From e773cc9f9f9d116c0b5a8a8c813c4d890743ca5c Mon Sep 17 00:00:00 2001
From: Martin Kim <46072231+martinkim0@users.noreply.github.com>
Date: Fri, 2 Feb 2024 09:23:50 -0800
Subject: [PATCH] Correct and rerun hub intro tutorial (#221)

---
 hub/scvi_hub_intro_and_download.ipynb | 98 ++++++++++++++++-----------
 1 file changed, 59 insertions(+), 39 deletions(-)

diff --git a/hub/scvi_hub_intro_and_download.ipynb b/hub/scvi_hub_intro_and_download.ipynb
index d78f605..6b2194c 100644
--- a/hub/scvi_hub_intro_and_download.ipynb
+++ b/hub/scvi_hub_intro_and_download.ipynb
@@ -17,7 +17,9 @@
    "id": "c78df63c",
    "metadata": {},
    "source": [
-    "Uncomment the following lines in Google Colab in order to install `scvi-tools`:"
+    "```{note}\n",
+    "Running the following cell will install tutorial dependencies on Google Colab only. It will have no effect on environments other than Google Colab.\n",
+    "```"
    ]
   },
   {
@@ -25,12 +27,27 @@
    "execution_count": 1,
    "id": "26d9e3c8",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/martinkim/bin/miniforge3/envs/scvi-11/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",
+    "!pip install --quiet scvi-colab\n",
+    "from scvi_colab import install\n",
     "\n",
-    "# install()"
+    "install()"
    ]
   },
   {
@@ -53,11 +70,18 @@
    "id": "ce72c6b4",
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "Seed set to 0\n"
+     ]
+    },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Last run with scvi-tools version: 1.0.3\n"
+      "Last run with scvi-tools version: 1.1.0rc2\n"
      ]
     }
    ],
@@ -71,7 +95,9 @@
    "id": "2e161542",
    "metadata": {},
    "source": [
-    "You can modify `save_dir` below to change where the data files for this tutorial are saved."
+    "```{note}\n",
+    "You can modify `save_dir` below to change where the data files for this tutorial are saved.\n",
+    "```"
    ]
   },
   {
@@ -308,7 +334,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "c62bff650893402387f2453e03750c93",
+       "model_id": "1ea49f2e748948ed951d11724087c5bc",
        "version_major": 2,
        "version_minor": 0
       },
@@ -322,12 +348,12 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "6219bc54fb6548dfbdbf06736ade3349",
+       "model_id": "373dd1ad49a6458b9ea00ee1d0b4ec02",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "Downloading (…)38b80e180/adata.h5ad:   0%|          | 0.00/526k [00:00<?, ?B/s]"
+       "adata.h5ad:   0%|          | 0.00/1.01M [00:00<?, ?B/s]"
       ]
      },
      "metadata": {},
@@ -336,12 +362,12 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "af24e629ac1846ebacabe1b8295ec0f9",
+       "model_id": "e27f8cc038e84d2d81611fb2c7caecbf",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "Downloading (…)quired_metadata.json:   0%|          | 0.00/165 [00:00<?, ?B/s]"
+       "model.pt:   0%|          | 0.00/304k [00:00<?, ?B/s]"
       ]
      },
      "metadata": {},
@@ -350,12 +376,12 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "f57ba8aaf8364d22bb7351b79869d823",
+       "model_id": "a3a76ba3278c4834aa30e929ca987ac8",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "Downloading model.pt:   0%|          | 0.00/304k [00:00<?, ?B/s]"
+       "_scvi_required_metadata.json:   0%|          | 0.00/172 [00:00<?, ?B/s]"
       ]
      },
      "metadata": {},
@@ -364,7 +390,7 @@
    ],
    "source": [
     "hmo = HubModel.pull_from_huggingface_hub(\n",
-    "    repo_name=\"scvi-tools/demo-model\",\n",
+    "    repo_name=\"scvi-tools/test-scvi\",\n",
     "    cache_dir=save_dir.name,\n",
     "    revision=\"main\",\n",
     ")"
@@ -395,8 +421,22 @@
      "text": [
       "\u001b[34mINFO    \u001b[0m Loading model\u001b[33m...\u001b[0m                                                                                          \n",
       "\u001b[34mINFO    \u001b[0m File                                                                                                      \n",
-      "         \u001b[35m/tmp/tmpmuir791g/models--scvi-tools--demo-model/snapshots/59afc89bcc6ceb43e91e8e98d21805a38b80e180/\u001b[0m\u001b[95mmodel.p\u001b[0m\n",
-      "         \u001b[95mt\u001b[0m already downloaded                                                                                      \n"
+      "         \u001b[35m/tmp/tmprdl64_l0/models--scvi-tools--test-scvi/snapshots/e6d2074cc12961f99af4e72b7ae5d0e63e2cb99d/\u001b[0m\u001b[95mmodel.pt\u001b[0m\n",
+      "         already downloaded                                                                                        \n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/martinkim/bin/miniforge3/envs/scvi-11/lib/python3.11/site-packages/anndata/__init__.py:51: FutureWarning: `anndata.read` is deprecated, use `anndata.read_h5ad` instead. `ad.read` will be removed in mid 2024.\n",
+      "  warnings.warn(\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"
      ]
     },
     {
@@ -452,7 +492,7 @@
        "AnnData object with n_obs × n_vars = 400 × 100\n",
        "    obs: 'batch', 'labels', '_scvi_batch', '_scvi_labels'\n",
        "    uns: '_scvi_manager_uuid', '_scvi_uuid', 'protein_names'\n",
-       "    obsm: 'protein_expression'"
+       "    obsm: 'accessibility', 'protein_expression'"
       ]
      },
      "execution_count": 8,
@@ -536,26 +576,6 @@
     "\n",
     "Please browse the scvi-tools tutorials for explicit examples using scvi-hub in workflows."
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "931009ca",
-   "metadata": {},
-   "source": [
-    "## Clean up\n",
-    "\n",
-    "Uncomment the following line to remove all data files created in this tutorial:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 9,
-   "id": "b9a1ddf8",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# save_dir.cleanup()"
-   ]
   }
  ],
  "metadata": {
@@ -574,7 +594,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.4"
+   "version": "3.11.7"
   },
   "vscode": {
    "interpreter": {