Update installation lines

Author: keller-mark

notebooks/01-Single-Spatial-View.ipynb

@@ -976,24 +976,7 @@
    },
    "outputs": [],
    "source": [
-    "!pip install \"spatialdata-plot==0.4.0\""
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "2e65c668-49de-4883-9451-a50083932813",
-   "metadata": {
-    "colab": {
-     "base_uri": "https://localhost:8080/",
-     "height": 1000
-    },
-    "id": "TIV0fdvoewL8",
-    "outputId": "6ba23ae9-97b6-4bc0-931e-df0916738739"
-   },
-   "outputs": [],
-   "source": [
-    "!pip install \"easy_vitessce==0.0.12\""
+    "!pip install \"spatialdata-plot==0.4.0\" \"easy_vitessce==0.0.12\""
    ]
   },
   {

notebooks/02-Multiple-Views.ipynb

@@ -30,7 +30,7 @@
    },
    "outputs": [],
    "source": [
-    "!pip install \"vitessce[all]==3.9.2\" \"scanpy\" \"easy-vitessce==0.0.11\""
+    "!pip install \"vitessce[all]==3.9.2\" \"scanpy\" \"easy-vitessce==0.0.12\""
    ]
   },
   {
@@ -119,10 +119,12 @@
     "from os.path import join, isdir\n",
     "import scanpy as sc\n",
     "\n",
-    "from vitessce.data_utils import optimize_adata, VAR_CHUNK_SIZE\n",
+    "from vitessce.data_utils import VAR_CHUNK_SIZE\n",
     "\n",
     "# Load Scanpy's built-in reduced PBMC dataset.\n",
     "adata = sc.datasets.pbmc68k_reduced()\n",
+    "sc.tl.tsne(adata)\n",
+    "\n",
     "print(adata)\n",
     "print(\"\\nAvailable embeddings:\", list(adata.obsm.keys()))\n",
     "print(\"Available obs columns:\", list(adata.obs.columns))"
@@ -267,7 +269,7 @@
     "    vconcat, hconcat,\n",
     ")\n",
     "\n",
-    "vc2 = VitessceConfig(schema_version=\"1.0.18\", name=\"Visium example with Spatial + Non-Spatial Views\")\n",
+    "vc2 = VitessceConfig(schema_version=\"1.0.18\", name=\"Visium example\")\n",
     "\n",
     "wrapper = SpatialDataWrapper(\n",
     "    sdata_store=sdata_filepath,\n",