diff --git a/.cruft.json b/.cruft.json
index 4b913167..b178710f 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "77339226581ec535e1972984083ae70b702e7bec",
-  "checkout": null,
+  "commit": "6518dfa1abde7379ea7255daf0ce09c23f2b4c94",
+  "checkout": "v0.8.0",
   "context": {
     "cookiecutter": {
       "project_name": "mudata",
@@ -13,6 +13,7 @@
       "github_repo": "mudata",
       "license": "BSD 3-Clause License",
       "ide_integration": false,
+      "issue_categorization": "issue types",
       "_copy_without_render": [
         ".github/workflows/build.yaml",
         ".github/workflows/test.yaml",
@@ -36,8 +37,10 @@
         "trim_blocks": true
       },
       "_template": "https://github.com/scverse/cookiecutter-scverse",
-      "_commit": "77339226581ec535e1972984083ae70b702e7bec"
-    }
+      "_commit": "4d6aa34fd5be7523ca3bd49fbd81a882dde01d1f"
+    },
+    "_commit": "6518dfa1abde7379ea7255daf0ce09c23f2b4c94",
+    "_template": "https://github.com/scverse/cookiecutter-scverse"
   },
   "directory": null
 }
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
index b3a4e4bc..c072948c 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -14,11 +14,12 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+permissions:
+  contents: read
+
 jobs:
   package:
     runs-on: ubuntu-latest
-    permissions:
-      contents: read
     steps:
       - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
index 30b097c0..aa634229 100644
--- a/.github/workflows/release.yaml
+++ b/.github/workflows/release.yaml
@@ -21,6 +21,7 @@ jobs:
       name: pypi
       url: https://pypi.org/p/mudata
     permissions:
+      contents: read
       id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
       - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index ff2b9aa9..3fc3e3d9 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -26,7 +26,7 @@ jobs:
   # Check [[tool.hatch.envs.hatch-test.matrix]] in pyproject.toml and https://hatch.pypa.io/latest/environment/ for
   # more details.
   get-environments:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-slim
     outputs:
       envs: ${{ steps.get-envs.outputs.envs }}
     steps:
@@ -56,6 +56,7 @@ jobs:
     needs: get-environments
     permissions:
        id-token: write  # for codecov OIDC
+       contents: read
 
     strategy:
       fail-fast: false
@@ -79,6 +80,8 @@ jobs:
           python-version: ${{ matrix.env.python }}
       - name: create hatch environment
         run: uvx hatch env create ${{ matrix.env.name }}
+      - name: list all all installed package versions
+        run: uvx hatch run ${{ matrix.env.name }}:uv pip list
       - name: run tests using hatch
         env:
           MPLBACKEND: agg
@@ -87,7 +90,7 @@ jobs:
         run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto
       - name: generate coverage report
         run: |
-          # See https://coverage.readthedocs.io/en/latest/config.html#run-patch
+          # See https://coverage.readthedocs.io/page/config.html#run-patch
           test -f .coverage || uvx hatch run ${{ matrix.env.name }}:cov-combine
           uvx hatch run ${{ matrix.env.name }}:cov-report   # report visibly
           uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 5f265d91..e43dcdd9 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -12,7 +12,7 @@ repos:
       - id: biome-format
         exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.25.2
+    rev: v2.25.3
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index bd0b1f5b..67eb948d 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -1,4 +1,4 @@
-# https://docs.readthedocs.io/en/stable/config-file/v2.html
+# https://docs.readthedocs.io/page/config-file/v2.html
 version: 2
 build:
   os: ubuntu-24.04
diff --git a/docs/_static/.gitkeep b/docs/_static/.gitkeep
new file mode 100644
index 00000000..e69de29b
diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css
new file mode 100644
index 00000000..b8c8d47f
--- /dev/null
+++ b/docs/_static/css/custom.css
@@ -0,0 +1,4 @@
+/* Reduce the font size in data frames - See https://github.com/scverse/cookiecutter-scverse/issues/193 */
+div.cell_output table.dataframe {
+    font-size: 0.8em;
+}
diff --git a/docs/conf.py b/docs/conf.py
index 26d8c121..f450255d 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -2,7 +2,7 @@
 
 # This file only contains a selection of the most common options. For a full
 # list see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
+# https://www.sphinx-doc.org/page/usage/configuration.html
 
 # -- Path setup --------------------------------------------------------------
 import shutil
diff --git a/docs/contributing.md b/docs/contributing.md
index d6361cfc..7d0d49fa 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -9,7 +9,7 @@ the [scientific Python tutorials][], or the [scanpy developer guide][].
 
