test(engine): make TestDrainTimeout deterministic + preserve subclass type in @ontology_entity by Aureliolo · Pull Request #1729 · Aureliolo/synthorg

Aureliolo · 2026-05-03T12:43:03Z

Summary

Fix the timing-sensitive TestDrainTimeout::test_drain_timeout_resolves_pending_futures flake hit by PR #1727's Test (Python 3.14) job, plus a foundational fix to the @ontology_entity decorator that surfaced as Pyright false-positives in the same file.

Root cause (test flake)

PR #1545 (commit 13f3db679, "TOCTOU races + resource leaks") changed TaskEngine.stop() to install an outer hard-deadline at 2 × timeout and re-raise TimeoutError when cleanup exceeds it. The pre-existing test called await eng.stop(timeout=0.05) and expected stop() to return cleanly, leaving only ~50 ms for cancellation + future-cleanup. Under xdist load on slow Ubuntu CI runners, cleanup intermittently overruns 50 ms, the outer hard-deadline fires, and TimeoutError escapes to the test as 1 failed, 27881 passed.

Changes

tests/unit/engine/test_task_engine_integration.py

Bump stop(timeout=…) from 0.05 to 0.5. Same contract is exercised (inner drain still fires, queued futures still resolve to shutdown failure) without race sensitivity. Cleanup margin grows from 50 ms to 500 ms — comfortably above the few milliseconds the cleanup actually needs.
Inline comment ties the budget to the 2 × timeout hard-deadline ratio so the next reader doesn't lower it back.

src/synthorg/ontology/decorator.py

The decorator's positional overload returned type[BaseModel], erasing concrete subclass identity. Pyright reported false-positive "no attribute" diagnostics on every @ontology_entity-decorated class (Task, Artifact, Agent, Project, Role, MeetingRecord, OrgFact, etc.). Mypy was lenient because the alternative overload returned Any.
Switched to PEP 695 inline type parameters (def ontology_entity[T: BaseModel](cls: type[T], /) -> type[T]: ...), bound to BaseModel. Static analysers now resolve Task as type[Task] instead of type[BaseModel].

Test plan

Targeted test 5 consecutive runs, including one slow run (31 s) that mirrors the CI-runner pressure that flaked the original — 5/5 PASSED.
Full file tests/unit/engine/test_task_engine_integration.py — 11/11 PASSED in 12 s.
Full strict mypy: Success: no issues found in 3626 source files.
Ruff lint + format clean.
Pre-push gates green: mypy (affected modules), pytest unit (affected modules), forbidden-literal gate, persistence-boundary gate, typed-boundary contract, cost-recording chokepoint.

Review coverage

This PR was opened directly via the GitHub MCP tool because a parallel /pre-pr-review is running in another terminal on a different branch. The full pre-PR review pipeline (specialist agents, triage gate) was not invoked. The changes are narrow and verified by the gates listed above.

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The decorator's positional overload returned type[BaseModel], which erased the concrete subclass type. Pyright reported false-positive 'no attribute' diagnostics on every @ontology_entity-decorated class (Task, Artifact, Agent, Project, Role, MeetingRecord, OrgFact, etc.). Mypy was lenient because the alternative overload returned Any. Use PEP 695 inline type parameters bound to BaseModel so the decorated class identity flows through to consumers. Static analysers now resolve Task as type[Task] instead of type[BaseModel].

stop(timeout=T) installs an outer hard-deadline at 2*T and re-raises TimeoutError when cleanup exceeds it. The original 50 ms budget left only ~50 ms for cancellation plus future-cleanup, which raced under xdist load on slow CI runners and surfaced as TimeoutError escaping stop() (e.g. PR #1727 hit this). Bump the budget to 500 ms so the cleanup margin is 500 ms instead of 50 ms. The same contract is exercised (inner drain still fires, queued futures still resolve to shutdown failure) without race sensitivity. Inline comment explains the budget choice tied to the hard-deadline ratio so the next reader does not lower it back.

github-actions · 2026-05-03T12:43:15Z

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coderabbitai · 2026-05-03T12:43:20Z

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🔇 Additional comments (3)

src/synthorg/ontology/decorator.py (2)

25-26: Type-only import placement is correct.

Callable under TYPE_CHECKING is appropriate here and keeps runtime imports lean while supporting overload typing.

132-151: Generic overloads are a strong typing improvement.

The new type[T]-preserving overloads correctly keep concrete model subclass types across both decorator usage patterns.

tests/unit/engine/test_task_engine_integration.py (1)

320-336: Looks good — the larger stop timeout matches the engine’s 2× hard-deadline behavior.

