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josh-gree/repro.py

Created September 6, 2025 21:47
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repro.py
# /// script
# requires-python = ">=3.13"
# dependencies = [
# "inmoose",
# "numpy",
# "pandas",
# ]
# ///
"""Explicit reproduction of pycombat_norm IndexError."""
import numpy as np
import pandas as pd
from inmoose.pycombat.pycombat_norm import pycombat_norm
# Create data that triggers the bug
np.random.seed(42)
# 20 samples, 5 genes - exact failing case
data = pd.DataFrame(
np.random.normal(0, 1, (20, 5)), columns=[f"gene_{i}" for i in range(5)]
).T # Transpose to (genes × samples)
batch = ["reference"] * 10 + ["prediction"] * 10
print("Data shape (genes × samples):", data.shape)
print("Batch labels:", batch)
try:
result = pycombat_norm(data, batch, ref_batch="reference")
print("Success!")
except Exception as e:
print(f"Error: {e}")
print(f"Error type: {type(e).__name__}")
Raw
repro.py.lock
version = 1
revision = 3
requires-python = ">=3.13"
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