feat(validation): add stratified sampling by ring size

src/macro_lactone_toolkit/validation/sampling.py

@@ -0,0 +1,55 @@
+from __future__ import annotations
+
+import pandas as pd
+
+from macro_lactone_toolkit import MacroLactoneAnalyzer
+
+
+def stratified_sample_by_ring_size(
+    df: pd.DataFrame,
+    sample_ratio: float,
+    smiles_col: str = "smiles",
+    random_state: int = 42,
+) -> pd.DataFrame:
+    """
+    Perform stratified sampling by ring size.
+
+    First classifies all molecules, then samples 10% from each ring size layer.
+    """
+    analyzer = MacroLactoneAnalyzer()
+
+    # Classify all molecules
+    classifications = []
+    ring_sizes = []
+
+    for smiles in df[smiles_col]:
+        result = analyzer.classify_macrocycle(smiles)
+        classifications.append(result.classification)
+        ring_sizes.append(result.ring_size)
+
+    df = df.copy()
+    df["_classification"] = classifications
+    df["_ring_size"] = ring_sizes
+
+    # Group by ring size and sample from each group
+    sampled_groups = []
+
+    for ring_size in range(12, 21):
+        group = df[df["_ring_size"] == ring_size]
+        if len(group) > 0:
+            n_samples = max(1, int(len(group) * sample_ratio))
+            sampled = group.sample(n=min(n_samples, len(group)), random_state=random_state)
+            sampled_groups.append(sampled)
+
+    # Also sample from unknown ring size (None)
+    unknown_group = df[df["_ring_size"].isna()]
+    if len(unknown_group) > 0:
+        n_samples = max(1, int(len(unknown_group) * sample_ratio))
+        sampled = unknown_group.sample(n=min(n_samples, len(unknown_group)), random_state=random_state)
+        sampled_groups.append(sampled)
+
+    if not sampled_groups:
+        return pd.DataFrame()
+
+    result = pd.concat(sampled_groups, ignore_index=True)
+    return result

tests/validation/test_sampling.py

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+import pandas as pd
+import pytest
+
+from macro_lactone_toolkit.validation.sampling import stratified_sample_by_ring_size
+
+
+def test_stratified_sample():
+    # Create test data with known ring sizes
+    data = {
+        "smiles": [
+            "O=C1CCCCCCCCCCCCCCO1",  # 16-membered
+            "O=C1CCCCCCCCCCCCO1",     # 14-membered
+            "O=C1CCCCCCCCCCCCCCCCO1", # 18-membered
+        ],
+        "id": ["A", "B", "C"],
+    }
+    df = pd.DataFrame(data)
+
+    sampled = stratified_sample_by_ring_size(df, sample_ratio=0.5, random_state=42)
+
+    # Should get at least 1 from each ring size (50% of 1 = 1)
+    assert len(sampled) >= 1
+    assert len(sampled) <= 3