Fix contrastivevi tutorial (#202)

scrna/contrastiveVI_tutorial.ipynb

@@ -59,6 +59,7 @@
     "import tempfile\n",
     "\n",
     "import numpy as np\n",
+    "import requests\n",
     "import scanpy as sc\n",
     "import scvi\n",
     "import torch"
@@ -160,6 +161,19 @@
     "As an extra preprocessing step, we'll calculate cell cycle labels to be used later in our analysis:"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_cell_cycle_genes() -> list:\n",
+    "    # Canonical list of cell cycle genes\n",
+    "    url = \"https://raw.githubusercontent.com/scverse/scanpy_usage/master/180209_cell_cycle/data/regev_lab_cell_cycle_genes.txt\"\n",
+    "    cell_cycle_genes = requests.get(url).text.split(\"\\n\")[:-1]\n",
+    "    return cell_cycle_genes"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -172,10 +186,7 @@
    },
    "outputs": [],
    "source": [
-    "# Canonical list of cell cycle genes\n",
-    "!wget https://raw.githubusercontent.com/scverse/scanpy_usage/master/180209_cell_cycle/data/regev_lab_cell_cycle_genes.txt\n",
-    "\n",
-    "cell_cycle_genes = [x.strip() for x in open(\"./regev_lab_cell_cycle_genes.txt\")]\n",
+    "cell_cycle_genes = get_cell_cycle_genes()\n",
     "\n",
     "s_genes = cell_cycle_genes[:43]\n",
     "g2m_genes = cell_cycle_genes[43:]\n",