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.github/release.yml

@@ -4,6 +4,7 @@ changelog:
       - release-ignore
     authors:
       - pre-commit-ci
+      - pre-commit-ci[bot]
   categories:
     - title: Added
       labels:

.github/workflows/benchmarks.yml

@@ -8,8 +8,8 @@ name: Benchmarks
 on:
   pull_request:
     types: [labeled]
-  schedule:
-    - cron: "6 6 * * 0" # every sunday
+  #  schedule:
+  #    - cron: "6 6 * * 0" # every sunday
   workflow_dispatch:
     inputs:
       base_ref:
@@ -59,11 +59,11 @@ jobs:
     steps:
       # We need the full repo to avoid this issue
       # https://github.com/actions/checkout/issues/23
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         name: Install Python
         with:
           python-version: "3.11"
@@ -140,7 +140,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           PLATFORM: ${{ matrix.runs-on }}
-          PYTHON: "3.9"
+          PYTHON: "3.11"
           BACKEND: ${{ matrix.benchmark-name }}
           RUN_ID: ${{ github.run_id }}
           TITLE: "[test-bot] Benchmark tests failing"
@@ -170,7 +170,7 @@ jobs:
 
           fi
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v7
         if: always()
         with:
           name: asv-benchmark-results-${{ github.run_id }}-${{ github.run_number }}-${{ github.run_attempt }}-${{ matrix.benchmark-name }}
@@ -182,13 +182,13 @@ jobs:
     if: always()
     steps:
       - name: Download artifact
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           pattern: asv-benchmark-results*
           path: asv_result
           merge-multiple: true
       - name: Upload artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: asv-benchmark-results-${{ github.run_id }}-${{ github.run_number }}-${{ github.run_attempt }}
           path: asv_result

.github/workflows/benchmarks_report.yml

@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: "Download artifact"
-        uses: actions/github-script@v7
+        uses: actions/github-script@v9
         with:
           script: |
             let allArtifacts = await github.rest.actions.listWorkflowRunArtifacts({
@@ -68,7 +68,7 @@ jobs:
 
       - name: "Comment on PR"
         if: env.PR_NUMBER != ''
-        uses: actions/github-script@v7
+        uses: actions/github-script@v9
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           script: |
@@ -84,7 +84,7 @@ jobs:
 
       - name: "Remove run-benchmarks label"
         if: env.PR_NUMBER != ''
-        uses: actions/github-script@v7
+        uses: actions/github-script@v9
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           script: |

.github/workflows/release.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     if: startsWith(github.ref, 'refs/tags/v')
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - uses: hynek/build-and-inspect-python-package@v2
 
   upload-to-pypi:
@@ -21,7 +21,7 @@ jobs:
 
     steps:
       - name: Download built artifact to dist/
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           name: Packages
           path: dist

.github/workflows/test.yml

@@ -24,13 +24,13 @@ jobs:
       fail-fast: false
       matrix:
         platform: [ubuntu-latest, macos-latest] # [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.10", "3.12"]
+        python-version: ["3.11", "3.13"]
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -62,86 +62,11 @@ jobs:
           PLATFORM: ${{ matrix.platform }}
 
       - name: Coverage
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
 
       - name: Archive figures generated during testing
         if: always()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: plotting-results-${{ matrix.python-version }}-${{ matrix.platform }}
-          path: /home/runner/work/napari-spatialdata/napari-spatialdata/tests/plots/*
-
-  test_benchmarks:
-    name: test benchmarks
-    runs-on: ubuntu-latest
-    timeout-minutes: 60
-    env:
-      GIT_LFS_SKIP_SMUDGE: 1
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-          ref: ${{ github.ref }}
-
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.11
-          cache-dependency-path: pyproject.toml
-
-      - name: Install dependencies with 'pre' extras (since the above doesn't check pre-releases)
-        run: |
-          python -m pip install --upgrade pip
-          pip install .[pre]
-
-      - uses: tlambert03/setup-qt-libs@v1
-
-      - uses: octokit/request-action@v2.x
-        # here we get hash of the latest release commit to compare with PR
-        id: latest_release
-        with:
-          route: GET /repos/{owner}/{repo}/releases/latest
-          owner: scverse
-          repo: napari-spatialdata
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: install dependencies
-        run: |
-          pip install --upgrade pip
-          pip install "asv[virtualenv]"
-        env:
-          PIP_CONSTRAINT: benchmarks/benchmark.txt
-
-      - name: asv machine
-        run: asv machine --yes
-
-      - name: Run benchmarks PR
-        uses: aganders3/headless-gui@v2
-        with:
-          run: |
-            asv run --show-stderr --quick  --attribute timeout=300 HEAD^!
-        env:
-          PR: 1 # prevents asv from running very compute-intensive benchmarks
-          PIP_CONSTRAINT: ${{ github.workspace }}/benchmarks/benchmark.txt
-
-      - name: Fetch latest main
-        run: git fetch origin main
-
-      - name: Fetch latest release commit
-        run: git fetch origin ${{ fromJSON(steps.latest_release.outputs.data).target_commitish }}
-
-      - name: Ensure local main exists
-        run: |
-          CURRENT_BRANCH=$(git rev-parse --abbrev-ref HEAD)
-          if [ "$CURRENT_BRANCH" != "main" ]; then
-            git branch main origin/main
-          fi
-
-      - name: Run benchmarks latest release
-        uses: aganders3/headless-gui@v2
-        with:
-          run: |
-            asv run --show-stderr --quick --attribute timeout=300 ${{ fromJSON(steps.latest_release.outputs.data).target_commitish }}^!
-        env:
-          PR: 1 # prevents asv from running very compute-intensive benchmarks
-          PIP_CONSTRAINT: ${{ github.workspace }}/benchmarks/benchmark.txt
+          path: /Users/runner/work/napari-spatialdata/napari-spatialdata/tests/plots/generated/*

