🧪 Add tests for _ensure_registrations

docs/02-architecture/generated/module-dependency-map.json

@@ -1,12 +1,12 @@
 {
   "summary": {
     "scanned_modules": 1947,
-    "total_internal_imports": 7697,
+    "total_internal_imports": 7698,
     "layer_edges": 13,
     "cross_layer_group_edges": 60,
     "cross_layer_group_edges_total": 330,
     "violations": 0,
-    "source_fingerprint": "b95d700be542d6171fe3d5e1dff5df0d020d8352626bdaf7c63638f61c4fbbe9"
+    "source_fingerprint": "65812f7c9b0d268bdf97a7966535ffae61d04808363fa1d00a86f6736980fba2"
   },
   "layer_edges": [
     {
@@ -18,7 +18,7 @@
     {
       "source": "application",
       "target": "domain",
-      "imports": 1154,
+      "imports": 1155,
       "allowed": true
     },
     {
@@ -122,7 +122,7 @@
     {
       "source": "application.services",
       "target": "domain.control_plane",
-      "imports": 75
+      "imports": 76
     },
     {
       "source": "application.composite",

docs/02-architecture/generated/module-dependency-map.md

@@ -6,7 +6,7 @@
 ## Summary
 
 - Scanned modules: `1947`
-- Internal import edges (raw): `7697`
+- Internal import edges (raw): `7698`
 - Aggregated layer edges: `13`
 - Layer policy violations: `0`
 - Cross-layer module-group edges (total): `330`
@@ -22,7 +22,7 @@ flowchart LR
     composition[composition]
     interfaces[interfaces]
     application -->|1319 OK| application
-    application -->|1154 OK| domain
+    application -->|1155 OK| domain
     composition -->|287 OK| application
     composition -->|689 OK| composition
     composition -->|445 OK| domain
@@ -41,7 +41,7 @@ flowchart LR
 | From             | To               | Imports | Policy  |
 | ---------------- | ---------------- | ------: | ------- |
 | `application`    | `application`    |    1319 | allowed |
-| `application`    | `domain`         |    1154 | allowed |
+| `application`    | `domain`         |    1155 | allowed |
 | `composition`    | `application`    |     287 | allowed |
 | `composition`    | `composition`    |     689 | allowed |
 | `composition`    | `domain`         |     445 | allowed |
@@ -64,7 +64,7 @@ flowchart LR
 | `infrastructure.adapters`      | `domain.ports`                  |      88 |
 | `application.pipelines`        | `domain.types`                  |      82 |
 | `application.core`             | `domain.ports`                  |      78 |
-| `application.services`         | `domain.control_plane`          |      75 |
+| `application.services`         | `domain.control_plane`          |      76 |
 | `application.composite`        | `domain.ports`                  |      74 |
 | `application.services`         | `domain.ports`                  |      73 |
 | `infrastructure.storage`       | `domain.types`                  |      69 |

src/bioetl/application/pipelines/chembl/target_helpers.py

@@ -126,8 +126,7 @@ def project_component_xrefs(cls, xrefs: list[JsonDict]) -> dict[str, str]:
             )
 
         return {
-            column: cls.pipe_or_unknown(values)
-            for column, values in buckets.items()
+            column: cls.pipe_or_unknown(values) for column, values in buckets.items()
         }
 
     @classmethod
@@ -178,7 +177,9 @@ def synonym_target_field(syn_type: object) -> str | None:
         if normalized_type == "EC_NUMBER":
             return "target_ec_numbers"
 
-        if normalized_type == "GENE_SYMBOL" or normalized_type.startswith("GENE_SYMBOL_"):
+        if normalized_type == "GENE_SYMBOL" or normalized_type.startswith(
+            "GENE_SYMBOL_"
+        ):
             return "target_gene_synonyms"
 
         return None
@@ -266,9 +267,7 @@ def project_component_synonyms(
             "target_gene_synonyms": cls.pipe_or_unknown(
                 buckets["target_gene_synonyms"]
             ),
-            "target_ec_numbers": cls.pipe_or_unknown(
-                buckets["target_ec_numbers"]
-            ),
+            "target_ec_numbers": cls.pipe_or_unknown(buckets["target_ec_numbers"]),
         }
 
 

src/bioetl/application/pipelines/chembl/target_transformer.py

@@ -120,9 +120,7 @@ def _extract_business_data(
         # Extract primary component_id (first element) for enricher join key
         component_ids = flattened_components.get("component_ids")
         primary_component_id = component_ids[0] if component_ids else None
-        projected_synonyms = SynonymHelper.project_component_synonyms(
-            target_components
-        )
+        projected_synonyms = SynonymHelper.project_component_synonyms(target_components)
         component_xrefs = XrefHelper.collect_component_xrefs(target_components)
         xref_projection = XrefHelper.project_component_xrefs(component_xrefs)
 
