chore: Bump BMZ dependency to 0.9.0

pyproject.toml

@@ -44,7 +44,7 @@ dependencies = [
     'numpy<2.0.0',
     'torch>=2.0,<=2.7.1',
     'torchvision<=0.22.1',
-    'bioimageio.core==0.7',
+    'bioimageio.core==0.9.0',
     'tifffile<=2025.5.10',
     'psutil<=7.0.0',
     'pydantic>=2.11,<=2.12',
@@ -55,7 +55,6 @@ dependencies = [
     'zarr<3.0.0',
     'pillow<=11.2.1',
     'matplotlib<=3.10.3',
-    'xarray<2025.3.0',
 ]
 
 [project.optional-dependencies]

src/careamics/model_io/bioimage/model_description.py

@@ -4,15 +4,14 @@
 from typing import Optional, Union
 
 import numpy as np
-from bioimageio.spec._internal.io import resolve_and_extract
+from bioimageio.spec._internal.io import extract
 from bioimageio.spec.model.v0_5 import (
     ArchitectureFromLibraryDescr,
     Author,
     AxisBase,
     AxisId,
     BatchAxis,
     ChannelAxis,
-    EnvironmentFileDescr,
     FileDescr,
     FixedZeroMeanUnitVarianceAlongAxisKwargs,
     FixedZeroMeanUnitVarianceDescr,
@@ -269,7 +268,7 @@ def create_model_description(
             source=weights_path,
             architecture=architecture_descr,
             pytorch_version=Version(torch_version),
-            dependencies=EnvironmentFileDescr(source=env_path),
+            dependencies=FileDescr(source=Path(env_path)),
         ),
     )
 
@@ -322,17 +321,19 @@ def extract_model_path(model_desc: ModelDescr) -> tuple[Path, Path]:
     """
     if model_desc.weights.pytorch_state_dict is None:
         raise ValueError("No model weights found in model description.")
-    weights_path = resolve_and_extract(
-        model_desc.weights.pytorch_state_dict.source
-    ).path
+
+    # extract the zip model and return the directory
+    model_dir = extract(model_desc.root)
+
+    weights_path = model_dir.joinpath(model_desc.weights.pytorch_state_dict.source.path)
 
     for file in model_desc.attachments:
         file_path = file.source if isinstance(file.source, Path) else file.source.path
         if file_path is None:
             continue
         file_path = Path(file_path)
         if file_path.name == "careamics.yaml":
-            config_path = resolve_and_extract(file.source).path
+            config_path = model_dir.joinpath(file.source.path)
             break
     else:
         raise ValueError("Configuration file not found.")

src/careamics/model_io/bmz_io.py

@@ -187,7 +187,7 @@ def export_to_bmz(
 
         # test model description
         test_kwargs = (
-            model_description.config.get("bioimageio", {})
+            model_description.config.bioimageio.model_dump()
             .get("test_kwargs", {})
             .get("pytorch_state_dict", {})
         )