scverse · timtreis · May 16, 2024 · May 16, 2024 · May 16, 2024 · May 16, 2024
diff --git a/pyproject.toml b/pyproject.toml
@@ -47,6 +47,7 @@ docs = [
 test = [
     "pytest",
     "pytest-cov",
+    "pooch", # for scipy.datasets module
 ]
 # this will be used by readthedocs and will make pip also look for pre-releases, generally installing the latest available version
 pre = [

diff --git a/pyproject.toml.rej b/pyproject.toml.rej
diff --git a/tests/_images/Extent_correct_plot_after_transformations.png b/tests/_images/Extent_correct_plot_after_transformations.png
diff --git a/tests/_images/Extent_extent_calculation_respects_element_selection_circles.png b/tests/_images/Extent_extent_calculation_respects_element_selection_circles.png
diff --git a/...s/Extent_extent_calculation_respects_element_selection_circles_and_polygons.png b/...s/Extent_extent_calculation_respects_element_selection_circles_and_polygons.png
diff --git a/tests/_images/Extent_extent_calculation_respects_element_selection_polygons.png b/tests/_images/Extent_extent_calculation_respects_element_selection_polygons.png
diff --git a/tests/_images/Extent_extent_of_img_full_canvas.png b/tests/_images/Extent_extent_of_img_full_canvas.png
diff --git a/tests/_images/Extent_extent_of_img_is_correct_after_spatial_query.png b/tests/_images/Extent_extent_of_img_is_correct_after_spatial_query.png
diff --git a/tests/_images/Extent_extent_of_partial_canvas_on_full_canvas.png b/tests/_images/Extent_extent_of_partial_canvas_on_full_canvas.png
diff --git a/tests/_images/Extent_extent_of_points_partial_canvas.png b/tests/_images/Extent_extent_of_points_partial_canvas.png
diff --git a/tests/_images/Extent_extent_of_polygons_is_correct_after_spatial_query.png b/tests/_images/Extent_extent_of_polygons_is_correct_after_spatial_query.png
diff --git a/tests/_images/Extent_extent_of_polygons_on_img_is_correct_after_spatial_query.png b/tests/_images/Extent_extent_of_polygons_on_img_is_correct_after_spatial_query.png
diff --git a/tests/_images/Images_can_do_rasterization.png b/tests/_images/Images_can_do_rasterization.png
diff --git a/tests/_images/Images_can_normalize_image.png b/tests/_images/Images_can_normalize_image.png
diff --git a/tests/_images/Images_can_pass_cmap.png b/tests/_images/Images_can_pass_cmap.png
diff --git a/tests/_images/Images_can_pass_cmap_list.png b/tests/_images/Images_can_pass_cmap_list.png
diff --git a/tests/_images/Images_can_pass_cmap_to_each_channel.png b/tests/_images/Images_can_pass_cmap_to_each_channel.png
diff --git a/tests/_images/Images_can_pass_cmap_to_single_channel.png b/tests/_images/Images_can_pass_cmap_to_single_channel.png
diff --git a/tests/_images/Images_can_pass_color_to_each_channel.png b/tests/_images/Images_can_pass_color_to_each_channel.png
diff --git a/tests/_images/Images_can_pass_color_to_single_channel.png b/tests/_images/Images_can_pass_color_to_single_channel.png
diff --git a/tests/_images/Images_can_pass_str_cmap.png b/tests/_images/Images_can_pass_str_cmap.png
diff --git a/tests/_images/Images_can_pass_str_cmap_list.png b/tests/_images/Images_can_pass_str_cmap_list.png
diff --git a/tests/_images/Images_can_render_a_single_channel_from_image.png b/tests/_images/Images_can_render_a_single_channel_from_image.png
diff --git a/tests/_images/Images_can_render_given_scale_of_multiscale_image.png b/tests/_images/Images_can_render_given_scale_of_multiscale_image.png
diff --git a/tests/_images/Images_can_render_image.png b/tests/_images/Images_can_render_image.png
diff --git a/tests/_images/Images_can_render_multiscale_image.png b/tests/_images/Images_can_render_multiscale_image.png
diff --git a/tests/_images/Images_can_render_two_channels_from_image.png b/tests/_images/Images_can_render_two_channels_from_image.png
diff --git a/tests/_images/Images_can_stack_render_images.png b/tests/_images/Images_can_stack_render_images.png
diff --git a/tests/_images/Images_can_stop_rasterization_with_scale_full.png b/tests/_images/Images_can_stop_rasterization_with_scale_full.png
diff --git a/tests/_images/Labels_can_color_labels.png b/tests/_images/Labels_can_color_labels.png
diff --git a/tests/_images/Labels_can_color_labels_by_continuous_variable.png b/tests/_images/Labels_can_color_labels_by_continuous_variable.png
