diff --git a/quick_start/data_loading.ipynb b/quick_start/data_loading.ipynb
index 4762e7e..f40cc39 100644
--- a/quick_start/data_loading.ipynb
+++ b/quick_start/data_loading.ipynb
@@ -32,10 +32,10 @@
"execution_count": 1,
"metadata": {
"execution": {
- "iopub.execute_input": "2024-02-12T17:58:06.623052Z",
- "iopub.status.busy": "2024-02-12T17:58:06.622842Z",
- "iopub.status.idle": "2024-02-12T17:58:08.847159Z",
- "shell.execute_reply": "2024-02-12T17:58:08.846706Z"
+ "iopub.execute_input": "2024-09-23T19:16:28.311814Z",
+ "iopub.status.busy": "2024-09-23T19:16:28.311712Z",
+ "iopub.status.idle": "2024-09-23T19:16:29.336772Z",
+ "shell.execute_reply": "2024-09-23T19:16:29.336373Z"
}
},
"outputs": [
@@ -43,7 +43,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "\u001b[33mWARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv\u001b[0m\u001b[33m\r\n",
+ "\u001b[33mWARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable.It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.\u001b[0m\u001b[33m\r\n",
"\u001b[0m"
]
},
@@ -51,7 +51,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "/env/lib/python3.11/site-packages/scvi_colab/_core.py:41: UserWarning: \n",
+ "/usr/local/lib/python3.12/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",
@@ -78,15 +78,38 @@
"height": 382
},
"execution": {
- "iopub.execute_input": "2024-02-12T17:58:08.848818Z",
- "iopub.status.busy": "2024-02-12T17:58:08.848700Z",
- "iopub.status.idle": "2024-02-12T17:58:17.616550Z",
- "shell.execute_reply": "2024-02-12T17:58:17.615973Z"
+ "iopub.execute_input": "2024-09-23T19:16:29.337936Z",
+ "iopub.status.busy": "2024-09-23T19:16:29.337831Z",
+ "iopub.status.idle": "2024-09-23T19:16:45.530710Z",
+ "shell.execute_reply": "2024-09-23T19:16:45.530293Z"
},
"id": "N3oQkal_sLcr",
"outputId": "2ab53643-9881-4376-9f0e-d22ab67c6b9c"
},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/usr/local/lib/python3.12/site-packages/leidenalg/VertexPartition.py:388: SyntaxWarning: invalid escape sequence '\\m'\n",
+ " \"\"\" Implements modularity. This quality function is well-defined only for positive edge weights.\n",
+ "/usr/local/lib/python3.12/site-packages/leidenalg/VertexPartition.py:761: SyntaxWarning: invalid escape sequence '\\m'\n",
+ " \"\"\" Implements Reichardt and Bornholdt's Potts model with a configuration null model.\n",
+ "/usr/local/lib/python3.12/site-packages/leidenalg/Optimiser.py:7: SyntaxWarning: invalid escape sequence '\\g'\n",
+ " \"\"\" Class for doing community detection using the Leiden algorithm.\n",
+ "/usr/local/lib/python3.12/site-packages/leidenalg/Optimiser.py:305: SyntaxWarning: invalid escape sequence '\\s'\n",
+ " \"\"\" Optimise the given partitions simultaneously.\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/usr/local/lib/python3.12/site-packages/pyro/ops/stats.py:514: SyntaxWarning: invalid escape sequence '\\g'\n",
+ " \"\"\"\n"
+ ]
+ }
+ ],
"source": [
"import os\n",
"import tempfile\n",
@@ -106,10 +129,10 @@
"execution_count": 3,
"metadata": {
"execution": {
- "iopub.execute_input": "2024-02-12T17:58:17.618452Z",
- "iopub.status.busy": "2024-02-12T17:58:17.618148Z",
