Enabling widget testing and deprecated testing old widgets

tox.ini

@@ -36,7 +36,7 @@ deps =
     pyqt5
     git+https://github.com/hadim/pytrackmate.git
 commands =
-    pytest -v --color=yes --cov=ultrack --cov-report=xml --durations=15 --ignore=ultrack/widgets
+    pytest -v --color=yes --cov=ultrack --cov-report=xml --durations=15
 
 [testenv:lint]
 description = Runs all linting tasks

ultrack/api/app.py

@@ -130,7 +130,7 @@ async def start_experiment(ws: WebSocket, exp: Experiment) -> None:
     update_experiment(exp)
     await app.state.queue.join()
     await app.state.queue.put(exp)
-    await ws.send_json(json.loads(exp.json()))
+    await ws.send_json(json.loads(exp.model_dump_json()))
     UltrackWebsocketLogger.register_interruption_handler(exp.id)
     exp.status = ExperimentStatus.INITIALIZING
     update_experiment(exp)
@@ -157,7 +157,7 @@ async def finish_experiment(ws: WebSocket, exp: Experiment) -> Experiment:
     app.state.queue.task_done()
     if ws.client_state == WebSocketState.CONNECTED:
         # send the final state
-        await ws.send_json(json.loads(exp.json()))
+        await ws.send_json(json.loads(exp.model_dump_json()))
     return exp
 
 

ultrack/api/utils/api.py

@@ -209,7 +209,7 @@ async def run_thread():
                 experiment.err_log = _mimic_carriage_return(self.stderr.getvalue())
             if websocket.state == WebSocketState.DISCONNECTED:
                 return False
-            await websocket.send_json(json.loads(experiment.json()))
+            await websocket.send_json(json.loads(experiment.model_dump_json()))
             return True
 
         def between_callback(stop_logger_event: threading.Event):

ultrack/core/gt_matching.py

@@ -291,7 +291,7 @@ def match_to_ground_truth(
         return df_nodes
 
     # optimize configuration
-    opt_config = config.copy(deep=True)
+    opt_config = config.model_copy(deep=True)
     gt_df = df_nodes[df_nodes["gt_track_id"] > 0]
 
     if len(gt_df) == 0:

ultrack/widgets/_test/test_division_annotation_widget.py

@@ -11,6 +11,8 @@
 from ultrack.core.database import NodeDB, VarAnnotation
 from ultrack.widgets import DivisionAnnotationWidget
 
+pytest.skip(reason="DEPRECATED", allow_module_level=True)
+
 
 @pytest.mark.parametrize(
     "config_content",

ultrack/widgets/_test/test_hypotheses_viz_widget.py

@@ -12,6 +12,8 @@
 from ultrack.core.segmentation.node import Node
 from ultrack.widgets import HypothesesVizWidget
 
+pytest.skip(reason="DEPRECATED", allow_module_level=True)
+
 
 def _is_sorted(nodes: Dict[int, Node]) -> bool:
     nodes = list(nodes.values())

ultrack/widgets/_test/test_labels_to_edges_widget.py

@@ -2,10 +2,12 @@
 
 import napari
 import numpy as np
+import pytest
 
-from ultrack.utils._test.test_edge import multiple_labels  # noqa: F401
 from ultrack.widgets import LabelsToContoursWidget
 
+pytest.skip(reason="DEPRECATED", allow_module_level=True)
+
 
 def test_labels_to_contours_widget(
     make_napari_viewer: Callable[[], napari.Viewer],

ultrack/widgets/_test/test_node_annotation_widget.py

@@ -2,6 +2,7 @@
 from typing import Callable, Tuple
 
 import napari
+import pytest
 import zarr
 from sqlalchemy import create_engine
 from sqlalchemy.orm import Session
@@ -10,6 +11,8 @@
 from ultrack.core.database import NodeDB, NodeSegmAnnotation
 from ultrack.widgets import NodeAnnotationWidget
 
+pytest.skip(reason="DEPRECATED", allow_module_level=True)
+
 
 def test_node_annotation_widget(
     make_napari_viewer: Callable[[], napari.Viewer],

ultrack/widgets/_test/test_track_inspection_widget.py

@@ -9,6 +9,8 @@
 from ultrack.config import MainConfig
 from ultrack.widgets import TrackInspectionWidget
 
+pytest.skip(reason="DEPRECATED", allow_module_level=True)
+
 
 @pytest.mark.parametrize(
     "config_content,timelapse_mock_data",

ultrack/widgets/ultrackwidget/_legacy/_test/test_widgets.py

@@ -4,10 +4,13 @@
 
 import higra as hg
 import napari
+import pytest
 
 from ultrack.config import MainConfig
 from ultrack.widgets.ultrackwidget import UltrackWidget
 
+pytest.skip(reason="DEPRECATED", allow_module_level=True)
+
 
 def test_ultrack_widget(
     make_napari_viewer: Callable[[], napari.Viewer],

ultrack/widgets/ultrackwidget/data_forms.py

@@ -13,7 +13,7 @@
     QWidget,
 )
 
-from ultrack.config import CFG_ALIAS_TO_ATTR, MainConfig
+from ultrack.config.config import CFG_ALIAS_TO_ATTR, MainConfig
 from ultrack.widgets.ultrackwidget.components.blankable_number_edit import (
     BlankableNumberEdit,
 )