backend_fixtures: @@ -95,7 +95,7 @@ def pytest_collection_modifyitems(config, items): # ============================================================================= -# Container Fixtures - Auto-start MySQL and MinIO via testcontainers +# Container Fixtures - Auto-start MySQL, PostgreSQL, and S3 via testcontainers # ============================================================================= # Check if we should use external containers (for CI or manual docker-compose) @@ -164,36 +164,50 @@ def postgres_container(): @pytest.fixture(scope="session") -def minio_container(): - """Start MinIO container for the test session (or use external).""" +def s3_container(): + """Start an S3-compatible object store for the test session (or use external).""" if USE_EXTERNAL_CONTAINERS: # Use external container - return None, credentials come from env - logger.info("Using external MinIO container") + logger.info("Using external S3 container") yield None return - from testcontainers.minio import MinioContainer - - # MinIO withdrew its public images: `minio/minio` on Docker Hub is gone - # entirely (any tag, not just `latest`) and `quay.io/minio/minio` now - # requires authentication. Chainguard publishes a maintained build that - # needs no credentials and is drop-in for this fixture. Overridable so a - # deployment can point at its own mirror without editing tests. - container = MinioContainer( - image=os.environ.get("DJ_TEST_MINIO_IMAGE", "cgr.dev/chainguard/minio:latest"), - access_key="datajoint", - secret_key="datajoint", + import time + + from testcontainers.core.container import DockerContainer + + # SeaweedFS replaces MinIO, which withdrew its public images and archived + # its source (#1560). It matched MinIO on s3fs directory emulation + # (isdir/walk/find over prefixes and zero-byte markers), which GC depends + # on. Overridable so a deployment can point at its own mirror. + container = ( + DockerContainer(os.environ.get("DJ_TEST_S3_IMAGE", "chrislusf/seaweedfs:4.48")) + .with_command("server -s3 -ip.bind=0.0.0.0") + .with_env("AWS_ACCESS_KEY_ID", "datajoint") + .with_env("AWS_SECRET_ACCESS_KEY", "datajoint") + .with_exposed_ports(8333) ) container.start() host = container.get_container_host_ip() - port = container.get_exposed_port(9000) - logger.info(f"MinIO container started at {host}:{port}") + port = container.get_exposed_port(8333) + # The S3 gateway starts after the master, volume, and filer servers + deadline = time.monotonic() + 60 + while True: + try: + urllib3.PoolManager().request("GET", f"http://{host}:{port}/", retries=False, timeout=1) + break + except urllib3.exceptions.HTTPError: + if time.monotonic() > deadline: + container.stop() + raise + time.sleep(0.5) + logger.info(f"S3 container started at {host}:{port}") yield container container.stop() - logger.info("MinIO container stopped") + logger.info("S3 container stopped") # ============================================================================= @@ -253,12 +267,12 @@ def db_creds_test(mysql_container) -> Dict: @pytest.fixture(scope="session") -def s3_creds(minio_container) -> Dict: - """S3/MinIO credentials from container or environment.""" - if minio_container is not None: +def s3_creds(s3_container) -> Dict: + """S3 credentials from container or environment.""" + if s3_container is not None: # From testcontainer - host = minio_container.get_container_host_ip() - port = minio_container.get_exposed_port(9000) + host = s3_container.get_container_host_ip() + port = s3_container.get_exposed_port(8333) return dict( endpoint=f"{host}:{port}", access_key="datajoint", @@ -268,7 +282,7 @@ def s3_creds(minio_container) -> Dict: else: # From environment (external container) return dict( - endpoint=os.environ.get("S3_ENDPOINT", "localhost:9000"), + endpoint=os.environ.get("S3_ENDPOINT", "localhost:8333"), access_key=os.environ.get("S3_ACCESS_KEY", "datajoint"), secret_key=os.environ.get("S3_SECRET_KEY", "datajoint"), bucket=os.environ.get("S3_BUCKET", "datajoint.test"), @@ -487,7 +501,7 @@ def connection_test(connection_root, prefix, db_creds_test): # ============================================================================= -# S3/MinIO Fixtures +# S3 Fixtures # ============================================================================= @@ -509,7 +523,7 @@ def stores_config(s3_creds, tmpdir_factory): bucket=s3_creds.get("bucket", "datajoint-test"), location="dj/repo", stage=str(tmpdir_factory.mktemp("repo-s3")), - secure=False, # MinIO runs without SSL in tests + secure=False, # The test S3 server runs without SSL ), "local": dict(protocol="file", location=str(tmpdir_factory.mktemp("local"))), "share": dict( @@ -519,7 +533,7 @@ def stores_config(s3_creds, tmpdir_factory): secret_key=s3_creds["secret_key"], bucket=s3_creds.get("bucket", "datajoint-test"), location="dj/store/repo", - secure=False, # MinIO runs without SSL in tests + secure=False, # The test S3 server runs without SSL ), } @@ -566,7 +580,7 @@ def http_client(): @pytest.fixture(scope="session") def s3fs_client(s3_creds): - """Initialize s3fs filesystem for MinIO.""" + """Initialize s3fs filesystem for the test S3 server.""" import s3fs return s3fs.S3FileSystem( @@ -577,8 +591,8 @@ def s3fs_client(s3_creds): @pytest.fixture(scope="session") -def