| 🟡 |
bioimageio format validation |
| status |
valid-format |
| source |
https://hypha.aicell.io/bioimage-io/artifacts/charismatic-whale/files/rdf.yaml?version=v0 |
| id |
charismatic-whale |
| version |
1.0.1 |
| applied format |
model 0.5.10 |
| bioimageio.spec |
0.5.10.2 |
|
Location |
Details |
| ✔️ |
|
Successfully created `ModelDescr` instance. |
| ✔️ |
|
bioimageio.spec format validation model 0.5.10 |
| ⚠ |
inputs.0.sample_tensor |
Needs to be filled for FAIR compliance |
| ⚠ |
outputs.0.sample_tensor |
Needs to be filled for FAIR compliance |
| ❌ |
weights.torchscript |
Conda environment creation |
| ❌ |
weights.torchscript |
Command '['conda', 'env', 'create', '--yes', '--file=/tmp/tmpo5yp_vsq/torchscript/env.yaml', '--name=9c82d2cec5a94707cc26ef020f54bbee82474f4bbc61da4ec4e0890677f85751', '--quiet']' returned non-zero exit status 1. |
|
|
See Traceback 1. |
|
weights.torchscript |
recommended conda environment (Conda environment creation) |
|
|
%YAML 1.2
---
channels:
- conda-forge
- nodefaults
dependencies:
- conda-forge::bioimageio.core>=0.9.4
- numpy <2
- pip
- pytorch==2.2.0
- torchvision==0.17.0
|
|
weights.torchscript |
conda compare (Conda environment creation) |
|
|
/usr/share/miniconda/lib/python3.13/site-packages/conda/env/env.py:288: FutureWarning: The
environment file is not fully CEP 24 compliant is deprecated and will be removed in 26.9. In the
future, this configuration will be rejected. Please fix the following errors in order to make
the configuration valid: - Invalid type for 'name', expected a str deprecated.topic(
bioimageio.core not found numpy not found pip not found pytorch 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:443 in _test │
│ │
│ 440 │ │ raise RuntimeError("Conda not available") from e │
│ 441 │ │
│ 442 │ try: │
│ ❱ 443 │ │ run_command([CONDA_CMD, "run", "-n", env_name, "python", "--version"]) │
│ 444 │ except Exception: │
│ 445 │ │ working_dir.mkdir(parents=True, exist_ok=True) │
│ 446 │ │ path = working_dir / "env.yaml" │
│ │
│ /home/runner/.local/lib/python3.12/site-packages/bioimageio/core/_resource_tests.py:203 in defau │
│ │
│ 200 │
│ 201 def default_run_command(args: Sequence[str]): │
│ 202 │ logger.info("running '{}'...", " ".join(args)) │
│ ❱ 203 │ _ = subprocess.check_call(args) │
│ 204 │
│ 205 │
│ 206 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', '9c82d2cec5a94707cc26ef020f54bbee82474f4bbc61da4ec4e0890677f85751', '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:450 in _test │
│ │
│ 447 │ │ try: │
│ 448 │ │ │ _ = path.write_bytes(encoded_env) │
│ 449 │ │ │ logger.debug("written conda env to {}", path) │
│ ❱ 450 │ │ │ run_command( │
│ 451 │ │ │ │ [ │
│ 452 │ │ │ │ │ CONDA_CMD, │
│ 453 │ │ │ │ │ "env", │
│ │
│ /home/runner/.local/lib/python3.12/site-packages/bioimageio/core/_resource_tests.py:203 in defau │
│ │
│ 200 │
│ 201 def default_run_command(args: Sequence[str]): │
│ 202 │ logger.info("running '{}'...", " ".join(args)) │
│ ❱ 203 │ _ = subprocess.check_call(args) │
│ 204 │
│ 205 │
│ 206 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/tmpo5yp_vsq/torchscript/env.yaml', '--name=9c82d2cec5a94707cc26ef020f54bbee82474f4bbc61da4ec4e0890677f85751', '--quiet']' returned non-zero exit status 1.