From 6969d124274cad16a294cc6969ddf25b0c42a0cc Mon Sep 17 00:00:00 2001
From: "scverse-pr-creator[bot]"
 <272303624+scverse-pr-creator[bot]@users.noreply.github.com>
Date: Fri, 24 Jul 2026 10:51:25 +0000
Subject: [PATCH 1/4] Update instance repo from cookiecutter template

---
 .cruft.json             | 4 ++--
 .pre-commit-config.yaml | 8 ++++++--
 docs/contributing.md    | 6 ++++--
 docs/template_usage.md  | 2 +-
 pyproject.toml          | 4 +++-
 5 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/.cruft.json b/.cruft.json
index 09f389b..ca33885 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,6 +1,6 @@
 {
   "template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
-  "commit": "31733e798d89018e590c2586962c153d38057dad",
+  "commit": "d7f546e69b928578a358d78950333563f6934c26",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -37,7 +37,7 @@
         "trim_blocks": true
       },
       "_template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
-      "_commit": "31733e798d89018e590c2586962c153d38057dad"
+      "_commit": "d7f546e69b928578a358d78950333563f6934c26"
     }
   },
   "directory": null
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 0284b58..7bc56f9 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -11,18 +11,19 @@ repos:
     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: v2.25.3
     hooks:
       - id: pyproject-fmt
+        groups: [format]
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.15.22
     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
@@ -39,9 +40,12 @@ repos:
       - 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
diff --git a/docs/contributing.md b/docs/contributing.md
index 798c1c5..7afcf9b 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-static-analysis: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 1a769ab..2524d9d 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 fmt` 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 1661a3b..828d28a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -34,7 +34,6 @@ urls.Source = "https://github.com/scverse/cookiecutter-scverse-instance"
 [dependency-groups]
 dev = [
   "mypy",
-  "prek",
   "twine>=4.0.2",
 ]
 test = [
@@ -77,6 +76,9 @@ envs.hatch-test.overrides.matrix.deps.env-vars = [
   { value = "allow", key = "UV_PRERELEASE", if = [ "pre" ] },
 ]
 envs.hatch-test.dependency-groups = [ "dev", "test" ]
+envs.hatch-static-analysis.dependencies = [ "prek" ]
+envs.hatch-static-analysis.scripts.format-fix = "prek run -a --group=format"
+envs.hatch-static-analysis.scripts.lint-fix = "prek run -a --no-group=format"
 
 [tool.ruff]
 line-length = 120

From 067ee38c6d72c45b194392b8f8e9fd6e10c09af7 Mon Sep 17 00:00:00 2001
From: "scverse-pr-creator[bot]"
 <272303624+scverse-pr-creator[bot]@users.noreply.github.com>
Date: Fri, 24 Jul 2026 11:18:58 +0000
Subject: [PATCH 2/4] Update instance repo from cookiecutter template

---
 .pre-commit-config.yaml |  3 ++-
 docs/template_usage.md  |  2 +-
 pyproject.toml          | 17 +++++++++++++----
 3 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 7bc56f9..2f7ed62 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -28,12 +28,13 @@ repos:
     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:
diff --git a/docs/template_usage.md b/docs/template_usage.md
index 2524d9d..b191b70 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`.
-Set up the git hook once by running `prek install` (e.g. `uvx prek install`), then `hatch fmt` to format and 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 828d28a..627ca78 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -33,7 +33,6 @@ urls.Source = "https://github.com/scverse/cookiecutter-scverse-instance"
 
 [dependency-groups]
 dev = [
-  "mypy",
   "twine>=4.0.2",
 ]
 test = [
@@ -56,6 +55,10 @@ doc = [
   "sphinxcontrib-katex",
   "sphinxext-opengraph",
 ]
+typecheck = [
+  "mypy",
+  # add any stub packages that you might need here
+]
 
 [tool.hatch]
 envs.default.installer = "uv"
@@ -76,9 +79,15 @@ envs.hatch-test.overrides.matrix.deps.env-vars = [
   { value = "allow", key = "UV_PRERELEASE", if = [ "pre" ] },
 ]
 envs.hatch-test.dependency-groups = [ "dev", "test" ]
-envs.hatch-static-analysis.dependencies = [ "prek" ]
-envs.hatch-static-analysis.scripts.format-fix = "prek run -a --group=format"
-envs.hatch-static-analysis.scripts.lint-fix = "prek run -a --no-group=format"
+envs.hatch-check-fmt.dependencies = [ "prek" ]
+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-fix = "prek run -a --no-group=format --no-group=typecheck"
+envs.hatch-check-types.dependencies = [ "mypy" ]
+envs.hatch-check-types.scripts.check = [ "mypy" ]
+
+[tool.mypy]
+files = [ "src", "tests" ]
 
 [tool.ruff]
 line-length = 120

From dd0f039c8ce818c139532fd030fd485c45f91014 Mon Sep 17 00:00:00 2001
From: "scverse-pr-creator[bot]"
 <272303624+scverse-pr-creator[bot]@users.noreply.github.com>
Date: Fri, 24 Jul 2026 11:21:21 +0000
Subject: [PATCH 3/4] Update instance repo from cookiecutter template

---
 docs/contributing.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/contributing.md b/docs/contributing.md
index 7afcf9b..f31c190 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -156,7 +156,7 @@ See [pre-commit checks](template_usage.md#pre-commit-checks) for a full list of
 To enable the checks locally, run
 
 ```bash
-hatch run hatch-static-analysis:prek install
+hatch run hatch-check-code:prek install
 # or
 uvx prek install
 ```

From 03a37f7f27611251cefc1ec77db5dbba710a7375 Mon Sep 17 00:00:00 2001
From: "scverse-pr-creator[bot]"
 <272303624+scverse-pr-creator[bot]@users.noreply.github.com>
Date: Fri, 24 Jul 2026 11:24:38 +0000
Subject: [PATCH 4/4] Update instance repo from cookiecutter template

---
 .cruft.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.cruft.json b/.cruft.json
index ca33885..d6a03e3 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,6 +1,6 @@
 {
   "template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
-  "commit": "d7f546e69b928578a358d78950333563f6934c26",
+  "commit": "ba8ba4359df21973a17be78d182f4a7361727098",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -37,7 +37,7 @@
         "trim_blocks": true
       },
       "_template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
-      "_commit": "d7f546e69b928578a358d78950333563f6934c26"
+      "_commit": "ba8ba4359df21973a17be78d182f4a7361727098"
     }
   },
   "directory": null