diff --git a/tests/_images/Labels_can_do_rasterization.png b/tests/_images/Labels_can_do_rasterization.png
diff --git a/tests/_images/Labels_can_render_given_scale_of_multiscale_labels.png b/tests/_images/Labels_can_render_given_scale_of_multiscale_labels.png
diff --git a/tests/_images/Labels_can_render_labels.png b/tests/_images/Labels_can_render_labels.png
diff --git a/tests/_images/Labels_can_render_multiscale_labels.png b/tests/_images/Labels_can_render_multiscale_labels.png
diff --git a/tests/_images/Labels_can_stack_render_labels.png b/tests/_images/Labels_can_stack_render_labels.png
diff --git a/tests/_images/Labels_can_stop_rasterization_with_scale_full.png b/tests/_images/Labels_can_stop_rasterization_with_scale_full.png
diff --git a/tests/_images/Labels_label_categorical_color.png b/tests/_images/Labels_label_categorical_color.png
diff --git a/tests/_images/Labels_multiscale_label_categorical_color.png b/tests/_images/Labels_multiscale_label_categorical_color.png
diff --git a/.../_images/NotebooksTransformations_can_render_transformations_raccoon_affine.png b/.../_images/NotebooksTransformations_can_render_transformations_raccoon_affine.png
diff --git a/...ges/NotebooksTransformations_can_render_transformations_raccoon_composition.png b/...ges/NotebooksTransformations_can_render_transformations_raccoon_composition.png
diff --git a/..._images/NotebooksTransformations_can_render_transformations_raccoon_inverse.png b/..._images/NotebooksTransformations_can_render_transformations_raccoon_inverse.png
diff --git a/..._images/NotebooksTransformations_can_render_transformations_raccoon_mapaxis.png b/..._images/NotebooksTransformations_can_render_transformations_raccoon_mapaxis.png
diff --git a/..._images/NotebooksTransformations_can_render_transformations_raccoon_overlay.png b/..._images/NotebooksTransformations_can_render_transformations_raccoon_overlay.png
diff --git a/...images/NotebooksTransformations_can_render_transformations_raccoon_rotation.png b/...images/NotebooksTransformations_can_render_transformations_raccoon_rotation.png
diff --git a/...s/_images/NotebooksTransformations_can_render_transformations_raccoon_scale.png b/...s/_images/NotebooksTransformations_can_render_transformations_raccoon_scale.png
diff --git a/...s/_images/NotebooksTransformations_can_render_transformations_raccoon_split.png b/...s/_images/NotebooksTransformations_can_render_transformations_raccoon_split.png
diff --git a/...ges/NotebooksTransformations_can_render_transformations_raccoon_translation.png b/...ges/NotebooksTransformations_can_render_transformations_raccoon_translation.png
diff --git a/tests/_images/Points_can_filter_with_groups.png b/tests/_images/Points_can_filter_with_groups.png
diff --git a/tests/_images/Points_can_filter_with_groups_default_palette.png b/tests/_images/Points_can_filter_with_groups_default_palette.png
diff --git a/tests/_images/Points_can_render_points.png b/tests/_images/Points_can_render_points.png
diff --git a/tests/_images/Points_can_stack_render_points.png b/tests/_images/Points_can_stack_render_points.png
diff --git a/tests/_images/Points_color_recognises_actual_color_as_color.png b/tests/_images/Points_color_recognises_actual_color_as_color.png
diff --git a/tests/_images/Points_coloring_with_cmap.png b/tests/_images/Points_coloring_with_cmap.png
diff --git a/tests/_images/Points_coloring_with_palette.png b/tests/_images/Points_coloring_with_palette.png
diff --git a/tests/_images/Points_points_categorical_color.png b/tests/_images/Points_points_categorical_color.png
diff --git a/tests/_images/Points_points_coercable_categorical_color.png b/tests/_images/Points_points_coercable_categorical_color.png
diff --git a/tests/_images/Shapes_can_color_from_geodataframe.png b/tests/_images/Shapes_can_color_from_geodataframe.png
diff --git a/tests/_images/Shapes_can_color_two_queried_shapes_elements_by_annotation.png b/tests/_images/Shapes_can_color_two_queried_shapes_elements_by_annotation.png
diff --git a/tests/_images/Shapes_can_color_two_shapes_elements_by_annotation.png b/tests/_images/Shapes_can_color_two_shapes_elements_by_annotation.png
