chores: format files by suggestion of running ruff

Author: ecarrenolozano

.pre-commit-config.yaml

@@ -22,7 +22,7 @@ default_stages:
 repos:
     # Fast Python linter and formatter with auto-fix support
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.3
+    rev: v0.12.5
     hooks:
     -   id: ruff-check
         args: [--fix, --show-fixes]

notebooks/quickstart_demo.ipynb

@@ -367,7 +367,9 @@
     "name_id_go = 'go'\n",
     "format_go = 'obo'\n",
     "\n",
-    "gene_ontology = ontology_loader.load_from_registry(name_id=name_id_go, format=format_go)\n",
+    "gene_ontology = ontology_loader.load_from_registry(\n",
+    "    name_id=name_id_go, format=format_go\n",
+    ")\n",
     "\n",
     "print(f'Loaded ontology: {name_id_go}.{format_go}')\n",
     "print(f'Number of terms: {len(gene_ontology.terms())}')"
@@ -579,7 +581,7 @@
    "outputs": [],
    "source": [
     "# Load \"chebi\" ontology previosly downloaded\n",
-    "#chebi = loader.load_from_registry(name_id=\"chebi\", format=\"owl\")"
+    "# chebi = loader.load_from_registry(name_id=\"chebi\", format=\"owl\")"
    ]
   },
   {
@@ -599,9 +601,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "path='../data/out/go_version1.obo'\n",
+    "path = '../data/out/go_version1.obo'\n",
     "\n",
-    "Path(path).exists()\n"
+    "Path(path).exists()"
    ]
   },
   {