bug: ahref update (#4449)

* bug: ahref update

* fix: linter

* fix: typo fix

Author: dpanigra

notebooks/community/alphagenome/cloudai_alphagenome_finetune.ipynb

@@ -50,7 +50,8 @@
       "source": [
         "# AlphaGenome Finetuning Tutorial using Google Cloud Platform\n",
         "\n",
-        "This notebook demonstrates how to finetune an AlphaGenome model on custom genomic tracks.\n",
+        "This notebook demonstrates how to finetune an AlphaGenome model on custom genomic tracks. This notebook adds the Google Cloud Platform utilities to the Google DeepMind's \n",
+        "<a href=\"https://github.com/google-deepmind/alphagenome_research/blob/main/colabs/finetune.ipynb\">AlphaGenome Finetuning Tutorial</a>.\n",
         "\n",
         "**What you'll learn:**\n",
         "\n",

notebooks/community/alphagenome/cloudai_alphagenome_vai_quickstart.ipynb

@@ -37,7 +37,7 @@
         "    </a>\n",
         "  </td>\n",
         "  <td style=\"text-align: center\">\n",
-        "    <a href=\"https://console.cloud.google.com/vertex-ai/colab/import/https:%2F%2Fraw.githubusercontent.com%2FGoogleCloudPlatform%2Fvertex-ai-samples%2Fmain%2Fnotebooks%2Fcommunity%2alphagenome%2Fcloudai_alphagenome_vai_quickstart.ipynb\">\n",
+        "    <a href=\"https://console.cloud.google.com/vertex-ai/colab/import/https:%2F%2Fraw.githubusercontent.com%2FGoogleCloudPlatform%2Fvertex-ai-samples%2Fmain%2Fnotebooks%2Fcommunity%2Falphagenome%2Fcloudai_alphagenome_vai_quickstart.ipynb\">\n",
         "      <img width=\"32px\" src=\"https://lh3.googleusercontent.com/JmcxdQi-qOpctIvWKgPtrzZdJJK-J3sWE1RsfjZNwshCFgE_9fULcNpuXYTilIR2hjwN\" alt=\"Google Cloud Colab Enterprise logo\"><br> Open in Colab Enterprise\n",
         "    </a>\n",
         "  </td>\n",
@@ -4458,14 +4458,14 @@
       "outputs": [],
       "source": [
         "def extract_k562(adata):\n",
-        "  values = adata.X[:, adata.var['ontology_curie'] == 'EFO:0002067']\n",
-        "  assert values.size == 1\n",
-        "  return values.flatten()[0]\n",
+        "    values = adata.X[:, adata.var[\"ontology_curie\"] == \"EFO:0002067\"]\n",
+        "    assert values.size == 1\n",
+        "    return values.flatten()[0]\n",
         "\n",
         "\n",
         "ism_result = ism.ism_matrix(\n",
         "    [extract_k562(x[0]) for x in variant_scores],\n",
-        "    variants=[v[0].uns['variant'] for v in variant_scores],\n",
+        "    variants=[v[0].uns[\"variant\"] for v in variant_scores],\n",
         ")"
       ]
     },
@@ -4637,9 +4637,7 @@
         }
       ],
       "source": [
-        "interval = Interval(\n",
-        "    chromosome=\"chr19\", start=2**20, end=2**20 + 2**20, strand=\".\"\n",
-        ")\n",
+        "interval = Interval(chromosome=\"chr19\", start=2**20, end=2**20 + 2**20, strand=\".\")\n",
         "\n",
         "scores = dna_model.score_interval(\n",
         "    interval,\n",