diff --git a/.cruft.json b/.cruft.json
index f7f1f4bb..330e025d 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,6 +1,6 @@
 {
   "template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
-  "commit": "707f3faab836f9272912f92188b63b31da70c064",
+  "commit": "b1491b8903480508809046cac5889510da46f395",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -37,7 +37,7 @@
         "trim_blocks": true
       },
       "_template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
-      "_commit": "707f3faab836f9272912f92188b63b31da70c064"
+      "_commit": "b1491b8903480508809046cac5889510da46f395"
     }
   },
   "directory": null
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c6d9c514..1ae6fdf3 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,48 +7,53 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.5.5
+    rev: v2.5.6
     hooks:
       - id: biome-format
         exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
+        groups: [format]
   - repo: https://github.com/tox-dev/pyproject-fmt
     rev: v2.26.0
     hooks:
       - id: pyproject-fmt
+        groups: [format]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.16.0
+    rev: v0.16.1
     hooks:
       - id: ruff-check
-        types_or: [python, pyi, jupyter]
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
-        types_or: [python, pyi, jupyter]
+        groups: [format]
   - repo: local
     hooks:
       - id: mypy
         name: mypy
-        entry: uv run --group test mypy src tests
+        entry: hatch check types
         language: system
         types: [python]
         files: ^(src|tests)/
         require_serial: true
         pass_filenames: false
+        groups: [typecheck]
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
       - id: detect-private-key
       - id: check-ast
       - id: end-of-file-fixer
+        groups: [format]
       - id: mixed-line-ending
         args: [--fix=lf]
+        groups: [format]
       - id: trailing-whitespace
+        groups: [format]
       - id: check-case-conflict
       # Check that there are no merge conflicts (could be generated by template sync)
       - id: check-merge-conflict
         args: [--assume-in-merge]
 
   - repo: https://github.com/zizmorcore/zizmor-pre-commit
-    rev: v1.28.0
+    rev: v1.29.0
     hooks:
       - id: zizmor
         args: [--no-progress, --fix]
diff --git a/docs/contributing.md b/docs/contributing.md
index 798c1c5e..f31c190c 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -153,10 +153,12 @@ We recommend running them with [prek][], a fast, drop-in replacement for `pre-co
 On every commit, the checks will either automatically fix issues with the code, or raise an error message.
 See [pre-commit checks](template_usage.md#pre-commit-checks) for a full list of checks enabled for this repository.
 
-To enable the checks locally, install [prek][] (e.g. with `uv tool install prek`) and run
+To enable the checks locally, run
 
 ```bash
-prek install
+hatch run hatch-check-code:prek install
+# or
+uvx prek install
 ```
 
 in the root of the repository.
diff --git a/docs/template_usage.md b/docs/template_usage.md
index 1a769aba..b191b706 100644
--- a/docs/template_usage.md
+++ b/docs/template_usage.md
@@ -194,7 +194,7 @@ This template uses a number of pre-commit checks.
 In this section we'll detail what is used, where they're defined, and how to modify these checks.
 
 To run the checks locally, we recommend [prek][], a fast, drop-in replacement for `pre-commit` that reads the same `.pre-commit-config.yaml`.
-Install it (e.g. with `uv tool install prek`) and run `prek install` once to set up the git hook, then `prek run --all-files` to check the whole repository.
+Set up the git hook once by running `prek install` (e.g. `uvx prek install`), then `hatch check --fix` to format and check the whole repository.
 
 
 ### Overview of pre-commit hooks used by the template
diff --git a/pyproject.toml b/pyproject.toml
index 7e62ad01..c4bbda6d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -34,8 +34,6 @@ urls.Source = "https://github.com/scverse/cookiecutter-scverse-instance"
 
 [dependency-groups]
 dev = [
-  "mypy",
-  "prek",
   "twine>=4.0.2",
 ]
 test = [
@@ -58,6 +56,10 @@ doc = [
   "sphinxcontrib-katex",
   "sphinxext-opengraph",
 ]
+typecheck = [
+  "mypy",
+  "pandas-stubs",
+]
 
 [tool.hatch]
 envs.default.installer = "uv"
@@ -78,6 +80,14 @@ envs.hatch-test.overrides.matrix.deps.env-vars = [
   { value = "allow", key = "UV_PRERELEASE", if = [ "pre" ] },
 ]
 envs.hatch-test.dependency-groups = [ "dev", "test" ]
+envs.hatch-check-fmt.dependencies = [ "prek" ]
+envs.hatch-check-fmt.scripts.format-check = "echo 'try `hatch check fmt --fix`'; false"
+envs.hatch-check-fmt.scripts.format-fix = "prek run -a --group=format --no-group=typecheck"
+envs.hatch-check-code.dependencies = [ "prek" ]
+envs.hatch-check-code.scripts.lint-check = "echo 'try `hatch check code --fix`'; false"
+envs.hatch-check-code.scripts.lint-fix = "prek run -a --no-group=format --no-group=typecheck"
+envs.hatch-check-types.scripts.check = [ "mypy" ]
+envs.hatch-check-types.dependency-groups = [ "typecheck", "test" ]
 
 [tool.ruff]
 line-length = 120
@@ -117,6 +127,9 @@ lint.per-file-ignores."docs/*" = [ "I" ]
 lint.per-file-ignores."tests/*" = [ "D" ]
 lint.pydocstyle.convention = "numpy"
 
+[tool.mypy]
+files = [ "src", "tests" ]
+
 [tool.pytest]
 addopts = [
   "--import-mode=importlib", # allow using test files with same name