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jbloomlab / dms_variants

Analyze deep mutational scanning of barcoded variants.
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deprecation warning #85

Open jbloom opened 1 year ago

jbloom commented 1 year ago

The code currently gives this warning:

/fh/fast/bloom_j/software/miniconda3/envs/dms-vep-pipeline/lib/python3.11/site-packages/dms_variants/codonvarianttable.py:1779: FutureWarning: In a future version, the Index constructor will not infer numeric dtypes when passed object-dtype sequences (matching Series behavior)
jbloom commented 7 months ago

Not yet addressed, closed by accident.

jgallowa07 commented 1 day ago

I think this might be related but I just installed dms_variants == 1.6.0 and when I tried

import dms_variants.codon_variant_table

I got

    from mizani.utils import multitype_sort
ImportError: cannot import name 'multitype_sort' from 'mizani.utils' (/home/jgallowa/miniforge3/envs/multidms-dev/lib/python3.9/site-packages/mizani/utils.py)

The underlying problem seems to be with plotnine. Looking into a solution for this now.

jgallowa07 commented 1 day ago

It works for me if I pin mizani, a dependency of plotnine, to 011.4. Maybe worth raising an issue with plotnine, as the problem is coming from there.

jbloom commented 1 day ago

Yes, do you want to raise the plotnine issue?