stardist / stardist

StarDist - Object Detection with Star-convex Shapes

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`export_bioimageio()` generates a default dependency file not required by bioimage.io

qin-yu opened this issue · comments

The default behavior of export_bioimageio() is to generate an environment.yaml file, documenting the environment in which the function is executed. While this feature could prove beneficial to certain users, I believe it should be an optional aspect, especially considering that bioimage.io does not mandate it for TensorFlow models.

Currently, a workaround for me involves specifying "dependencies": None in the overwrite_spec_kwargs dictionary. However, the existence of a default config file led me to take it for granted initially, resulting in unwanted reuploads and DOI records on Zenodo, and unnecessary installation of environments for bioimage.io's CI on GitHub. Additionally, even if an update is made without the environment.yaml file, the file persists and must be manually deleted.

To streamline the export process and enhance clarity for new users, I suggest adding a parameter, such as generate_default_deps=False, allowing users to opt out of this feature by default while retaining the option for those who find it valuable.

PS: A bug in generated environment.yaml file has been reported into #252