afloresep · afloresep · Apr 30, 2026 · Apr 30, 2026 · Apr 30, 2026 · Apr 30, 2026
diff --git a/notebooks/01_quickstart.ipynb b/notebooks/01_quickstart.ipynb
@@ -69,7 +69,7 @@
     }
    ],
    "source": [
-    "model = TMAP(metric=\"jaccard\", n_neighbors=20, kc=50, seed=42).fit(fps)\n",
+    "model = TMAP(metric=\"jaccard\",seed=42).fit(fps)\n",
     "\n",
     "print(model.embedding_.shape)\n",
     "print(model.tree_.edges.shape)\n"
@@ -84,6 +84,14 @@
     "Use `to_widget()` when you want an interactive Jupyter view.\n"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "ede8ead6",
+   "metadata": {},
+   "source": [
+    "Note: If this is your first time using the notebook view (jupyter-scatter) you might need to restart the notebook or the VSCode extensions after installing."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 3,
@@ -93,19 +101,19 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/var/folders/zw/c0mr_7jx7t3bz1k6_9n9wh3r0000gn/T/ipykernel_83682/684963885.py:5: UserWarning: Edges are not supported in notebook mode yet and will be ignored.\n",
+      "/var/folders/zw/c0mr_7jx7t3bz1k6_9n9wh3r0000gn/T/ipykernel_37637/684963885.py:5: UserWarning: Edges are not supported in notebook mode yet and will be ignored.\n",
       "  widget = viz.to_widget(width=1000, height=650, controls=True)\n"
      ]
     },
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "c968a1fae2dd4ca6b4b08e5e79da193e",
+       "model_id": "252e412c35304bca8b89c728ad5a8115",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "VBox(children=(HBox(children=(VBox(children=(<jscatter.widgets.button.Button object at 0x13fd45e80>, <jscatter…"
+       "VBox(children=(HBox(children=(VBox(children=(<jscatter.widgets.button.Button object at 0x17eafdc10>, <jscatter…"
       ]
      },
      "execution_count": 3,
@@ -133,9 +141,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "quickstart_molecules.html\n"
+     ]
+    }
+   ],
    "source": [
     "path = viz.write_html(\"quickstart_molecules.html\")\n",
     "print(path)\n"

diff --git a/notebooks/08_cheminformatics.ipynb → notebooks/02_cheminformatics.ipynb b/notebooks/08_cheminformatics.ipynb → notebooks/02_cheminformatics.ipynb
diff --git a/notebooks/03_continuous_embeddings.ipynb b/notebooks/03_continuous_embeddings.ipynb
diff --git a/notebooks/04_new_functionalities.ipynb b/notebooks/04_new_functionalities.ipynb
diff --git a/notebooks/05_single_cell.ipynb → notebooks/04_single_cell.ipynb b/notebooks/05_single_cell.ipynb → notebooks/04_single_cell.ipynb
diff --git a/notebooks/07_faq.ipynb → notebooks/05_faq.ipynb b/notebooks/07_faq.ipynb → notebooks/05_faq.ipynb
diff --git a/notebooks/06_metric_guide.ipynb b/notebooks/06_metric_guide.ipynb
diff --git a/notebooks/02_minhash_deep_dive.ipynb → notebooks/06_minhash_deep_dive.ipynb b/notebooks/02_minhash_deep_dive.ipynb → notebooks/06_minhash_deep_dive.ipynb