From df3514e26f50a07986d6a4098a9ca512141b3c8e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 9 Feb 2026 18:33:17 +0000
Subject: [PATCH 01/12] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/biomejs/pre-commit: v2.3.10 → v2.3.14](https://github.com/biomejs/pre-commit/compare/v2.3.10...v2.3.14)
- [github.com/tox-dev/pyproject-fmt: v2.12.1 → v2.14.2](https://github.com/tox-dev/pyproject-fmt/compare/v2.12.1...v2.14.2)
- [github.com/astral-sh/ruff-pre-commit: v0.14.14 → v0.15.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.14...v0.15.0)
---
 .pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index fe5759d2..70fe7b61 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: v2.14.2
     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]

From 8fab83bea8a0fdffced6d3e4e7f9ad0f09652b0a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 9 Feb 2026 18:33:43 +0000
Subject: [PATCH 02/12] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 scripts/pyproject.toml | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/scripts/pyproject.toml b/scripts/pyproject.toml
index 1c4cb416..67cf912f 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" ]
@@ -93,11 +91,11 @@ lint.isort.required-imports = [ "from __future__ import annotations" ]
 [tool.pyproject-fmt]
 column_width = 120
 
-[tool.pytest.ini_options]
-addopts = [
+[tool.pytest]
+ini_options.addopts = [
   "--import-mode=importlib",
 ]
-filterwarnings = [
+ini_options.filterwarnings = [
   "error",
   # https://github.com/man-group/pytest-plugins/issues/224
   "ignore::DeprecationWarning:pytest_shutil",

From 75599b822ebd7746ff600a098fa6fc0e6d463297 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 9 Feb 2026 18:37:46 +0000
Subject: [PATCH 03/12] Apply automatic changes

---
 {{cookiecutter.project_name}}/.pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/{{cookiecutter.project_name}}/.pre-commit-config.yaml b/{{cookiecutter.project_name}}/.pre-commit-config.yaml
index 74ce081b..82c5c710 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: v2.15.0
     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]

From 5f419963ea2ec6ff81817126e3361b0b4df3fd5d Mon Sep 17 00:00:00 2001
From: "Philipp A." <flying-sheep@web.de>
Date: Tue, 10 Feb 2026 09:44:54 +0100
Subject: [PATCH 04/12] no more ini

---
 scripts/pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/pyproject.toml b/scripts/pyproject.toml
index 67cf912f..57c3ef3b 100644
--- a/scripts/pyproject.toml
+++ b/scripts/pyproject.toml
@@ -92,10 +92,10 @@ lint.isort.required-imports = [ "from __future__ import annotations" ]
 column_width = 120
 
 [tool.pytest]
-ini_options.addopts = [
+addopts = [
   "--import-mode=importlib",
 ]
-ini_options.filterwarnings = [
+filterwarnings = [
   "error",
   # https://github.com/man-group/pytest-plugins/issues/224
   "ignore::DeprecationWarning:pytest_shutil",

From 1bf6582f72cc5e2620fe31bf81df04c98f9c10c4 Mon Sep 17 00:00:00 2001
From: "Philipp A." <flying-sheep@web.de>
Date: Tue, 10 Feb 2026 10:05:17 +0100
Subject: [PATCH 05/12] bump

---
 .pre-commit-config.yaml                               | 2 +-
 {{cookiecutter.project_name}}/.pre-commit-config.yaml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 70fe7b61..7ab7de54 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ repos:
       - id: biome-format
   # Hooks that are run for scripts
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.14.2
+    rev: v2.15.1
     hooks:
       - id: pyproject-fmt
         files: ^scripts/pyproject\.toml$
diff --git a/{{cookiecutter.project_name}}/.pre-commit-config.yaml b/{{cookiecutter.project_name}}/.pre-commit-config.yaml
index 82c5c710..e47a4f7a 100644
--- a/{{cookiecutter.project_name}}/.pre-commit-config.yaml
+++ b/{{cookiecutter.project_name}}/.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: v2.15.0
+    rev: v2.15.1
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit

From 44e54664b103e6be7465840393f62cab0dc0b76a Mon Sep 17 00:00:00 2001
From: "Philipp A." <flying-sheep@web.de>
Date: Tue, 10 Feb 2026 10:10:03 +0100
Subject: [PATCH 06/12] fmt

---
 .../assets/cookiecutter-scverse-instance.json |  2 +-
 {{cookiecutter.project_name}}/pyproject.toml  | 50 +++++++------------
 2 files changed, 20 insertions(+), 32 deletions(-)

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/{{cookiecutter.project_name}}/pyproject.toml b/{{cookiecutter.project_name}}/pyproject.toml
index 3de9ac3a..af840ec4 100644
--- a/{{cookiecutter.project_name}}/pyproject.toml
+++ b/{{cookiecutter.project_name}}/pyproject.toml
@@ -65,33 +65,23 @@ 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 = [
+hatch-test.overrides.matrix.deps.env-vars = [
   { key = "UV_PRERELEASE", value = "allow", if = [ "pre" ] },
 ]
 
@@ -99,9 +89,7 @@ matrix.deps.env-vars = [
 line-length = 120
 src = [ "src" ]
 extend-include = [ "*.ipynb" ]
-
 format.docstring-code-format = true
-
 lint.select = [
   "B",      # flake8-bugbear
   "BLE",    # flake8-blind-except
@@ -142,12 +130,12 @@ 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 = [

From 55ef642aeceaf4ee951adc27752619eb3f41a7d6 Mon Sep 17 00:00:00 2001
From: "Philipp A." <flying-sheep@web.de>
Date: Tue, 10 Feb 2026 10:12:44 +0100
Subject: [PATCH 07/12] whoops

---
 {{cookiecutter.project_name}}/pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/{{cookiecutter.project_name}}/pyproject.toml b/{{cookiecutter.project_name}}/pyproject.toml
index af840ec4..2146bf1e 100644
--- a/{{cookiecutter.project_name}}/pyproject.toml
+++ b/{{cookiecutter.project_name}}/pyproject.toml
@@ -81,7 +81,7 @@ envs.hatch-test.matrix = [
 ]
 # If the matrix variable `deps` is set to "pre",
 # set the environment variable `UV_PRERELEASE` to "allow".
-hatch-test.overrides.matrix.deps.env-vars = [
+envs.hatch-test.overrides.matrix.deps.env-vars = [
   { key = "UV_PRERELEASE", value = "allow", if = [ "pre" ] },
 ]
 

From 74ab287c56edc7425855d2c75a45862b389f3d7c Mon Sep 17 00:00:00 2001
From: "Philipp A." <flying-sheep@web.de>
Date: Tue, 10 Feb 2026 10:16:08 +0100
Subject: [PATCH 08/12] fmt

---
 {{cookiecutter.project_name}}/pyproject.toml | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/{{cookiecutter.project_name}}/pyproject.toml b/{{cookiecutter.project_name}}/pyproject.toml
index 2146bf1e..a3db4a97 100644
--- a/{{cookiecutter.project_name}}/pyproject.toml
+++ b/{{cookiecutter.project_name}}/pyproject.toml
@@ -59,12 +59,6 @@ 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"
 envs.default.dependency-groups = [ "dev" ]
@@ -84,6 +78,10 @@ envs.hatch-test.matrix = [
 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

From 5bc3fafbc3db1c0e04881441220bdf718f6796b9 Mon Sep 17 00:00:00 2001
From: "Philipp A." <flying-sheep@web.de>
Date: Tue, 10 Feb 2026 10:18:30 +0100
Subject: [PATCH 09/12] whitespace bullshit

