napari-spatialdata 0.5.6__tar.gz → 0.6.0__tar.gz

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/.github/release.yml

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

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/.github/workflows/test.yml

@@ -69,7 +69,7 @@ jobs:
         uses: actions/upload-artifact@v4
         with:
           name: plotting-results-${{ matrix.python-version }}-${{ matrix.platform }}
-          path: /home/runner/work/napari-spatialdata/napari-spatialdata/tests/plots/*
+          path: /Users/runner/work/napari-spatialdata/napari-spatialdata/tests/plots/generated/*
 
   test_benchmarks:
     name: test benchmarks

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/.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

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/.pre-commit-config.yaml

@@ -7,7 +7,7 @@ default_stages:
 minimum_pre_commit_version: 2.9.3
 repos:
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.15.0
+    rev: v1.17.1
     hooks:
       - id: mypy
         additional_dependencies: [numpy>=1.23]
@@ -22,7 +22,7 @@ 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
@@ -30,8 +30,8 @@ repos:
       - 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]
@@ -49,7 +49,11 @@ repos:
     hooks:
       - id: blacken-docs
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.6
+    rev: v0.12.8
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.20.0
+    hooks:
+      - id: pyupgrade

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napari-spatialdata
-Version: 0.5.6
+Version: 0.6.0
 Summary: Interactive visualization of spatial omics data with napari
 Home-page: https://github.com/scverse/napari-spatialdata.git
 Author: giovanni palla
@@ -27,11 +27,11 @@ License-File: LICENSE
 Requires-Dist: anndata
 Requires-Dist: click
 Requires-Dist: cycler
-Requires-Dist: dask>=2024.4.1
+Requires-Dist: dask<=2024.11.2,>=2024.4.1
 Requires-Dist: geopandas
 Requires-Dist: loguru
 Requires-Dist: matplotlib
-Requires-Dist: napari<0.5.6,>=0.4.19.post1
+Requires-Dist: napari>=0.6.2
 Requires-Dist: napari-matplotlib
 Requires-Dist: numba
 Requires-Dist: numpy
@@ -50,6 +50,8 @@ Requires-Dist: typing_extensions>=4.8.0
 Requires-Dist: vispy
 Requires-Dist: xarray
 Requires-Dist: xarray-datatree
+Provides-Extra: bermuda
+Requires-Dist: bermuda; extra == "bermuda"
 Provides-Extra: test
 Requires-Dist: loguru; extra == "test"
 Requires-Dist: pytest; extra == "test"
@@ -72,7 +74,7 @@ Requires-Dist: sphinx-qt-documentation; extra == "doc"
 Requires-Dist: myst-nb; extra == "doc"
 Requires-Dist: squidpy; extra == "doc"
 Provides-Extra: readthedocs
-Requires-Dist: pydantic<2; extra == "readthedocs"
+Requires-Dist: pydantic>2; extra == "readthedocs"
 Provides-Extra: pre
 Requires-Dist: spatialdata>=0.1.0-pre0; extra == "pre"
 Provides-Extra: all
@@ -91,10 +93,14 @@ Dynamic: license-file
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/napari-spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/napari-spatialdata/main)
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-spatialdata)](https://napari-hub.org/plugins/napari-spatialdata)
 [![DOI](https://zenodo.org/badge/477021400.svg)](https://zenodo.org/badge/latestdoi/477021400)
+[![Documentation][badge-pypi]][link-pypi]
+[![Anaconda-Server Badge](https://anaconda.org/conda-forge/napari-spatialdata/badges/version.svg)](https://anaconda.org/conda-forge/napari-spatialdata)
+
+[badge-pypi]: https://badge.fury.io/py/napari-spatialdata.svg
+[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
 
@@ -104,6 +110,13 @@ 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

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/README.md

@@ -10,10 +10,14 @@
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/napari-spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/napari-spatialdata/main)
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-spatialdata)](https://napari-hub.org/plugins/napari-spatialdata)
 [![DOI](https://zenodo.org/badge/477021400.svg)](https://zenodo.org/badge/latestdoi/477021400)
+[![Documentation][badge-pypi]][link-pypi]
+[![Anaconda-Server Badge](https://anaconda.org/conda-forge/napari-spatialdata/badges/version.svg)](https://anaconda.org/conda-forge/napari-spatialdata)
+
+[badge-pypi]: https://badge.fury.io/py/napari-spatialdata.svg
+[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
 
