Sync with cookiecutter-scverse v0.7.0

.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "87a407a65408d75a949c0b54b19fd287475a56f8",
-  "checkout": "v0.4.0",
+  "commit": "6ff5b92b5d44ea6d8a88e47538475718d467db95",
+  "checkout": "v0.7.0",
   "context": {
     "cookiecutter": {
       "project_name": "spatialdata-plot",
@@ -10,19 +10,33 @@
       "author_full_name": "scverse",
       "author_email": "scverse",
       "github_user": "scverse",
-      "project_repo": "https://github.com/scverse/spatialdata-plot",
+      "github_repo": "spatialdata-plot",
       "license": "BSD 3-Clause License",
+      "ide_integration": false,
       "_copy_without_render": [
         ".github/workflows/build.yaml",
         ".github/workflows/test.yaml",
         "docs/_templates/autosummary/**.rst"
       ],
+      "_exclude_on_template_update": [
+        "CHANGELOG.md",
+        "LICENSE",
+        "README.md",
+        "docs/api.md",
+        "docs/index.md",
+        "docs/notebooks/example.ipynb",
+        "docs/references.bib",
+        "docs/references.md",
+        "src/**",
+        "tests/**"
+      ],
       "_render_devdocs": false,
       "_jinja2_env_vars": {
         "lstrip_blocks": true,
         "trim_blocks": true
       },
-      "_template": "https://github.com/scverse/cookiecutter-scverse"
+      "_template": "https://github.com/scverse/cookiecutter-scverse",
+      "_commit": "6ff5b92b5d44ea6d8a88e47538475718d467db95"
     }
   },
   "directory": null

.editorconfig

@@ -8,10 +8,7 @@ charset = utf-8
 trim_trailing_whitespace = true
 insert_final_newline = true
 
-[*.{yml,yaml}]
-indent_size = 2
-
-[.cruft.json]
+[{*.{yml,yaml,toml},.cruft.json}]
 indent_size = 2
 
 [Makefile]

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,41 @@
+name: Bug report
+description: Report something that is broken or incorrect
+type: Bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
+        detailing how to provide the necessary information for us to reproduce your bug. In brief:
+          * Please provide exact steps how to reproduce the bug in a clean Python environment.
+          * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
+          * Replicate problems on public datasets or share data subsets when full sharing isn't possible.
+
+  - type: textarea
+    id: report
+    attributes:
+      label: Report
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: versions
+    attributes:
+      label: Versions
+      description: |
+        Which version of packages.
+
+        Please install `session-info2`, run the following command in a notebook,
+        click the "Copy as Markdown" button, then paste the results into the text box below.
+
+        ```python
+        In[1]: import session_info2; session_info2.session_info(dependencies=True)
+        ```
+
+        Alternatively, run this in a console:
+
+        ```python
+        >>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
+        ```
+      render: python

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Scverse Community Forum
+    url: https://discourse.scverse.org/
+    about: If you have questions about "How to do X", please ask them here.

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for spatialdata-plot
+type: Enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true

.github/workflows/build.yaml

@@ -0,0 +1,26 @@
+name: Check Build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Build package
+        run: uv build
+      - name: Check package
+        run: uvx twine check --strict dist/*.whl

.github/workflows/release.yaml

@@ -4,28 +4,43 @@ on:
   release:
     types: [published]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
-  package_and_release:
+  build:
     runs-on: ubuntu-latest
-    if: startsWith(github.ref, 'refs/tags/v')
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.12
-        uses: actions/setup-python@v5
+      - uses: actions/checkout@v5
         with:
-          python-version: "3.12"
-          cache: pip
-      - name: Install build dependencies
-        run: python -m pip install --upgrade pip wheel twine build
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
       - name: Build package
-        run: python -m build
+        run: uv build
       - name: Check package
-        run: twine check --strict dist/*.whl
-      - 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
+        run: uvx twine check --strict dist/*
+      - name: Upload build artifacts
+        uses: actions/upload-artifact@v4
         with:
-          password: ${{ secrets.PYPI_API_TOKEN }}
+          name: dist
+          path: dist/
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write # for PyPI trusted publishing
+    environment:
+      name: pypi
+      url: https://pypi.org/p/spatialdata-plot
+    steps:
+      - name: Download build artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test.yaml

