various fixes

Author: FynnBe

bioimageio/core/_resource_tests.py

@@ -428,7 +428,7 @@ def load_description_and_test(
                 )
             )
             or (c := source.validation_summary.details[0].context) is None
-            or not c["perform_io_checks"]
+            or not c.perform_io_checks
         ):
             logger.debug(
                 "deserializing source to ensure we validate and test using format {} and perform io checks",

bioimageio/core/backends/onnx_backend.py

@@ -23,9 +23,8 @@ def __init__(
         if model_description.weights.onnx is None:
             raise ValueError("No ONNX weights specified for {model_description.name}")
 
-        self._session = rt.InferenceSession(
-            str(download(model_description.weights.onnx.source).path)
-        )
+        local_path = download(model_description.weights.onnx.source).path
+        self._session = rt.InferenceSession(local_path.read_bytes())
         onnx_inputs = self._session.get_inputs()  # type: ignore
         self._input_names: List[str] = [ipt.name for ipt in onnx_inputs]  # type: ignore
 

bioimageio/core/backends/torchscript_backend.py

@@ -36,7 +36,9 @@ def __init__(
                 "Multiple devices for single torchscript model not yet implemented"
             )
 
-        self._model = torch.jit.load(weight_path)
+        with weight_path.open("rb") as f:
+            self._model = torch.jit.load(f)
+
         self._model.to(self.devices[0])
         self._model = self._model.eval()
 

tests/test_bioimageio_collection.py

@@ -43,6 +43,11 @@ def yield_bioimageio_yaml_urls() -> Iterable[ParameterSet]:
     "wild-rhino/0.1.0",  # requires careamics
     "dazzling-spider/0.1.0",  # requires careamics
     "humorous-fox/0.1.0",  # requires careamics
+    "ambitious-sloth/1.2",  # requires inferno
+    "dynamic-t-rex/1",  # model.v0_4.ScaleLinearKwargs with axes
+    "famous-fish/0.1.0",  # list index out of range `fl[3]`
+    "happy-elephant/0.1.0",  # list index out of range `fl[3]`
+    "affectionate-cow/0.1.0",  # custom dependencies
 }
 
 

tests/test_stat_calculators.py

@@ -1,8 +1,7 @@
-from typing import Tuple
+from typing import Optional, Tuple
 
 import numpy as np
 import pytest
-from git import Optional
 from xarray.testing import assert_allclose  # pyright: ignore[reportUnknownVariableType]
 
 from bioimageio.core.axis import AxisId