| 🟡 |
bioimageio format validation |
| status |
valid-format |
| source |
https://hypha.aicell.io/bioimage-io/artifacts/independent-shrimp/files/rdf.yaml?version=v0 |
| id |
10.5281/zenodo.6811491/6811492 |
| version |
1 |
| applied format |
model 0.4.10 |
| bioimageio.spec |
0.5.7.4 |
|
Location |
Details |
| ✔️ |
|
Successfully created `ModelDescr` instance. |
| ✔️ |
|
bioimageio.spec format validation model 0.4.10 |
| ⚠ |
weights.pytorch_state_dict.dependencies |
Custom dependencies (conda:environment.yaml) specified. Avoid this whenever possible to allow execution in a wider range of software environments. |
| ⚠ |
weights.pytorch_state_dict.pytorch_version |
missing. Please specify the PyTorch version these PyTorch state dict weights were created with. |
| ⚠ |
weights.torchscript.pytorch_version |
missing. Please specify the PyTorch version these Torchscript weights were created with. |
| ✔️ |
weights.pytorch_state_dict |
Found existing conda environment 'fe5c5ca5d72e353852afde2ce12a86fddf7a9a2d68b7f586310f01a815a50dee' |
| ❌ |
weights.pytorch_state_dict |
Reproduce test outputs from test inputs (pytorch_state_dict) |
| ❌ |
weights.pytorch_state_dict |
/usr/share/miniconda/envs/fe5c5ca5d72e353852afde2ce12a86fddf7a9a2d68b7f586310f01a815a50dee/lib/python3.10/site-packages/torch/lib/libtorch_cpu.so: undefined symbol: iJIT_NotifyEvent |
|
|
See Traceback 1. |
|
weights.pytorch_state_dict |
recommended conda environment (Reproduce test outputs from test inputs (pytorch_state_dict)) |
|
|
%YAML 1.2
---
name: torch-em-deploy
channels:
- pytorch
- conda-forge
- nodefaults
dependencies:
- conda-forge::bioimageio.core
- pip
- pytorch>=1.6,<2.0
|
|
weights.pytorch_state_dict |
conda compare (Reproduce test outputs from test inputs (pytorch_state_dict)) |
|
|
Success. All the packages in the specification file are present in the environment with matching
version and build string. |
| ❌ |
weights.torchscript |
Conda environment creation |
| ❌ |
weights.torchscript |
Command '['conda', 'env', 'create', '--yes', '--file=/tmp/tmpi3fyqsk6/torchscript/env.yaml', '--name=8e61e58e234408358ebe72e5f3a59a6fb1adb59db8e7656f72bc034a857c269d', '--quiet']' returned non-zero exit status 1. |
|
|
See Traceback 2. |
|
weights.torchscript |
recommended conda environment (Conda environment creation) |
|
|
%YAML 1.2
---
channels:
- conda-forge
- nodefaults
dependencies:
- conda-forge::bioimageio.core>=0.9.4
- mkl ==2024.0.0
- numpy <2
- pip
- pytorch==1.10.1
- setuptools <70.0.0
- torchaudio==0.10.1
- torchvision==0.11.2
|
|
weights.torchscript |
conda compare (Conda environment creation) |
|
|
bioimageio.core not found mkl not found numpy not found pip not found pytorch not found
setuptools not found torchaudio not found torchvision not found |
Traceback 1
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /usr/share/miniconda/envs/fe5c5ca5d72e353852afde2ce12a86fddf7a9a2d68b7f586310f01a815a50dee/lib/p │
│ │
│ 781 │ │ test_input = get_test_input_sample(model) │
│ 782 │ │ expected = get_test_output_sample(model) │
│ 783 │ │ │
│ ❱ 784 │ │ with create_prediction_pipeline( │
│ 785 │ │ │ bioimageio_model=model, devices=devices, weight_format=weight_format │
│ 786 │ │ ) as prediction_pipeline: │
│ 787 │ │ │ results = prediction_pipeline.predict_sample_without_blocking(test_input) │
│ │
│ /usr/share/miniconda/envs/fe5c5ca5d72e353852afde2ce12a86fddf7a9a2d68b7f586310f01a815a50dee/lib/p │
│ │
│ 368 │ │ │ f"deprecated create_prediction_pipeline kwargs: {set(deprecated_kwargs)}" │
│ 369 │ │ ) │
│ 370 │ │
│ ❱ 371 │ model_adapter = model_adapter or create_model_adapter( │
│ 372 │ │ model_description=bioimageio_model, │
│ 373 │ │ devices=devices, │
│ 374 │ │ weight_format_priority_order=weights_format and (weights_format,), │
│ │
│ /usr/share/miniconda/envs/fe5c5ca5d72e353852afde2ce12a86fddf7a9a2d68b7f586310f01a815a50dee/lib/p │
│ │
│ 166 │ │ assert errors │
│ 167 │ │ if len(weight_format_priority_order) == 1: │
│ 168 │ │ │ assert len(errors) == 1 │
