chore: lint

AllenNeuralDynamics · Sep 26, 2024 · e9e3c46 · e9e3c46
1 parent 3909043
commit e9e3c46
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Showing 2 changed files with 31 additions and 101 deletions.
diff --git a/examples/quality_control.py b/examples/quality_control.py
@@ -13,93 +13,38 @@
     evaluation_description="Qualitative check that drift map shows minimal movement",
     evaluation_modality=Modality.ECEPHYS,
     evaluation_stage=Stage.PROCESSING,
-    evaluation_status=[
-        QCStatus(
-            evaluator="Fred Flintstone",
-            timestamp=t,
-            status=Status.FAIL
-        )
-    ],
+    evaluation_status=[QCStatus(evaluator="Fred Flintstone", timestamp=t, status=Status.FAIL)],
     qc_metrics=[
-        QCMetric(
-            name="Probe A drift",
-            value="High",
-            reference="ecephys-drift-map"
-        ),
-        QCMetric(
-            name="Probe B drift",
-            value="Low",
-            reference="ecephys-drift-map"
-        ),
-        QCMetric(
-            name="Probe C drift",
-            value="Low",
-            reference="ecephys-drift-map"
-        )
+        QCMetric(name="Probe A drift", value="High", reference="ecephys-drift-map"),
+        QCMetric(name="Probe B drift", value="Low", reference="ecephys-drift-map"),
+        QCMetric(name="Probe C drift", value="Low", reference="ecephys-drift-map"),
     ],
-    notes="Manually annotated: failed due to high drift on probe A"
+    notes="Manually annotated: failed due to high drift on probe A",
 )
 
 eval1 = QCEvaluation(
     evaluation_name="Video frame count check",
     evaluation_modality=Modality.BEHAVIOR_VIDEOS,
     evaluation_stage=Stage.RAW,
-    evaluation_status=[
-        QCStatus(
-            evaluator="Fred Flintstone",
-            timestamp=t,
-            status=Status.FAIL
-        )
-    ],
-    qc_metrics=[
-        QCMetric(
-            name="video_1_num_frames",
-            value=662
-        ),
-        QCMetric(
-            name="video_2_num_frames",
-            value=662
-        )
-    ],
-    notes="Pass when video_1_num_frames==video_2_num_frames"
+    evaluation_status=[QCStatus(evaluator="Fred Flintstone", timestamp=t, status=Status.FAIL)],
+    qc_metrics=[QCMetric(name="video_1_num_frames", value=662), QCMetric(name="video_2_num_frames", value=662)],
+    notes="Pass when video_1_num_frames==video_2_num_frames",
 )
 
 eval2 = QCEvaluation(
     evaluation_name="Probes present",
     evaluation_modality=Modality.ECEPHYS,
     evaluation_stage=Stage.RAW,
-    evaluation_status=[
-        QCStatus(
-            evaluator="Automated",
-            timestamp=t,
-            status=Status.PASS
-        )
-    ],
+    evaluation_status=[QCStatus(evaluator="Automated", timestamp=t, status=Status.PASS)],
     qc_metrics=[
-        QCMetric(
-            name="ProbeA_success",
-            value=True
-        ),
-        QCMetric(
-            name="ProbeB_success",
-            value=True
-        ),
-        QCMetric(
-            name="ProbeC_success",
-            value=True
-        )
+        QCMetric(name="ProbeA_success", value=True),
+        QCMetric(name="ProbeB_success", value=True),
+        QCMetric(name="ProbeC_success", value=True),
     ],
 )
 
 q = QualityControl(
-    overall_status=[
-        QCStatus(
-            evaluator="Automated",
-            timestamp=t,
-            status=Status.PASS
-        )
-    ],
-    evaluations=[eval0, eval1, eval2]
+    overall_status=[QCStatus(evaluator="Automated", timestamp=t, status=Status.PASS)], evaluations=[eval0, eval1, eval2]
 )
 
 serialized = q.model_dump_json()

diff --git a/tests/test_quality_control.py b/tests/test_quality_control.py
@@ -19,43 +19,28 @@ def test_constructors(self):
             q = QualityControl()
 
         test_eval = QCEvaluation(
-                evaluation_name="Drift map",
-                evaluation_status=[
-                    QCStatus(
-                        evaluator="Fred Flintstone",
-                        timestamp=date.fromisoformat("2020-10-10"),
-                        status=Status.PASS
-                    )
-                ],
-                evaluation_modality=Modality.ECEPHYS,
-                evaluation_stage=Stage.PROCESSING,
-                qc_metrics=[
-                    QCMetric(
-                        name="Multiple values example",
-                        value={"stuff": "in_a_dict"}
-                    ),
-                    QCMetric(
-                        name="Drift map pass/fail",
-                        value=False,
-                        description="Manual evaluation of whether the drift map looks good",
-                        references=["s3://some-data-somewhere"]
-                    )
-                ],
-            )
-
-        q = QualityControl(
-            overall_status=[
-                QCStatus(
-                    evaluator="Bob",
-                    timestamp=date.fromisoformat("2020-10-10"),
-                    status=Status.PASS
-                )
+            evaluation_name="Drift map",
+            evaluation_status=[
+                QCStatus(evaluator="Fred Flintstone", timestamp=date.fromisoformat("2020-10-10"), status=Status.PASS)
             ],
-            evaluations=[
-                test_eval
+            evaluation_modality=Modality.ECEPHYS,
+            evaluation_stage=Stage.PROCESSING,
+            qc_metrics=[
+                QCMetric(name="Multiple values example", value={"stuff": "in_a_dict"}),
+                QCMetric(
+                    name="Drift map pass/fail",
+                    value=False,
+                    description="Manual evaluation of whether the drift map looks good",
+                    references=["s3://some-data-somewhere"],
+                ),
             ],
         )
 
+        q = QualityControl(
+            overall_status=[QCStatus(evaluator="Bob", timestamp=date.fromisoformat("2020-10-10"), status=Status.PASS)],
+            evaluations=[test_eval],
+        )
+
         assert q is not None