Merge branch 'main' of https://github.com/scverse/napari-spatialdata

Author: LucaMarconato

.github/release.yml

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

src/napari_spatialdata/_viewer.py

@@ -18,7 +18,7 @@
 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
@@ -473,7 +473,7 @@ def get_sdata_image(self, sdata: SpatialData, key: str, selected_cs: str, multi:
         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))
 

tests/conftest.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import os
 import random
 import string
 from abc import ABC, ABCMeta
@@ -24,6 +25,8 @@
 
 from napari_spatialdata.utils._test_utils import export_figure, save_image
 
+OFFSCREEN = os.environ.get("QT_QPA_PLATFORM", "") == "offscreen"
+
 HERE: Path = Path(__file__).parent
 
 SEED = 42

tests/test_interactive.py

@@ -11,13 +11,14 @@
 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):
@@ -52,6 +53,7 @@ def test_switch_coordinate_system(self, sdata_blobs: SpatialData):
         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)
@@ -61,6 +63,7 @@ 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):
@@ -91,6 +94,7 @@ def test_add_text_to_polygons(self, sdata_blobs: SpatialData):
         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:

tests/test_spatialdata.py

@@ -24,6 +24,7 @@
 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(

tests/test_utils.py

@@ -15,6 +15,7 @@
     _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

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