│ ❱ 169 │ │ │ raise errors[0] │
│ 170 │ │ │
│ 171 │ │ else: │
│ 172 │ │ │ msg = ( │
│ │
│ /usr/share/miniconda/envs/fe5c5ca5d72e353852afde2ce12a86fddf7a9a2d68b7f586310f01a815a50dee/lib/p │
│ │
│ 107 │ │ │ if wf == "pytorch_state_dict": │
│ 108 │ │ │ │ assert weights.pytorch_state_dict is not None │
│ 109 │ │ │ │ try: │
│ ❱ 110 │ │ │ │ │ from .pytorch_backend import PytorchModelAdapter │
│ 111 │ │ │ │ │ │
│ 112 │ │ │ │ │ return PytorchModelAdapter( │
│ 113 │ │ │ │ │ │ model_description=model_description, devices=devices │
│ │
│ /usr/share/miniconda/envs/fe5c5ca5d72e353852afde2ce12a86fddf7a9a2d68b7f586310f01a815a50dee/lib/p │
│ │
│ 5 from pathlib import Path │
│ 6 from typing import Any, List, Literal, Optional, Sequence, Union │
│ 7 │
│ ❱ 8 import torch │
│ 9 from loguru import logger │
│ 10 from numpy.typing import NDArray │
│ 11 from torch import nn │
│ │
│ /usr/share/miniconda/envs/fe5c5ca5d72e353852afde2ce12a86fddf7a9a2d68b7f586310f01a815a50dee/lib/p │
│ │
│ 215 │ # See Note [Global dependencies] │
│ 216 │ if USE_GLOBAL_DEPS: │
│ 217 │ │ _load_global_deps() │
│ ❱ 218 │ from torch._C import * # noqa: F403 │
│ 219 │
│ 220 # Appease the type checker; ordinarily this binding is inserted by the │
│ 221 # torch._C module initialization code in C │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
ImportError: /usr/share/miniconda/envs/fe5c5ca5d72e353852afde2ce12a86fddf7a9a2d68b7f586310f01a815a50dee/lib/python3.10/site-packages/torch/lib/libtorch_cpu.so: undefined symbol: iJIT_NotifyEvent
Traceback 2
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /home/runner/.local/lib/python3.12/site-packages/bioimageio/core/_resource_tests.py:428 in _test │
│ │
│ 425 │ │ raise RuntimeError("Conda not available") from e │
│ 426 │ │
│ 427 │ try: │
│ ❱ 428 │ │ run_command([CONDA_CMD, "run", "-n", env_name, "python", "--version"]) │
│ 429 │ except Exception as e: │
│ 430 │ │ working_dir.mkdir(parents=True, exist_ok=True) │
│ 431 │ │ path = working_dir / "env.yaml" │
│ │
│ /home/runner/.local/lib/python3.12/site-packages/bioimageio/core/_resource_tests.py:198 in defau │
│ │
│ 195 │
│ 196 def default_run_command(args: Sequence[str]): │
│ 197 │ logger.info("running '{}'...", " ".join(args)) │
│ ❱ 198 │ _ = subprocess.check_call(args) │
│ 199 │
│ 200 │
│ 201 def test_description( │
│ │
│ /usr/lib/python3.12/subprocess.py:413 in check_call │
│ │
│ 410 │ │ cmd = kwargs.get("args") │
│ 411 │ │ if cmd is None: │
│ 412 │ │ │ cmd = popenargs[0] │
│ ❱ 413 │ │ raise CalledProcessError(retcode, cmd) │
│ 414 │ return 0 │
│ 415 │
│ 416 │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
CalledProcessError: Command '['conda', 'run', '-n', '8e61e58e234408358ebe72e5f3a59a6fb1adb59db8e7656f72bc034a857c269d', 'python', '--version']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /home/runner/.local/lib/python3.12/site-packages/bioimageio/core/_resource_tests.py:435 in _test │
│ │
│ 432 │ │ try: │
│ 433 │ │ │ _ = path.write_bytes(encoded_env) │
│ 434 │ │ │ logger.debug("written conda env to {}", path) │
│ ❱ 435 │ │ │ run_command( │
│ 436 │ │ │ │ [ │
│ 437 │ │ │ │ │ CONDA_CMD, │
│ 438 │ │ │ │ │ "env", │
│ │
│ /home/runner/.local/lib/python3.12/site-packages/bioimageio/core/_resource_tests.py:198 in defau │
│ │
│ 195 │
│ 196 def default_run_command(args: Sequence[str]): │
│ 197 │ logger.info("running '{}'...", " ".join(args)) │
│ ❱ 198 │ _ = subprocess.check_call(args) │
│ 199 │
│ 200 │
│ 201 def test_description( │
│ │
│ /usr/lib/python3.12/subprocess.py:413 in check_call │
│ │
│ 410 │ │ cmd = kwargs.get("args") │
│ 411 │ │ if cmd is None: │
│ 412 │ │ │ cmd = popenargs[0] │
│ ❱ 413 │ │ raise CalledProcessError(retcode, cmd) │
│ 414 │ return 0 │
│ 415 │
│ 416 │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
CalledProcessError: Command '['conda', 'env', 'create', '--yes', '--file=/tmp/tmpi3fyqsk6/torchscript/env.yaml', '--name=8e61e58e234408358ebe72e5f3a59a6fb1adb59db8e7656f72bc034a857c269d', '--quiet']' returned non-zero exit status 1.