René's URL Explorer Experiment

{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"Model test failed (affable-shark's onnx weights)","articleBody":"```\r\n!bioimageio test affable-shark\r\n```\r\nGetting the following issue.\r\nNoticed 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?\r\n\r\ncc @FynnBe \r\n\r\n\u003cdetails\u003e\r\n\u003csummary\u003eSee error log\u003c/summary\u003e\r\n```\r\ntesting affable-shark...\r\n2024-09-12 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\r\nDownloading 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'.\r\n100%|█████████████████████████████████████| 4.22k/4.22k [00:00\u003c00:00, 8.48MB/s]\r\nDownloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/affable-shark/1.1/files/zero_mean_unit_variance.ijm' to file '/home/jovyan/.cache/bioimageio/3c123c5162a87c48333c80f7389e99a7-zero_mean_unit_variance.ijm'.\r\n100%|█████████████████████████████████████████| 845/845 [00:00\u003c00:00, 1.29MB/s]\r\ncomputing SHA256 of 3c123c5162a87c48333c80f7389e99a7-zero_mean_unit_variance.ijm\r\nDownloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/affable-shark/1.1/files/documentation.md' to file '/home/jovyan/.cache/bioimageio/8c032152668b4aaa68f99fb56c067631-documentation.md'.\r\n100%|█████████████████████████████████████| 1.57k/1.57k [00:00\u003c00:00, 3.45MB/s]\r\nSHA256 hash of downloaded file: 9b8330e6fae8403efc7a44bb7365186c14fb6222b608791baab7a4e0352dbdcd\r\nUse this value as the 'known_hash' argument of 'pooch.retrieve' to ensure that the file hasn't changed if it is downloaded again in the future.\r\nDownloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/affable-shark/1.1/files/test_input_0.npy' to file '/home/jovyan/.cache/bioimageio/93e503596d7d0bbf5b3937cf1a80402b-test_input_0.npy'.\r\n100%|████████████████████████████████████████| 262k/262k [00:00\u003c00:00, 830MB/s]\r\ncomputing SHA256 of 93e503596d7d0bbf5b3937cf1a80402b-test_input_0.npy (result: c\r\nDownloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/affable-shark/1.1/files/sample_input_0.tif' to file '/home/jovyan/.cache/bioimageio/baeb9b3639733aa6ad5f8305149a3585-sample_input_0.tif'.\r\n100%|██████████████████████████████████████| 65.8k/65.8k [00:00\u003c00:00, 260MB/s]\r\ncomputing SHA256 of baeb9b3639733aa6ad5f8305149a3585-sample_input_0.tif (result:\r\nDownloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/affable-shark/1.1/files/test_output_0.npy' to file '/home/jovyan/.cache/bioimageio/858a63339bdb8f80ff310e077a5079bb-test_output_0.npy'.\r\n100%|███████████████████████████████████████| 524k/524k [00:00\u003c00:00, 2.06GB/s]\r\ncomputing SHA256 of 858a63339bdb8f80ff310e077a5079bb-test_output_0.npy (result: \r\nDownloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/affable-shark/1.1/files/sample_output_0.tif' to file '/home/jovyan/.cache/bioimageio/d22d18e9c3592839985cac2534ac4617-sample_output_0.tif'.\r\n100%|███████████████████████████████████████| 525k/525k [00:00\u003c00:00, 1.51GB/s]\r\ncomputing SHA256 of d22d18e9c3592839985cac2534ac4617-sample_output_0.tif (result\r\nDownloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/affable-shark/1.1/files/weights.onnx' to file '/home/jovyan/.cache/bioimageio/4f6534376602b6e094e1895b93c4ee74-weights.onnx'.\r\n100%|████████████████████████████████████████| 116M/116M [00:00\u003c00:00, 370GB/s]\r\ncomputing SHA256 of 4f6534376602b6e094e1895b93c4ee74-weights.onnx (result: df913\r\nDownloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/affable-shark/1.1/files/unet.py' to file '/home/jovyan/.cache/bioimageio/760a77af34fd5e3e1eebeff7e0669585-unet.py'.\r\n100%|█████████████████████████████████████| 20.9k/20.9k [00:00\u003c00:00, 41.7MB/s]\r\ncomputing SHA256 of 760a77af34fd5e3e1eebeff7e0669585-unet.py (result: 7f5b15948e\r\nDownloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/affable-shark/1.1/files/weights.pt' to file '/home/jovyan/.cache/bioimageio/78e469078bf5116258ceaf6f41001dd7-weights.pt'.\r\n100%|████████████████████████████████████████| 116M/116M [00:00\u003c00:00, 128GB/s]\r\ncomputing SHA256 of 78e469078bf5116258ceaf6f41001dd7-weights.pt (result: 608f52c\r\nDownloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/affable-shark/1.1/files/weights-torchscript.pt' to file '/home/jovyan/.cache/bioimageio/d44de80414e1fd1414b97beaaed935f5-weights-torchscript.pt'.