chores: clean up Ruff issues in quickstart_demo.ipynb

Author: ecarrenolozano

notebooks/quickstart_demo.ipynb

@@ -129,7 +129,7 @@
     "# 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",
@@ -167,7 +167,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "cache_dir = Path(\"../data/out\")"
+    "cache_dir = Path('../data/out')"
    ]
   },
   {
@@ -266,7 +266,7 @@
    "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')))"
    ]
   },
   {
@@ -282,7 +282,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(onto_registry.get_available_formats(ontology_id=\"chebi\"))"
+    "print(onto_registry.get_available_formats(ontology_id='chebi'))"
    ]
   },
   {
@@ -326,18 +326,18 @@
    "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}')"
    ]
   },
   {
@@ -376,13 +376,13 @@
    "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())}')"
    ]
   },
   {
@@ -400,7 +400,7 @@
    "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"
    ]
   },
   {
@@ -412,9 +412,9 @@
     "queries = OntologyQueries(gene_ontology)\n",
     "\n",
     "# Print term relations\n",
-    "print(f\"Term: {term_id}\")\n",
-    "print(f\"  Parents     : {queries.ancestors(term_id)}\")\n",
-    "print(f\"  Children    : {queries.descendants(term_id)}\")\n",
+    "print(f'Term: {term_id}')\n",
+    "print(f'  Parents     : {queries.ancestors(term_id)}')\n",
+    "print(f'  Children    : {queries.descendants(term_id)}')\n",
     "\n",
     "\n",
     "# print(f\"  Ancestors   : {queries.ancestors(term_id)}\")\n",
@@ -458,7 +458,7 @@
    "outputs": [],
    "source": [
     "# Load the ontogragh catalog of ontologies\n",
-    "onto_registry = op.registry(\"../data/out\")"
+    "onto_registry = op.registry('../data/out')"
    ]
   },
   {
@@ -508,7 +508,7 @@
    "outputs": [],
    "source": [
     "# You can get the metadata of each ontology and store it in a variable. At the same time, you can print it using `show_metadata=True`\n",
-    "go_metadata = onto_registry.get_ontology_metadata(\"go\", show_metadata=True)"
+    "go_metadata = onto_registry.get_ontology_metadata('go', show_metadata=True)"
    ]
   },
   {
@@ -518,7 +518,7 @@
    "outputs": [],
    "source": [
     "# The catalog contains different formats for the same ontology. You can verify all the formats available for a specific ontology.\n",
-    "onto_registry.get_available_formats(\"chebi\")"
+    "onto_registry.get_available_formats('chebi')"
    ]
   },
   {