From 1cb3efdd48651f234c48734aaf6b10b665a5aaba Mon Sep 17 00:00:00 2001
From: Zargham Ahmad <zargham.ahmad12@gmail.com>
Date: Sun, 24 Sep 2023 23:47:10 +0200
Subject: [PATCH 1/3] updated formatter.py

---
 tools/matchms/formatter.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/tools/matchms/formatter.py b/tools/matchms/formatter.py
index 7bb4b452..113a7cea 100644
--- a/tools/matchms/formatter.py
+++ b/tools/matchms/formatter.py
@@ -13,11 +13,13 @@ def scores_to_dataframe(scores):
         DataFrame: Scores
         DataFrame: Matches
     """
-    dataframe = DataFrame(columns=['query', 'reference', *scores.scores.score_names])
+    data = []
 
     for i, (row, col) in enumerate(zip(scores.scores.row, scores.scores.col)):
-        dataframe.loc[i] = [scores.queries[col].metadata['compound_name'], scores.references[row].metadata['compound_name'], *scores.scores.data[i]]
-
+        data.append([scores.queries[col].metadata['compound_name'], scores.references[row].metadata['compound_name'], *scores.scores.data[i]])
+    
+    dataframe = DataFrame(data, columns=['query', 'reference', *scores.scores.score_names])
+    
     return dataframe
 
 

From 90cae260899f63e782c482ffeefc26ebcc782f8f Mon Sep 17 00:00:00 2001
From: Zargham Ahmad <zargham.ahmad12@gmail.com>
Date: Mon, 25 Sep 2023 18:19:39 +0200
Subject: [PATCH 2/3] remove whitespace

---
 tools/matchms/formatter.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/matchms/formatter.py b/tools/matchms/formatter.py
index 113a7cea..0d58ecec 100644
--- a/tools/matchms/formatter.py
+++ b/tools/matchms/formatter.py
@@ -17,9 +17,9 @@ def scores_to_dataframe(scores):
 
     for i, (row, col) in enumerate(zip(scores.scores.row, scores.scores.col)):
         data.append([scores.queries[col].metadata['compound_name'], scores.references[row].metadata['compound_name'], *scores.scores.data[i]])
-    
+
     dataframe = DataFrame(data, columns=['query', 'reference', *scores.scores.score_names])
-    
+
     return dataframe
 
 

From 0ab31125b136f2273fc760060de3d28da295e6a2 Mon Sep 17 00:00:00 2001
From: Zargham Ahmad <46793118+zargham-ahmad@users.noreply.github.com>
Date: Wed, 27 Sep 2023 14:39:20 +0200
Subject: [PATCH 3/3] bump galaxy version matchms_formatter.xml

---
 tools/matchms/matchms_formatter.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/matchms/matchms_formatter.xml b/tools/matchms/matchms_formatter.xml
index 3ba3822d..10abc2f5 100644
--- a/tools/matchms/matchms_formatter.xml
+++ b/tools/matchms/matchms_formatter.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>reformat scores object of matchms to long format table</description>
 
     <macros>