stardist / stardist

StarDist - Object Detection with Star-convex Shapes

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`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