Update template to v0.4.0

.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "586b1652162ff7994b0070a034023d64289ae416",
-  "checkout": "v0.3.1",
+  "commit": "87a407a65408d75a949c0b54b19fd287475a56f8",
+  "checkout": "v0.4.0",
   "context": {
     "cookiecutter": {
       "project_name": "scirpy",

.github/workflows/test.yaml

@@ -26,9 +26,9 @@ jobs:
           - os: ubuntu-latest
             python: "3.9"
           - os: ubuntu-latest
-            python: "3.11"
+            python: "3.12"
           - os: ubuntu-latest
-            python: "3.11"
+            python: "3.12"
             pip-flags: "--pre"
             name: PRE-RELEASE DEPENDENCIES
 
@@ -52,10 +52,7 @@ jobs:
           python -m pip install --upgrade pip wheel
       - name: Install dependencies
         run: |
-          # Workaround issue with scikit-bio
-          # This will work in the next release, see https://github.com/biocore/scikit-bio/pull/1813
-          pip install git+https://github.com/grst/scikit-bio.git@main
-          pip install ${{ matrix.pip-flags }} ".[dev,test,rpack,dandelion]"
+          pip install ${{ matrix.pip-flags }} ".[dev,test,rpack,dandelion,diversity]"
       - name: Test
         env:
           MPLBACKEND: agg

.gitignore

@@ -6,6 +6,7 @@ notebooks
 tutorial
 /data
 .idea
+/node_modules/
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

docs/conf.py

@@ -1,5 +1,5 @@
 # Configuration file for the Sphinx documentation builder.
-#
+
 # This file only contains a selection of the most common options. For a full
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html

docs/contributing.md

@@ -51,7 +51,7 @@ and [prettier][prettier-editors].
 ## Writing tests
 
 ```{note}
-Remember to first install the package with `pip install '-e[dev,test]'`
+Remember to first install the package with `pip install -e '.[dev,test]'`
 ```
 
 This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] for every function added

pyproject.toml

@@ -52,7 +52,7 @@ doc = [
     "docutils>=0.8,!=0.18.*,!=0.19.*",
     'sphinx>=4',
     "sphinx-book-theme>=1.0.0",
-    "myst-nb",
+    "myst-nb>=1.1.0",
     'sphinxcontrib-bibtex>=1.0.0',
     "sphinx-autodoc-typehints",
     # for tutorial
@@ -148,7 +148,7 @@ ignore = [
     "D107",
     # Errors from function calls in argument defaults. These are fine when the result is immutable.
     "B008",
-    # __magic__ methods are are often self-explanatory, allow missing docstrings
+    # __magic__ methods are often self-explanatory, allow missing docstrings
     "D105",
     # first line should end with a period [Bug: doesn't work with single-line docstrings]
     "D400",