Core Compatibility Report: kind-badger/v0¤
| 🟡 | bioimageio format validation |
|---|---|
| status | valid-format |
| source | https://hypha.aicell.io/bioimage-io/artifacts/kind-badger/files/rdf.yaml?version=v0 |
| id | kind-badger |
| format version | model 0.5.6 |
| bioimageio.spec | 0.5.6.0 |
| Location | Details | |
|---|---|---|
| ✔️ | Successfully created `ModelDescr` instance. | |
| ✔️ | bioimageio.spec format validation model 0.5.6 | |
| ⚠ | inputs.0.sample_tensor |
Needs to be filled for FAIR compliance |
| ⚠ | outputs.0.sample_tensor |
Needs to be filled for FAIR compliance |
| ❌ | weights.pytorch_state_dict |
Conda environment creation |
| ❌ | weights.pytorch_state_dict |
Command '['conda', 'env', 'create', '--yes', '--file=/tmp/tmpxr_hqayw/pytorch_state_dict/env.yaml', '--name=755f1c5d5db340315cccd209a1aa696b22de3bea219e0f714c8617e638911938', '--quiet']' returned non-zero exit status 1. |
| See Traceback 1. | ||
weights.pytorch_state_dict |
recommended conda environment (Conda environment creation) |
|
%YAML 1.2
---
channels:
- conda-forge
- nodefaults
dependencies:
- conda-forge::bioimageio.core
- numpy >=2,<3
- pip
- pytorch==2.9.1
- torchaudio
- torchvision
|
||
weights.pytorch_state_dict |
conda compare (Conda environment creation) |
|
bioimageio.core not found numpy not found pip not found pytorch not found torchaudio not found torchvision not found |
Traceback 1
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /home/runner/.local/lib/python3.12/site-packages/bioimageio/core/_resource_tests.py:412 in _test │
│ │
│ 409 │ │ raise RuntimeError("Conda not available") from e │
│ 410 │ │
│ 411 │ try: │
│ ❱ 412 │ │ run_command([CONDA_CMD, "run", "-n", env_name, "python", "--version"]) │
│ 413 │ except Exception as e: │
│ 414 │ │ working_dir.mkdir(parents=True, exist_ok=True) │
│ 415 │ │ path = working_dir / "env.yaml" │
│ │
│ /home/runner/.local/lib/python3.12/site-packages/bioimageio/core/_resource_tests.py:197 in defau │
│ │
│ 194 │
│ 195 def default_run_command(args: Sequence[str]): │
│ 196 │ logger.info("running '{}'...", " ".join(args)) │
│ ❱ 197 │ _ = subprocess.check_call(args) │
│ 198 │
│ 199 │
│ 200 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', '755f1c5d5db340315cccd209a1aa696b22de3bea219e0f714c8617e638911938', '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:419 in _test │
│ │
│ 416 │ │ try: │
│ 417 │ │ │ _ = path.write_bytes(encoded_env) │
│ 418 │ │ │ logger.debug("written conda env to {}", path) │
│ ❱ 419 │ │ │ run_command( │
│ 420 │ │ │ │ [ │
│ 421 │ │ │ │ │ CONDA_CMD, │
│ 422 │ │ │ │ │ "env", │
│ │
│ /home/runner/.local/lib/python3.12/site-packages/bioimageio/core/_resource_tests.py:197 in defau │
│ │
│ 194 │
│ 195 def default_run_command(args: Sequence[str]): │
│ 196 │ logger.info("running '{}'...", " ".join(args)) │
│ ❱ 197 │ _ = subprocess.check_call(args) │
│ 198 │
│ 199 │
│ 200 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/tmpxr_hqayw/pytorch_state_dict/env.yaml', '--name=755f1c5d5db340315cccd209a1aa696b22de3bea219e0f714c8617e638911938', '--quiet']' returned non-zero exit status 1.