core-bioimage-io-python
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bioimage-io
Model test failed
!bioimageio test affable-shark
Getting the following issue. Noticed that it's because of the environment is not configured correctly, is there a universal conda env which can handle not all but most of the models? Should I just use the dev env?
cc @FynnBe
See error log
``` testing affable-shark... 2024-09-12 17:15:13.365 | INFO | bioimageio.spec._internal.io_utils:open_bioimageio_yaml:112 - loading affable-shark from https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/affable-shark/1.1/files/rdf.yaml Downloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/affable-shark/1.1/files/rdf.yaml' to file '/home/jovyan/.cache/bioimageio/c1d5091838f82f59738702f2d8a938ed-rdf.yaml'. 100%|█████████████████████████████████████| 4.22k/4.22k [00:00❌ bioimageio validation failed━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ source https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.…
format version model 0.5.3
bioimageio.spec 0.5.3.2
bioimageio.core 0.6.8
❓ location detail
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
✔️ initialized ModelDescr
to describe model 0.5.3
✔️ bioimageio.spec format
validation model 0.5.3
🔍 context.perform_io_che… True
🔍 context.root https://uk1s3.embassy.e…
🔍 context.known_files.ze… 767f2c3a50e36365c30b9e4…
🔍 context.known_files.te… c29bd6e16e3f7856217b407…
🔍 context.known_files.sa… a24b3c708b6ca6825494eb7…
🔍 context.known_files.te… 510181f38930e59e4fd8ecc…
🔍 context.known_files.sa… e8f99aabe8405427f515eba…
🔍 context.known_files.we… df913b85947f5132bcdaf81…
🔍 context.known_files.un… 7f5b15948e8e2c91f78dcff…
🔍 context.known_files.we… 608f52cd7f5119f7a7b8272…
🔍 context.known_files.we… 8410950508655a300793b38…
🔍 context.warning_level error
⚠ documentation No '# Validation'
(sub)section found in
documentation.md.
❌ Reproduce test outputs
from test inputs
❌ weights.onnx The 'onnx' model adapter
could not be created in
this environment:
ImportError(failed to
import onnxruntime: No
module named
'onnxruntime').
|
| | | ]8;id=839366;_resource_tests.py_resource_tests.py]8;;,
line 161, in _test_model_inference with create_prediction_pipeline(
| | | |
]8;id=688587;_prediction_pipeline.py_prediction_pipeline.py]8;;, line 333, in create_prediction_pipeline
model_adapter = model_adapter or create_model_adapter( | | |
| ]8;id=670151;_model_adapter.py_model_adapter.py]8;;, line 138, in create raise ValueError(
| | | |
| | ❌ | | Run onnx inference
for parametrized inputs
| | ❌ | weights.onnx | The 'onnx' model
adapter could not be created in this environment: ImportError(failed to import
onnxruntime: No module named 'onnxruntime').
|
| | | ]8;id=227383;_resource_tests.py_resource_tests.py]8;;,
line 296, in _test_model_inference_parametrized with
create_prediction_pipeline( | | |
| ]8;id=394538;_prediction_pipeline.py_prediction_pipeline.py]8;;, line 333, in create_prediction_pipeline
model_adapter = model_adapter or create_model_adapter( | | |
| ]8;id=235797;_model_adapter.py_model_adapter.py]8;;, line 138, in create raise ValueError(
| | | |
| | ❌ | | Reproduce test
outputs from test inputs
| | ❌ | weights.pytorch_state_dict | The
'pytorch_state_dict' model adapter could not be created in this environment:
ImportError(failed to import torch: No module named 'torch').
|
| | | ]8;id=608868;_resource_tests.py_resource_tests.py]8;;,
line 161, in _test_model_inference with create_prediction_pipeline(
| | | |
]8;id=593174;_prediction_pipeline.py_prediction_pipeline.py]8;;, line 333, in create_prediction_pipeline
model_adapter = model_adapter or create_model_adapter( | | |
| ]8;id=396184;_model_adapter.py_model_adapter.py]8;;, line 138, in create raise ValueError(
| | | |
| | ❌ | | Run
pytorch_state_dict inference for parametrized inputs
| | ❌ | weights.pytorch_state_dict | The
'pytorch_state_dict' model adapter could not be created in this environment:
ImportError(failed to import torch: No module named 'torch').
|
| | | ]8;id=13371;_resource_tests.py_resource_tests.py]8;;,
line 296, in _test_model_inference_parametrized with
create_prediction_pipeline( | | |
| ]8;id=137629;_prediction_pipeline.py_prediction_pipeline.py]8;;, line 333, in create_prediction_pipeline
model_adapter = model_adapter or create_model_adapter( | | |
| ]8;id=975301;_model_adapter.py_model_adapter.py]8;;, line 138, in create raise ValueError(
| | | |
| | ❌ | | Reproduce test
outputs from test inputs
| | ❌ | weights.torchscript | The 'torchscript'
model adapter could not be created in this environment: ImportError(failed to
import torch: No module named 'torch').
|
| | | ]8;id=429218;_resource_tests.py_resource_tests.py]8;;,
line 161, in _test_model_inference with create_prediction_pipeline(
| | | |
]8;id=163549;_prediction_pipeline.py_prediction_pipeline.py]8;;, line 333, in create_prediction_pipeline
model_adapter = model_adapter or create_model_adapter( | | |
| ]8;id=43384;_model_adapter.py_model_adapter.py]8;;, line 138, in create raise ValueError(
| | | |
| | ❌ | | Run torchscript
inference for parametrized inputs
| | ❌ | weights.torchscript | The 'torchscript'
model adapter could not be created in this environment: ImportError(failed to
import torch: No module named 'torch').
|
| | | ]8;id=935828;_resource_tests.py_resource_tests.py]8;;,
line 296, in _test_model_inference_parametrized with
create_prediction_pipeline( | | |
| ]8;id=672681;_prediction_pipeline.py_prediction_pipeline.py]8;;, line 333, in create_prediction_pipeline
model_adapter = model_adapter or create_model_adapter( | | |
| ]8;id=379847;_model_adapter.py_model_adapter.py]8;;, line 138, in create raise ValueError(
| | | |
</details>
