chore: Bump BMZ dependency to 0.9.0 (#508)

## Description

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reviewers to
understand the code and have the correct mindset when examining changes.
-->

> [!NOTE]  
> **tldr**: Depend on BMZ latest version

### Background - why do we need this PR?

<!-- What problem are you solving? Describe in a few sentences the state
before
this PR. Use code examples if useful. -->

Currently, we fixed `xarray` dependency bc of the BMZ, and we depend on
an old BMZ version. This allows us to depend on the latest version
(`0.8.0` was incompatible bc of bioimageio.specs lagging dependency on
Pydantic).

### Overview - what changed?

<!-- What aspects and mechanisms of the code base changed? Describe only
the general
idea and overarching features. -->

Dependency on BMZ.

### Implementation - how did you implement the changes?

<!-- How did you solve the issue technically? Explain why you chose this
approach and
provide code examples if applicable (e.g. change in the API for users).
-->

Update `pyproject.toml` and some BMZ API calls.

## Changes Made

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### New features or files
- `NewClass` added to `new_file.py`
- `new_function` added to `existing_file.py`

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### Modified features or files

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- `pyproject.toml`
- `model_description.py`


## How has this been tested?

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description of the tests added to the PR or code snippet to reproduce
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CI and local.

## Related Issues

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#495 (comment)


Thanks @mese79 !!!

---

**Please ensure your PR meets the following requirements:**

- [x] Code builds and passes tests locally, including doctests
- [ ] New tests have been added (for bug fixes/features)
- [x] Pre-commit passes
- [ ] PR to the documentation exists (for bug fixes / features)

---------

Co-authored-by: Mehdi Seifi <mehdiseifi@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: 3 people

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", {})
         )