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Improve transparency by warning when max_cohort_size triggers downsampling #930

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Improve transparency by warning when max_cohort_size triggers downsampling #930

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9bf82a9
feat: warn when cohort downsampling occurs (fixes #912)
adilraza99 Feb 23, 2026
a026446
Merge branch 'master' into GH912-cohort-downsampling-warning
jonbrenas Feb 23, 2026
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7 changes: 7 additions & 0 deletions malariagen_data/anoph/snp_data.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
import warnings
from functools import lru_cache
from typing import Any, Dict, List, Optional, Tuple, Union

Expand Down Expand Up @@ -1253,6 +1254,12 @@ def _snp_calls(
if max_cohort_size is not None:
n_samples = ds.sizes["samples"]
if n_samples > max_cohort_size:
warnings.warn(
f"Cohort downsampled from {n_samples} to {max_cohort_size} "
"samples. Set max_cohort_size=None to disable downsampling.",
UserWarning,
stacklevel=2,
)
rng = np.random.default_rng(seed=random_seed)
loc_downsample = rng.choice(
n_samples, size=max_cohort_size, replace=False
Expand Down