minio_client(s3_creds, s3fs_client, teardown=False): - """S3 filesystem with test bucket created (legacy name for compatibility).""" +def s3_client(s3_creds, s3fs_client, teardown=False): + """S3 filesystem with the test bucket created.""" bucket = s3_creds["bucket"] # Create bucket if it doesn't exist diff --git a/tests/integration/test_attach.py b/tests/integration/test_attach.py index f7ad953fe..d3881d69d 100644 --- a/tests/integration/test_attach.py +++ b/tests/integration/test_attach.py @@ -5,7 +5,7 @@ from tests.schema_external import Attach -def test_attach_attributes(schema_ext, minio_client, tmpdir_factory): +def test_attach_attributes(schema_ext, s3_client, tmpdir_factory): """Test saving files in attachments""" import datajoint as dj @@ -46,7 +46,7 @@ def test_attach_attributes(schema_ext, minio_client, tmpdir_factory): assert p2 == path2[0] -def test_return_string(schema_ext, minio_client, tmpdir_factory): +def test_return_string(schema_ext, s3_client, tmpdir_factory): """Test returning string on fetch""" import datajoint as dj diff --git a/tests/integration/test_codecs.py b/tests/integration/test_codecs.py index 22365e841..a33abdffb 100644 --- a/tests/integration/test_codecs.py +++ b/tests/integration/test_codecs.py @@ -72,7 +72,7 @@ def test_codec_graph(schema_codec): c.delete() -def test_codec_chained(schema_codec, minio_client): +def test_codec_chained(schema_codec, s3_client): """Test codec chaining (layout -> blob).""" c = Connectivity() c.delete() diff --git a/tests/integration/test_npy_codec.py b/tests/integration/test_npy_codec.py index badd28cbe..eac472dd9 100644 --- a/tests/integration/test_npy_codec.py +++ b/tests/integration/test_npy_codec.py @@ -257,14 +257,14 @@ def test_codec_validate_rejects_object_dtype(self): # ============================================================================= -# Integration Tests (require database + MinIO) +# Integration Tests (require database + S3) # ============================================================================= class TestNpyCodecIntegration: """Integration tests for NpyCodec with real storage.""" - def test_insert_fetch_roundtrip(self, schema_npy, minio_client): + def test_insert_fetch_roundtrip(self, schema_npy, s3_client): """Basic insert and fetch should preserve array data.""" rec = Recording() rec.delete() @@ -284,7 +284,7 @@ def test_insert_fetch_roundtrip(self, schema_npy, minio_client): rec.delete() - def test_npy_ref_caching(self, schema_npy, minio_client): + def test_npy_ref_caching(self, schema_npy, s3_client): """NpyRef should cache loaded data.""" rec = Recording() rec.delete() @@ -304,7 +304,7 @@ def test_npy_ref_caching(self, schema_npy, minio_client): rec.delete() - def test_npy_ref_array_protocol(self, schema_npy, minio_client): + def test_npy_ref_array_protocol(self, schema_npy, s3_client): """NpyRef should work transparently in numpy operations.""" rec = Recording() rec.delete() @@ -331,7 +331,7 @@ def test_npy_ref_array_protocol(self, schema_npy, minio_client): rec.delete() - def test_npy_ref_indexing(self, schema_npy, minio_client): + def test_npy_ref_indexing(self, schema_npy, s3_client): """NpyRef should support indexing/slicing.""" rec = Recording() rec.delete() @@ -351,7 +351,7 @@ def test_npy_ref_indexing(self, schema_npy, minio_client): rec.delete() - def test_bulk_fetch_lazy(self, schema_npy, minio_client): + def test_bulk_fetch_lazy(self, schema_npy, s3_client): """Fetching via to_dicts should return NpyRefs that are lazy.""" rec = Recording() rec.delete() @@ -381,7 +381,7 @@ def test_bulk_fetch_lazy(self, schema_npy, minio_client): rec.delete() - def test_different_dtypes(self, schema_npy, minio_client): + def test_different_dtypes(self, schema_npy, s3_client): """NpyCodec should handle various numpy dtypes.""" rec = Recording() rec.delete() @@ -405,7 +405,7 @@ def test_different_dtypes(self, schema_npy, minio_client): rec.delete() - def test_multidimensional_arrays(self, schema_npy, minio_client): + def test_multidimensional_arrays(self, schema_npy, s3_client): """NpyCodec should handle various array shapes.""" rec = Recording() rec.delete() @@ -430,7 +430,7 @@ def test_multidimensional_arrays(self, schema_npy, minio_client): rec.delete() - def test_schema_addressed_path(self, schema_npy, minio_client): + def test_schema_addressed_path(self, schema_npy, s3_client): """NpyCodec should store files with .npy extension.""" rec = Recording() rec.delete() @@ -453,7 +453,7 @@ def test_schema_addressed_path(self, schema_npy, minio_client): class TestNpyCodecEdgeCases: """Edge case tests for NpyCodec.""" - def test_empty_array(self, schema_npy, minio_client): + def test_empty_array(self, schema_npy, s3_client): """NpyCodec should handle empty arrays.""" rec = Recording() rec.delete() @@ -470,7 +470,7 @@ def test_empty_array(self, schema_npy, minio_client): rec.delete() - def test_large_array(self, schema_npy, minio_client): + def test_large_array(self, schema_npy, s3_client): """NpyCodec should handle large arrays.""" rec = Recording() rec.delete() @@ -488,7 +488,7 @@ def test_large_array(self, schema_npy, minio_client): rec.delete() - def test_structured_array(self, schema_npy, minio_client): + def test_structured_array(self, schema_npy, s3_client): """NpyCodec should handle structured arrays.""" rec = Recording() rec.delete()