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Breaking changes to ibis #77

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emdann opened this issue May 23, 2024 · 1 comment · May be fixed by #79
Open

Breaking changes to ibis #77

emdann opened this issue May 23, 2024 · 1 comment · May be fixed by #79
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@emdann
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emdann commented May 23, 2024 •
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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
@emdann emdann added the bug Something isn't working label May 23, 2024
This was referenced Nov 28, 2024
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@pablo-gar
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pablo-gar commented Nov 28, 2024 •
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This is caused by passing an empty filter. Fixed here #79

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