From 0d0c6a6ad061f1f20e7b982051415857f898f527 Mon Sep 17 00:00:00 2001
From: Charlotte Rich-Griffin <25774602+crichgriffin@users.noreply.github.com>
Date: Wed, 12 Apr 2023 11:49:28 +0100
Subject: [PATCH] add logging to track change in nnb

---
 panpipes/python_scripts/batch_correct_bbknn.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/panpipes/python_scripts/batch_correct_bbknn.py b/panpipes/python_scripts/batch_correct_bbknn.py
index 508d7e6f..d05900cf 100644
--- a/panpipes/python_scripts/batch_correct_bbknn.py
+++ b/panpipes/python_scripts/batch_correct_bbknn.py
@@ -61,9 +61,13 @@
 
     # make sure that batch is a categorical
     adata.obs["comb_columns"] = adata.obs["comb_columns"].astype("category")
+    # test the minimum number of neighbours needed for the function to not break,
+    # the safe point is 40 in my tests
     nn_test = nnb * len(adata.obs["comb_columns"].unique())
     if nn_test > 40:
         nnb = nnb - 1
+        L.info("reducing the numbers within batch to %i as the number of batches is high, \
+               and bbknn will likely crash" % nnb)
         if nnb < 1:
             sys.exit("can't work with 0 neighbors_within_batch")
     # run bbknn