diff --git a/tests/_images/Shapes_can_filter_with_groups.png b/tests/_images/Shapes_can_filter_with_groups.png
diff --git a/tests/_images/Shapes_can_plot_queried_with_annotation_despite_random_shuffling.png b/tests/_images/Shapes_can_plot_queried_with_annotation_despite_random_shuffling.png
diff --git a/tests/_images/Shapes_can_plot_shapes_after_spatial_query.png b/tests/_images/Shapes_can_plot_shapes_after_spatial_query.png
diff --git a/tests/_images/Shapes_can_plot_with_annotation_despite_random_shuffling.png b/tests/_images/Shapes_can_plot_with_annotation_despite_random_shuffling.png
diff --git a/tests/_images/Shapes_can_render_circles.png b/tests/_images/Shapes_can_render_circles.png
diff --git a/tests/_images/Shapes_can_render_circles_with_colored_outline.png b/tests/_images/Shapes_can_render_circles_with_colored_outline.png
diff --git a/tests/_images/Shapes_can_render_circles_with_default_outline_width.png b/tests/_images/Shapes_can_render_circles_with_default_outline_width.png
diff --git a/tests/_images/Shapes_can_render_circles_with_outline.png b/tests/_images/Shapes_can_render_circles_with_outline.png
diff --git a/tests/_images/Shapes_can_render_circles_with_specified_outline_width.png b/tests/_images/Shapes_can_render_circles_with_specified_outline_width.png
diff --git a/tests/_images/Shapes_can_render_empty_geometry.png b/tests/_images/Shapes_can_render_empty_geometry.png
diff --git a/tests/_images/Shapes_can_render_multipolygons.png b/tests/_images/Shapes_can_render_multipolygons.png
diff --git a/tests/_images/Shapes_can_render_polygons.png b/tests/_images/Shapes_can_render_polygons.png
diff --git a/tests/_images/Shapes_can_render_polygons_with_outline.png b/tests/_images/Shapes_can_render_polygons_with_outline.png
diff --git a/tests/_images/Shapes_can_render_polygons_with_rgb_colored_outline.png b/tests/_images/Shapes_can_render_polygons_with_rgb_colored_outline.png
diff --git a/tests/_images/Shapes_can_render_polygons_with_rgba_colored_outline.png b/tests/_images/Shapes_can_render_polygons_with_rgba_colored_outline.png
diff --git a/tests/_images/Shapes_can_render_polygons_with_str_colored_outline.png b/tests/_images/Shapes_can_render_polygons_with_str_colored_outline.png
diff --git a/tests/_images/Shapes_can_scale_shapes.png b/tests/_images/Shapes_can_scale_shapes.png
diff --git a/tests/_images/Shapes_can_stack_render_shapes.png b/tests/_images/Shapes_can_stack_render_shapes.png
diff --git a/tests/_images/Shapes_color_recognises_actual_color_as_color.png b/tests/_images/Shapes_color_recognises_actual_color_as_color.png
diff --git a/tests/_images/Shapes_colorbar_can_be_normalised.png b/tests/_images/Shapes_colorbar_can_be_normalised.png
diff --git a/tests/_images/Shapes_colorbar_respects_input_limits.png b/tests/_images/Shapes_colorbar_respects_input_limits.png
diff --git a/tests/_images/Shapes_coloring_with_palette.png b/tests/_images/Shapes_coloring_with_palette.png
diff --git a/tests/_images/Shapes_shapes_categorical_color.png b/tests/_images/Shapes_shapes_categorical_color.png
diff --git a/tests/_images/Shapes_shapes_coercable_categorical_color.png b/tests/_images/Shapes_shapes_coercable_categorical_color.png
diff --git a/tests/_images/Show_pad_extent_adds_padding.png b/tests/_images/Show_pad_extent_adds_padding.png
diff --git a/tests/_images/Upstream_can_render_transformations_raccoon_mapaxis.png b/tests/_images/Upstream_can_render_transformations_raccoon_mapaxis.png
diff --git a/tests/_images/Upstream_can_render_transformations_raccoon_overlay.png b/tests/_images/Upstream_can_render_transformations_raccoon_overlay.png
diff --git a/tests/_images/Upstream_can_render_transformations_raccoon_scale.png b/tests/_images/Upstream_can_render_transformations_raccoon_scale.png
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -14,7 +14,6 @@
 from geopandas import GeoDataFrame
 from matplotlib.testing.compare import compare_images
 from multiscale_spatial_image import MultiscaleSpatialImage
-from numpy.random import default_rng
 from shapely.geometry import MultiPolygon, Polygon
 from spatial_image import SpatialImage
 from spatialdata import SpatialData
@@ -35,9 +34,9 @@
 EXPECTED = HERE / "_images"
 ACTUAL = HERE / "figures"
 TOL = 60
-DPI = 40
+DPI = 80
 