@@ -163,15 +161,9 @@ def _extract_business_data(
             if component_xrefs
             else None,
             "target_xref_pdb_ids": xref_projection["target_xref_pdb_ids"],
-            "target_xref_go_component": xref_projection[
-                "target_xref_go_component"
-            ],
-            "target_xref_go_function": xref_projection[
-                "target_xref_go_function"
-            ],
-            "target_xref_go_process": xref_projection[
-                "target_xref_go_process"
-            ],
+            "target_xref_go_component": xref_projection["target_xref_go_component"],
+            "target_xref_go_function": xref_projection["target_xref_go_function"],
+            "target_xref_go_process": xref_projection["target_xref_go_process"],
             "target_xref_reactome_ids": xref_projection["target_xref_reactome_ids"],
             # Flattened components
             **serialized_flattened_components,

src/bioetl/infrastructure/storage/silver/operations/delta_operations.py

@@ -103,11 +103,14 @@ async def _write_delete_impl(
     request: _DeltaWriteRequest,
 ) -> None:
     """Write data in delete mode (overwrite table)."""
-    policy = getattr(
-        host,
-        "_merge_resilience_policy",
-        DEFAULT_SILVER_MERGE_POLICY,
-    ) or DEFAULT_SILVER_MERGE_POLICY
+    policy = (
+        getattr(
+            host,
+            "_merge_resilience_policy",
+            DEFAULT_SILVER_MERGE_POLICY,
+        )
+        or DEFAULT_SILVER_MERGE_POLICY
+    )
     await _write_plain_delta_request(
         load_module=host._load_silver_writer_module,
         request=request,
@@ -122,11 +125,14 @@ async def _write_append_impl(
     request: _DeltaWriteRequest,
 ) -> None:
     """Write data in append mode."""
-    policy = getattr(
-        host,
-        "_merge_resilience_policy",
-        DEFAULT_SILVER_MERGE_POLICY,
-    ) or DEFAULT_SILVER_MERGE_POLICY
+    policy = (
+        getattr(
+            host,
+            "_merge_resilience_policy",
+            DEFAULT_SILVER_MERGE_POLICY,
+        )
+        or DEFAULT_SILVER_MERGE_POLICY
+    )
     await _write_plain_delta_request(
         load_module=host._load_silver_writer_module,
         request=request,

src/memory/validation.py

@@ -8,11 +8,11 @@
 from typing import Any
 
 from memory.notes import (
+    NOTE_READ_TIMEOUT_SECONDS,
     extract_markdown_headings,
     normalize_text_key,
     parse_markdown_note,
     parse_markdown_note_metadata,
-    NOTE_READ_TIMEOUT_SECONDS,
 )
 from memory.resources import (
     CATALOG_DIR,

tests/architecture/test_adapter_contracts.py

@@ -20,13 +20,11 @@
 import shutil
 import subprocess
 from concurrent.futures import ThreadPoolExecutor
-from importlib import import_module
 from pathlib import Path
 from unittest.mock import AsyncMock, MagicMock
 
 import pytest
 
-from bioetl.domain.ports import FilterableDataSourcePort
 
 ADAPTER_MIXIN_CANONICAL_FILES = frozenset(
     {

tests/architecture/test_application_services_lazy_facade_governance.py

@@ -202,7 +202,9 @@ def _run_command_with_stdout_file(
                     start_time = time.time()  # Reset for kill timeout
                 if killed and (time.time() - start_time > kill_timeout):
                     process.terminate()
-                    raise OSError(f"Command timed out after {timeout}s and failed to terminate: {' '.join(command)}")
+                    raise OSError(
+                        f"Command timed out after {timeout}s and failed to terminate: {' '.join(command)}"
+                    )
                 time.sleep(poll_interval)
 
             completed = subprocess.CompletedProcess(

tests/architecture/test_composite_dq_externalization.py

@@ -113,10 +113,10 @@ def test_external_composite_dq_bundle_is_not_threshold_only(
             f"Composite DQ config must declare non-empty required_fields: {external_path}"
         )
         assert (
-            isinstance(field_validations, list)
-            and field_validations
-            or isinstance(cross_field_validations, list)
-            and cross_field_validations
+            (isinstance(field_validations, list)
+            and field_validations)
+            or (isinstance(cross_field_validations, list)
+            and cross_field_validations)
         ), (
             "Composite DQ config must declare field or cross-field validation "
             f"bundles: {external_path}"

tests/architecture/test_deprecation_warnings.py

@@ -54,9 +54,9 @@ def test_deprecation_warning_ignores_are_not_hidden_in_test_modules() -> None:
 
 def test_runner_assembly_has_no_deprecated_fsm_bootstrap_warning() -> None:
     """Composite runner assembly should require explicit FSM helper injection."""
-    source = (ROOT / Path(
-        "src/bioetl/composition/bootstrap/runtime/runner_assembly.py"
-    )).read_text(encoding="utf-8")
+    source = (
+        ROOT / Path("src/bioetl/composition/bootstrap/runtime/runner_assembly.py")
+    ).read_text(encoding="utf-8")
     assert (
         "Creating CompositePipelineRunner without fsm_state_helper is deprecated"
         not in source
@@ -66,14 +66,12 @@ def test_runner_assembly_has_no_deprecated_fsm_bootstrap_warning() -> None:
 
