pin anndata==0.10.8 at start

workshop.ipynb

@@ -15,16 +15,32 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b73128e6-6f93-4920-b770-9de2b8266a10",
+   "id": "ca755138-cd74-4bda-aadc-b8b4b3a5868d",
    "metadata": {
     "id": "fxGSU7epkxsh"
    },
    "source": [
-    "### TileDB-SOMA / Census Hello World\n",
-    "\n",
-    "Load the necessary libraries (sample requirements file [here][requirements-nb.txt]):\n",
-    "\n",
-    "[requirements-nb.txt]: https://github.com/TileDB-Inc/scverse-ml-workshop-2024/blob/main/requirements-nb.txt"
+    "### TileDB-SOMA / Census Hello World"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "39c45052-4a48-4168-9c5a-f5fe941972d2",
+   "metadata": {},
+   "source": [
+    "Pin `anndata==0.10.8` (required for `scvi` later in this notebook, cf. [mudata#77](https://github.com/scverse/mudata/issues/77), [census#1276](https://github.com/chanzuckerberg/cellxgene-census/pull/1276); should only be necessary temporarily)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e7c9bab3-0ba4-427a-978e-b9911d36fb9d",
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "!pip install -q anndata==0.10.8"
    ]
   },
   {
@@ -5853,7 +5869,7 @@
     }
    ],
    "source": [
-    "!pip install anndata==0.10.8 flax==0.8.5 tiledb-vector-search 'git+https://github.com/ryan-williams/[email protected]#subdirectory=api/python/cellxgene_census'"
+    "!pip install anndata==0.10.8 leidenalg flax==0.8.5 tiledb-vector-search 'git+https://github.com/ryan-williams/[email protected]#subdirectory=api/python/cellxgene_census'"
    ]
   },
   {
@@ -6022,26 +6038,6 @@
     "And for visualization, compute leiden clusters on the scVI embeddings. These will come at handy later on."
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 72,
-   "id": "c20607f3-583b-4127-9c3b-7c8b1bc97648",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Requirement already satisfied: leidenalg in /home/ubuntu/.pyenv/versions/3.9.19/envs/scverse-ml-workshop-2024-3.9.19/lib/python3.9/site-packages (0.10.2)\n",
-      "Requirement already satisfied: igraph<0.12,>=0.10.0 in /home/ubuntu/.pyenv/versions/3.9.19/envs/scverse-ml-workshop-2024-3.9.19/lib/python3.9/site-packages (from leidenalg) (0.11.6)\n",
-      "Requirement already satisfied: texttable>=1.6.2 in /home/ubuntu/.pyenv/versions/3.9.19/envs/scverse-ml-workshop-2024-3.9.19/lib/python3.9/site-packages (from igraph<0.12,>=0.10.0->leidenalg) (1.7.0)\n"
-     ]
-    }
-   ],
-   "source": [
-    "!pip install leidenalg"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 73,