`export_bioimageio()` causes config file error
qin-yu opened this issue · comments
Describe the bug
The current export_bioimageio()
function generates a config file containing an erroneous line of code, leading to errors. e.g. if I install a minimal conda environment for exporting StarDist model, the default environment.yaml file generated by export_bioimageio()
contains a line - bioimageio.core>=0.5.0; extra == "bioimageio"
, which causes a failed check in bioimage.io after submitting the exported model.
error': 'Failed to install conda environment:\n'
'channels: [defaults, conda-forge]\n'
'dependencies:\n'
'- python>=3.7,<3.8\n'
'- bioimageio.core>=0.5.0; extra == "bioimageio"\n'
'- pip\n'
"- pip: [stardist>=0.8.3, 'tensorflow>=1.[15](https://github.com/bioimage-io/collection-bioimage-io/actions/runs/6476544517/job/17585511761?pr=648#step:9:16),<2']\n"
"name: '8429[20](https://github.com/bioimage-io/collection-bioimage-io/actions/runs/6476544517/job/17585511761?pr=648#step:9:21)5'\n",
'id': 'validation_summary_tensorflow_saved_model_bundle',
'name': 'install test environment',
'status': 'failed'
To reproduce
Standard use of export_bioimageio()
in a minimal environment causes the issue.
Expected behavior
bioimageio.core
's requirement should be - bioimageio.core>=0.5.0
Environment (please complete the following information):
- StarDist version 0.8.3
- TensorFlow version 1.15.3
- OS: Linux
This will be fixed together with the next export_bioimageio()
issue