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- New .github/workflows/test.yml with parallel unit-tests and integration-tests jobs; integration job uses a Redis service container on port 6379. - New docker-compose-redis.yml for running Redis locally during development. - New tests/test_integration.py with 27 tests across 6 classes (status, get_normalized_nodes, semantic_types, curie_prefixes, setid, query, conflations), all marked pytest.mark.integration; data-loading placeholder present for Phase 2. - Updated tests/conftest.py to add session-scoped integration_client fixture with Redis availability check and TestClient context manager. - Updated tests/test_callback.py to skip test_async_query_callback (requires external callback-app container). - Updated pytest.ini to register integration and callback_integration markers and document the plain-pytest limitation from test_norm/test_setid module-level app.state mutation. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
NodeLoader.__init__ and get_config now accept an optional config_file parameter (defaults to the project-root config.json, preserving existing behavior). This removes the need for monkeypatching in tests and lets the integration test fixture and CI loading step pass tests/data/config.json directly. Also adds tests/data/config.json pointing at the Gene/Protein compendia and GeneProtein conflation under tests/data/, and wires it into the integration_client fixture and the GitHub Actions loading step. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
bmt.utils.format_element was renamed to bmt.util.format in the installed version (bmt==1.4.3); update the import in loader.py and normalizer.py. Integration tests are marked xfail because bmt-lite raises ValueError when Toolkit() is called with a schema URL in startup_event (server.py:75). Add tests/README.md documenting this and the unawaited-coroutine issue in test_loader.py::test_nn_load. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
I just don't like 'em.
bmt-lite-v3.1.0 was overwriting bmt/__init__.py in the shared namespace, causing Toolkit(url) to raise ValueError. Fix: uninstall bmt-lite and reinstall bmt cleanly. This also lets us revert the bmt.utils->bmt.util rename (format_element is back), and remove the xfail marker from all integration tests. Also fix test_unknown_semantic_type: the endpoint returns a "Not found" sentinel for unknown types rather than an empty dict; update the assertion to match the real behavior. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
aioredis 2.x defines TimeoutError(asyncio.TimeoutError, builtins.TimeoutError) which raises TypeError on Python 3.11+ where the two are the same type. The codebase uses the aioredis 1.x API (create_redis_pool, aioredis.commands.Redis) so 2.x would also break at runtime. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Without pins, CI installs pydantic v2 + matching newer fastapi/reasoner-pydantic. The codebase uses pydantic v1 APIs (class-based Config, min_items, etc.) and reasoner-pydantic 4.x, which are incompatible with pydantic v2. fastapi 0.100+ dropped pydantic v1 support. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
fastapi<0.100 was too broad: fastapi 0.99.x pulls in starlette 0.27+ which uses httpx as the TestClient backend. A newer httpx then dropped the app= kwarg, breaking TestClient(app) in all tests. fastapi==0.83.0 pins starlette==0.19.1 (requests-based TestClient), which is the version the test suite was written against. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
starlette 0.19.1 TestClient calls anyio.start_blocking_portal(), which was removed in anyio 4.x. CI was getting anyio 4.12.1 while the locally working version is 3.7.1. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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WIP