fix: update notebook with suggestions given by ruff tool.

Author: ecarrenolozano

notebooks/quickstart_demo.ipynb

@@ -129,13 +129,11 @@
     "# 1. Standard library imports\n",
     "import sys\n",
     "\n",
-    "sys.path.append(\"/home/ecarreno/SSC-Projects/b_REPOSITORIES/ontograph\")\n",
+    "sys.path.append('/home/ecarreno/SSC-Projects/b_REPOSITORIES/ontograph')\n",
     "\n",
     "from pathlib import Path\n",
     "\n",
     "# 2. Related third party imports\n",
-    "import pronto\n",
-    "\n",
     "# 3. Local application/library specific imports\n",
     "from ontograph.downloader import PoochDownloaderAdapter\n",
     "from ontograph.ontology_query import OntologyQueries\n",
@@ -158,7 +156,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "cache_dir = Path(\"../data/out\")"
+    "cache_dir = Path('../data/out')"
    ]
   },
   {
@@ -224,7 +222,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "for index, ontology in enumerate(onto_registry.list_available_ontologies()):\n",
+    "for ontology in onto_registry.list_available_ontologies():\n",
     "    print(ontology)"
    ]
   },
@@ -243,7 +241,7 @@
    "source": [
     "# This function looks if the given ontology has a link with a given extension\n",
     "\n",
-    "print(\"Link: {}\".format(onto_registry.get_download_url(\"chebi\", \"obo\")))"
+    "print('Link: {}'.format(onto_registry.get_download_url('chebi', 'obo')))"
    ]
   },
   {
@@ -259,7 +257,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(onto_registry.get_available_formats(ontology_id=\"chebi\"))"
+    "print(onto_registry.get_available_formats(ontology_id='chebi'))"
    ]
   },
   {
@@ -303,18 +301,18 @@
    "source": [
     "# Put the ontologies and their formats as a dictionary\n",
     "resources = [\n",
-    "    {\"name_id\": \"chebi\", \"format\": \"owl\"},\n",
-    "    {\"name_id\": \"go\", \"format\": \"obo\"},\n",
-    "    {\"name_id\": \"ado\", \"format\": \"owl\"},\n",
+    "    {'name_id': 'chebi', 'format': 'owl'},\n",
+    "    {'name_id': 'go', 'format': 'obo'},\n",
+    "    {'name_id': 'ado', 'format': 'owl'},\n",
     "]\n",
     "\n",
     "# Use the downloader, it has a cache in case you have already downloaded the ontologies.\n",
     "batch_results = downloader.fetch_batch(resources)\n",
     "\n",
     "# Print all the paths where your ontologies are located\n",
-    "print(\"Ontologies in cache:\")\n",
+    "print('Ontologies in cache:')\n",
     "for ontology_name, ontology_path in batch_results.items():\n",
-    "    print(f\"\\t{ontology_name}: {ontology_path}\")"
+    "    print(f'\\t{ontology_name}: {ontology_path}')"
    ]
   },
   {
@@ -353,13 +351,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "name_id_go = \"go\"\n",
-    "format_go = \"obo\"\n",
+    "name_id_go = 'go'\n",
+    "format_go = 'obo'\n",
     "\n",
     "gene_ontology = ontology_loader.load(name_id=name_id_go, format=format_go)\n",
     "\n",
-    "print(f\"Loaded ontology: {name_id_go}.{format_go}\")\n",
-    "print(f\"Number of terms: {len(gene_ontology.terms())}\")"
+    "print(f'Loaded ontology: {name_id_go}.{format_go}')\n",
+    "print(f'Number of terms: {len(gene_ontology.terms())}')"
    ]
   },
   {
@@ -377,7 +375,7 @@
    "source": [
     "# term_id = \"GO:0008150\" # biological_process\n",
     "# term_id = \"GO:0160266\"  # anestrus phase\n",
-    "term_id = \"GO:0070360\"  # symbiont-mediated actin polymerization-dependent cell-to-cell migration in host"
+    "term_id = 'GO:0070360'  # symbiont-mediated actin polymerization-dependent cell-to-cell migration in host"
    ]
   },
   {
@@ -389,9 +387,9 @@
     "queries = OntologyQueries(gene_ontology)\n",
     "\n",
     "# Print term relations\n",
-    "print(f\"Term: {term_id}\")\n",
-    "print(f\"  Parents     : {queries.parents(term_id)}\")\n",
-    "print(f\"  Children    : {queries.children(term_id)}\")\n",
+    "print(f'Term: {term_id}')\n",
+    "print(f'  Parents     : {queries.parents(term_id)}')\n",
+    "print(f'  Children    : {queries.children(term_id)}')\n",
     "\n",
     "\n",
     "# print(f\"  Ancestors   : {queries.ancestors(term_id)}\")\n",