From a1c21ed34c07f8f939cc30bf15d5ef6cc0e74938 Mon Sep 17 00:00:00 2001
From: eusimeo <116293153+eusimeo@users.noreply.github.com>
Date: Wed, 8 Jul 2026 15:48:48 +0200
Subject: [PATCH 1/2] Update pandas dependency.py

Updated the code from lines 700ish and on to be compatible with newer pandas versions
---
 src/grid.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/src/grid.py b/src/grid.py
index ec1cb4c..52ecd15 100644
--- a/src/grid.py
+++ b/src/grid.py
@@ -709,9 +709,19 @@ def reinitialization(self,initialization,microbes_pp,output,mode,pulse,*args):
         # calculate frequency of every taxon 
         frequencies = cum_abundance/cum_abundance.sum()
         frequencies = frequencies.fillna(0)
+        frequencies = frequencies.clip(lower=0, upper=1)          # guard against any stray negative/over-1 values (sum of 1) 
+        frequencies = frequencies / frequencies.sum() if frequencies.sum() > 0 else frequencies  # renormalize to exactly 1
+
+        #print("sum of frequencies:", frequencies.sum())
+        #print("any NaN?", frequencies.isna().any())
+        #print("min/max:", frequencies.min(), frequencies.max())
+        #print("dtype:", frequencies.dtype)
         
         # last: assign microbes to each grid box randomly based on prior densities
         choose_taxa = np.zeros((self.n_taxa,self.gridsize), dtype='int8')
         for i in range(self.n_taxa):
-            choose_taxa[i,:] = np.random.binomial(1, frequencies[i], self.gridsize)
-        self.Microbes.loc[np.ravel(choose_taxa,order='F')==0] = np.float32(0) # NOTE order='F'
\ No newline at end of file
+            freq=np.float64(frequencies.iloc[1]) #working independent of indexing (based on location not index labels)
+            p_vec = np.array([freq, 1.0 - freq], dtype=np.float64) #solve numoy issues
+            p_vec = p_vec / p_vec.sum()
+            choose_taxa[i,:] = np.random.choice([1,0], self.gridsize, replace=True, p=p_vec)
+        self.Microbes.loc[np.ravel(choose_taxa,order='F')==0] = np.float32(0) # NOTE order='F'

From d6fae256fb123026dc14ef95deeaca4b1faa08a1 Mon Sep 17 00:00:00 2001
From: Jeth Walkup <161084507+jgwalkup@users.noreply.github.com>
Date: Wed, 8 Jul 2026 10:09:02 -0400
Subject: [PATCH 2/2] Clean up grid.py by removing commented debug code

Removed debug print statements for frequencies.
---
 src/grid.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/src/grid.py b/src/grid.py
index 52ecd15..d0ca2c7 100644
--- a/src/grid.py
+++ b/src/grid.py
@@ -712,11 +712,6 @@ def reinitialization(self,initialization,microbes_pp,output,mode,pulse,*args):
         frequencies = frequencies.clip(lower=0, upper=1)          # guard against any stray negative/over-1 values (sum of 1) 
         frequencies = frequencies / frequencies.sum() if frequencies.sum() > 0 else frequencies  # renormalize to exactly 1
 
-        #print("sum of frequencies:", frequencies.sum())
-        #print("any NaN?", frequencies.isna().any())
-        #print("min/max:", frequencies.min(), frequencies.max())
-        #print("dtype:", frequencies.dtype)
-        
         # last: assign microbes to each grid box randomly based on prior densities
         choose_taxa = np.zeros((self.n_taxa,self.gridsize), dtype='int8')
         for i in range(self.n_taxa):