@@ -23,6 +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

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/docs/conf.py

@@ -23,7 +23,7 @@ print(napari_spatialdata.__file__)  # noqa: T201
 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}"
 

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/setup.cfg

@@ -34,11 +34,11 @@ install_requires =
 	anndata
 	click
 	cycler
-	dask>=2024.4.1
+	dask>=2024.4.1,<=2024.11.2
 	geopandas
 	loguru
 	matplotlib
-	napari>=0.4.19.post1,<0.5.6
+	napari>=0.6.2
 	napari-matplotlib
 	numba
 	numpy
@@ -61,6 +61,8 @@ package_dir =
 	=src
 
 [options.extras_require]
+bermuda = 
+	bermuda
 test = 
 	loguru
 	pytest
@@ -83,7 +85,7 @@ doc =
 	myst-nb
 	squidpy
 readthedocs = 
-	pydantic<2
+	pydantic>2
 pre = 
 	spatialdata>=0.1.0-pre0
 all = 

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/src/napari_spatialdata/_model.py

@@ -246,7 +246,7 @@ class DataModel:
         return self._adata_layer
 
     @adata_layer.setter
-    def adata_layer(self, adata_layer: str) -> None:
+    def adata_layer(self, adata_layer: str | None) -> None:
         self._adata_layer = adata_layer
 
     @property

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/src/napari_spatialdata/_scatterwidgets.py

@@ -114,7 +114,7 @@ class ScatterListWidget(AListWidget):
         elif self.getAttribute() == "obsm":
             if TYPE_CHECKING:
                 assert isinstance(text, int | str)
-            self.text = text  # type: ignore[assignment]
+            self.text = text
             super().setIndex(text)
 
     @property

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/src/napari_spatialdata/_version.py

@@ -1,7 +1,14 @@
 # file generated by setuptools-scm
 # don't change, don't track in version control
 
-__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
 
 TYPE_CHECKING = False
 if TYPE_CHECKING:
@@ -9,13 +16,19 @@ if TYPE_CHECKING:
     from typing import Union
 
     VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
 else:
     VERSION_TUPLE = object
+    COMMIT_ID = object
 
 version: str
 __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
 
-__version__ = version = '0.5.6'
-__version_tuple__ = version_tuple = (0, 5, 6)
+__version__ = version = '0.6.0'
+__version_tuple__ = version_tuple = (0, 6, 0)
+
+__commit_id__ = commit_id = 'gc95e3e271'

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/src/napari_spatialdata/_view.py

@@ -426,7 +426,7 @@ class QtAdataViewWidget(QWidget):
         super().__init__()
 
         self._viewer = napari_viewer
-        self._model = model if model else napari_viewer.window._dock_widgets["SpatialData"].widget().viewer_model._model
+        self._model = model if model else napari_viewer.window.dock_widgets["SpatialData"].viewer_model.model
 
         self._select_layer()
         self._viewer.layers.selection.events.changed.connect(self._select_layer)

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/src/napari_spatialdata/_viewer.py

@@ -18,7 +18,7 @@ from shapely import Polygon
 from spatialdata import get_element_annotators, get_element_instances
 from spatialdata._core.query.relational_query import _left_join_spatialelement_table
 from spatialdata._types import ArrayLike
-from spatialdata.models import PointsModel, ShapesModel, TableModel, force_2d, get_channels
+from spatialdata.models import PointsModel, ShapesModel, TableModel, force_2d, get_channel_names
 from spatialdata.transformations import Affine, Identity
 