- "iopub.status.idle": "2024-02-12T17:58:17.621597Z",
- "shell.execute_reply": "2024-02-12T17:58:17.621257Z"
+ "iopub.execute_input": "2024-09-23T19:16:45.532819Z",
+ "iopub.status.busy": "2024-09-23T19:16:45.532452Z",
+ "iopub.status.idle": "2024-09-23T19:16:45.535907Z",
+ "shell.execute_reply": "2024-09-23T19:16:45.535647Z"
}
},
"outputs": [
@@ -124,7 +147,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Last run with scvi-tools version: 1.1.0\n"
+ "Last run with scvi-tools version: 1.2.0\n"
]
}
],
@@ -147,10 +170,10 @@
"execution_count": 4,
"metadata": {
"execution": {
- "iopub.execute_input": "2024-02-12T17:58:17.623032Z",
- "iopub.status.busy": "2024-02-12T17:58:17.622916Z",
- "iopub.status.idle": "2024-02-12T17:58:17.631198Z",
- "shell.execute_reply": "2024-02-12T17:58:17.630930Z"
+ "iopub.execute_input": "2024-09-23T19:16:45.536832Z",
+ "iopub.status.busy": "2024-09-23T19:16:45.536740Z",
+ "iopub.status.idle": "2024-09-23T19:16:45.549170Z",
+ "shell.execute_reply": "2024-09-23T19:16:45.548782Z"
}
},
"outputs": [],
@@ -195,17 +218,17 @@
"execution_count": 5,
"metadata": {
"execution": {
- "iopub.execute_input": "2024-02-12T17:58:17.632650Z",
- "iopub.status.busy": "2024-02-12T17:58:17.632538Z",
- "iopub.status.idle": "2024-02-12T17:58:20.227617Z",
- "shell.execute_reply": "2024-02-12T17:58:20.227137Z"
+ "iopub.execute_input": "2024-09-23T19:16:45.550745Z",
+ "iopub.status.busy": "2024-09-23T19:16:45.550652Z",
+ "iopub.status.idle": "2024-09-23T19:16:47.144881Z",
+ "shell.execute_reply": "2024-09-23T19:16:47.144514Z"
}
},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "12d5cdc27a4e48f38d0b5c9eaf57694a",
+ "model_id": "0e5f1682b0f14518b6283c3e9935c09c",
"version_major": 2,
"version_minor": 0
},
@@ -216,14 +239,6 @@
"metadata": {},
"output_type": "display_data"
},
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "/env/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"
- ]
- },
{
"data": {
"text/plain": [
@@ -261,10 +276,10 @@
"height": 237
},
"execution": {
- "iopub.execute_input": "2024-02-12T17:58:20.229173Z",
- "iopub.status.busy": "2024-02-12T17:58:20.229051Z",
- "iopub.status.idle": "2024-02-12T17:58:20.233828Z",
- "shell.execute_reply": "2024-02-12T17:58:20.233555Z"
+ "iopub.execute_input": "2024-09-23T19:16:47.146123Z",
+ "iopub.status.busy": "2024-09-23T19:16:47.146010Z",
+ "iopub.status.idle": "2024-09-23T19:16:47.154262Z",
+ "shell.execute_reply": "2024-09-23T19:16:47.153980Z"
},
"id": "JmqvrG8AxCrO",
"outputId": "8252b5ae-9f5d-434b-e308-766f95f6b994"
@@ -358,10 +373,10 @@
"execution_count": 7,
"metadata": {
"execution": {
- "iopub.execute_input": "2024-02-12T17:58:20.235263Z",
- "iopub.status.busy": "2024-02-12T17:58:20.235151Z",
- "iopub.status.idle": "2024-02-12T17:58:20.237395Z",
- "shell.execute_reply": "2024-02-12T17:58:20.237114Z"
+ "iopub.execute_input": "2024-09-23T19:16:47.155331Z",
+ "iopub.status.busy": "2024-09-23T19:16:47.155218Z",
+ "iopub.status.idle": "2024-09-23T19:16:47.157232Z",
+ "shell.execute_reply": "2024-09-23T19:16:47.156962Z"
}
},
"outputs": [],
@@ -383,10 +398,10 @@
"execution_count": 8,
"metadata": {
"execution": {