-RNG = default_rng()
+RNG = np.random.default_rng(seed=42)
 
 
 @pytest.fixture()
@@ -375,12 +374,19 @@ def compare(cls, basename: str, tolerance: Optional[float] = None):
         ACTUAL.mkdir(parents=True, exist_ok=True)
         out_path = ACTUAL / f"{basename}.png"
 
+        width, height = 400, 300  # fixed dimensions so runners don't change
+        fig = plt.gcf()
+        fig.set_size_inches(width / DPI, height / DPI)
+        fig.set_dpi(DPI)
+
+        # Apply constrained layout and save the plot
+        fig.set_constrained_layout(True)
         plt.savefig(out_path, dpi=DPI)
         plt.close()
 
         if tolerance is None:
             # see https://github.com/scverse/squidpy/pull/302
-            tolerance = 2 * TOL if "Napari" in str(basename) else TOL
+            tolerance = 2 * TOL if "Napari" in basename else TOL
 
         res = compare_images(str(EXPECTED / f"{basename}.png"), str(out_path), tolerance)
 

diff --git a/tests/pl/test_get_extent.py b/tests/pl/test_get_extent.py
@@ -11,12 +11,14 @@
 from spatialdata.models import PointsModel, ShapesModel
 from spatialdata.transformations import Affine, set_transformation
 
-from tests.conftest import PlotTester, PlotTesterMeta
+from tests.conftest import DPI, PlotTester, PlotTesterMeta
 
