Update instance repo from cookiecutter template

Author: github-actions[bot]

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
-  "commit": "f49bf20fd799812e085e747682323ebab7a7fc2c",
+  "commit": "3b1f898cbe747b0bd0884163112251c26d9f2472",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -36,7 +36,7 @@
         "trim_blocks": true
       },
       "_template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
-      "_commit": "f49bf20fd799812e085e747682323ebab7a7fc2c"
+      "_commit": "3b1f898cbe747b0bd0884163112251c26d9f2472"
     }
   },
   "directory": null

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v1.9.4
+    rev: v2.0.0-beta.5
     hooks:
       - id: biome-format
         exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
@@ -16,7 +16,7 @@ repos:
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.12
+    rev: v0.11.13
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]