---
 {{cookiecutter.project_name}}/pyproject.toml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/{{cookiecutter.project_name}}/pyproject.toml b/{{cookiecutter.project_name}}/pyproject.toml
index a3db4a97..c77792a1 100644
--- a/{{cookiecutter.project_name}}/pyproject.toml
+++ b/{{cookiecutter.project_name}}/pyproject.toml
@@ -78,10 +78,9 @@ envs.hatch-test.matrix = [
 envs.hatch-test.overrides.matrix.deps.env-vars = [
   { key = "UV_PRERELEASE", value = "allow", if = [ "pre" ] },
 ]
-{% if cookiecutter.project_name.lower().replace("-", "_") != cookiecutter.package_name -%}
+{%- if cookiecutter.project_name.lower().replace("-", "_") != cookiecutter.package_name %}
 build.targets.wheel.packages = [ "src/{{ cookiecutter.package_name }}" ]
-
-{% endif -%}
+{%- endif %}
 
 [tool.ruff]
 line-length = 120

From 9731eee7fbd31e02c09aac035d2ef192820e4f11 Mon Sep 17 00:00:00 2001
From: "Philipp A." <flying-sheep@web.de>
Date: Tue, 10 Feb 2026 10:23:10 +0100
Subject: [PATCH 10/12] argh

---
 {{cookiecutter.project_name}}/pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/{{cookiecutter.project_name}}/pyproject.toml b/{{cookiecutter.project_name}}/pyproject.toml
index c77792a1..f26dfeaa 100644
--- a/{{cookiecutter.project_name}}/pyproject.toml
+++ b/{{cookiecutter.project_name}}/pyproject.toml
@@ -78,10 +78,10 @@ envs.hatch-test.matrix = [
 envs.hatch-test.overrides.matrix.deps.env-vars = [
   { key = "UV_PRERELEASE", value = "allow", if = [ "pre" ] },
 ]
-{%- if cookiecutter.project_name.lower().replace("-", "_") != cookiecutter.package_name %}
+{% if cookiecutter.project_name.lower().replace("-", "_") != cookiecutter.package_name -%}
 build.targets.wheel.packages = [ "src/{{ cookiecutter.package_name }}" ]
-{%- endif %}
 
+{%- endif %}
 [tool.ruff]
 line-length = 120
 src = [ "src" ]

From 4fe8e88f6d0908d8a56ca5fcf589e78e4d8f5461 Mon Sep 17 00:00:00 2001
From: "Philipp A." <flying-sheep@web.de>
Date: Tue, 10 Feb 2026 10:24:29 +0100
Subject: [PATCH 11/12] maybe trim works

---
 {{cookiecutter.project_name}}/pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/{{cookiecutter.project_name}}/pyproject.toml b/{{cookiecutter.project_name}}/pyproject.toml
index f26dfeaa..0e44f053 100644
--- a/{{cookiecutter.project_name}}/pyproject.toml
+++ b/{{cookiecutter.project_name}}/pyproject.toml
@@ -80,8 +80,8 @@ envs.hatch-test.overrides.matrix.deps.env-vars = [
 ]
 {% 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" ]

From 76b62e6611dc10085a04ba7f653fe35cc18238bc Mon Sep 17 00:00:00 2001
From: "Philipp A." <flying-sheep@web.de>
Date: Tue, 10 Feb 2026 10:27:54 +0100
Subject: [PATCH 12/12] hmm

---
 {{cookiecutter.project_name}}/pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/{{cookiecutter.project_name}}/pyproject.toml b/{{cookiecutter.project_name}}/pyproject.toml
index 0e44f053..52763fb7 100644
--- a/{{cookiecutter.project_name}}/pyproject.toml
+++ b/{{cookiecutter.project_name}}/pyproject.toml
@@ -80,7 +80,7 @@ envs.hatch-test.overrides.matrix.deps.env-vars = [
 ]
 {% if cookiecutter.project_name.lower().replace("-", "_") != cookiecutter.package_name -%}
 build.targets.wheel.packages = [ "src/{{ cookiecutter.package_name }}" ]
-{%- endif %}
+{% endif %}
 
 [tool.ruff]
 line-length = 120