From 2d3508a670c0cf46357e5fbdf1ea836d87e5d7d2 Mon Sep 17 00:00:00 2001
From: Marius Lange <marius.lange@bsse.ethz.ch>
Date: Fri, 24 Apr 2026 14:59:08 -0600
Subject: [PATCH] chore: sync with cookiecutter-scverse v0.7.0

Sync remaining template v0.7.0 changes that were deferred from earlier
sync PRs:

- Issue templates: `labels:` -> `type:` (GitHub issue-type field;
  matches the template). Values capitalised as in the template
  ("Bug", "Enhancement").
- `build.yaml` / `release.yaml`: bump actions to checkout@v5 and
  setup-uv@v7, drop `cache-dependency-glob` (handled automatically by
  setup-uv@v7) and the per-workflow strict-bash `defaults.run` block
  (not in the template).
- `.readthedocs.yaml`: bump RTD Python to 3.13 and add `nodejs: latest`
  under `tools` (new upstream default).
- `.cruft.json`: bump pinned template commit/checkout to v0.7.0
  (6ff5b92).

Deliberately NOT synced (keeps this PR focused and non-risky):
- Codecov OIDC migration
- Sphinx `-W` strict build flag
- katex docs extension

Tracking: closes #73.
---
 .cruft.json                                |  6 +++---
 .github/ISSUE_TEMPLATE/bug_report.yml      |  2 +-
 .github/ISSUE_TEMPLATE/feature_request.yml |  2 +-
 .github/workflows/build.yaml               | 11 ++---------
 .github/workflows/release.yaml             | 11 ++---------
 .readthedocs.yaml                          |  3 ++-
 6 files changed, 11 insertions(+), 24 deletions(-)

diff --git a/.cruft.json b/.cruft.json
index f27f963..1f33811 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec",
-  "checkout": "v0.6.0",
+  "commit": "6ff5b92b5d44ea6d8a88e47538475718d467db95",
+  "checkout": "v0.7.0",
   "context": {
     "cookiecutter": {
       "project_name": "cell-annotator",
@@ -36,7 +36,7 @@
         "trim_blocks": true
       },
       "_template": "https://github.com/scverse/cookiecutter-scverse",
-      "_commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec"
+      "_commit": "6ff5b92b5d44ea6d8a88e47538475718d467db95"
     }
   },
   "directory": null
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index 3ca1ccb..c91d8e9 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -1,6 +1,6 @@
 name: Bug report
 description: Report something that is broken or incorrect
-labels: bug
+type: Bug
 body:
   - type: markdown
     attributes:
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
index 8e5b875..6f13514 100644
--- a/.github/ISSUE_TEMPLATE/feature_request.yml
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -1,6 +1,6 @@
 name: Feature request
 description: Propose a new feature for cell-annotator
-labels: enhancement
+type: Enhancement
 body:
   - type: textarea
     id: description
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
index 83e01a1..c6ecc2f 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -10,23 +10,16 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
-defaults:
-  run:
-    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
-    shell: bash -euo pipefail {0}
-
 jobs:
   package:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           filter: blob:none
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
-        with:
-          cache-dependency-glob: pyproject.toml
+        uses: astral-sh/setup-uv@v7
       - name: Build package
         run: uv build
       - name: Check package
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
index 1b93b0d..0bc2162 100644
--- a/.github/workflows/release.yaml
+++ b/.github/workflows/release.yaml
@@ -4,11 +4,6 @@ on:
   release:
     types: [published]
 
-defaults:
-  run:
-    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
-    shell: bash -euo pipefail {0}
-
 # Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
 jobs:
   release:
@@ -20,14 +15,12 @@ jobs:
     permissions:
       id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           filter: blob:none
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
-        with:
-          cache-dependency-glob: pyproject.toml
+        uses: astral-sh/setup-uv@v7
       - name: Build package
         run: uv build
       - name: Publish package distributions to PyPI
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index c3f3f96..6c28477 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -3,7 +3,8 @@ version: 2
 build:
   os: ubuntu-24.04
   tools:
-    python: "3.12"
+    python: "3.13"
+    nodejs: latest
   jobs:
     create_environment:
       - asdf plugin add uv