From 15a499485ede152b6d432b7c91f1084e9e11bd8f Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 26 Jun 2024 16:08:07 +0200
Subject: [PATCH] resolve deprecation warning in base.table
Use np.isnan instead of scipy.isnan. Starting from scipy 1.12
(or earlier), scipy.isnan was definitely deprecated. This made the
SpearmanCorrel function silently return None which triggered a failing
unit test that was reported by Andrius Merkys.
---
modules/base/pymod/table.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/modules/base/pymod/table.py b/modules/base/pymod/table.py
index 1e20e4eae..f5adc6a10 100644
--- a/modules/base/pymod/table.py
+++ b/modules/base/pymod/table.py
@@ -2172,6 +2172,7 @@ Statistics for column %(col)s
"""
try:
import scipy.stats.mstats
+ import numpy as np
if IsStringLike(col1) and IsStringLike(col2):
col1 = self.GetColIndex(col1)
@@ -2183,7 +2184,7 @@ Statistics for column %(col)s
vals2.append(v2)
try:
correl = scipy.stats.mstats.spearmanr(vals1, vals2)[0]
- if scipy.isnan(correl):
+ if np.isnan(correl):
return None
return correl
except:
--
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