This keeps the test focused on the same drain/cleanup contract while giving enough headroom to avoid the CI/xdist race without materially slowing the suite.

Walkthrough

This pull request updates the type stubs for the @ontology_entity decorator in src/synthorg/ontology/decorator.py to use generic type parameter T for better static type preservation. The no-argument overload now returns type[T] and the keyword-argument overload returns Callable[[type[T]], type[T]], replacing previous type[BaseModel] and Any return types. The runtime implementation behavior remains unchanged. Additionally, a test timeout in tests/unit/engine/test_task_engine_integration.py is increased from 0.05 to 0.5 seconds with added explanatory comments clarifying the drain and hard-deadline timeout mechanics.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly summarizes the main changes: making the TestDrainTimeout test deterministic and preserving subclass type in `@ontology_entity` decorator.
Description check	✅ Passed	The description provides detailed context and rationale for both changes, thoroughly explaining the root cause of the test flake and the typing fix.
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codspeed-hq · 2026-05-03T12:45:33Z

Merging this PR will not alter performance

✅ 33 untouched benchmarks
⏩ 21 skipped benchmarks¹

_{Comparing fix/test-drain-timeout-flaky (2aca184) with main (5cb1212)}

21 benchmarks were skipped, so the baseline results were used instead. If they were deleted from the codebase, click here and archive them to remove them from the performance reports. ↩

gemini-code-assist

Code Review

This pull request updates the ontology_entity decorator to use PEP 695 generic syntax, aiming to preserve concrete subclass types in static analysis, and increases a test timeout to improve CI stability. The review identifies critical runtime issues: Callable and BaseModel are imported only during type checking but are required at runtime for signature evaluation, which will cause NameError exceptions. Furthermore, the decorator factory overload is flagged for potential type erasure since the generic parameter T cannot be inferred from the factory's arguments.

gemini-code-assist · 2026-05-03T12:46:51Z

 logger = get_logger(__name__)

 if TYPE_CHECKING:
+    from collections.abc import Callable


The Callable import is placed inside a TYPE_CHECKING block, but it is used in the runtime signatures of the ontology_entity overloads (e.g., line 151). Since this module does not use from __future__ import annotations, these signatures are evaluated when the module is loaded, which will result in a NameError at runtime. This import should be moved outside the TYPE_CHECKING block.

Suggested change

logger = get_logger(__name__)

if TYPE_CHECKING:

from collections.abc import Callable

from collections.abc import Callable

logger = get_logger(__name__)

if TYPE_CHECKING:

gemini-code-assist · 2026-05-03T12:46:52Z

+# false-positive "no attribute" diagnostics.
 @overload
-def ontology_entity(cls: type[BaseModel], /) -> type[BaseModel]: ...
+def ontology_entity[T: BaseModel](cls: type[T], /) -> type[T]: ...


The PEP 695 type parameter T uses BaseModel as its bound. In Python 3.12+, bounds of type parameters are evaluated at runtime when the function is defined. Since BaseModel is only imported within a TYPE_CHECKING block (line 27) and annotations are not deferred via from __future__ import annotations, this will cause a NameError at runtime. Additionally, the use of EntityTier and EntitySource in the subsequent overload's signature will trigger similar errors. To fix this while avoiding circular imports, you may need to use the traditional TypeVar syntax with a string forward reference for the bound: T = TypeVar("T", bound="BaseModel").

gemini-code-assist · 2026-05-03T12:46:52Z

+def ontology_entity[T: BaseModel](
    *,
    entity_name: str | None = None,
    tier: EntityTier | None = None,
    source: EntitySource | None = None,
-) -> Any: ...
+) -> Callable[[type[T]], type[T]]: ...


The second overload for ontology_entity (the decorator factory) appears to erase the concrete subclass type in static analysis. The type parameter T is scoped to the ontology_entity function and is bound when the factory is called. Because T is not used in the factory's arguments, it cannot be inferred and will default to its bound (BaseModel). Consequently, the returned callable is typed as Callable[[type[BaseModel]], type[BaseModel]], which erases the specific identity of the decorated class. To preserve the subclass type, the returned callable itself should be generic (e.g., by using a Protocol with a generic __call__ or using a module-level TypeVar).

codecov · 2026-05-03T12:52:46Z

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✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.73%. Comparing base (5cb1212) to head (2aca184).
⚠️ Report is 1 commits behind head on main.
✅ All tests successful. No failed tests found.

