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biolink / ontobio

python library for working with ontologies and ontology associations
https://ontobio.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
118 stars 30 forks source link

Graph.node removed in networkX 2.4 #554

Closed kshefchek closed 2 years ago

kshefchek commented 3 years ago

See https://networkx.org/documentation/stable/release/release_2.4.html#deprecations

We currently use this in obograph_util. I suggest we anchor to 2.3 and then fix this. This is breaking the monarch ui evidence views.

matentzn commented 2 years ago

Can we fix this issue in the code? Having ontobio pin versions really makes it hard to have it co-exist with other libraries further down the stack.

deepakunni3 commented 2 years ago

@kshefchek Could you also let us know if PR #585 fixed the issues you were seeing with Monarch UI evidence views?

cmungall commented 2 years ago

Thank you @deepakunni3 for #585 !!!

kshefchek commented 2 years ago

everything is working on the monarch side, thanks @deepakunni3 !

deepakunni3 commented 2 years ago

Happy to help @cmungall! Glad that it was quick fix.

Thanks @kshefchek for checking 🎉