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scverse / genomic-features

Genomic Features in Python from BioConductor's AnnotationHub
https://genomic-features.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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Breaking changes to ibis #77

Open emdann opened 1 month ago

emdann commented 1 month ago

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New ibis release breaks the core gene function (see also in CI)

ensdb = genomic_features.ensembl.annotation(species="Hsapiens", version="108")
genes = ensdb.genes()

throws

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/oak/stanford/groups/pritch/users/emma/miniforge3/envs/perturb-vs-tissue-env/lib/python3.10/site-packages/genomic_features/ensembl/ensembldb.py", line 123, in genes
    query = self.db.table("gene").filter(filter.convert())
  File "/oak/stanford/groups/pritch/users/emma/miniforge3/envs/perturb-vs-tissue-env/lib/python3.10/site-packages/ibis/expr/types/relations.py", line 2486, in filter
    raise com.IbisInputError("You must pass at least one predicate to filter")
ibis.common.exceptions.IbisInputError: You must pass at least one predicate to filter

Quick fix: downgrading to ibis-framework[sqlite, duckdb]==8.0.0