Update instance repo from cookiecutter template

Author: github-actions[bot]

.cruft.json

@@ -1,12 +1,12 @@
 {
   "template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
-  "commit": "8642a1825348e6236ec62151c55dd90c7197ae08",
+  "commit": "cbf6b45007d28c0cf4faf528f99f46b53565a92f",
   "checkout": null,
   "context": {
     "cookiecutter": {
       "project_name": "cookiecutter-scverse-instance",
       "package_name": "cookiecutter_scverse_instance",
-      "project_description": "An example repo generated from the `cookiecutter-scverse` template. Feel free to look around this repo and check out the docs to find out if the template works for you!",
+      "project_description": "An example repo generated from the `cookiecutter-scverse` template.",
       "author_full_name": "scverse community",
       "author_email": "core-team@scverse.org",
       "github_user": "scverse",
@@ -36,7 +36,7 @@
         "trim_blocks": true
       },
       "_template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
-      "_commit": "8642a1825348e6236ec62151c55dd90c7197ae08"
+      "_commit": "cbf6b45007d28c0cf4faf528f99f46b53565a92f"
     }
   },
   "directory": null

.pre-commit-config.yaml

@@ -7,16 +7,16 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.3.10
+    rev: v2.3.14
     hooks:
       - id: biome-format
         exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.12.1
+    rev: v2.15.1
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.14
+    rev: v0.15.0
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]

README.md

@@ -6,7 +6,7 @@
 [badge-tests]: https://img.shields.io/github/actions/workflow/status/scverse/cookiecutter-scverse-instance/test.yaml?branch=main
 [badge-docs]: https://img.shields.io/readthedocs/cookiecutter-scverse-instance
 
-An example repo generated from the `cookiecutter-scverse` template. Feel free to look around this repo and check out the docs to find out if the template works for you!
+An example repo generated from the `cookiecutter-scverse` template.
 
 ## Getting started
 

pyproject.toml

@@ -5,7 +5,7 @@ requires = [ "hatchling" ]
 [project]
 name = "cookiecutter-scverse-instance"
 version = "0.0.1"
-description = "An example repo generated from the `cookiecutter-scverse` template. Feel free to look around this repo and check out the docs to find out if the template works for you!"
+description = "An example repo generated from the `cookiecutter-scverse` template."
 readme = "README.md"
 license = { file = "LICENSE" }
 maintainers = [
@@ -57,43 +57,31 @@ doc = [
   "sphinxext-opengraph",
 ]
 
-[tool.hatch.envs.default]
-installer = "uv"
-dependency-groups = [ "dev" ]
-
-[tool.hatch.envs.docs]
-dependency-groups = [ "doc" ]
-scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
-scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
-scripts.clean = "git clean -fdX -- {args:docs}"
-
-[tool.hatch.envs.hatch-test]
-dependency-groups = [ "dev", "test" ]
-
-# Test the lowest and highest supported Python versions with normal deps
-[[tool.hatch.envs.hatch-test.matrix]]
-deps = [ "stable" ]
-python = [ "3.11", "3.14" ]
-
-# Test the newest supported Python version also with pre-release deps
-[[tool.hatch.envs.hatch-test.matrix]]
-deps = [ "pre" ]
-python = [ "3.14" ]
-
-[tool.hatch.envs.hatch-test.overrides]
+[tool.hatch]
+envs.default.installer = "uv"
+envs.default.dependency-groups = [ "dev" ]
+envs.docs.dependency-groups = [ "doc" ]
+envs.docs.scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
+envs.docs.scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
+envs.docs.scripts.clean = "git clean -fdX -- {args:docs}"
+envs.hatch-test.dependency-groups = [ "dev", "test" ]
+envs.hatch-test.matrix = [
+  # Test the lowest and highest supported Python versions with normal deps
+  { deps = [ "stable" ], python = [ "3.11", "3.14" ] },
+  # Test the newest supported Python version also with pre-release deps
+  { deps = [ "pre" ], python = [ "3.14" ] },
+]
 # If the matrix variable `deps` is set to "pre",
 # set the environment variable `UV_PRERELEASE` to "allow".
-matrix.deps.env-vars = [
+envs.hatch-test.overrides.matrix.deps.env-vars = [
   { key = "UV_PRERELEASE", value = "allow", if = [ "pre" ] },
 ]
 
 [tool.ruff]
 line-length = 120
 src = [ "src" ]
 extend-include = [ "*.ipynb" ]
-
 format.docstring-code-format = true
-
 lint.select = [
   "B",      # flake8-bugbear
   "BLE",    # flake8-blind-except
@@ -134,12 +122,12 @@ addopts = [
   "--import-mode=importlib", # allow using test files with same name
 ]
 
-[tool.coverage.run]
-source = [ "cookiecutter_scverse_instance" ]
-patch = [ "subprocess" ]
-omit = [
+[tool.coverage]
+run.omit = [
   "**/test_*.py",
 ]
+run.patch = [ "subprocess" ]
+run.source = [ "cookiecutter_scverse_instance" ]
 
 [tool.cruft]
 skip = [