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shuzhao-li-lab / PythonCentricPipelineForMetabolomics

Python pipeline for metabolomics data preprocessing, QC, standardization and annotation
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scipy dependency in matchms #72

Closed shuzhao-li closed 1 month ago

shuzhao-li commented 1 month ago

I'm using matchms 0.27.0, which calls a deprecated function in scipy (1.14.0)

ImportError: cannot import name 'get_index_dtype' from 'scipy.sparse'

I had to downgrade scipy to get through this:

pip install scipy==1.13.1

Maybe we should specify these versions in pcpfm install requirements.

jmmitc06 commented 1 month ago

Looks like v1.14 was released less than a month ago, never noticed a deprecation warning. I like that workaround for the time being. I've added it to the main branch but still need to push to pypi.