Closed YaphetKG closed 1 year ago
Hi @YaphetKG :)
Thank you for testing this out and submitting a ticket. That error comes when the version of linkml-runtime and linkml dependencies are out of date. I think jupyter-notebook inherits your virtual environment cache and also uses your local virtual environment. Can you do a !pip list
in the notebook and check what versions your linkml dependencies are on?
If I do this:
!pip install --no-cache-dir bmt==0.8.11
from bmt import Toolkit
import bmt
url = 'https://raw.githubusercontent.com/biolink/biolink-model/v3.0.1/biolink-model.yaml'
bmt = Toolkit(URL)
!pip list
I get:
linkml 1.3.2
linkml-dataops 0.1.0
linkml-runtime 1.3.2
The reachable_from
syntax is new to linkml 1.3.2, and we use it in biolink to constrain enumerations.
ah ok , let me try it thanks @sierra-moxon
It is working thanks for the hint @sierra-moxon
Is there any way to ensure that bmt > 0.8.8 always requires linkml > 1.3.2? I just ran into this problem because I upgraded to bmt 0.8.11 but my linkml is still at 1.2.10. My Python package config skills are weak, but I think you can add it to requirements.txt.
I recently did this
on a jupyter notebook , but it seems like there is a value error that is raised