 [pyopensci tutorials]: https://www.pyopensci.org/learn.html
 [scientific Python tutorials]: https://learn.scientific-python.org/development/tutorials/
-[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
+[scanpy developer guide]: https://scanpy.scverse.org/page/dev/
 
 :::{tip} The *hatch* project manager
 
@@ -46,11 +46,21 @@ hatch test  # defined in the table [tool.hatch.envs.hatch-test] in pyproject.tom
 hatch run docs:build  # defined in the table [tool.hatch.envs.docs]
 ```
 
-When using an IDE such as VS Code,
-you’ll have to point the editor at the paths to the virtual environments manually.
-The environment you typically want to use as your main development environment is the `hatch-test`
-environment with the latest Python version.
+### VS Code
 
+If you are using VS code, install the [hatch-code][] extension.
+Additionally, make sure that the `vscode-python-environments` extension is installed (should be by default)
+and `"python.useEnvironmentsExtension": true` is activated in your `settings.json`.
+
+Next, open the "Python Environment Managers" sidebar.
+You can do so by opening the command palette (Ctrl+Shift+P) and searching for `Python: Focus on Environment Managers View`.
+It will show a collapsible list where you can expand "Hatch"
+and activate an environment by clicking on the checkmark next to it.
+As the main development environment, we recommend to use `hatch-test` with the latest supported Python version.
+
+### Other IDEs
+
+For other IDEs, you’ll have to point the editor at the paths to the virtual environments manually.
 To get a list of all environments for your projects, run
 
 ```bash
@@ -63,7 +73,7 @@ This will list “Standalone” environments and a table of “Matrix” environ
 +------------+---------+--------------------------+----------+---------------------------------+-------------+
 | Name       | Type    | Envs                     | Features | Dependencies                    | Scripts     |
 +------------+---------+--------------------------+----------+---------------------------------+-------------+
-| hatch-test | virtual | hatch-test.py3.11-stable | dev      | coverage-enable-subprocess==1.0 | cov-combine |
+| hatch-test | virtual | hatch-test.py3.12-stable | dev      | coverage-enable-subprocess==1.0 | cov-combine |
 |            |         | hatch-test.py3.14-stable | test     | coverage[toml]~=7.4             | cov-report  |
 |            |         | hatch-test.py3.14-pre    |          | pytest-mock~=3.12               | run         |
 |            |         |                          |          | pytest-randomly~=3.15           | run-cov     |
@@ -74,6 +84,7 @@ This will list “Standalone” environments and a table of “Matrix” environ
 ```
 
 From the `Envs` column, select the environment name you want to use for development.
+As the main development environment, we recommend to use `hatch-test` with the latest supported Python version.
 In this example, it would be `hatch-test.py3.14-stable`.
 
 Next, create the environment with
@@ -88,10 +99,7 @@ Then, obtain the path to the environment using
 hatch env find hatch-test.py3.14-stable
 ```
 
-In case you are using VScode, now open the command palette (Ctrl+Shift+P) and search for `Python: Select Interpreter`.
-Choose `Enter Interpreter Path` and paste the path to the virtual environment from above.
-
-In this future, this may become easier through a hatch vscode extension.
+and manually point it to the python binary.
 
 ::::
 
@@ -134,24 +142,26 @@ The `.venv` directory is typically automatically discovered by IDEs such as VS C
 :::::
 
 [hatch environments]: https://hatch.pypa.io/latest/tutorials/environment/basic-usage/
+[hatch-code]: https://marketplace.visualstudio.com/items?itemName=PyPA.hatch
 [uv]: https://docs.astral.sh/uv/
 
 ## Code-style
 
-This package uses [pre-commit][] to enforce consistent code-styles.
-On every commit, pre-commit checks will either automatically fix issues with the code, or raise an error message.
+This package uses [pre-commit][]-style hooks to enforce consistent code-styles.
+We recommend running them with [prek][], a fast, drop-in replacement for `pre-commit` that reads the same `.pre-commit-config.yaml`.
+On every commit, the checks will either automatically fix issues with the code, or raise an error message.
 
