From 989491fda6ce24ac706ffff9c1ee35bd174976cb Mon Sep 17 00:00:00 2001
From: scverse-bot <None>
Date: Thu, 22 Feb 2024 18:39:48 +0000
Subject: [PATCH] Update template to v0.3.1

---
 .cruft.json                    |  7 ++++---
 .github/workflows/release.yaml |  2 +-
 docs/contributing.md           |  3 ++-
 pyproject.toml                 | 16 +++++++++-------
 4 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/.cruft.json b/.cruft.json
index b07da1e..0912980 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "2f766dd6b8cef64e3a127bd316dd61415fbc37b6",
-  "checkout": null,
+  "commit": "586b1652162ff7994b0070a034023d64289ae416",
+  "checkout": "v0.3.1",
   "context": {
     "cookiecutter": {
       "project_name": "scCoral",
@@ -13,7 +13,8 @@
       "project_repo": "https://github.com/lucas-diedrich/sccoral",
       "license": "MIT License",
       "_copy_without_render": [
-        ".github/workflows/**.yaml",
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
         "docs/_templates/autosummary/**.rst"
       ],
       "_render_devdocs": false,
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
index bd82eb5..e013feb 100644
--- a/.github/workflows/release.yaml
+++ b/.github/workflows/release.yaml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     environment:
       name: pypi
-      url: https://pypi.org/p/{{ cookiecutter.package_name }}
+      url: https://pypi.org/p/sccoral
     permissions:
       id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
diff --git a/docs/contributing.md b/docs/contributing.md
index 9df103f..ac9bcdb 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -93,7 +93,7 @@ Before making a release, you need to update the version number in the `pyproject
 > Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
 
 Once you are done, commit and push your changes and navigate to the "Releases" page of this project on GitHub.
-Specify `vX.X.X` as a tag name and create a release. For more information, see [managing Github releases][]. This will automatically create a git tag and trigger a Github workflow that creates a release on PyPI.
+Specify `vX.X.X` as a tag name and create a release. For more information, see [managing GitHub releases][]. This will automatically create a git tag and trigger a Github workflow that creates a release on PyPI.
 
 ## Writing documentation
 
@@ -157,3 +157,4 @@ open _build/html/index.html
 [numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
 [sphinx autodoc typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
 [pypi]: https://pypi.org/
+[managing GitHub releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository
diff --git a/pyproject.toml b/pyproject.toml
index faf3031..1e1b06d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -66,8 +66,14 @@ addopts = [
 ]
 
 [tool.ruff]
-src = ["src"]
 line-length = 120
+src = ["src"]
+extend-include = ["*.ipynb"]
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.ruff.lint]
 select = [
     "F",  # Errors detected by Pyflakes
     "E",  # Error detected by Pycodestyle
@@ -108,15 +114,11 @@ ignore = [
     # We want docstrings to start immediately after the opening triple quote
     "D213",
 ]
-extend-include = ["*.ipynb"]
-
-[tool.ruff.format]
-docstring-code-format = true
 
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "docs/*" = ["I"]
 "tests/*" = ["D"]
 "*/__init__.py" = ["F401"]