diff --git a/src/python/diff3_analysis.ipynb b/src/python/diff3_analysis.ipynb
deleted file mode 100644
index 013ab8e1d8..0000000000
--- a/src/python/diff3_analysis.ipynb
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from diff3_analysis import diff3_analysis\n",
-    "import os\n",
-    "\n",
-    "row_nums = [\n",
-    "    582, 427, 930, 70, 128, 1444, 1177, 849, 1425, 1642, 1897, 862, 943, 1442, 1120,\n",
-    "    111, 693, 535, 354, 530, 845, 654, 921, 464, 1006, 707, 485, 1928, 809, 1329, 65, 1890, 100, 247, 2038, 900\n",
-    "]\n",
-    "\n",
-    "merge_tools = [\"gitmerge_ort\", \n",
-    "    \"gitmerge_ort_adjacent\", \n",
-    "    \"gitmerge_ort_ignorespace\", \n",
-    "    \"gitmerge_ort_imports\", \n",
-    "    \"gitmerge_ort_imports_ignorespace\", \n",
-    "    \"gitmerge_resolve\",\n",
-    "    \"gitmerge_recursive_histogram\", \n",
-    "    \"gitmerge_recursive_ignorespace\", \n",
-    "    \"gitmerge_recursive_minimal\", \n",
-    "    \"gitmerge_recursive_myers\", \n",
-    "    \"gitmerge_recursive_patience\",\n",
-    "    \"git_hires_merge\",\n",
-    "    \"spork\", \n",
-    "    \"intellimerge\"]\n",
-    "\n",
-    "# Ensure the base output directory exists\n",
-    "base_output_dir = \"./merge_conflict_analysis_diffs\"\n",
-    "\n",
-    "for row_num in row_nums:\n",
-    "    for merge_tool in merge_tools:\n",
-    "        # Create a subdirectory for this specific results_index\n",
-    "        repo_output_dir = os.path.join(base_output_dir, str(row_num), merge_tool)\n",
-    "        os.makedirs(repo_output_dir, exist_ok=True)\n",
-    "        diff3_analysis(merge_tool, row_num, repo_output_dir)\n"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "research",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.18"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 2
-}
diff --git a/src/python/run_diff3_analysis.py b/src/python/run_diff3_analysis.py
new file mode 100644
index 0000000000..8c7fd259a6
--- /dev/null
+++ b/src/python/run_diff3_analysis.py
@@ -0,0 +1,74 @@
+from diff3_analysis import diff3_analysis
+import os
+
+# Mixed conflict and pass examples from results_greatest_hits/result.csv
+# Randomly chosen sample of mixed results from dataset
+row_nums = [
+    582,
+    427,
+    930,
+    70,
+    128,
+    1444,
+    1177,
+    849,
+    1425,
+    1642,
+    1897,
+    862,
+    943,
+    1442,
+    1120,
+    111,
+    693,
+    535,
+    354,
+    530,
+    845,
+    654,
+    921,
+    464,
+    1006,
+    707,
+    485,
+    1928,
+    809,
+    1329,
+    65,
+    1890,
+    100,
+    247,
+    2038,
+    900,
+]
+
+# All merge tools
+merge_tools = [
+    "gitmerge_ort",
+    "gitmerge_ort_adjacent",
+    "gitmerge_ort_ignorespace",
+    "gitmerge_ort_imports",
+    "gitmerge_ort_imports_ignorespace",
+    "gitmerge_resolve",
+    "gitmerge_recursive_histogram",
+    "gitmerge_recursive_ignorespace",
+    "gitmerge_recursive_minimal",
+    "gitmerge_recursive_myers",
+    "gitmerge_recursive_patience",
+    "git_hires_merge",
+    "spork",
+    "intellimerge",
+]
+
+
+def run_analysis():
+    # Ensure the base output directory exists
+    base_output_dir = "./merge_conflict_analysis_diffs"
+
+    # Loop through each conflict, recreating merges to repo_output_dir
+    for row_num in row_nums:
+        for merge_tool in merge_tools:
+            # Create a subdirectory for this specific results_index
+            repo_output_dir = os.path.join(base_output_dir, str(row_num), merge_tool)
+            os.makedirs(repo_output_dir, exist_ok=True)
+            diff3_analysis(merge_tool, row_num, repo_output_dir)