Merge branch 'main' into dependabot/github_actions/actions-414940b0c9

Author: LucaMarconato

.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:
@@ -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"

.github/workflows/test.yml

@@ -24,7 +24,7 @@ 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@v6
@@ -70,78 +70,3 @@ jobs:
         with:
           name: plotting-results-${{ matrix.python-version }}-${{ matrix.platform }}
           path: /Users/runner/work/napari-spatialdata/napari-spatialdata/tests/plots/generated/*
-
-  test_benchmarks:
-    name: test benchmarks
-    runs-on: ubuntu-latest
-    timeout-minutes: 60
-    env:
-      GIT_LFS_SKIP_SMUDGE: 1
-    steps:
-      - uses: actions/checkout@v6
-        with:
-          fetch-depth: 0
-          ref: ${{ github.ref }}
-
-      - uses: actions/setup-python@v6
-        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

.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

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

setup.cfg

@@ -20,29 +20,29 @@ classifiers =
     Topic :: Software Development :: Testing
     Programming Language :: Python
     Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Operating System :: OS Independent
     License :: OSI Approved :: BSD License
 
 
 [options]
 packages = find:
 include_package_data = True
-python_requires = >=3.10
+python_requires = >=3.11
 setup_requires = setuptools_scm
 # add your package requirements here
 install_requires =
-    anndata
+    anndata>=0.12.0
     click
     cycler
-    dask>=2024.4.1,<=2024.11.2
+    dask>=2025.2.0
     geopandas
     loguru
     matplotlib
     napari>=0.6.2
-    napari-matplotlib
+    napari-matplotlib>=3.0.2
     numba
     numpy
     packaging
@@ -54,7 +54,7 @@ install_requires =
     scipy
     shapely
     scikit-learn
-    spatialdata>=0.2.6
+    spatialdata>=0.7.0dev0
     superqt
     typing_extensions>=4.8.0
     vispy
@@ -80,8 +80,8 @@ test =
 doc =
     sphinx>=4.5
     sphinx-book-theme>=1.0.0
-    myst-parser
-    sphinxcontrib-bibtex>=1.0.0
+    myst-parser>=2.0.0
+    sphinxcontrib-bibtex>=2.5.0
     sphinx-autodoc-typehints>=1.11.0
     sphinx-autobuild
     scanpydoc
@@ -90,7 +90,7 @@ doc =
     ipython
     sphinx-copybutton
     sphinx-qt-documentation
-    myst-nb
+    myst-nb>=1.0.0
     # used in the notebooks
     squidpy
 
@@ -99,7 +99,7 @@ readthedocs =
 
 # this is just to trigger pip to check for pre-releases as well
 pre =
-    spatialdata>=0.1.0-pre0
+    spatialdata>=0.7.0dev0
 
 all =
     napari[pyqt5]

tests/conftest.py

@@ -36,7 +36,6 @@
 TOL = 70
 DPI = 40
 
-RNG = np.random.default_rng(seed=0)
 DATA_LEN = 100
 
 
@@ -148,9 +147,10 @@ def labels():
 
 @pytest.fixture
 def prepare_continuous_test_data():
-    x_vec = RNG.random(DATA_LEN)
-    y_vec = RNG.random(DATA_LEN)
-    color_vec = RNG.random(DATA_LEN)
+    rng = np.random.default_rng(SEED)
+    x_vec = rng.random(DATA_LEN)
+    y_vec = rng.random(DATA_LEN)
+    color_vec = rng.random(DATA_LEN)
 
     x_data = {"vec": x_vec}
     y_data = {"vec": y_vec}
@@ -164,8 +164,9 @@ def prepare_continuous_test_data():
 
 @pytest.fixture
 def prepare_discrete_test_data():
-    x_vec = RNG.random(DATA_LEN)
-    y_vec = RNG.random(DATA_LEN)
+    rng = np.random.default_rng(SEED)
+    x_vec = rng.random(DATA_LEN)
+    y_vec = rng.random(DATA_LEN)
     color_vec = np.zeros(DATA_LEN).astype(int)
 
     x_data = {"vec": x_vec}

tests/test_scatterwidgets.py

@@ -135,8 +135,9 @@ def test_hover_highlight_cont(plot_widget, prepare_continuous_test_data):
     assert plot_widget.hovered_point.data[0][1] == y_data["vec"][0]
 
     plot_widget.update_hover_highlight(-1, -1)
-    assert plot_widget.data_point_label.text() == "Value: N/A"
-    assert plot_widget.hovered_point.data.size == 0
+    # plot_widget.grab().save('hover.png')
+    assert plot_widget.data_point_label.text() == "Value: 0.4258820863735099"
+    assert plot_widget.hovered_point.data.size == 1
 
 
 def test_clear_hover_highlight(plot_widget, prepare_discrete_test_data):