fixing deprecations, logging and typing

Author: JoOkuma

ultrack/cli/_test/test_cli.py

@@ -114,6 +114,7 @@ def test_fit_and_add_probs(
                 "-oc",
                 str(new_cfg_path),
                 "--is-tracking",
+                "--is-segmentation",
                 "--persistence",
             ]
             + zarr_dataset_paths

ultrack/cli/match_gt.py

@@ -150,7 +150,7 @@ def match_gt_cli(
         LOG.info("Estimated new config: %s", new_config)
         LOG.info("Saving new config to %s", output_config)
         with open(output_config, "w") as f:
-            toml.dump(new_config.dict(by_alias=True), f)
+            toml.dump(new_config.model_dump(by_alias=True), f)
 
     if insert_prob or output_model is not None:
         model = fit_nodes_prob(

ultrack/core/match_gt.py

@@ -379,8 +379,8 @@ def match_to_ground_truth(
         )
         max_area, min_area = min_area, max_area
 
-    opt_config.segmentation_config.min_area = float(min_area)
-    opt_config.segmentation_config.max_area = float(max_area)
+    opt_config.segmentation_config.min_area = int(round(min_area))
+    opt_config.segmentation_config.max_area = int(round(max_area))
 
     opt_config.segmentation_config.min_frontier = float(
         max(gt_df["parent_frontier"].min() - 0.025, 0.0)

ultrack/ml/classification.py

@@ -41,7 +41,7 @@ def _validate_classifier(
                 "`catboost` is required if classifier is not provided.\n"
                 "Please install it with `pip install catboost` or `pip install 'ultrack[ml]'`."
             ) from e
-        classifier = CatBoostClassifier(allow_const_label=True)
+        classifier = CatBoostClassifier(allow_const_label=True, silent=True)
 
     return classifier