Add RSC

.github/workflows/make-tutorials-json.yml

@@ -20,7 +20,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           filter: blob:none
           fetch-depth: 0

.readthedocs.yaml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-24.04
   tools:
-    python: "3.12"
+    python: "3.14"
   jobs:
     create_environment:
       - asdf plugin add uv

docs/notebooks/scverse_data_interoperability.ipynb

@@ -121,7 +121,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.12"
+   "version": "3.13.13"
   }
  },
  "nbformat": 4,

docs/notebooks/tutorial_concatenation_anndata_mudata.ipynb

@@ -61,11 +61,11 @@
     {
      "data": {
       "text/plain": [
-       "['pbmc10k_multiome',\n",
-       " 'brain9k_multiome',\n",
+       "['pbmc3k_multiome',\n",
+       " 'pbmc10k_multiome',\n",
        " 'brain3k_multiome',\n",
        " 'pbmc5k_citeseq',\n",
-       " 'pbmc3k_multiome']"
+       " 'brain9k_multiome']"
       ]
      },
      "execution_count": 2,
@@ -96,15 +96,15 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/mudatasets/core.py:203: UserWarning: Dataset is in the 10X .h5 format and can't be loaded as backed.\n",
+      "/home/runner/miniconda3/envs/tutorials/lib/python3.13/site-packages/mudatasets/core.py:203: UserWarning: Dataset is in the 10X .h5 format and can't be loaded as backed.\n",
       "  warn(\"Dataset is in the 10X .h5 format and can't be loaded as backed.\")\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
+      "/home/runner/miniconda3/envs/tutorials/lib/python3.13/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
       "  from .autonotebook import tqdm as notebook_tqdm\n"
      ]
     },
@@ -119,18 +119,12 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/anndata/_core/anndata.py:1813: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
+      "/home/runner/miniconda3/envs/tutorials/lib/python3.13/site-packages/anndata/_core/anndata.py:1880: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
       "  utils.warn_names_duplicates(\"var\")\n",
-      "/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/anndata/_core/anndata.py:1813: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
-      "  utils.warn_names_duplicates(\"var\")\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/mudata/_core/mudata.py:947: UserWarning: var_names are not unique. To make them unique, call `.var_names_make_unique`.\n",
-      "  warnings.warn(\n"
+      "/home/runner/miniconda3/envs/tutorials/lib/python3.13/site-packages/anndata/_core/anndata.py:1880: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
+      "  utils.warn_names_duplicates(\"var\")\n",
+      "/home/runner/miniconda3/envs/tutorials/lib/python3.13/site-packages/mudata/_core/mudata.py:565: UserWarning: var_names are not unique. To make them unique, call `.var_names_make_unique`.\n",
+      "  self._update_attr_legacy(attr, axis, join_common, **kwargs)\n"
      ]
     }
    ],
@@ -150,18 +144,18 @@
        "<pre>MuData object with n_obs × n_vars = 5247 × 33570\n",
        "  var:\t&#x27;gene_ids&#x27;, &#x27;feature_types&#x27;, &#x27;genome&#x27;, &#x27;pattern&#x27;, &#x27;read&#x27;, &#x27;sequence&#x27;\n",
        "  2 modalities\n",
-       "    rna:\t5247 x 33538\n",
+       "    rna:\t5247 × 33538\n",
        "      var:\t&#x27;gene_ids&#x27;, &#x27;feature_types&#x27;, &#x27;genome&#x27;, &#x27;pattern&#x27;, &#x27;read&#x27;, &#x27;sequence&#x27;\n",
-       "    prot:\t5247 x 32\n",
+       "    prot:\t5247 × 32\n",
        "      var:\t&#x27;gene_ids&#x27;, &#x27;feature_types&#x27;, &#x27;genome&#x27;, &#x27;pattern&#x27;, &#x27;read&#x27;, &#x27;sequence&#x27;</pre>"
       ],
       "text/plain": [
        "MuData object with n_obs × n_vars = 5247 × 33570\n",
        "  var:\t'gene_ids', 'feature_types', 'genome', 'pattern', 'read', 'sequence'\n",
        "  2 modalities\n",
-       "    rna:\t5247 x 33538\n",
+       "    rna:\t5247 × 33538\n",
        "      var:\t'gene_ids', 'feature_types', 'genome', 'pattern', 'read', 'sequence'\n",
-       "    prot:\t5247 x 32\n",
+       "    prot:\t5247 × 32\n",
        "      var:\t'gene_ids', 'feature_types', 'genome', 'pattern', 'read', 'sequence'"
       ]
      },
@@ -235,18 +229,18 @@
        "<pre>MuData object with n_obs × n_vars = 300 × 1032\n",
        "  var:\t&#x27;gene_ids&#x27;, &#x27;feature_types&#x27;, &#x27;genome&#x27;, &#x27;pattern&#x27;, &#x27;read&#x27;, &#x27;sequence&#x27;\n",
        "  2 modalities\n",
-       "    prot:\t300 x 32\n",
+       "    prot:\t300 × 32\n",
        "      var:\t&#x27;gene_ids&#x27;, &#x27;feature_types&#x27;, &#x27;genome&#x27;, &#x27;pattern&#x27;, &#x27;read&#x27;, &#x27;sequence&#x27;\n",
-       "    rna:\t300 x 1000\n",
+       "    rna:\t300 × 1000\n",
        "      var:\t&#x27;gene_ids&#x27;, &#x27;feature_types&#x27;, &#x27;genome&#x27;, &#x27;pattern&#x27;, &#x27;read&#x27;, &#x27;sequence&#x27;</pre>"
       ],
       "text/plain": [
        "MuData object with n_obs × n_vars = 300 × 1032\n",
        "  var:\t'gene_ids', 'feature_types', 'genome', 'pattern', 'read', 'sequence'\n",
        "  2 modalities\n",
-       "    prot:\t300 x 32\n",
+       "    prot:\t300 × 32\n",
        "      var:\t'gene_ids', 'feature_types', 'genome', 'pattern', 'read', 'sequence'\n",
-       "    rna:\t300 x 1000\n",
+       "    rna:\t300 × 1000\n",
        "      var:\t'gene_ids', 'feature_types', 'genome', 'pattern', 'read', 'sequence'"
       ]
      },
@@ -270,18 +264,18 @@
        "<pre>MuData object with n_obs × n_vars = 400 × 1015\n",
        "  var:\t&#x27;gene_ids&#x27;, &#x27;feature_types&#x27;, &#x27;genome&#x27;, &#x27;pattern&#x27;, &#x27;read&#x27;, &#x27;sequence&#x27;\n",
        "  2 modalities\n",
-       "    prot:\t400 x 15\n",
+       "    prot:\t400 × 15\n",
        "      var:\t&#x27;gene_ids&#x27;, &#x27;feature_types&#x27;, &#x27;genome&#x27;, &#x27;pattern&#x27;, &#x27;read&#x27;, &#x27;sequence&#x27;\n",
-       "    rna:\t400 x 1000\n",
+       "    rna:\t400 × 1000\n",
        "      var:\t&#x27;gene_ids&#x27;, &#x27;feature_types&#x27;, &#x27;genome&#x27;, &#x27;pattern&#x27;, &#x27;read&#x27;, &#x27;sequence&#x27;</pre>"
       ],
       "text/plain": [
        "MuData object with n_obs × n_vars = 400 × 1015\n",
        "  var:\t'gene_ids', 'feature_types', 'genome', 'pattern', 'read', 'sequence'\n",
        "  2 modalities\n",
-       "    prot:\t400 x 15\n",
+       "    prot:\t400 × 15\n",
        "      var:\t'gene_ids', 'feature_types', 'genome', 'pattern', 'read', 'sequence'\n",
-       "    rna:\t400 x 1000\n",
+       "    rna:\t400 × 1000\n",
        "      var:\t'gene_ids', 'feature_types', 'genome', 'pattern', 'read', 'sequence'"
       ]
      },
@@ -543,14 +537,14 @@
       "text/html": [
        "<pre>MuData object with n_obs × n_vars = 700 × 1687\n",
        "  2 modalities\n",
-       "    rna:\t700 x 1655\n",
-       "    prot:\t700 x 32</pre>"
+       "    rna:\t700 × 1655\n",
+       "    prot:\t700 × 32</pre>"
       ],
       "text/plain": [
        "MuData object with n_obs × n_vars = 700 × 1687\n",
        "  2 modalities\n",
-       "    rna:\t700 x 1655\n",
-       "    prot:\t700 x 32"
+       "    rna:\t700 × 1655\n",
+       "    prot:\t700 × 32"
       ]
      },
      "execution_count": 19,
@@ -954,7 +948,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.12"
+   "version": "3.13.13"
   },
   "vscode": {
    "interpreter": {

environment.yml

@@ -3,7 +3,7 @@ name: tutorials
 channels:
   - conda-forge
 dependencies:
-  - python=3.12
+  - python=3.13
   - jupyter-cache
   - ipykernel
   - ipython

tutorial-registry/tutorials/rapids-singlecell-gpu/meta.yaml

@@ -0,0 +1,18 @@
+name: GPU-accelerated single-cell analysis with rapids-singlecell
+description: |
+  This tutorial demonstrates a complete single-cell RNA-seq workflow on the GPU
+  using rapids-singlecell as a drop-in replacement for scanpy, covering
+  preprocessing, clustering, batch correction, and differential expression.
+link: https://rapids-singlecell.readthedocs.io/en/latest/notebooks/01_basic_workflow.html
+image: icon.svg
+primary_category: scRNA-seq
+order: 80
+tags:
+  - preprocessing
+  - quality control
+  - visualization
+  - differential expression
+packages:
+  - rapids-singlecell
+authors:
+  - Intron7

tutorial-registry/validate.py

@@ -139,7 +139,7 @@ def make_output(
         json.dump(result, sys.stdout, indent=2)
 
 
-def main(schema_file: Path, meta_dir: Path, categories_file: Path, *, outdir: Path | None = None):
+def main(schema_file: Path, meta_dir: Path, categories_file: Path, *, outdir: Path | None = None) -> None:
     """Validate and create output directory."""
     tutorials = list(validate_tutorials(schema_file, meta_dir))
     categories = load_categories(categories_file)