- "iopub.execute_input": "2024-02-12T17:58:20.238838Z",
- "iopub.status.busy": "2024-02-12T17:58:20.238671Z",
- "iopub.status.idle": "2024-02-12T17:58:21.159121Z",
- "shell.execute_reply": "2024-02-12T17:58:21.158692Z"
+ "iopub.execute_input": "2024-09-23T19:16:47.158262Z",
+ "iopub.status.busy": "2024-09-23T19:16:47.158159Z",
+ "iopub.status.idle": "2024-09-23T19:16:48.415108Z",
+ "shell.execute_reply": "2024-09-23T19:16:48.414712Z"
}
},
"outputs": [
@@ -394,7 +409,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "Downloading data from 'https://cf.10xgenomics.com/samples/cell-exp/3.0.2/5k_pbmc_protein_v3/5k_pbmc_protein_v3_filtered_feature_bc_matrix.h5' to file '/tmp/tmpniq7jd5c/pbmc5k_protein_filtered_feature_bc_matrix.h5'.\n"
+ "Downloading data from 'https://cf.10xgenomics.com/samples/cell-exp/3.0.2/5k_pbmc_protein_v3/5k_pbmc_protein_v3_filtered_feature_bc_matrix.h5' to file '/tmp/tmpjfn__qb9/pbmc5k_protein_filtered_feature_bc_matrix.h5'.\n"
]
}
],
@@ -419,10 +434,10 @@
"height": 34
},
"execution": {
- "iopub.execute_input": "2024-02-12T17:58:21.160721Z",
- "iopub.status.busy": "2024-02-12T17:58:21.160600Z",
- "iopub.status.idle": "2024-02-12T17:58:21.808616Z",
- "shell.execute_reply": "2024-02-12T17:58:21.808184Z"
+ "iopub.execute_input": "2024-09-23T19:16:48.416721Z",
+ "iopub.status.busy": "2024-09-23T19:16:48.416608Z",
+ "iopub.status.idle": "2024-09-23T19:16:49.001663Z",
+ "shell.execute_reply": "2024-09-23T19:16:49.001391Z"
},
"id": "TypCa4tExtyp",
"outputId": "5cf6a4c5-de7d-4c7e-8114-47ce4fcfe19f"
@@ -432,13 +447,23 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "/env/lib/python3.11/site-packages/anndata/_core/anndata.py:1908: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
+ "/usr/local/lib/python3.12/site-packages/anndata/_core/anndata.py:1756: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
" utils.warn_names_duplicates(\"var\")\n",
- "/env/lib/python3.11/site-packages/anndata/_core/anndata.py:1908: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
+ "/usr/local/lib/python3.12/site-packages/anndata/_core/anndata.py:1756: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
" utils.warn_names_duplicates(\"var\")\n",
- "/env/lib/python3.11/site-packages/mudata/_core/mudata.py:479: UserWarning: var_names are not unique. To make them unique, call `.var_names_make_unique`.\n",
+ "/usr/local/lib/python3.12/site-packages/mudata/_core/mudata.py:1531: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.\n",
+ " self._update_attr(\"var\", axis=0, join_common=join_common)\n",
+ "/usr/local/lib/python3.12/site-packages/mudata/_core/mudata.py:915: UserWarning: var_names are not unique. To make them unique, call `.var_names_make_unique`.\n",
" warnings.warn(\n"
]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/usr/local/lib/python3.12/site-packages/mudata/_core/mudata.py:1429: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.\n",
+ " self._update_attr(\"obs\", axis=1, join_common=join_common)\n"
+ ]
}
],
"source": [
@@ -450,10 +475,10 @@
"execution_count": 10,
"metadata": {
"execution": {
- "iopub.execute_input": "2024-02-12T17:58:21.810276Z",
- "iopub.status.busy": "2024-02-12T17:58:21.810128Z",
- "iopub.status.idle": "2024-02-12T17:58:21.812987Z",
- "shell.execute_reply": "2024-02-12T17:58:21.812561Z"
+ "iopub.execute_input": "2024-09-23T19:16:49.002731Z",
+ "iopub.status.busy": "2024-09-23T19:16:49.002603Z",
+ "iopub.status.idle": "2024-09-23T19:16:49.004797Z",
+ "shell.execute_reply": "2024-09-23T19:16:49.004615Z"
}
},
"outputs": [
@@ -461,21 +486,21 @@
"data": {
"text/html": [
"MuData object with n_obs × n_vars = 5247 × 33570\n",
- " var:\t'gene_ids', 'feature_types', 'genome'\n",
+ " var:\t'gene_ids', 'feature_types', 'genome', 'pattern', 'read', 'sequence'\n",
" 2 modalities\n",
" rna:\t5247 x 33538\n",
- " var:\t'gene_ids', 'feature_types', 'genome'\n",
+ " var:\t'gene_ids', 'feature_types', 'genome', 'pattern', 'read', 'sequence'\n",
" prot:\t5247 x 32\n",
- " var:\t'gene_ids', 'feature_types', 'genome'"
+ " var:\t'gene_ids', 'feature_types', 'genome', 'pattern', 'read', 'sequence'"
],
"text/plain": [
"MuData object with n_obs × n_vars = 5247 × 33570\n",
- " var:\t'gene_ids', 'feature_types', 'genome'\n",
+ " var:\t'gene_ids', 'feature_types', 'genome', 'pattern', 'read', 'sequence'\n",
" 2 modalities\n",
" rna:\t5247 x 33538\n",
- " var:\t'gene_ids', 'feature_types', 'genome'\n",
+ " var:\t'gene_ids', 'feature_types', 'genome', 'pattern', 'read', 'sequence'\n",
" prot:\t5247 x 32\n",
- " var:\t'gene_ids', 'feature_types', 'genome'"
+ " var:\t'gene_ids', 'feature_types', 'genome', 'pattern', 'read', 'sequence'"
]
},
"execution_count": 10,
@@ -501,10 +526,10 @@
"execution_count": 11,
"metadata": {
"execution": {
- "iopub.execute_input": "2024-02-12T17:58:21.814474Z",
- "iopub.status.busy": "2024-02-12T17:58:21.814284Z",
- "iopub.status.idle": "2024-02-12T17:58:21.838191Z",
- "shell.execute_reply": "2024-02-12T17:58:21.837804Z"
+ "iopub.execute_input": "2024-09-23T19:16:49.005630Z",
+ "iopub.status.busy": "2024-09-23T19:16:49.005546Z",
+ "iopub.status.idle": "2024-09-23T19:16:49.034688Z",
+ "shell.execute_reply": "2024-09-23T19:16:49.034484Z"
},
"id": "fK451tYtx-cH"
},
@@ -527,10 +552,10 @@
"execution_count": 12,
"metadata": {
"execution": {
- "iopub.execute_input": "2024-02-12T17:58:21.839580Z",
- "iopub.status.busy": "2024-02-12T17:58:21.839419Z",
- "iopub.status.idle": "2024-02-12T17:58:21.982755Z",
- "shell.execute_reply": "2024-02-12T17:58:21.982323Z"
+ "iopub.execute_input": "2024-09-23T19:16:49.035539Z",
+ "iopub.status.busy": "2024-09-23T19:16:49.035455Z",
+ "iopub.status.idle": "2024-09-23T19:16:49.136503Z",
+ "shell.execute_reply": "2024-09-23T19:16:49.136122Z"
}
},
"outputs": [],
@@ -556,10 +581,10 @@
"height": 206
},
"execution": {
- "iopub.execute_input": "2024-02-12T17:58:21.984462Z",
- "iopub.status.busy": "2024-02-12T17:58:21.984341Z",
- "iopub.status.idle": "2024-02-12T17:58:21.988543Z",
- "shell.execute_reply": "2024-02-12T17:58:21.988272Z"
+ "iopub.execute_input": "2024-09-23T19:16:49.138507Z",
+ "iopub.status.busy": "2024-09-23T19:16:49.138389Z",
+ "iopub.status.idle": "2024-09-23T19:16:49.142009Z",
+ "shell.execute_reply": "2024-09-23T19:16:49.141795Z"
},
"id": "iIhwaX1az1rB",
"outputId": "f21bf106-6cee-4475-d3a0-0b65fed6995c"
@@ -652,10 +677,10 @@
"height": 86
},
"execution": {
- "iopub.execute_input": "2024-02-12T17:58:21.989952Z",
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- "iopub.status.idle": "2024-02-12T17:58:22.090957Z",
- "shell.execute_reply": "2024-02-12T17:58:22.090521Z"
+ "iopub.execute_input": "2024-09-23T19:16:49.142907Z",
+ "iopub.status.busy": "2024-09-23T19:16:49.142814Z",
+ "iopub.status.idle": "2024-09-23T19:16:49.227357Z",
+ "shell.execute_reply": "2024-09-23T19:16:49.227038Z"
},
"id": "eUN2B0pm0iah",
"outputId": "28a116f8-c3fd-4f47-adcf-4c619aaa2799"
@@ -693,10 +718,10 @@
"execution_count": 15,
"metadata": {
"execution": {
- "iopub.execute_input": "2024-02-12T17:58:22.092604Z",
- "iopub.status.busy": "2024-02-12T17:58:22.092462Z",
- "iopub.status.idle": "2024-02-12T17:58:22.106781Z",
- "shell.execute_reply": "2024-02-12T17:58:22.106518Z"
+ "iopub.execute_input": "2024-09-23T19:16:49.228420Z",
+ "iopub.status.busy": "2024-09-23T19:16:49.228308Z",
+ "iopub.status.idle": "2024-09-23T19:16:49.240620Z",
+ "shell.execute_reply": "2024-09-23T19:16:49.240341Z"
},
"id": "lwdhWVBe00mW"
},
@@ -719,10 +744,10 @@
"execution_count": 16,
"metadata": {
"execution": {
- "iopub.execute_input": "2024-02-12T17:58:22.108235Z",
- "iopub.status.busy": "2024-02-12T17:58:22.108126Z",
- "iopub.status.idle": "2024-02-12T17:58:22.213224Z",
- "shell.execute_reply": "2024-02-12T17:58:22.212776Z"
+ "iopub.execute_input": "2024-09-23T19:16:49.242185Z",
+ "iopub.status.busy": "2024-09-23T19:16:49.242092Z",
+ "iopub.status.idle": "2024-09-23T19:16:49.262026Z",
+ "shell.execute_reply": "2024-09-23T19:16:49.261661Z"
},
"id": "T81mge-w1KHF"
},
@@ -746,10 +771,10 @@
"execution_count": 17,
"metadata": {
"execution": {
- "iopub.execute_input": "2024-02-12T17:58:22.214929Z",
- "iopub.status.busy": "2024-02-12T17:58:22.214806Z",
- "iopub.status.idle": "2024-02-12T17:58:22.217107Z",
- "shell.execute_reply": "2024-02-12T17:58:22.216830Z"
+ "iopub.execute_input": "2024-09-23T19:16:49.263686Z",
+ "iopub.status.busy": "2024-09-23T19:16:49.263576Z",
+ "iopub.status.idle": "2024-09-23T19:16:49.265688Z",
+ "shell.execute_reply": "2024-09-23T19:16:49.265474Z"
},
"id": "ZbwQTY_h1QT2"
},
@@ -773,17 +798,27 @@
"execution_count": 18,
"metadata": {
"execution": {
- "iopub.execute_input": "2024-02-12T17:58:22.218623Z",
- "iopub.status.busy": "2024-02-12T17:58:22.218414Z",
- "iopub.status.idle": "2024-02-12T17:58:22.306969Z",
- "shell.execute_reply": "2024-02-12T17:58:22.306664Z"
+ "iopub.execute_input": "2024-09-23T19:16:49.266673Z",
+ "iopub.status.busy": "2024-09-23T19:16:49.266586Z",
+ "iopub.status.idle": "2024-09-23T19:16:49.342333Z",
+ "shell.execute_reply": "2024-09-23T19:16:49.342090Z"
}
},
"outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/usr/local/lib/python3.12/site-packages/mudata/_core/mudata.py:1531: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.\n",
+ " self._update_attr(\"var\", axis=0, join_common=join_common)\n",
+ "/usr/local/lib/python3.12/site-packages/mudata/_core/mudata.py:1429: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.\n",
+ " self._update_attr(\"obs\", axis=1, join_common=join_common)\n"