.gitignore

@@ -117,3 +117,4 @@ tests/plots/generated
 
 # Local temp script for testing user bugs (Luca)
 temp/
+uv.lock

.mypy.ini

@@ -1,7 +1,6 @@
 [mypy]
 mypy_path = napari-spatialdata
 python_version = 3.10
-plugins = numpy.typing.mypy_plugin
 
 ignore_errors = False
 warn_redundant_casts = True

.pre-commit-config.yaml

@@ -7,13 +7,13 @@ default_stages:
 minimum_pre_commit_version: 2.9.3
 repos:
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.15.0
+    rev: v1.20.2
     hooks:
       - id: mypy
         additional_dependencies: [numpy>=1.23]
         exclude: docs
-  - repo: https://github.com/psf/black
-    rev: 25.1.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 26.3.1
     hooks:
       - id: black
         additional_dependencies: [toml]
@@ -22,16 +22,16 @@ repos:
     hooks:
       - id: prettier
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: detect-private-key
       - id: check-merge-conflict
       - id: check-ast
       - id: check-symlinks
       - id: check-added-large-files
       - id: check-executables-have-shebangs
-      - id: fix-encoding-pragma
-        args: [--remove]
+      #      - id: fix-encoding-pragma
+      #        args: [--remove]
       - id: end-of-file-fixer
       - id: mixed-line-ending
         args: [--fix=lf]
@@ -45,11 +45,15 @@ repos:
       - id: check-toml
       - id: requirements-txt-fixer
   - repo: https://github.com/asottile/blacken-docs
-    rev: 1.19.1
+    rev: 1.20.0
     hooks:
       - id: blacken-docs
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.6
+    rev: v0.15.12
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.21.2
+    hooks:
+      - id: pyupgrade

.readthedocs.yaml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.11"
 sphinx:
   configuration: docs/conf.py
   fail_on_warning: false
@@ -12,7 +12,7 @@ python:
     - method: pip
       path: .
       extra_requirements:
-        - "doc"
+        - "docs"
         - "all"
         - "readthedocs"
         - "pre"

README.md

@@ -17,8 +17,7 @@
 [link-pypi]: https://pypi.org/project/napari-spatialdata/
 
 This repository contains a napari plugin for interactively exploring and annotating
-SpatialData objects. Here you can find the [napari-spatialdata documentation]
-(https://spatialdata.scverse.org/projects/napari/en/stable/notebooks/spatialdata.html). `napari-spatialdata` is part of the `SpatialData` ecosystem. To learn more about SpatialData, please see the [spatialdata documentation](https://spatialdata.scverse.org/).
+SpatialData objects. Here you can find the [napari-spatialdata documentation](https://spatialdata.scverse.org/projects/napari/en/stable/notebooks/spatialdata.html). `napari-spatialdata` is part of the `SpatialData` ecosystem. To learn more about SpatialData, please see the [spatialdata documentation](https://spatialdata.scverse.org/).
 
 ## Installation
 
@@ -28,6 +27,13 @@ You can install `napari-spatialdata` via [pip]:
 
 The `all` command will install the qt bindings `PyQt5`.
 
+Napari now also includes multiple triangulation backends. These improve the speed by which a napari 'Shapes' layer gets
+loaded (this does not improve the speed of editing large numbers of shapes yet!). See also the napari
+[documentation](https://napari.org/stable/guides/triangulation.html) and already slightly older [blog post](https://napari.org/island-dispatch/blog/triangles_speedup_beta.html). For installation via
+pip:
+
+    pip install napari-spatialdata[all, bermuda]
+
 You can find more details on this in the [installation instructions](https://spatialdata.scverse.org/en/stable/installation.html).
 
 ## Using napari-spatialdata as default zarr reader

asv.conf.json

@@ -16,7 +16,7 @@
   // Install using default qt install
   "build_command": ["python -V"], // skip build stage
   "install_command": [
-    "in-dir={env_dir} python -m pip install {build_dir}[all,test]"
+    "in-dir={env_dir} python -m pip install --pre {build_dir}[all,test,pre]"
   ],
   "uninstall_command": [
     "in-dir={env_dir} python -m pip uninstall -y {project}"

benchmarks/benchmark.txt

@@ -22,7 +22,7 @@ json5==0.9.25
     # via asv
 mamba==0.11.3
     # via -r benchmark.in
-packaging==24.1
+packaging>=24.2
     # via
     #   asv
     #   build

docs/conf.py

@@ -23,7 +23,7 @@
 info = metadata("napari-spatialdata")
 project_name = info["Name"]
 author = info["Author"]
-copyright = f"{datetime.now():%Y}, {author}."
+copyright = f"{datetime.now():%Y}, {author}"
 version = info["Version"]
 repository_url = f"https://github.com/scverse/{project_name}"
 

docs/contributing.md

@@ -1,3 +1,25 @@
 # Contributing guide
 
 Please refer to the [contribution guide from the `spatialdata` repository](https://github.com/scverse/spatialdata/blob/main/docs/contributing.md).
+
+## Debugging napari GUI tests
+
+To visually inspect what a test is rendering in napari:
+
+1. Change `make_napari_viewer()` to `make_napari_viewer(show=True)`
+2. Add `napari.run()` before the end of the test (before the assertions)
+
+Example:
+
+```python
+import napari
+
+
+def test_my_visualization(make_napari_viewer):
+    viewer = make_napari_viewer(show=True)
+    # ... setup code ...
+    napari.run()
+    # assertions...
+```
+
+Remember to revert these changes before committing.