Merge branch 'main' into test/mock-service-find

Author: olivermeyer

compass.yml

@@ -0,0 +1,77 @@
+name: python-sdk
+id: ari:cloud:compass:fff788d2-8a2a-4c36-a884-dde2bb4a2b49:component/f65912bc-77bd-4e1f-b333-1a9e8f0ac32c/aca547e5-2577-4f9d-9aaa-cf360acc976c
+description: 🔬 Python SDK providing access to the Aignostics Platform. Includes Aignostics Launchpad (Desktop Application), Aignostics CLI (Command-Line Interface), example notebooks, and Aignostics Client Library.
+configVersion: 1
+typeId: APPLICATION
+ownerId: ari:cloud:identity::team/b1cfb598-3138-4c2a-8b6a-19fb1078645b
+fields:
+  tier: 4
+links:
+  - name: null
+    type: REPOSITORY
+    url: https://github.com/aignostics/python-sdk
+relationships:
+  DEPENDS_ON: []
+labels:
+  - aignostics
+  - atlas
+  - dicom
+  - digital-pathology
+  - image-data-commons
+  - language:python
+  - machine-learning
+  - marimo
+  - medical-imaging
+  - nicegui
+  - oe-python-template
+  - openslide
+  - pydantic
+  - pydicom
+  - qupath
+  - source:github
+  - typer
+  - uv
+  - whole-slide-imaging
+customFields:
+  - name: CSV Approved
+    type: boolean
+    value: false
+  - name: Component Key
+    type: text
+    value: null
+  - name: Deployment Branch
+    type: text
+    value: null
+  - name: Development Branch
+    type: text
+    value: null
+  - name: FinOps Label
+    type: text
+    value: null
+  - name: Has external API
+    type: boolean
+    value: false
+  - name: Has external CLI
+    type: boolean
+    value: false
+  - name: Has external graphical UI
+    type: boolean
+    value: false
+  - name: Has internal API
+    type: boolean
+    value: false
+  - name: Has internal CLI
+    type: boolean
+    value: false
+  - name: Has internal graphical UI
+    type: boolean
+    value: false
+  - name: Is independently deployable
+    type: boolean
+    value: false
+  - name: Path in Repository
+    type: text
+    value: null
+  - name: Process Level
+    type: single_select
+    value: null

tests/aignostics/qupath/gui_test.py

@@ -302,7 +302,6 @@ async def test_gui_run_qupath_install_to_inspect(  # noqa: C901, PLR0912, PLR091
         # Check for (1) spot added to QuPath project, (2) heatmaps added, (3) spot annotated
         try:
             project_info = json.loads(output)
-            annotations_total = 0
             spot_found = False
             spot_width = None
             spot_height = None
@@ -329,7 +328,7 @@ async def test_gui_run_qupath_install_to_inspect(  # noqa: C901, PLR0912, PLR091
             ), (
                 f"Expected approximately {SPOT_0_EXPECTED_CELLS_CLASSIFIED[0]} "
                 f"({SPOT_0_EXPECTED_CELLS_CLASSIFIED[1]}% tolerance) annotations in the QuPath results, "
-                f"but found {annotations_total}"
+                f"but found {spot_annotations}"
             )
         except json.JSONDecodeError as e:
             pytest.fail(f"Failed to parse QuPath inspect output as JSON: {e}\nOutput: {output!r}\n")

tests/constants_test.py

@@ -97,7 +97,7 @@
         TEST_APPLICATION_VERSION = "0.0.6"
 
         HETA_APPLICATION_ID = "he-tme"
-        HETA_APPLICATION_VERSION = "1.0.0"
+        HETA_APPLICATION_VERSION = "1.1.0"
         TEST_APPLICATION_VERSION_USE_LATEST_FALLBACK_SKIP = True
 
         PIPELINE_GPU_TYPE = "L4"
@@ -112,28 +112,28 @@
         SPECIAL_APPLICATION_VERSION = "0.99.0"
 
         SPOT_0_EXPECTED_RESULT_FILES = [
-            ("tissue_qc_segmentation_map_image.tiff", 1540764, 10),
-            ("tissue_qc_geojson_polygons.json", 160668, 10),
-            ("tissue_segmentation_geojson_polygons.json", 853784, 10),
-            ("readout_generation_slide_readouts.csv", 302252, 10),
-            ("readout_generation_cell_readouts.csv", 1472661, 10),
-            ("cell_classification_geojson_polygons.json", 9939791, 10),
-            ("tissue_segmentation_segmentation_map_image.tiff", 2807584, 10),
-            ("tissue_segmentation_csv_class_information.csv", 451, 10),
-            ("tissue_qc_csv_class_information.csv", 284, 10),
+            ("tissue_qc_segmentation_map_image.tiff", 1642856, 10),
+            ("tissue_qc_geojson_polygons.json", 259955, 10),
+            ("tissue_segmentation_geojson_polygons.json", 887003, 10),
+            ("readout_generation_slide_readouts.csv", 303217, 10),
+            ("readout_generation_cell_readouts.csv", 1658344, 10),
+            ("cell_classification_geojson_polygons.json", 11218951, 10),
+            ("tissue_segmentation_segmentation_map_image.tiff", 2945078, 10),
+            ("tissue_segmentation_csv_class_information.csv", 452, 10),
+            ("tissue_qc_csv_class_information.csv", 285, 10),
         ]
-        SPOT_0_EXPECTED_CELLS_CLASSIFIED = (35160, 10)
+        SPOT_0_EXPECTED_CELLS_CLASSIFIED = (39798, 10)
 
         SPOT_1_EXPECTED_RESULT_FILES = [
-            ("tissue_qc_segmentation_map_image.tiff", 440122, 10),
-            ("tissue_qc_geojson_polygons.json", 139943, 10),
-            ("tissue_segmentation_geojson_polygons.json", 175419, 10),
-            ("readout_generation_slide_readouts.csv", 300408, 10),
-            ("readout_generation_cell_readouts.csv", 2384271, 10),
-            ("cell_classification_geojson_polygons.json", 16384866, 10),
-            ("tissue_segmentation_segmentation_map_image.tiff", 508552, 10),
-            ("tissue_segmentation_csv_class_information.csv", 443, 10),
-            ("tissue_qc_csv_class_information.csv", 284, 10),
+            ("tissue_qc_segmentation_map_image.tiff", 469040, 10),
+            ("tissue_qc_geojson_polygons.json", 177779, 10),
+            ("tissue_segmentation_geojson_polygons.json", 205951, 10),
+            ("readout_generation_slide_readouts.csv", 299654, 10),
+            ("readout_generation_cell_readouts.csv", 2387860, 10),
+            ("cell_classification_geojson_polygons.json", 16687724, 10),
+            ("tissue_segmentation_segmentation_map_image.tiff", 536582, 10),
+            ("tissue_segmentation_csv_class_information.csv", 441, 10),
+            ("tissue_qc_csv_class_information.csv", 286, 10),
         ]
 
     case _: