diff --git a/.github/assets/cookiecutter-scverse-instance.json b/.github/assets/cookiecutter-scverse-instance.json
index 3371cb54..d9c9f605 100644
--- a/.github/assets/cookiecutter-scverse-instance.json
+++ b/.github/assets/cookiecutter-scverse-instance.json
@@ -1,7 +1,7 @@
 {
     "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",
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index fe5759d2..7ab7de54 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,17 +1,17 @@
 repos:
   # Hooks that are run everywhere
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.3.10
+    rev: v2.3.14
     hooks:
       - id: biome-format
   # Hooks that are run for scripts
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.12.1
+    rev: v2.15.1
     hooks:
       - id: pyproject-fmt
         files: ^scripts/pyproject\.toml$
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.14
+    rev: v0.15.0
     hooks:
       - id: ruff-check
         args: [--fix, --exit-non-zero-on-fix]
diff --git a/scripts/pyproject.toml b/scripts/pyproject.toml
index 1c4cb416..57c3ef3b 100644
--- a/scripts/pyproject.toml
+++ b/scripts/pyproject.toml
@@ -34,15 +34,13 @@ urls.Source = "https://github.com/scverse/cookiecutter-scverse"
 scripts.make-rich-output = "scverse_template_scripts.make_rich_output:main"
 scripts.send-cruft-prs = "scverse_template_scripts.cruft_prs:cli"
 
-[tool.hatch.version]
-source = "vcs"
-fallback-version = "0.0"
+[tool.hatch]
+version.source = "vcs"
+version.fallback-version = "0.0"
 
 [tool.ruff]
 line-length = 120
-
 format.docstring-code-format = true
-
 lint.select = [
   "A",
   "ANN",
@@ -84,7 +82,7 @@ lint.unfixable = [
   "RUF001", # never “fix” “confusables”
 ]
 lint.allowed-confusables = [ "×", "’" ]
-lint.flake8-type-checking.exempt-modules = [  ]
+lint.flake8-type-checking.exempt-modules = []
 lint.flake8-type-checking.runtime-evaluated-decorators = [ "cyclopts.App.default" ]
 lint.flake8-type-checking.strict = true
 lint.isort.known-first-party = [ "scverse_template_scripts", "testing.scverse_template_scripts" ]
@@ -93,7 +91,7 @@ lint.isort.required-imports = [ "from __future__ import annotations" ]
 [tool.pyproject-fmt]
 column_width = 120
 
-[tool.pytest.ini_options]
+[tool.pytest]
 addopts = [
   "--import-mode=importlib",
 ]
diff --git a/{{cookiecutter.project_name}}/.pre-commit-config.yaml b/{{cookiecutter.project_name}}/.pre-commit-config.yaml
index 74ce081b..e47a4f7a 100644
--- a/{{cookiecutter.project_name}}/.pre-commit-config.yaml
+++ b/{{cookiecutter.project_name}}/.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]
diff --git a/{{cookiecutter.project_name}}/pyproject.toml b/{{cookiecutter.project_name}}/pyproject.toml
index 3de9ac3a..52763fb7 100644
--- a/{{cookiecutter.project_name}}/pyproject.toml
+++ b/{{cookiecutter.project_name}}/pyproject.toml
@@ -59,49 +59,34 @@ doc = [
   "sphinxext-opengraph",
 ]
 
-{% if cookiecutter.project_name.lower().replace("-", "_") != cookiecutter.package_name -%}
-[tool.hatch.build.targets.wheel]
-packages = [ "src/{{ cookiecutter.package_name }}" ]
-
-{% endif -%}
-
-[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" ] },
 ]
+{% if cookiecutter.project_name.lower().replace("-", "_") != cookiecutter.package_name -%}
+build.targets.wheel.packages = [ "src/{{ cookiecutter.package_name }}" ]
+{% endif %}
 
 [tool.ruff]
 line-length = 120
 src = [ "src" ]
 extend-include = [ "*.ipynb" ]
-
 format.docstring-code-format = true
-
 lint.select = [
   "B",      # flake8-bugbear
   "BLE",    # flake8-blind-except
@@ -142,12 +127,12 @@ addopts = [
   "--import-mode=importlib", # allow using test files with same name
 ]
 
-[tool.coverage.run]
-source = [ "{{ cookiecutter.package_name }}" ]
-patch = [ "subprocess" ]
-omit = [
+[tool.coverage]
+run.omit = [
   "**/test_*.py",
 ]
+run.patch = [ "subprocess" ]
+run.source = [ "{{ cookiecutter.package_name }}" ]
 
 [tool.cruft]
 skip = [