+ ]
+ },
{
"data": {
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- "MuData object with n_obs × n_vars = 7947 × 14309\n",
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@@ -795,7 +830,7 @@
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@@ -853,28 +888,15 @@
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- "iopub.status.idle": "2024-02-12T17:58:22.433418Z",
- "shell.execute_reply": "2024-02-12T17:58:22.432929Z"
+ "iopub.execute_input": "2024-09-23T19:16:49.343331Z",
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+ "iopub.status.idle": "2024-09-23T19:16:49.346023Z",
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},
"id": "V8eKOa4Uy1WP",
"outputId": "b26c6733-e4f7-46be-fdec-3cd467f6a7c2"
},
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- ":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"
- ]
- }
- ],
+ "outputs": [],
"source": [
"scvi.model.SCVI.setup_anndata(adata, layer=\"counts\", batch_key=\"batch\")"
]
@@ -921,28 +943,15 @@
"height": 225
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+ "iopub.status.idle": "2024-09-23T19:16:49.350368Z",
+ "shell.execute_reply": "2024-09-23T19:16:49.350161Z"
},
"id": "i7REZQil1o1u",
"outputId": "4a81b824-c6ca-46a9-830b-651406650cb4"
},
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- ":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"
- ]
- }
- ],
+ "outputs": [],
"source": [
"# totalVI requires dense protein data\n",
"pbmc5k.mod[\"prot\"].X = (\n",
@@ -971,10 +980,10 @@
"execution_count": 21,
"metadata": {
"execution": {
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- "shell.execute_reply": "2024-02-12T17:58:22.448001Z"
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+ "shell.execute_reply": "2024-09-23T19:16:49.356485Z"
}
},
"outputs": [
@@ -984,18 +993,6 @@
"text": [
"\u001b[34mINFO \u001b[0m Using column names from columns of adata.obsm\u001b[1m[\u001b[0m\u001b[32m'prot'\u001b[0m\u001b[1m]\u001b[0m \n"
]
- },
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- ":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"
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}
],
"source": [
@@ -1038,10 +1035,10 @@
"height": 644
},
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- "shell.execute_reply": "2024-02-12T17:58:22.815229Z"
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+ "iopub.status.busy": "2024-09-23T19:16:49.357498Z",
+ "iopub.status.idle": "2024-09-23T19:16:49.686600Z",
+ "shell.execute_reply": "2024-09-23T19:16:49.686283Z"
},
"id": "lJngLWo_F0qG",
"outputId": "fd5eba95-05bc-4ca6-c75d-343b1502add1"
@@ -1057,11 +1054,11 @@
{
"data": {
"text/html": [
- "Anndata setup with scvi-tools version 1.1.0.\n",
+ "Anndata setup with scvi-tools version 1.2.0.\n",
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],
"text/plain": [
- "Anndata setup with scvi-tools version \u001b[1;36m1.1\u001b[0m.\u001b[1;36m0\u001b[0m.\n"
+ "Anndata setup with scvi-tools version \u001b[1;36m1.2\u001b[0m.\u001b[1;36m6\u001b[0m.\n"
]
},
"metadata": {},
@@ -1274,7 +1271,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
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