| 🟡 |
bioimageio format validation |
| status |
valid-format |
| source |
https://hypha.aicell.io/bioimage-io/artifacts/resourceful-lizard/files/rdf.yaml?version=v0 |
| id |
resourceful-lizard |
| 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 |
| ⚠ |
documentation |
No '# Validation' (sub)section found in doc.md. |
| ⚠ |
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/tmp650mioe3/pytorch_state_dict/env.yaml', '--name=a5da52dafabdde7cdd7c07143428e76b22eb95ad536a51113bc0628f90346b5e', '--quiet']' returned non-zero exit status 1. |
|
|
See Traceback 1. |
|
weights.pytorch_state_dict |
recommended conda environment (Conda environment creation) |
|
|
See Recommended Conda Environment 1. |
|
weights.pytorch_state_dict |
conda compare (Conda environment creation) |
|
|
bioimageio.core not found cuda not found pip not found python not found pytorch not found
setuptools not found torchvision not found fsspec not found
//github.com/facebookresearch/segment-anything.git not found huggingface-hub not found
matplotlib not found packaging not found safetensors not found timm not found tqdm 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', 'a5da52dafabdde7cdd7c07143428e76b22eb95ad536a51113bc0628f90346b5e', '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/tmp650mioe3/pytorch_state_dict/env.yaml', '--name=a5da52dafabdde7cdd7c07143428e76b22eb95ad536a51113bc0628f90346b5e', '--quiet']' returned non-zero exit status 1.
Recommended Conda Environment 1
%YAML 1.2
---
channels:
- pytorch
- nvidia
- anaconda
- conda-forge
- nodefaults
dependencies:
- bioimageio.core
- cuda=11.8
- pip
- python=3.10
- pytorch
- setuptools
- torchvision
- pip:
- fsspec
- git+https://github.com/facebookresearch/segment-anything.git
- huggingface-hub
- matplotlib
- packaging
- safetensors
- timm
- tqdm