clean notebook

Docs/Analysis/_1_template_extraction.ipynb

@@ -64,7 +64,7 @@
     "\n",
     "\n",
     "def save_svg_to_file(svg_object):\n",
-    "    svg_data = svg_object.data  \n",
+    "    svg_data = svg_object.data\n",
     "    with tempfile.NamedTemporaryFile(delete=False, suffix=\".svg\") as tmpfile:\n",
     "        tmpfile.write(svg_data.encode(\"utf-8\"))\n",
     "        return tmpfile.name\n",
@@ -85,8 +85,6 @@
     "from pdf2image import convert_from_path\n",
     "\n",
     "\n",
-    "\n",
-    "\n",
     "def pdf_to_images(pdf_path, dpi=900):\n",
     "    \"\"\"\n",
     "    Converts PDFs to images with an option to specify the DPI for higher quality.\n",
@@ -198,7 +196,9 @@
     "\n",
     "\n",
     "titles = [\"A\", \"B\", \"C\"]\n",
-    "display_images_in_subplot(images, _its, _rc, titles, save_path=\"./fig/Fig1_old_aam_its_rc.pdf\")"
+    "display_images_in_subplot(\n",
+    "    images, _its, _rc, titles, save_path=\"./fig/Fig1_old_aam_its_rc.pdf\"\n",
+    ")"
    ]
   },
   {

Docs/Analysis/_2b_aam_analysis.ipynb

@@ -323,7 +323,9 @@
     "sys.path.append(\"../../\")\n",
     "from syntemp.SynUtils.utils import load_database\n",
     "\n",
-    "data = load_database(\"../../Data/AAM/results_benchmark/golden/golden_aam_reactions.json.gz\")"
+    "data = load_database(\n",
+    "    \"../../Data/AAM/results_benchmark/golden/golden_aam_reactions.json.gz\"\n",
+    ")"
    ]
   },
   {
@@ -582,7 +584,9 @@
     "sys.path.append(\"../../\")\n",
     "from syntemp.SynUtils.utils import load_database\n",
     "\n",
-    "final_df = pd.DataFrame(load_database(\"../../Data/AAM/results_benchmark/aam_benchmark.json.gz\"))"
+    "final_df = pd.DataFrame(\n",
+    "    load_database(\"../../Data/AAM/results_benchmark/aam_benchmark.json.gz\")\n",
+    ")"
    ]
   },
   {