added patch for rm permissions bug

Author: dmarx

pyttitools-PYTTI.ipynb

@@ -338,8 +338,19 @@
         "  if not path_exists('./pytti'):\n",
         "    !git clone https://github.com/pytti-tools/pytti-core.git pytti       &> /dev/null\n",
         "  else:\n",
-        "    !rm -r pytti\n",
-        "    !git clone https://github.com/pytti-tools/pytti-core.git pytti\n",
+        "    try:\n",
+        "      !rm -r pytti\n",
+        "      !git clone https://github.com/pytti-tools/pytti-core.git pytti\n",
+        "    except Exception as ex:\n",
+        "      logger.warning(\n",
+        "        str(ex)\n",
+        "      )\n",
+        "      logger.warning(\n",
+        "        \"A `pytti` folder already exists and could not be deleted.\"\n",
+        "        \"If you encounter problems, try deleting that folder and trying again.\"\n",
+        "        \"Please report this and any other issues here: \"\n",
+        "        \"https://github.com/pytti-tools/pytti-notebook/issues/new\",\n",
+        "        exc_info=True)\n",
         "  !pip install -r pytti/requirements.txt\n",
         "  !git clone https://github.com/shariqfarooq123/AdaBins.git        &> /dev/null\n",
         "  !git clone https://github.com/zacjiang/GMA.git                   &> /dev/null\n",