Update template to v0.3.1

.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "8e96abb5c3e2d5078c44713958da672711cf2a48",
-  "checkout": "v0.3.0",
+  "commit": "586b1652162ff7994b0070a034023d64289ae416",
+  "checkout": "v0.3.1",
   "context": {
     "cookiecutter": {
       "project_name": "spatialdata-plot",
@@ -13,7 +13,8 @@
       "project_repo": "https://github.com/scverse/spatialdata-plot",
       "license": "BSD 3-Clause License",
       "_copy_without_render": [
-        ".github/workflows/**.yaml",
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
         "docs/_templates/autosummary/**.rst"
       ],
       "_render_devdocs": false,

.github/workflows/release.yaml

@@ -4,28 +4,26 @@ on:
   release:
     types: [published]
 
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
 jobs:
   release:
-    # requires that you have put your twine API key in your
-    # github secrets (see readme for details)
+    name: Upload release to PyPI
     runs-on: ubuntu-latest
-    if: contains(github.ref, 'tags')
+    environment:
+      name: pypi
+      url: https://pypi.org/p/spatialdata_plot
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
-      - name: Checkout code
-        uses: actions/checkout@v3
-
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
         with:
-          python-version: "3.10"
-
-      - name: Install hatch
-        run: pip install hatch
-
-      - name: Build project for distribution
-        run: hatch build
-
-      - name: Publish a Python distribution to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+          filter: blob:none
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
         with:
-          password: ${{ secrets.PYPI_API_TOKEN }}
+          python-version: "3.x"
+          cache: "pip"
+      - run: pip install build
+      - run: python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.mypy.ini

@@ -25,4 +25,4 @@ no_warn_no_return = True
 
 show_error_codes = True
 show_column_numbers = True
-error_summary = True
+error_summary = True

.pre-commit-config.yaml

@@ -5,21 +5,11 @@ default_stages:
   - commit
   - push
 minimum_pre_commit_version: 2.16.0
-ci:
-  skip: []
 repos:
-  - repo: https://github.com/psf/black
-    rev: 24.3.0
-    hooks:
-      - id: black
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
-  - repo: https://github.com/asottile/blacken-docs
-    rev: 1.16.0
-    hooks:
-      - id: blacken-docs
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.9.0
     hooks:
@@ -30,4 +20,29 @@ repos:
     rev: v0.3.4
     hooks:
       - id: ruff
+        types_or: [python, pyi, jupyter]
         args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      # Check that there are no merge conflicts (could be generated by template sync)
+      - id: check-merge-conflict
+        args: [--assume-in-merge]
+  - repo: local
+    hooks:
+      - id: forbid-to-commit
+        name: Don't commit rej files
+        entry: |
+          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+          Fix the merge conflicts manually and remove the .rej files.
+        language: fail
+        files: '.*\.rej$'

docs/conf.py

@@ -59,6 +59,7 @@
     "sphinx.ext.mathjax",
     "IPython.sphinxext.ipython_console_highlighting",
     "sphinx_design",
+    "sphinxext.opengraph",
     *[p.stem for p in (HERE / "extensions").glob("*.py")],
 ]
 
@@ -130,6 +131,7 @@
 html_theme = "sphinx_book_theme"
 # html_theme = "sphinx_rtd_theme"
 html_static_path = ["_static"]
+html_css_files = ["css/custom.css"]
 html_title = project_name
 html_logo = "_static/img/spatialdata_horizontal.png"
 
@@ -145,19 +147,3 @@
     # you can add an exception to this list.
     ("py:class", "igraph.Graph"),
 ]
-
-
-def setup(app):
-    """App setup hook."""
-    app.add_config_value(
-        "recommonmark_config",
-        {
-            "auto_toc_tree_section": "Contents",
-            "enable_auto_toc_tree": True,
-            "enable_math": True,
-            "enable_inline_math": False,
-            "enable_eval_rst": True,
-        },
-        True,
-    )
-    app.add_css_file("css/custom.css")

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

docs/index.md

@@ -8,7 +8,6 @@
 
 api.md
 changelog.md
-template_usage.md
 contributing.md
 references.md
 ```

docs/notebooks/preprocessing.ipynb

@@ -131,9 +131,7 @@
     "tags": []
    },
    "outputs": [],
-   "source": [
-    "import spatialdata_plot"
-   ]
+   "source": []
   },
   {
    "cell_type": "markdown",