 from napari_spatialdata._model import DataModel
@@ -52,6 +52,12 @@ class SpatialDataViewer(QObject):
         self.sdata = sdata
         self._model = DataModel()
         self._layer_event_caches: dict[str, list[dict[str, Any]]] = {}
+        self.viewer.bind_key("Ctrl-L", self._inherit_metadata, overwrite=True)
+
+        logger.warning(
+            "Due to Shift-L being used as shortcut in napari, it is being deprecated and might not link a new layer"
+            " to an existing SpatialData object in the viewer. Please use ⌘-L on MacOS or else Ctrl-L.",
+        )
         self.viewer.bind_key("Shift-L", self._inherit_metadata, overwrite=True)
         self.viewer.bind_key("Shift-E", self._save_to_sdata, overwrite=True)
         self.viewer.layers.events.inserted.connect(self._on_layer_insert)
@@ -467,7 +473,7 @@ class SpatialDataViewer(QObject):
         affine = _get_transform(sdata.images[original_name], selected_cs)
         rgb_image, rgb = _adjust_channels_order(element=sdata.images[original_name])
 
-        channels = ("RGB(A)",) if rgb else get_channels(sdata.images[original_name])
+        channels = ("RGB(A)",) if rgb else get_channel_names(sdata.images[original_name])
 
         adata = AnnData(shape=(0, len(channels)), var=pd.DataFrame(index=channels))
 

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/src/napari_spatialdata/utils/_test_utils.py

@@ -71,26 +71,22 @@ def click_list_widget_item(
             raise ValueError(f"{click} is not a valid click")
 
 
-def take_screenshot(viewer: napari.Viewer, canvas_only: bool = False) -> ArrayLike | Any:
-    """Take screenshot of the Napari viewer.
+def export_figure(viewer: napari.Viewer) -> ArrayLike | Any:
+    """Export figure from the data displayed in the Napari viewer.
 
     Parameters
     ----------
     viewer
         Instance of napari Viewer.
-    canvas_only
-        If True, only the canvas is saved, not the viewer window.
 
     Returns
     -------
-    The screenshot as an array.
+    The exported figure as an array.
     """
-    logger.info("Taking screenshot of viewer")
-    # to distinguish between the black of the image background and the black of the napari background (now white)
-    # TODO (melonora): remove when napari allows for getting rid of margins.
+    logger.info("Export figure of data in viewer canvas")
     old_theme = viewer.theme
     viewer.theme = "light"
-    interactive_screenshot = viewer.screenshot(canvas_only=canvas_only, size=(202, 284))
+    interactive_screenshot = viewer.export_figure()
     viewer.theme = old_theme
     viewer.close()
 

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/src/napari_spatialdata/utils/_utils.py

@@ -487,7 +487,7 @@ def get_napari_version() -> packaging.version.Version:
 
 
 @contextmanager
-def block_signals(widget: QObject) -> Generator[None, None, None]:
+def block_signals(widget: QObject) -> Generator[None]:
     try:
         widget.blockSignals(True)
         yield

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/src/napari_spatialdata.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napari-spatialdata
-Version: 0.5.6
+Version: 0.6.0
 Summary: Interactive visualization of spatial omics data with napari
 Home-page: https://github.com/scverse/napari-spatialdata.git
 Author: giovanni palla
@@ -27,11 +27,11 @@ License-File: LICENSE
 Requires-Dist: anndata
 Requires-Dist: click
 Requires-Dist: cycler
-Requires-Dist: dask>=2024.4.1
+Requires-Dist: dask<=2024.11.2,>=2024.4.1
 Requires-Dist: geopandas
 Requires-Dist: loguru
 Requires-Dist: matplotlib
-Requires-Dist: napari<0.5.6,>=0.4.19.post1
+Requires-Dist: napari>=0.6.2
 Requires-Dist: napari-matplotlib
 Requires-Dist: numba
 Requires-Dist: numpy
@@ -50,6 +50,8 @@ Requires-Dist: typing_extensions>=4.8.0
 Requires-Dist: vispy
 Requires-Dist: xarray
 Requires-Dist: xarray-datatree
+Provides-Extra: bermuda
+Requires-Dist: bermuda; extra == "bermuda"
 Provides-Extra: test
 Requires-Dist: loguru; extra == "test"
 Requires-Dist: pytest; extra == "test"
@@ -72,7 +74,7 @@ Requires-Dist: sphinx-qt-documentation; extra == "doc"
 Requires-Dist: myst-nb; extra == "doc"
 Requires-Dist: squidpy; extra == "doc"
 Provides-Extra: readthedocs
-Requires-Dist: pydantic<2; extra == "readthedocs"
+Requires-Dist: pydantic>2; extra == "readthedocs"
 Provides-Extra: pre
 Requires-Dist: spatialdata>=0.1.0-pre0; extra == "pre"
 Provides-Extra: all
@@ -91,10 +93,14 @@ Dynamic: license-file
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/napari-spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/napari-spatialdata/main)
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-spatialdata)](https://napari-hub.org/plugins/napari-spatialdata)
 [![DOI](https://zenodo.org/badge/477021400.svg)](https://zenodo.org/badge/latestdoi/477021400)
+[![Documentation][badge-pypi]][link-pypi]
+[![Anaconda-Server Badge](https://anaconda.org/conda-forge/napari-spatialdata/badges/version.svg)](https://anaconda.org/conda-forge/napari-spatialdata)
+
+[badge-pypi]: https://badge.fury.io/py/napari-spatialdata.svg
+[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
 