 def test_composite_application_services_do_not_reintroduce_legacy_aliases() -> None:
     """Composite application helpers should expose canonical service names only."""
-    fsm_source = (ROOT / Path("src/bioetl/application/composite/fsm_helper.py")).read_text(
-        encoding="utf-8"
-    )
+    fsm_source = (
+        ROOT / Path("src/bioetl/application/composite/fsm_helper.py")
+    ).read_text(encoding="utf-8")
     dedup_source = (
         ROOT / Path("src/bioetl/application/composite/deduplication.py")
-    ).read_text(
-        encoding="utf-8"
-    )
+    ).read_text(encoding="utf-8")
 
     assert "class FSMStateHelper(" not in fsm_source
     assert '"FSMStateHelper"' not in fsm_source

tests/helpers/__init__.py

@@ -27,8 +27,8 @@
     "assert_check_artifacts_passes_for_fresh_outputs",
     "assert_cli_succeeded",
     "assert_process_succeeded",
-    "assert_router_python_command",
     "assert_repeated_core_output_bytes_are_stable",
+    "assert_router_python_command",
     "assert_written_core_artifacts_are_deterministic",
     "repo_root",
     "run_main_in_process",

tests/integration/_consolidation_suite_support.py

@@ -27,7 +27,7 @@ def patch_quarantine_adapter_for_cached_fixture_replay(
 ) -> None:
     """Avoid quarantine-delta side effects during cached fixture replays."""
 
-    async def _write_many_without_delta(self, records):  # noqa: ANN001
+    async def _write_many_without_delta(self, records):
         stored = getattr(self, "_test_quarantine_records", [])
         stored.extend([self._normalize_record(record) for record in records])
         self._test_quarantine_records = stored

tests/integration/ci/reproducibility_contract_support.py

@@ -41,7 +41,7 @@ def __init__(self) -> None:
         self._items: dict[str, list[object]] = {}
 
     def append(self, entry: object) -> None:
-        manifest_id = getattr(entry, "manifest_id")
+        manifest_id = entry.manifest_id
         self._items.setdefault(manifest_id, []).append(entry)
 
     def list_entries(self, manifest_id: str) -> tuple[object, ...]:

tests/integration/determinism/test_reproducibility_determinism_gate.py

@@ -33,11 +33,19 @@ def _stable_manifest_payload(payload: dict) -> dict:
         "replay_capability": payload.get("replay_capability"),
         "launch_context": {
             key: payload.get("launch_context", {}).get(key)
-            for key in ("exact_replay", "execution_context", "required_persistence_profile")
+            for key in (
+                "exact_replay",
+                "execution_context",
+                "required_persistence_profile",
+            )
         },
         "runtime_config": {
             key: payload.get("runtime_config", {}).get(key)
-            for key in ("exact_replay", "execution_context", "required_persistence_profile")
+            for key in (
+                "exact_replay",
+                "execution_context",
+                "required_persistence_profile",
+            )
         },
         "code_provenance": {
             "contract_ref": payload["code_provenance"]["contract_ref"],
@@ -65,8 +73,15 @@ async def test_consolidation_determinism_replay_guard(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,
 ) -> None:
-    first_manifest, second_manifest, first_effective, second_effective, first_run_id, second_run_id = (
-        await run_tracked_fixture_replay_pair(tmp_path=tmp_path, monkeypatch=monkeypatch)
+    (
+        first_manifest,
+        second_manifest,
+        first_effective,
+        second_effective,
+        first_run_id,
+        second_run_id,
+    ) = await run_tracked_fixture_replay_pair(
+        tmp_path=tmp_path, monkeypatch=monkeypatch
     )
 
     assert first_manifest["run_id"] != second_manifest["run_id"]
@@ -76,7 +91,10 @@ async def test_consolidation_determinism_replay_guard(
 
     assert first_manifest["replay_capability"] == "exact_replay_supported"
     assert second_manifest["replay_capability"] == "exact_replay_supported"
-    assert first_manifest["execution_fingerprint"] == second_manifest["execution_fingerprint"]
+    assert (
+        first_manifest["execution_fingerprint"]
+        == second_manifest["execution_fingerprint"]
+    )
     assert first_manifest["launch_context"]["exact_replay"] is True
     assert second_manifest["launch_context"]["exact_replay"] is True
 
@@ -98,9 +116,9 @@ async def test_consolidation_determinism_replay_guard(
         first_manifest["code_provenance"]["dq_contract_compatibility_hash"]
         == second_manifest["code_provenance"]["dq_contract_compatibility_hash"]
     )
-    assert _canonical_manifest_fingerprint(first_manifest) == _canonical_manifest_fingerprint(
-        second_manifest
-    )
+    assert _canonical_manifest_fingerprint(
+        first_manifest
+    ) == _canonical_manifest_fingerprint(second_manifest)
     assert first_effective["artifact_id"] == second_effective["artifact_id"]
 
     evidence_dir = tmp_path / "reports" / "reproducibility"