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fix: add DeprecationWarning to geneset() and snp_dataset() #1286

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fix: add DeprecationWarning to geneset() and snp_dataset() #1286

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44b61ec
fix: add DeprecationWarning to geneset() and snp_dataset()
Tanisha127 Apr 12, 2026
4f7db8f
Merge branch 'master' into fix/deprecation-warnings-geneset-snp-dataset
Tanisha127 Apr 12, 2026
389e133
fix: apply ruff-format formatting
Tanisha127 Apr 12, 2026
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8 changes: 8 additions & 0 deletions malariagen_data/anoph/genome_features.py
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Expand Up @@ -68,6 +68,14 @@ def _geneset_gff3_path(self):

def geneset(self, *args, **kwargs): # pragma: no cover
"""Deprecated, this method has been renamed to genome_features()."""
import warnings

warnings.warn(
"geneset() is deprecated and will be removed in a future version. "
"Use genome_features() instead.",
DeprecationWarning,
stacklevel=2,
)
return self.genome_features(*args, **kwargs)

def _genome_features(self, *, attributes: Tuple[str, ...]):
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8 changes: 8 additions & 0 deletions malariagen_data/anoph/snp_data.py
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Expand Up @@ -1380,6 +1380,14 @@ def _snp_calls(

def snp_dataset(self, *args, **kwargs): # pragma: no cover
"""Deprecated, this method has been renamed to snp_calls()."""
import warnings

warnings.warn(
"snp_dataset() is deprecated and will be removed in a future version. "
"Use snp_calls() instead.",
DeprecationWarning,
stacklevel=2,
)
return self.snp_calls(*args, **kwargs)

def _prep_region_cache_param(
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