From 7037c5a821aad3c01ee768a1b3cd7e21f05003e5 Mon Sep 17 00:00:00 2001
From: John Huddleston <huddlej@gmail.com>
Date: Tue, 23 Jan 2024 14:49:20 -0800
Subject: [PATCH] Manually disable normalized stress for MDS

Suppress a user warning from scikit-learn's MDS implementation caused by
not setting the `normalized_stress` value in v1.3. The default value changed
from `False` to `"auto"` in v1.4, but we want the original default
anyway so we set it here.
---
 src/pathogen_embed/pathogen_embed.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/pathogen_embed/pathogen_embed.py b/src/pathogen_embed/pathogen_embed.py
index 3838a39..dd5945c 100644
--- a/src/pathogen_embed/pathogen_embed.py
+++ b/src/pathogen_embed/pathogen_embed.py
@@ -284,6 +284,7 @@ def embed(args):
             "n_jobs": 1,
             "n_init": 2,
             "random_state" : args.random_seed,
+            "normalized_stress": False,
         }
 
     # Override defaults with parameter values passed through embedding parameters, if