\r\n100%|████████████████████████████████████████| 116M/116M [00:00\u003c00:00, 252GB/s]\r\ncomputing SHA256 of d44de80414e1fd1414b97beaaed935f5-weights-torchscript.pt (res\r\n2024-09-12 17:15:46.533 | INFO     | bioimageio.core._resource_tests:_test_model_inference:147 - starting 'Reproduce test outputs from test inputs'\r\n/srv/conda/envs/notebook/lib/python3.10/site-packages/bioimageio/core/_resource_tests.py:407: UserWarning: The argument `decimal` has been depricated in favour of `relative_tolerance` and `absolute_tolerance`, with different validation logic, using `numpy.testing.assert_allclose, see 'https://numpy.org/doc/stable/reference/generated/numpy.testing.assert_allclose.html'. Passing a value for `decimal` will cause validation to revert to the old behaviour.\r\n  warnings.warn(\r\n2024-09-12 17:15:46.540 | INFO     | bioimageio.core._resource_tests:_test_model_inference_parametrized:242 - Testing inference with 6 different input tensor sizes\r\n2024-09-12 17:15:46.544 | INFO     | bioimageio.core._resource_tests:_test_model_inference:147 - starting 'Reproduce test outputs from test inputs'\r\n2024-09-12 17:15:46.555 | INFO     | bioimageio.core._resource_tests:_test_model_inference_parametrized:242 - Testing inference with 6 different input tensor sizes\r\n2024-09-12 17:15:46.557 | INFO     | bioimageio.core._resource_tests:_test_model_inference:147 - starting 'Reproduce test outputs from test inputs'\r\n2024-09-12 17:15:46.566 | INFO     | bioimageio.core._resource_tests:_test_model_inference_parametrized:242 - Testing inference with 6 different input tensor sizes\r\n\r\n                                                                                \r\n  ❌                bioimageio validation failed                                \r\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ \r\n  source            [https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.…](https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.%E2%80%A6)  \r\n  format version    model 0.5.3                                                 \r\n  bioimageio.spec   0.5.3.2                                                     \r\n  bioimageio.core   0.6.8                                                       \r\n                                                                                \r\n\r\n                                                                                \r\n  ❓                        location                  detail                    \r\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ \r\n  ✔️                                                   initialized ModelDescr    \r\n                                                      to describe model 0.5.3   \r\n                                                                                \r\n  ✔️                                                   bioimageio.spec format    \r\n                                                      validation model 0.5.3    \r\n  🔍                        context.perform_io_che…   True                      \r\n  🔍                        context.root              [https://uk1s3.embassy.e…](https://uk1s3.embassy.e%E2%80%A6/)  \r\n  🔍                        context.known_files.ze…   767f2c3a50e36365c30b9e4…  \r\n  🔍                        context.known_files.te…   c29bd6e16e3f7856217b407…  \r\n  🔍                        context.known_files.sa…   a24b3c708b6ca6825494eb7…  \r\n  🔍                        context.known_files.te…   510181f38930e59e4fd8ecc…  \r\n  🔍                        context.known_files.sa…   e8f99aabe8405427f515eba…  \r\n  🔍                        context.known_files.we…   df913b85947f5132bcdaf81…  \r\n  🔍                        context.known_files.un…   7f5b15948e8e2c91f78dcff…  \r\n  🔍                        context.known_files.we…   608f52cd7f5119f7a7b8272…  \r\n  🔍                        context.known_files.we…   8410950508655a300793b38…  \r\n  🔍                        context.warning_level     error                     \r\n  ⚠                         documentation             No '# Validation'         \r\n                                                      (sub)section found in     \r\n                                                      documentation.md.         \r\n                                                                                \r\n  ❌                                                  Reproduce test outputs    \r\n                                                      from test inputs          \r\n  ❌                        weights.onnx              The 'onnx' model adapter  \r\n                                                      could not be created in   \r\n                                                      this environment:         \r\n  ImportError(failed to                                                         \r\n  import onnxruntime: No                                                        \r\n  module named                                                                  \r\n  'onnxruntime').                                                               \r\n                                                                                \r\n\r\n                                                                                \r\n                                                                                \r\n                           |                                                    \r\n                                                                                \r\n\r\n\r\n\r\n\r\n|     |                                                 | \u001B]8;id=839366;_resource_tests.py\u001B\\_resource_tests.py\u001B]8;;\u001B\\,   \r\nline 161, in _test_model_inference    with create_prediction_pipeline(          \r\n| |     |                                                 |                     \r\n\u001B]8;id=688587;_prediction_pipeline.py\u001B\\_prediction_pipeline.py\u001B]8;;\u001B\\, line 333, in create_prediction_pipeline                \r\nmodel_adapter = model_adapter or create_model_adapter( | |     |                \r\n| \u001B]8;id=670151;_model_adapter.py\u001B\\_model_adapter.py\u001B]8;;\u001B\\, line 138, in create    raise ValueError(                   \r\n| |     |                                                 |                     \r\n| | ❌   |                                                 | Run onnx inference \r\nfor parametrized inputs                                                         \r\n| | ❌   | weights.onnx                                  | The 'onnx' model     \r\nadapter could not be created in this environment: ImportError(failed to import  \r\nonnxruntime: No module named 'onnxruntime').                                    \r\n\r\n                                                                                \r\n                                                                                \r\n                           |                                                    \r\n                                                                                \r\n\r\n\r\n\r\n\r\n|     |                                                 | \u001B]8;id=227383;_resource_tests.py\u001B\\_resource_tests.py\u001B]8;;\u001B\\,   \r\nline 296, in _test_model_inference_parametrized    with                         \r\ncreate_prediction_pipeline(                              | |     |              \r\n| \u001B]8;id=394538;_prediction_pipeline.py\u001B\\_prediction_pipeline.py\u001B]8;;\u001B\\, line 333, in create_prediction_pipeline              \r\nmodel_adapter = model_adapter or create_model_adapter( | |     |                \r\n| \u001B]8;id=235797;_model_adapter.py\u001B\\_model_adapter.py\u001B]8;;\u001B\\, line 138, in create    raise ValueError(                   \r\n| |     |                                                 |                     \r\n| | ❌   |                                                 | Reproduce test     \r\noutputs from test inputs                                                        \r\n| | ❌   | weights.pytorch_state_dict                    | The                  \r\n'pytorch_state_dict' model adapter could not be created in this environment:    \r\nImportError(failed to import torch: No module named 'torch').                   \r\n\r\n                                                                                \r\n                                                                                \r\n                         |                                                      \r\n                                                                                \r\n\r\n\r\n\r\n\r\n|     |                                                 | \u001B]8;id=608868;_resource_tests.py\u001B\\_resource_tests.py\u001B]8;;\u001B\\,   \r\nline 161, in _test_model_inference    with create_prediction_pipeline(          \r\n| |     |                                                 |                     \r\n\u001B]8;id=593174;_prediction_pipeline.py\u001B\\_prediction_pipeline.py\u001B]8;;\u001B\\, line 333, in create_prediction_pipeline                \r\nmodel_adapter = model_adapter or create_model_adapter( | |     |                \r\n| \u001B]8;id=396184;_model_adapter.py\u001B\\_model_adapter.py\u001B]8;;\u001B\\, line 138, in create    raise ValueError(                   \r\n| |     |                                                 |                     \r\n| | ❌   |                                                 | Run                \r\npytorch_state_dict inference for parametrized inputs                            \r\n| | ❌   | weights.pytorch_state_dict                    | The                  \r\n'pytorch_state_dict' model adapter could not be created in this environment:    \r\nImportError(failed to import torch: No module named 'torch').                   \r\n\r\n                                                                                \r\n                                                                                \r\n                         |                                                      \r\n                                                                                \r\n\r\n\r\n\r\n\r\n|     |                                                 | \u001B]8;id=13371;_resource_tests.py\u001B\\_resource_tests.py\u001B]8;;\u001B\\,   \r\nline 296, in _test_model_inference_parametrized    with                         \r\ncreate_prediction_pipeline(                              | |     |              \r\n| \u001B]8;id=137629;_prediction_pipeline.py\u001B\\_prediction_pipeline.py\u001B]8;;\u001B\\, line 333, in create_prediction_pipeline              \r\nmodel_adapter = model_adapter or create_model_adapter( | |     |                \r\n| \u001B]8;id=975301;_model_adapter.py\u001B\\_model_adapter.py\u001B]8;;\u001B\\, line 138, in create    raise ValueError(                   \r\n| |     |                                                 |                     \r\n| | ❌   |                                                 | Reproduce test     \r\noutputs from test inputs                                                        \r\n| | ❌   | weights.torchscript                           | The 'torchscript'    \r\nmodel adapter could not be created in this environment: ImportError(failed to   \r\nimport torch: No module named 'torch').                                         \r\n\r\n                                                                                \r\n                                                                                \r\n                                |                                               \r\n                                                                                \r\n\r\n\r\n\r\n\r\n|     |                                                 | \u001B]8;id=429218;_resource_tests.py\u001B\\_resource_tests.py\u001B]8;;\u001B\\,   \r\nline 161, in _test_model_inference    with create_prediction_pipeline(          \r\n| |     |                                                 |                     \r\n\u001B]8;id=163549;_prediction_pipeline.py\u001B\\_prediction_pipeline.py\u001B]8;;\u001B\\, line 333, in create_prediction_pipeline                \r\nmodel_adapter = model_adapter or create_model_adapter( | |     |                \r\n| \u001B]8;id=43384;_model_adapter.py\u001B\\_model_adapter.py\u001B]8;;\u001B\\, line 138, in create    raise ValueError(                   \r\n| |     |                                                 |                     \r\n| | ❌   |                                                 | Run torchscript    \r\ninference for parametrized inputs                                               \r\n| | ❌   | weights.torchscript                           | The 'torchscript'    \r\nmodel adapter could not be created in this environment: ImportError(failed to   \r\nimport torch: No module named 'torch').                                         \r\n\r\n                                                                                \r\n                                                                                \r\n                                |                                               \r\n                                                                                \r\n\r\n\r\n\r\n\r\n|     |                                                 | \u001B]8;id=935828;_resource_tests.py\u001B\\_resource_tests.py\u001B]8;;\u001B\\,   \r\nline 296, in _test_model_inference_parametrized    with                         \r\ncreate_prediction_pipeline(                              | |     |              \r\n| \u001B]8;id=672681;_prediction_pipeline.py\u001B\\_prediction_pipeline.py\u001B]8;;\u001B\\, line 333, in create_prediction_pipeline              \r\nmodel_adapter = model_adapter or create_model_adapter( | |     |                \r\n| \u001B]8;id=379847;_model_adapter.py\u001B\\_model_adapter.py\u001B]8;;\u001B\\, line 138, in create    raise ValueError(                   \r\n| |     |                                                 |\r\n```\r\n\r\n\r\n\u003c/details\u003e\r\n\r\n","author":{"url":"https://github.com/oeway","@type":"Person","name":"oeway"},"datePublished":"2024-09-12T17:17:55.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":2},"url":"https://github.com/421/core-bioimage-io-python/issues/421"}