fix: include nbstripout, update ruff legacy pre-commit command

Author: iulusoy

.pre-commit-config.yaml

@@ -24,7 +24,7 @@ repos:
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.12.0
     hooks:
-    -   id: ruff
+    -   id: ruff-check
         args: [--fix, --show-fixes]
         stages: [pre-commit]
         files: \.py$
@@ -95,3 +95,9 @@ repos:
         -   '4'
         stages: [pre-commit]
         files: \.ya?ml$
+
+# clean output from jupyter notebooks
+-   repo: https://github.com/kynan/nbstripout
+    rev: 0.8.1
+    hooks:
+    -   id: nbstripout

notebooks/template_notebooks.ipynb

@@ -284,15 +284,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Added to sys.path: /home/edwin/SSC-Projects/b_REPOSITORIES/ontograph\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import sys\n",
     "import os\n",
@@ -308,38 +300,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Downloading data from 'http://purl.obolibrary.org/obo/go.obo' to file '/home/edwin/.ontograph_cache/go.obo'.\n",
-      "SHA256 hash of downloaded file: 0908af70601dd41f2c55f664ca5d5959e939162362e9a5573c6794b5d850e601\n",
-      "Use this value as the 'known_hash' argument of 'pooch.retrieve' to ensure that the file hasn't changed if it is downloaded again in the future.\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "{'name': 'go', 'version': 'releases/2025-06-01', 'format': '1.2'}\n"
-     ]
-    },
-    {
-     "ename": "AttributeError",
-     "evalue": "'Ontology' object has no attribute 'roots'",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[3], line 7\u001b[0m\n\u001b[1;32m      4\u001b[0m gene_ontology \u001b[38;5;241m=\u001b[39m client\u001b[38;5;241m.\u001b[39mload(name_id\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mgo\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28mformat\u001b[39m\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mobo\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m      6\u001b[0m \u001b[38;5;28mprint\u001b[39m(gene_ontology\u001b[38;5;241m.\u001b[39mmetadata())\n\u001b[0;32m----> 7\u001b[0m \u001b[38;5;28mprint\u001b[39m([root\u001b[38;5;241m.\u001b[39mid \u001b[38;5;28;01mfor\u001b[39;00m root \u001b[38;5;129;01min\u001b[39;00m \u001b[43mgene_ontology\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mroots\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m])\n",
-      "File \u001b[0;32m~/SSC-Projects/b_REPOSITORIES/ontograph/ontograph/api/client.py:51\u001b[0m, in \u001b[0;36mOntologyWrapper.roots\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m     50\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21mroots\u001b[39m(\u001b[38;5;28mself\u001b[39m):\n\u001b[0;32m---> 51\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mlist\u001b[39m(\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43montology\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mroots\u001b[49m())\n",
-      "\u001b[0;31mAttributeError\u001b[0m: 'Ontology' object has no attribute 'roots'"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "from ontograph.api.client import OntologyClient\n",
     "\n",