Problem
geneset() and snp_dataset() have docstrings saying they are deprecated,
but they never call warnings.warn(). Users get zero indication at runtime
that they should switch to the new methods.
Steps to Reproduce
import warnings
warnings.simplefilter("always")
ag3.geneset() # no DeprecationWarning raised
ag3.snp_dataset() # no DeprecationWarning raised
Expected Behaviour
Both methods should raise DeprecationWarning pointing users to the
replacement methods genome_features() and snp_calls().
Files Affected
malariagen_data/anoph/genome_features.py — geneset()
malariagen_data/anoph/snp_data.py — snp_dataset()
Fix
Added warnings.warn(..., DeprecationWarning, stacklevel=2) to both methods.
Problem
geneset()andsnp_dataset()have docstrings saying they are deprecated,but they never call
warnings.warn(). Users get zero indication at runtimethat they should switch to the new methods.
Steps to Reproduce
Expected Behaviour
Both methods should raise
DeprecationWarningpointing users to thereplacement methods
genome_features()andsnp_calls().Files Affected
malariagen_data/anoph/genome_features.py—geneset()malariagen_data/anoph/snp_data.py—snp_dataset()Fix
Added
warnings.warn(..., DeprecationWarning, stacklevel=2)to both methods.