@@ -104,6 +110,13 @@ 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

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/src/napari_spatialdata.egg-info/requires.txt

@@ -1,11 +1,11 @@
 anndata
 click
 cycler
-dask>=2024.4.1
+dask<=2024.11.2,>=2024.4.1
 geopandas
 loguru
 matplotlib
-napari<0.5.6,>=0.4.19.post1
+napari>=0.6.2
 napari-matplotlib
 numba
 numpy
@@ -28,6 +28,9 @@ xarray-datatree
 [all]
 napari[pyqt5]
 
+[bermuda]
+bermuda
+
 [doc]
 sphinx>=4.5
 sphinx-book-theme>=1.0.0
@@ -47,7 +50,7 @@ squidpy
 spatialdata>=0.1.0-pre0
 
 [readthedocs]
-pydantic<2
+pydantic>2
 
 [test]
 loguru

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/tests/conftest.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import os
 import random
 import string
 from abc import ABC, ABCMeta
@@ -22,7 +23,9 @@ from spatialdata._types import ArrayLike
 from spatialdata.datasets import blobs
 from spatialdata.models import TableModel
 
-from napari_spatialdata.utils._test_utils import save_image, take_screenshot
+from napari_spatialdata.utils._test_utils import export_figure, save_image
+
+OFFSCREEN = os.environ.get("QT_QPA_PLATFORM", "") == "offscreen"
 
 HERE: Path = Path(__file__).parent
 
@@ -214,7 +217,7 @@ class PlotTester(ABC):
         out_path = ACTUAL / f"{basename}.png"
 
         viewer = napari.current_viewer()
-        save_image(take_screenshot(viewer, canvas_only=True), out_path)
+        save_image(export_figure(viewer), str(out_path))
 
         if tolerance is None:
             # see https://github.com/theislab/squidpy/pull/302

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/tests/test_cli.py

@@ -1,5 +1,6 @@
 from pathlib import Path
 
+import pytest
 from click.testing import CliRunner
 from napari.viewer import Viewer
 from spatialdata.datasets import blobs
@@ -14,6 +15,7 @@ def test_view_exists():
     Viewer.close_all()
 
 
+@pytest.mark.usefixtures("mock_app_model")
 def test_view_path_not_exists():
     runner = CliRunner()
     with runner.isolated_filesystem():
@@ -26,6 +28,8 @@ def test_view_path_not_exists():
         Viewer.close_all()
 
 
+# added due to this https://github.com/napari/napari/issues/8214#issuecomment-3188565917
+@pytest.mark.usefixtures("mock_app_model")
 def test_view_path_is_dir():
     runner = CliRunner()
     with runner.isolated_filesystem():

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/tests/test_interactive.py

@@ -11,13 +11,15 @@ from spatialdata import SpatialData
 from spatialdata.models import Image2DModel
 
 from napari_spatialdata._interactive import Interactive
-from tests.conftest import PlotTester, PlotTesterMeta
+from tests.conftest import OFFSCREEN, PlotTester, PlotTesterMeta
 
 ARM_PROBLEM = (
     parse_version(version("numpy")) < parse_version("2") and sys.platform == "darwin" and platform.machine() == "arm64"
 )
 