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@@           Coverage Diff           @@
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  Branches     8991     8991           
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+ Misses      13452    13449    -3     
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@Ontology

## Highlights > _AI-generated summary (model: `openai/gpt-4.1-mini` via GitHub Models). Commit-based changelog below._ ### What you'll notice - Frontend and UX polishing improves user interface responsiveness and visual consistency. - API hygiene and validation enhancements provide smoother and more reliable interactions. ### What's new - Introduced typed-boundary helpers enabling better type safety and parse_typed workflows. - Added codebase-audit skill prompt tuning for improved project auditing. ### Under the hood - Eliminated flaky tests caused by module-level state for more stable test outcomes. - Unified image tag management under CLI and Renovate for consistent dependency updates. - Added cross-PR file-overlap analysis to the review dependency pull request skill. - Updated multiple dependencies including Python, Web, CLI, and container libraries. - Improved CI tooling and lock file maintenance for better build reliability.  :robot: I have created a release *beep* *boop* --- ## [0.7.8](v0.7.7...v0.7.8) (2026-05-03) ### Features * **api:** typed-boundary helper + codebase-audit skill prompt tuning ([#1712](#1712)) ([40ee65b](40ee65b)) * **boundary:** RFC [#1711](#1711) Phases 2 + 3 — typed boundaries via parse_typed ([#1720](#1720)) ([7b9f409](7b9f409)) ### Bug Fixes * **api:** audit cleanup B -- API hygiene & validation ([#1719](#1719)) ([3d790d9](3d790d9)) * audit cleanup C - persistence, concurrency & data integrity ([#1708](#1708)) ([#1717](#1717)) ([bcce097](bcce097)) * **test:** exterminate xdist-flaky tests with module-level state ([#1713](#1713)) ([#1721](#1721)) ([8d258dd](8d258dd)) * **web:** audit cleanup E -- frontend & UX polish ([#1710](#1710)) ([#1718](#1718)) ([3a3591a](3a3591a)) ### Refactoring * **cli:** single source of truth for DHI image tags + Renovate manager ([#1723](#1723)) ([57980a2](57980a2)) ### Documentation * audit cleanup D -- public-facing & docs sync ([#1709](#1709)) ([#1715](#1715)) ([ade03b7](ade03b7)) ### Tests * **engine:** make TestDrainTimeout deterministic + preserve subclass type in [@Ontology](https://github.com/ontology)_entity ([#1729](#1729)) ([b00fb05](b00fb05)) ### CI/CD * Update CI tool dependencies ([#1703](#1703)) ([355a9ff](355a9ff)) ### Maintenance * add cross-PR file-overlap analysis to review-dep-pr skill ([#1722](#1722)) ([3861d8a](3861d8a)) * **ci:** unify apko-version under workflow env so Renovate manages it everywhere ([#1724](#1724)) ([9c0a7fd](9c0a7fd)) * consolidate DHI image-pin custom regex managers ([#1726](#1726)) ([b8b0cba](b8b0cba)) * **deps:** update dependency chainguard-dev/melange to v0.50.4 ([#1701](#1701)) ([8cbf83a](8cbf83a)) * Lock file maintenance ([#1705](#1705)) ([414cfea](414cfea)) * Lock file maintenance ([#1727](#1727)) ([5cb1212](5cb1212)) * Update CLI dependencies ([#1702](#1702)) ([9fb57b9](9fb57b9)) * Update Container dependencies ([#1698](#1698)) ([6d24fd6](6d24fd6)) * Update dependency @eslint-react/eslint-plugin to v5 ([#1704](#1704)) ([1cb1294](1cb1294)) * Update Python dependencies ([#1699](#1699)) ([8e7af3a](8e7af3a)) * Update Python dependencies to v4.15.0 ([#1725](#1725)) ([69164c8](69164c8)) * Update Web dependencies ([#1700](#1700)) ([715300d](715300d)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). --------- Co-authored-by: synthorg-repo-bot[bot] <279117679+synthorg-repo-bot[bot]@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

Aureliolo added 2 commits May 3, 2026 14:37

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Aureliolo merged commit b00fb05 into main May 3, 2026
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chore(main): release 0.7.8 #1714

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test(engine): make TestDrainTimeout deterministic + preserve subclass type in @ontology_entity#1729

test(engine): make TestDrainTimeout deterministic + preserve subclass type in @ontology_entity#1729
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Aureliolo commented May 3, 2026

Summary

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