Merge pull request #479 from scverse/pre-commit-ci-update-config

[pre-commit.ci] pre-commit autoupdate

Author: ori-kron-wis

.pre-commit-config.yaml

@@ -34,7 +34,7 @@ repos:
           )$
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.12
+    rev: v0.13.0
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

use_cases/autotune_scvi.ipynb

@@ -278,7 +278,7 @@
     "model_cls.setup_anndata(\n",
     "    adata,\n",
     "    layer=\"counts\",\n",
-    "    labels_key=\"cell_type\", \n",
+    "    labels_key=\"cell_type\",\n",
     "    batch_key=\"cell_source\",\n",
     "    categorical_covariate_keys=[\"donor\"],\n",
     "    continuous_covariate_keys=[\"percent_mito\", \"percent_ribo\"],\n",
@@ -750,7 +750,7 @@
     "    scib_subsample_rows=10000,\n",
     "    local_mode=True,\n",
     "    ignore_reinit_error=True,\n",
-    "    solver=\"randomized\"\n",
+    "    solver=\"randomized\",\n",
     ")"
    ]
   },
@@ -1037,8 +1037,9 @@
     }
    ],
    "source": [
-    "#Manual Check:\n",
+    "# Manual Check:\n",
     "from scib_metrics.benchmark import Benchmarker\n",
+    "\n",
     "bm = Benchmarker(\n",
     "    adata,\n",
     "    batch_key=\"cell_source\",\n",