 
+@pytest.mark.skipif(OFFSCREEN, reason="Not running in offscreen mode")
+@pytest.mark.usefixtures("mock_app_model")
 class TestImages(PlotTester, metaclass=PlotTesterMeta):
     def test_plot_can_add_element_image(self, sdata_blobs: SpatialData):
         blobs_image = Image2DModel.parse(sdata_blobs["blobs_image"], c_coords=("r", "g", "b"))
@@ -51,6 +53,8 @@ class TestImages(PlotTester, metaclass=PlotTesterMeta):
         Viewer.close_all()
 
 
+@pytest.mark.skipif(OFFSCREEN, reason="Not running in offscreen mode")
+@pytest.mark.usefixtures("mock_app_model")
 def test_plot_can_add_element_switch_cs(sdata_blobs: SpatialData):
     i = Interactive(sdata=sdata_blobs, headless=True)
     i.add_element(element="blobs_image", element_coordinate_system="global", view_element_system=True)
@@ -59,6 +63,8 @@ def test_plot_can_add_element_switch_cs(sdata_blobs: SpatialData):
     Viewer.close_all()
 
 
+@pytest.mark.skipif(OFFSCREEN, reason="Not running in offscreen mode")
+@pytest.mark.usefixtures("mock_app_model")
 class TestInteractive(PlotTester, metaclass=PlotTesterMeta):
     def test_get_layer_existing(self, sdata_blobs: SpatialData):
         i = Interactive(sdata=sdata_blobs, headless=True)
@@ -88,6 +94,7 @@ class TestInteractive(PlotTester, metaclass=PlotTesterMeta):
         Viewer.close_all()
 
 
+@pytest.mark.skipif(OFFSCREEN, reason="Not running in offscreen mode")
 @pytest.mark.skipif(ARM_PROBLEM, reason="Test will segfault on ARM with numpy < 2")
 @pytest.mark.use_thread_loader
 def test_load_data_in_thread(make_napari_viewer: Callable[[], Viewer], sdata_blobs: SpatialData, qtbot: QtBot) -> None:

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/tests/test_scatterwidgets.py

@@ -7,6 +7,9 @@ from shapely.geometry import Polygon
 from napari_spatialdata._model import DataModel
 from napari_spatialdata._scatterwidgets import PlotWidget
 
+pytestmark = pytest.mark.usefixtures("mock_app_model")
+
+
 DATA_LEN = 100
 
 
@@ -281,6 +284,8 @@ def test_add_roi_to_plot(qtbot, plot_widget, prepare_discrete_test_data):
     assert len(rois) == 1, "There should be exactly one ROI in the scatter_plot"
 
 
+# sometimes this test fails due to a faulty clean-up, for example in the last failing
+# commit here: https://github.com/scverse/napari-spatialdata/pull/360
 def test_remove_roi_double_click(qtbot, plot_widget, prepare_discrete_test_data):
     """Test changing coordinates and removing ROI."""
     roi = pg.RectROI([0, 0], [1, 1])

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/tests/test_spatialdata.py

@@ -24,6 +24,7 @@ from napari_spatialdata import QtAdataViewWidget
 from napari_spatialdata._sdata_widgets import CoordinateSystemWidget, ElementWidget, SdataWidget
 from napari_spatialdata.constants import config
 from napari_spatialdata.utils._test_utils import click_list_widget_item, get_center_pos_listitem
+from tests.conftest import OFFSCREEN
 
 RNG = np.random.default_rng(seed=0)
 
@@ -94,6 +95,7 @@ def test_sdatawidget_labels(qtbot, make_napari_viewer: Any, blobs_extra_cs: Spat
     assert widget.viewer_model.viewer.layers[0].metadata.get("region_key") is not None
 
 
+@pytest.mark.skipif(OFFSCREEN, reason="Not running in offscreen mode")
 def test_sdatawidget_points(caplog, make_napari_viewer: Any, blobs_extra_cs: SpatialData):
     config.POINT_THRESHOLD = 400
     blobs_extra_cs.points["many_points"] = PointsModel.parse(
@@ -133,7 +135,7 @@ def test_sdatawidget_points(caplog, make_napari_viewer: Any, blobs_extra_cs: Spa
     with caplog.at_level(logging.INFO):
         assert (
             "Subsampling points because the number of points exceeds the currently supported 400."
-            in caplog.records[0].message
+            in caplog.records[1].message
         )
     assert widget.viewer_model.viewer.layers[1].metadata.get("adata").n_obs == 400
     del blobs_extra_cs.points["many_points"]