-To enable pre-commit locally, simply run
+To enable the checks locally, install [prek][] (e.g. with `uv tool install prek`) and run
 
 ```bash
-pre-commit install
+prek install
 ```
 
 in the root of the repository.
-Pre-commit will automatically download all dependencies when it is run for the first time.
+prek will automatically download all dependencies when it is run for the first time.
 
 Alternatively, you can rely on the [pre-commit.ci][] service enabled on GitHub.
-If you didn’t run `pre-commit` before pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
+If you didn’t run the checks before pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
 
 If pre-commit.ci added a commit on a branch you still have been working on locally, simply use
 
@@ -160,12 +170,13 @@ git pull --rebase
 ```
 
 to integrate the changes into yours.
-While the [pre-commit.ci][] is useful, we strongly encourage installing and running pre-commit locally first to understand its usage.
+While the [pre-commit.ci][] is useful, we strongly encourage installing and running the checks locally first to understand their usage.
 
 Finally, most editors have an _autoformat on save_ feature.
 Consider enabling this option for [ruff][ruff-editors] and [biome][biome-editors].
 
 [pre-commit]: https://pre-commit.com/
+[prek]: https://prek.j178.dev/
 [pre-commit.ci]: https://pre-commit.ci/
 [ruff-editors]: https://docs.astral.sh/ruff/integrations/
 [biome-editors]: https://biomejs.dev/guides/integrate-in-editor/
@@ -178,12 +189,8 @@ This package uses [pytest][] for automated testing.
 Please write {doc}`scanpy:dev/testing` for every function added to the package.
 
 Most IDEs integrate with pytest and provide a GUI to run tests.
-Just point yours to one of the environments returned by
-
-```bash
-hatch env create hatch-test  # create test environments for all supported versions
-hatch env find hatch-test  # list all possible test environment paths
-```
+If you set up your virtual environments as described in [installing dev dependencies](#installing-dev-dependencies),
+test cases should be automatically discovered by your IDE.
 
 Alternatively, you can run all tests from the command line by executing
 
@@ -273,11 +280,11 @@ This project uses [sphinx][] with the following features:
 
 See scanpy’s {doc}`scanpy:dev/documentation` for more information on how to write your own.
 
-[sphinx]: https://www.sphinx-doc.org/en/master/
-[myst]: https://myst-parser.readthedocs.io/en/latest/intro.html
-[myst-nb]: https://myst-nb.readthedocs.io/en/latest/
-[numpydoc-napoleon]: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
-[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
+[sphinx]: https://www.sphinx-doc.org/
+[myst]: https://myst-parser.readthedocs.io/page/intro.html
+[myst-nb]: https://myst-nb.readthedocs.io/
+[numpydoc-napoleon]: https://www.sphinx-doc.org/page/usage/extensions/napoleon.html
+[numpydoc]: https://numpydoc.readthedocs.io/page/format.html
 [sphinx-autodoc-typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
 
 ### Tutorials with myst-nb and jupyter notebooks
diff --git a/pyproject.toml b/pyproject.toml
index d4d3034a..330e0fa9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -45,7 +45,7 @@ urls.Source = "https://github.com/scverse/mudata"
 [dependency-groups]
 dev = [
   "mudata[io]",
-  "pre-commit",
+  "prek",
   "twine>=4.0.2",
 ]
 test = [
@@ -86,8 +86,10 @@ envs.docs.scripts.clean = "git clean -fdX -- {args:docs}"
 envs.docs.scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
 envs.docs.dependency-groups = [ "doc" ]
 envs.hatch-test.matrix = [
+  # Test the lowest and highest supported Python versions with normal deps
   { deps = [ "stable" ], python = [ "3.12", "3.14" ] },
-  { deps = [ "pre" ], python = [ "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".
@@ -163,6 +165,7 @@ run.source = [ "mudata" ]
 
 [tool.cruft]
 skip = [
+  ".git",
   "tests",
   "src/**/__init__.py",
   "src/**/basic.py",