@@ -3,73 +3,112 @@ name: Test
 on:
   push:
     branches: [main]
-    tags: ["v*"] # Push events to matching v*, i.e. v1.0, v20.15.10
+    tags: ["v*"]
   pull_request:
-    branches: ["*"]
+    branches: [main]
+  schedule:
+    - cron: "0 5 1,15 * *"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  MPLBACKEND: agg
 
 jobs:
-  test:
+  # Dynamically extract the test matrix from hatch so pyproject.toml is the single source of truth.
+  # See [[tool.hatch.envs.hatch-test.matrix]] in pyproject.toml.
+  get-environments:
     runs-on: ubuntu-latest
+    outputs:
+      envs: ${{ steps.get-envs.outputs.envs }}
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get test environments
+        id: get-envs
+        run: |
+          ENVS_JSON=$(uvx hatch env show --json | jq -c 'to_entries
+            | map(
+                select(.key | startswith("hatch-test"))
+                | {
+                    name: .key,
+                    label: (if (.key | contains("pre")) then .key + " (PRE-RELEASE DEPENDENCIES)" else .key end),
+                    python: .value.python
+                  }
+              )')
+          echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
+
+  test:
+    needs: get-environments
+    permissions:
+      id-token: write # for codecov OIDC
+
     strategy:
       fail-fast: false
       matrix:
-        env: ["dev-py311", "dev-py313"]
+        os: [ubuntu-latest]
+        env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
 
-    # Configure pytest-xdist
-    env:
-      OMP_NUM_THREADS: "1"
-      OPENBLAS_NUM_THREADS: "1"
-      MKL_NUM_THREADS: "1"
-      NUMEXPR_MAX_THREADS: "1"
-      MPLBACKEND: "agg"
-      DISPLAY: ":42"
-      PYTEST_ADDOPTS: "-n auto --dist=load --durations=10"
+    name: ${{ matrix.env.label }}
+    runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ contains(matrix.env.name, 'pre') }}
 
     steps:
-      - uses: actions/checkout@v4
-
-      # Cache rattler's shared package cache (speeds up downloads)
-      - name: Restore rattler cache
-        uses: actions/cache@v4
+      - uses: actions/checkout@v5
         with:
-          path: ~/.cache/rattler
-          key: rattler-${{ runner.os }}-${{ matrix.env }}-${{ hashFiles('pyproject.toml') }}
-          restore-keys: |
-            rattler-${{ runner.os }}-${{ matrix.env }}-
-            rattler-${{ runner.os }}-
-
-      # Install pixi and the requested environment
-      - uses: prefix-dev/setup-pixi@v0.9.0
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
         with:
-          environments: ${{ matrix.env }}
-          # We're not comitting the pixi-lock file
-          locked: false
-          cache: false
-          activate-environment: ${{ matrix.env }}
-
-      - name: Show versions
-        run: |
-          python --version
-          pixi --version
-
+          python-version: ${{ matrix.env.python }}
+      - name: Ensure figure directory exists
+        run: mkdir -p tests/figures
+      - name: Create hatch environment
+        run: uvx hatch env create ${{ matrix.env.name }}
       - name: Run tests
         env:
-          MPLBACKEND: agg
           DISPLAY: ":42"
+        run: >-
+          uvx hatch run ${{ matrix.env.name }}:${{
+            matrix.env.name == 'hatch-test.py3.14-stable' && 'run-cov' || 'run'
+          }} -v --color=yes ${{
+            matrix.env.name == 'hatch-test.py3.14-stable' && ' ' || '-n auto'
+          }}
+      - name: Generate coverage report
+        if: matrix.env.name == 'hatch-test.py3.14-stable'
         run: |
-          pytest -v --cov --color=yes --cov-report=xml
-
-      - name: Archive figures generated during testing
+          test -f .coverage || uvx hatch run ${{ matrix.env.name }}:cov-combine
+          uvx hatch run ${{ matrix.env.name }}:cov-report
+      - name: Archive visual test figures
         if: always()
         uses: actions/upload-artifact@v4
         with:
-          name: visual_test_results_${{ matrix.env }}
-          path: /home/runner/work/spatialdata-plot/spatialdata-plot/tests/figures/*
+          name: visual_test_results_${{ matrix.env.name }}
+          path: tests/figures/*
+      - name: Upload coverage
+        if: matrix.env.name == 'hatch-test.py3.14-stable'
+        uses: codecov/codecov-action@v5
+        with:
+          fail_ci_if_error: true
+          use_oidc: true
 
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
+  # Single required check for branch protection.
+  # See https://github.com/re-actors/alls-green#why
+  check:
+    name: Tests pass in all hatch environments
+    if: always()
+    needs:
+      - get-environments
+      - test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: re-actors/alls-green@release/v1
         with:
-          name: coverage
-          verbose: true
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          jobs: ${{ toJSON(needs) }}

.gitignore

@@ -6,8 +6,7 @@ buck-out/
 # Compiled files
 .venv/
 __pycache__/
-.mypy_cache/
-.ruff_cache/
+.*cache/
 /node_modules
 
 # Distribution / packaging
@@ -16,7 +15,6 @@ __pycache__/
 /*.egg-info/
 
 # Tests and coverage
-/.pytest_cache/
 /.cache/
 /data/
 *failed-diff.png
@@ -31,7 +29,6 @@ __pycache__/
 
 format.sh
 
-
 # test
 tests/figures/