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/tests/test_utils.py

@@ -15,6 +15,7 @@ from napari_spatialdata.utils._utils import (
     _position_cluster_labels,
     _set_palette,
 )
+from tests.conftest import OFFSCREEN
 
 
 def test_get_categorical(adata_labels: AnnData):
@@ -84,6 +85,7 @@ def test_min_max_norm(vec: np.ndarray) -> None:
     assert (out.min(), out.max()) == (0, 1)
 
 
+@pytest.mark.skipif(OFFSCREEN, reason="Not running in offscreen mode")
 def test_logger(caplog, prepare_continuous_test_data, adata_labels: AnnData, make_napari_viewer: Any):
     from napari_spatialdata._model import DataModel
     from napari_spatialdata._scatterwidgets import PlotWidget

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/tests/test_viewer.py

@@ -1,4 +1,5 @@
 import re
+import sys
 from pathlib import Path
 
 import numpy as np
@@ -32,7 +33,10 @@ def test_metadata_inheritance(qtbot, make_napari_viewer: any):
     layers = widget.viewer_model.viewer.layers
     sdatas = [layer.metadata["sdata"] for layer in layers if "sdata" in layer.metadata]
     assert all(sdatas[0] is sdata for sdata in sdatas[1:])
-    qtbot.keyPress(viewer.window._qt_viewer, Qt.Key_L, Qt.ShiftModifier)
+    if sys.platform == "darwin":
+        qtbot.keyPress(viewer.window._qt_viewer, Qt.Key_L, Qt.MetaModifier)
+    else:
+        qtbot.keyPress(viewer.window._qt_viewer, Qt.Key_L, Qt.ControlModifier)
 
     # Now we did let the shapes layer inherit sdata from another layer. The number of unique spatialdata objects
     # should still be one.

{napari_spatialdata-0.5.6 → napari_spatialdata-0.6.0}/tests/test_widgets.py

@@ -91,7 +91,7 @@ def test_change_layer(
     sdata_blobs: SpatialData,
 ) -> None:
     table = sdata_blobs["table"].copy()
-    table.obs["region"] = "blobs_labels"
+    table.obs["region"] = pd.Categorical(["blobs_labels"] * table.n_obs)
     table.uns["spatialdata_attrs"]["region"] = "blobs_labels"
     table.var_names = pd.Index([i + "_second" for i in table.var_names])
     sdata_blobs["second_table"] = table
@@ -267,6 +267,7 @@ def test_layer_selection(make_napari_viewer: Any, image: ArrayLike, widget: Any,
     assert widget.model.adata.n_obs == 0
 
 
+@pytest.mark.usefixtures("mock_app_model")
 def test_export_no_rois(adata_labels):
     """Test export for no rois situation."""
 
@@ -277,6 +278,7 @@ def test_export_no_rois(adata_labels):
     assert scatter_widget.status_label.text() == "Status: No rois selected."
 
 
+@pytest.mark.usefixtures("mock_app_model")
 def test_export_no_name(adata_labels, mocker):
     """Test export - no column name provided."""
 
@@ -290,6 +292,7 @@ def test_export_no_name(adata_labels, mocker):
     assert scatter_widget._model.adata.obs.equals(adata_labels.obs)
 
 
+@pytest.mark.usefixtures("mock_app_model")
 def test_new_annotation(adata_labels, annotation_values, mocker):
     """Test export - adding a new annotation."""
 
@@ -304,6 +307,7 @@ def test_new_annotation(adata_labels, annotation_values, mocker):
     assert np.array_equal(scatter_widget._model.adata.obs.test, annotation_values)
 
 
+@pytest.mark.usefixtures("mock_app_model")
 def test_old_annotation(adata_labels, annotation_values, mocker):
     """Test updating existing annotation."""