Merge pull request #351 from scverse/detached2

Update several tutorials so they will work in scvi-tools 1.2.0, py312…
scverse · Sep 25, 2024 · 80ddc92 · 80ddc92
2 parents e40dbe5 + a7f7215
commit 80ddc92
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Showing 6 changed files with 199 additions and 1,112 deletions.
diff --git a/.github/workflows/run_linux_cuda.yml b/.github/workflows/run_linux_cuda.yml
@@ -42,7 +42,6 @@ on:
           - spatial/gimvi_tutorial.ipynb
           - spatial/stereoscope_heart_LV_tutorial.ipynb
           - spatial/tangram_scvi_tools.ipynb
-          - tuning/autotune_new_model.ipynb
           - tuning/autotune_scvi.ipynb
 
       python-version:

diff --git a/.github/workflows/run_notebook_individual.yaml b/.github/workflows/run_notebook_individual.yaml
@@ -43,7 +43,6 @@ on:
           - spatial/gimvi_tutorial.ipynb
           - spatial/stereoscope_heart_LV_tutorial.ipynb
           - spatial/tangram_scvi_tools.ipynb
-          - tuning/autotune_new_model.ipynb
           - tuning/autotune_scvi.ipynb
       version:
         description: "latest/stable/semver/branch"

diff --git a/scrna/harmonization.ipynb b/scrna/harmonization.ipynb
@@ -7335,7 +7335,7 @@
    ],
    "source": [
     "SCANVI_MDE_KEY = \"X_scANVI_MDE\"\n",
-    "adata.obsm[SCANVI_MDE_KEY] = scvi.model.utils.mde(adata.obsm[SCANVI_LATENT_KEY])"
+    "adata.obsm[SCANVI_MDE_KEY] = scvi.model.utils.mde(adata.obsm[SCANVI_LATENT_KEY], accelerator=\"cpu\")"
    ]
   },
   {

diff --git a/spatial/cell2location_lymph_node_spatial_tutorial.ipynb b/spatial/cell2location_lymph_node_spatial_tutorial.ipynb
@@ -64,16 +64,42 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/opt/miniconda3/envs/scvi/lib/python3.11/site-packages/scvi_colab/_core.py:41: UserWarning: \n",
+      "                Not currently in Google Colab environment.\n",
+      "\n",
+      "                Please run with `run_outside_colab=True` to override.\n",
+      "\n",
+      "                Returning with no further action.\n",
+      "                \n",
+      "  warn(\n"
+     ]
+    }
+   ],
    "source": [
     "!pip install --quiet scvi-colab\n",
     "from scvi_colab import install\n",
     "\n",
     "install()"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# import os\n",
+    "# os.system(\"pip install git+https://github.com/BayraktarLab/cell2location.git\")\n",
+    "!pip install --quiet git+https://github.com/BayraktarLab/cell2location.git"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -1760,13 +1786,21 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "scvi-tools-dev",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
   "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
    "name": "python",
-   "version": "3.10.9"
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.9"
   },
   "vscode": {
    "interpreter": {
@@ -2805,5 +2839,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 0
+ "nbformat_minor": 4
 }