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bioimage-io / spec-bioimage-io

Specification for the bioimage.io model description file.
https://bioimage-io.github.io/spec-bioimage-io/
MIT License
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bioimageio.validate fails for the manifest.bioimage.io.yaml files #324

Open constantinpape opened 2 years ago

constantinpape commented 2 years ago

it fails for (at least) the first two entries in https://github.com/bioimage-io/collection-bioimage-io/blob/main/rdf.yaml#L30-L48:

https://github.com/HenriquesLab/ZeroCostDL4Mic: 

Error in manifest.bioimage.io.yaml:
("expected loaded resource to be a dictionary, but got type <class 'str'>: "
 'manifest.bioimage.io.yaml')

https://github.com/deepimagej/models/blob/master/manifest.bioimage.io.yaml

Error in manifest.bioimage.io...:
"'outputs'"
FynnBe commented 2 years ago

it fails for (at least) the first two entries in https://github.com/bioimage-io/collection-bioimage-io/blob/main/rdf.yaml#L30-L48:

this is not a valid collection... not sure if we want to update it here or in the spec to make it valid... I'll look into the collection repo first as we planned some more changes there and make sure that the collection specified there will be valid either way....

constantinpape commented 2 years ago

this is not a valid collection... not sure if we want to update it here or in the spec to make it valid... I'll look into the collection repo first as we planned some more changes there and make sure that the collection specified there will be valid either way....

I am not sure what's the best strategy, but the current state where rendering from a non-valid collection just works is very confusing because it's unclear how to fix it and the error messages are not helpful.

FynnBe commented 2 years ago

yes, but I suppose we have a limited amount of collection rdfs in use atm anyway... still, this needs a fix either way