+RNG = np.random.default_rng(seed=42)
 sc.pl.set_rcParams_defaults()
-sc.set_figure_params(dpi=40, color_map="viridis")
+sc.set_figure_params(dpi=DPI, color_map="viridis")
 matplotlib.use("agg")  # same as GitHub action runner
 _ = spatialdata_plot
+plt.tight_layout()
 
 # WARNING:
 # 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta

diff --git a/tests/pl/test_render_images.py b/tests/pl/test_render_images.py
@@ -1,14 +1,16 @@
 import dask.array as da
 import matplotlib
+import numpy as np
 import scanpy as sc
 import spatialdata_plot  # noqa: F401
 from spatial_image import to_spatial_image
 from spatialdata import SpatialData
 
-from tests.conftest import PlotTester, PlotTesterMeta
+from tests.conftest import DPI, PlotTester, PlotTesterMeta
 
+RNG = np.random.default_rng(seed=42)
 sc.pl.set_rcParams_defaults()
-sc.set_figure_params(dpi=40, color_map="viridis")
+sc.set_figure_params(dpi=DPI, color_map="viridis")
 matplotlib.use("agg")  # same as GitHub action runner
 _ = spatialdata_plot
 

diff --git a/tests/pl/test_render_labels.py b/tests/pl/test_render_labels.py
@@ -10,14 +10,14 @@
 from spatialdata._core.query.relational_query import _get_unique_label_values_as_index
 from spatialdata.models import TableModel
 
-from tests.conftest import PlotTester, PlotTesterMeta
+from tests.conftest import DPI, PlotTester, PlotTesterMeta
 
+RNG = np.random.default_rng(seed=42)
 sc.pl.set_rcParams_defaults()
-sc.set_figure_params(dpi=40, color_map="viridis")
+sc.set_figure_params(dpi=DPI, color_map="viridis")
 matplotlib.use("agg")  # same as GitHub action runner
 _ = spatialdata_plot
 
-RNG = np.random.default_rng(seed=42)
 # WARNING:
 # 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
 # 2. tests which produce a plot must be prefixed with `test_plot_`
@@ -72,7 +72,7 @@ def test_plot_can_stack_render_labels(self, sdata_blobs: SpatialData):
                 elements="blobs_labels", na_color="red", fill_alpha=1, outline_alpha=0, outline=False
             )
             .pl.render_labels(
-                elements="blobs_labels", na_color="blue", fill_alpha=0, outline_alpha=1, outline=True, contour_px=10
+                elements="blobs_labels", na_color="blue", fill_alpha=0, outline_alpha=1, outline=True, contour_px=15
             )
             .pl.show()
         )
@@ -118,6 +118,9 @@ def test_plot_label_categorical_color(self, sdata_blobs: SpatialData):
         sdata_blobs.pl.render_labels("blobs_labels", color="category").pl.show()
 
     def test_plot_multiscale_label_categorical_color(self, sdata_blobs: SpatialData):
+        # recreate RNG to get same plot acorss 3.9 and 3.10 workers
+        RNG = np.random.default_rng(seed=42)
+
         n_obs = max(_get_unique_label_values_as_index(sdata_blobs["blobs_multiscale_labels"]))
         adata = AnnData(
             RNG.normal(size=(n_obs, 10)), obs=pd.DataFrame(RNG.normal(size=(n_obs, 3)), columns=["a", "b", "c"])
@@ -133,19 +136,3 @@ def test_plot_multiscale_label_categorical_color(self, sdata_blobs: SpatialData)
 
