Prodigy Spacy scispacy versions

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Hello,

I'll be using Prodigy Spacy and scispacy in different capacities for a biomedical NER task. The current version of Prodigy that we have installed is 1.10.8 and I'll be submitting a request to have it upgraded to the latest version.

The latest version of Spacy is 3.2 and the latest version of Prodigy is 1.11.7 and both of these are compatible with each other. However, the latest version of scispacy is 0.4.0 which is incompatible with the latest version of Spacy 3.2 but proceeds to work with a upgrade warning. Furthermore, if I install scispacy (or its models) after installing spacy, spacy's version gets downgraded to 3.0.7 and it becomes incompatible with Prodigy.

I am wondering what is the best versions of all three Prodigy, spacy, scispacy that can work without problems (or even warnings). Unfortunately, I have limited scope of testing this because I'll be running this in a isolated sandbox environment with no internet access (and I would need to have support staff ingress anything I need). And I don't have access to Prodigy on my local computer.

Thanks.

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Hi @sudarshan85 , here are some suggestions that you can try. First, perhaps you can install a v1.11.x version of Prodigy if possible?

  • scispacy 0.4.0
  • spaCy 3.0.7 (compatible with scispacy) or 3.1.x
  • Prodigy v1.11.x (compatible with spaCy's v3.1).

Another suggestion is to try installing scispacy with all of its dependencies and upgrade spaCy (-> 3.1.x) to check if everything runs (if it does then it should be fine). Lastly, it might even be possible to install the scispacy models you're working on with the --no-deps flag.

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