bump spec

bioimageio/core/__init__.py

@@ -3,6 +3,7 @@
 """
 
 from bioimageio.spec import (
+    ValidationSummary,
     build_description,
     dump_description,
     load_dataset_description,
@@ -112,4 +113,5 @@
     "test_model",
     "test_resource",
     "validate_format",
+    "ValidationSummary",
 ]

bioimageio/core/backends/keras_backend.py

@@ -4,17 +4,18 @@
 from loguru import logger
 from numpy.typing import NDArray
 
-from bioimageio.spec._internal.io import download
-from bioimageio.spec._internal.type_guards import is_list, is_tuple
 from bioimageio.spec.model import v0_4, v0_5
 from bioimageio.spec.model.v0_5 import Version
+from bioimageio.spec.utils import download
 
 from .._settings import settings
 from ..digest_spec import get_axes_infos
+from ..utils._type_guards import is_list, is_tuple
 from ._model_adapter import ModelAdapter
 
 os.environ["KERAS_BACKEND"] = settings.keras_backend
 
+
 # by default, we use the keras integrated with tensorflow
 # TODO: check if we should prefer keras
 try:

bioimageio/core/backends/onnx_backend.py

@@ -5,11 +5,11 @@
 import onnxruntime as rt  # pyright: ignore[reportMissingTypeStubs]
 from numpy.typing import NDArray
 
-from bioimageio.spec._internal.type_guards import is_list, is_tuple
 from bioimageio.spec.model import v0_4, v0_5
 from bioimageio.spec.utils import download
 
 from ..model_adapters import ModelAdapter
+from ..utils._type_guards import is_list, is_tuple
 
 
 class ONNXModelAdapter(ModelAdapter):

bioimageio/core/backends/pytorch_backend.py

@@ -11,12 +11,13 @@
 from torch import nn
 from typing_extensions import assert_never
 
-from bioimageio.spec._internal.type_guards import is_list, is_ndarray, is_tuple
+from bioimageio.spec._internal.version_type import Version
 from bioimageio.spec.common import ZipPath
 from bioimageio.spec.model import AnyModelDescr, v0_4, v0_5
 from bioimageio.spec.utils import download
 
 from ..digest_spec import import_callable
+from ..utils._type_guards import is_list, is_ndarray, is_tuple
 from ._model_adapter import ModelAdapter
 
 
@@ -143,7 +144,10 @@ def load_torch_state_dict(
     model = model.to(devices[0])
     with path.open("rb") as f:
         assert not isinstance(f, TextIOWrapper)
-        state = torch.load(f, map_location=devices[0], weights_only=True)
+        if Version(str(torch.__version__)) < Version("1.13"):
+            state = torch.load(f, map_location=devices[0])
+        else:
+            state = torch.load(f, map_location=devices[0], weights_only=True)
 
     incompatible = model.load_state_dict(state)
     if (

bioimageio/core/backends/torchscript_backend.py

@@ -6,11 +6,11 @@
 import torch
 from numpy.typing import NDArray
 
-from bioimageio.spec._internal.type_guards import is_list, is_tuple
 from bioimageio.spec.model import v0_4, v0_5
 from bioimageio.spec.utils import download
 
 from ..model_adapters import ModelAdapter
+from ..utils._type_guards import is_list, is_tuple
 
 
 class TorchscriptModelAdapter(ModelAdapter):

bioimageio/core/utils/_type_guards.py

@@ -0,0 +1,8 @@
+"""use these type guards with caution!
+They widen the type to T[Any], which is not always correct."""
+
+from bioimageio.spec._internal import type_guards
+
+is_list = type_guards.is_list  # pyright: ignore[reportPrivateImportUsage]
+is_ndarray = type_guards.is_ndarray  # pyright: ignore[reportPrivateImportUsage]
+is_tuple = type_guards.is_tuple  # pyright: ignore[reportPrivateImportUsage]

dev/env-dev.yaml

@@ -5,7 +5,7 @@ channels:
   - nodefaults
   - pytorch
 dependencies:
-  - bioimageio.spec==0.5.4.1
+  - bioimageio.spec==0.5.4.2
   - black
   # - crick  # currently requires python<=3.9
   - h5py

dev/env-full.yaml

@@ -4,7 +4,7 @@ channels:
   - nodefaults
   - pytorch
 dependencies:
-  - bioimageio.spec==0.5.4.1
+  - bioimageio.spec==0.5.4.2
   - black
   # - careamics # TODO: add careamics for model testing (currently pins pydantic to <2.9)
   - cellpose # for model testing

dev/env-gpu.yaml

@@ -4,7 +4,7 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - bioimageio.spec==0.5.4.1
+  - bioimageio.spec==0.5.4.2
   - black
   - cellpose # for model testing
   # - crick  # currently requires python<=3.9

dev/env-py38.yaml

@@ -5,7 +5,7 @@ channels:
   - nodefaults
   - pytorch
 dependencies:
-  - bioimageio.spec==0.5.4.1
+  - bioimageio.spec==0.5.4.2
   - black
   - crick # uncommented
   - h5py

setup.py

@@ -30,7 +30,7 @@
     ],
     packages=find_namespace_packages(exclude=["tests"]),
     install_requires=[
-        "bioimageio.spec ==0.5.4.1",
+        "bioimageio.spec ==0.5.4.2",
         "h5py",
         "imagecodecs",
         "imageio>=2.10",
@@ -67,7 +67,7 @@
                 "packaging>=17.0",
                 "pdoc",
                 "pre-commit",
-                "pyright==1.1.396",
+                "pyright==1.1.398",
                 "segment-anything",  # for model testing
                 "timm",  # for model testing
                 # "crick",  # currently requires python<=3.9

tests/test_bioimageio_collection.py

@@ -40,7 +40,6 @@ def yield_bioimageio_yaml_urls() -> Iterable[ParameterSet]:
 
 
 KNOWN_INVALID: Collection[str] = {
-    "affable-shark/1.1",  # onnx weights expect fixed input shape
     "affectionate-cow/0.1.0",  # custom dependencies
     "ambitious-sloth/1.2",  # requires inferno
     "committed-turkey/1.2",  # error deserializing VarianceScaling