Merge branch 'main' into pre-commit-ci-update-config

Author: ori-kron-wis

.github/workflows/run_linux_cuda.yml

@@ -59,7 +59,7 @@ on:
       python-version:
         description: Python version
         required: true
-        default: "3.12"
+        default: "3.13"
         type: choice
         options:
           - "3.13"

.github/workflows/run_notebook.yaml

@@ -17,7 +17,7 @@ jobs:
     runs-on: [self-hosted, Linux, X64, CUDA]
 
     container:
-      image: ghcr.io/scverse/scvi-tools:py3.12-cu12-${{ inputs.version }}-tutorials
+      image: ghcr.io/scverse/scvi-tools:py3.13-cu12-${{ inputs.version }}-tutorials
       options: --user root --gpus all
 
     timeout-minutes: 600 # lenient timeout for scbasset tutorial

multimodal/totalVI_reference_mapping.ipynb

@@ -201,28 +201,27 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "adata = scvi.data.pbmc_seurat_v4_cite_seq(\n",
+    "    save_path=save_dir.name,\n",
+    "    mask_protein_batches=5,\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
    "metadata": {
     "colab": {
      "base_uri": "https://localhost:8080/"
     },
-    "execution": {
-     "iopub.execute_input": "2024-02-12T17:44:05.419836Z",
-     "iopub.status.busy": "2024-02-12T17:44:05.419692Z",
-     "iopub.status.idle": "2024-02-12T17:46:05.952898Z",
-     "shell.execute_reply": "2024-02-12T17:46:05.952435Z"
-    },
     "id": "dqFHL3TugIPi",
     "outputId": "b1471da0-8e2d-4e69-8479-a43985e7dd75"
    },
    "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\u001b[34mINFO    \u001b[0m Downloading file at \u001b[35m/tmp/tmpkyrakh_v/\u001b[0m\u001b[95mpbmc_seurat_v4.h5ad\u001b[0m                                                  \n"
-     ]
-    },
     {
      "name": "stdout",
      "output_type": "stream",
@@ -7200,10 +7199,6 @@
     }
    ],
    "source": [
-    "adata = scvi.data.pbmc_seurat_v4_cite_seq(\n",
-    "    save_path=save_dir.name,\n",
-    "    mask_protein_batches=5,\n",
-    ")\n",
     "adata.layers[\"counts\"] = adata.X.copy()\n",
     "sc.pp.normalize_total(adata, target_sum=1e4)\n",
     "sc.pp.log1p(adata)\n",
@@ -8305,69 +8300,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": null,
    "metadata": {
     "colab": {
      "base_uri": "https://localhost:8080/"
     },
-    "execution": {
-     "iopub.execute_input": "2024-02-12T17:50:08.588345Z",
-     "iopub.status.busy": "2024-02-12T17:50:08.588175Z",
-     "iopub.status.idle": "2024-02-12T17:58:11.125253Z",
-     "shell.execute_reply": "2024-02-12T17:58:11.124828Z"
-    },
     "id": "6JFgKTnmWM_D",
     "outputId": "c171ad12-db4e-4137-d24d-ffc9fb7e6733"
    },
    "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\u001b[34mINFO    \u001b[0m Found batches with missing protein expression                                                             \n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\u001b[34mINFO    \u001b[0m Computing empirical prior initialization for protein background.                                          \n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "<frozen abc>:119: FutureWarning: SparseDataset is deprecated and will be removed in late 2024. It has been replaced by the public classes CSRDataset and CSCDataset.\n",
-      "\n",
-      "For instance checks, use `isinstance(X, (anndata.experimental.CSRDataset, anndata.experimental.CSCDataset))` instead.\n",
-      "\n",
-      "For creation, use `anndata.experimental.sparse_dataset(X)` instead.\n",
-      "\n",
-      "<frozen abc>:119: FutureWarning: SparseDataset is deprecated and will be removed in late 2024. It has been replaced by the public classes CSRDataset and CSCDataset.\n",
-      "\n",
-      "For instance checks, use `isinstance(X, (anndata.experimental.CSRDataset, anndata.experimental.CSCDataset))` instead.\n",
-      "\n",
-      "For creation, use `anndata.experimental.sparse_dataset(X)` instead.\n",
-      "\n",
-      "/env/lib/python3.11/site-packages/scvi/model/base/_utils.py:126: UserWarning: Some proteins have all 0 counts in some batches. These proteins will be treated as missing measurements; however, this can occur due to experimental design/biology. Reinitialize the model with `override_missing_proteins=True`,to override this behavior.\n",
-      "  model = cls(adata, **non_kwargs, **kwargs)\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "GPU available: True (cuda), used: True\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "TPU available: False, using: 0 TPU cores\n"
-     ]
-    },
     {
      "name": "stderr",
      "output_type": "stream",
@@ -12415,7 +12356,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.12.7"
   },
   "toc": {
    "base_numbering": 1,