From 96f3523a43ddfc25a05ce971c6da8f0858041080 Mon Sep 17 00:00:00 2001
From: Yiding Lu <45527994+OBJECT907@users.noreply.github.com>
Date: Sat, 28 Feb 2026 10:44:30 +0800
Subject: [PATCH] Add epsilon adjustment to fold_change and percent_change

Updated fold_change and percent_change functions to include epsilon adjustment to prevent division by zero.
---
 src/pdex/_math.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/pdex/_math.py b/src/pdex/_math.py
index 2503d20..bc96fcc 100644
--- a/src/pdex/_math.py
+++ b/src/pdex/_math.py
@@ -106,15 +106,15 @@ def bulk_matrix_geometric(
 
 
 @nb.njit(parallel=True)
-def fold_change(x: np.ndarray, y: np.ndarray) -> np.ndarray:
+def fold_change(x: np.ndarray, y: np.ndarray, eps=1e-4) -> np.ndarray:
     """Calculates the log2-fold change between two arrays."""
-    return np.log2(x / y)
+    return np.log2((x + eps) / (y + eps))
 
 
 @nb.njit(parallel=True)
-def percent_change(x: np.ndarray, y: np.ndarray) -> np.ndarray:
+def percent_change(x: np.ndarray, y: np.ndarray, eps=1e-4) -> np.ndarray:
     """Calculates the change between two arrays."""
-    return (x - y) / y
+    return (x - y) / (y + eps)
 
 
 def mwu(