         sdata_blobs["other_table"].obs["category"] = sdata_blobs["other_table"].obs["category"].astype("category")
         sdata_blobs.pl.render_labels("blobs_multiscale_labels", color="category").pl.show()
-
-    # def test_plot_multiscale_label_coercable_categorical_color(self, sdata_blobs: SpatialData):
-    #     n_obs = max(_get_unique_label_values_as_index(sdata_blobs["blobs_multiscale_labels"]))
-    #     adata = AnnData(
-    #         RNG.normal(size=(n_obs, 10)), obs=pd.DataFrame(RNG.normal(size=(n_obs, 3)), columns=["a", "b", "c"])
-    #     )
-    #     adata.obs["instance_id"] = np.arange(adata.n_obs)
-    #     adata.obs["category"] = RNG.choice(["a", "b", "c"], size=adata.n_obs)
-    #     adata.obs["instance_id"] = list(range(adata.n_obs))
-    #     adata.obs["region"] = "blobs_multiscale_labels"
-    #     table = TableModel.parse(
-    #         adata=adata, region_key="region", instance_key="instance_id", region="blobs_multiscale_labels"
-    #     )
-    #     sdata_blobs["other_table"] = table
-    #
-    #     sdata_blobs.pl.render_labels("blobs_multiscale_labels", color="category").pl.show()
diff --git a/tests/pl/test_render_points.py b/tests/pl/test_render_points.py
@@ -7,11 +7,11 @@
 from spatialdata import SpatialData
 from spatialdata.models import TableModel
 
-from tests.conftest import PlotTester, PlotTesterMeta
+from tests.conftest import DPI, PlotTester, PlotTesterMeta
 
 RNG = np.random.default_rng(seed=42)
 sc.pl.set_rcParams_defaults()
-sc.set_figure_params(dpi=40, color_map="viridis")
+sc.set_figure_params(dpi=DPI, color_map="viridis")
 matplotlib.use("agg")  # same as GitHub action runner
 _ = spatialdata_plot
 

diff --git a/tests/pl/test_render_shapes.py b/tests/pl/test_render_shapes.py
@@ -10,14 +10,14 @@
 from spatialdata import SpatialData
 from spatialdata.models import ShapesModel, TableModel
 
-from tests.conftest import PlotTester, PlotTesterMeta
+from tests.conftest import DPI, PlotTester, PlotTesterMeta
 
+RNG = np.random.default_rng(seed=42)
 sc.pl.set_rcParams_defaults()
-sc.set_figure_params(dpi=40, color_map="viridis")
+sc.set_figure_params(dpi=DPI, color_map="viridis")
 matplotlib.use("agg")  # same as GitHub action runner
 _ = spatialdata_plot
 
-RNG = np.random.default_rng(seed=42)
 # WARNING:
 # 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
 # 2. tests which produce a plot must be prefixed with `test_plot_`

diff --git a/tests/pl/test_show.py b/tests/pl/test_show.py
@@ -1,12 +1,14 @@
 import matplotlib
+import numpy as np
 import scanpy as sc
 import spatialdata_plot  # noqa: F401
 from spatialdata import SpatialData
 
-from tests.conftest import PlotTester, PlotTesterMeta
+from tests.conftest import DPI, PlotTester, PlotTesterMeta
 
+RNG = np.random.default_rng(seed=42)
 sc.pl.set_rcParams_defaults()
-sc.set_figure_params(dpi=40, color_map="viridis")
+sc.set_figure_params(dpi=DPI, color_map="viridis")
 matplotlib.use("agg")  # same as GitHub action runner
 _ = spatialdata_plot
 

diff --git a/tests/pl/test_upstream_plots.py b/tests/pl/test_upstream_plots.py
@@ -2,6 +2,7 @@
 
 import matplotlib
 import matplotlib.pyplot as plt
+import numpy as np
 import scanpy as sc
 import spatialdata_plot  # noqa: F401
 from spatialdata import SpatialData
@@ -14,10 +15,11 @@
     set_transformation,
 )
 
-from tests.conftest import PlotTester, PlotTesterMeta
+from tests.conftest import DPI, PlotTester, PlotTesterMeta
 
-sc.pl.set_rcParams_defaults()
-sc.set_figure_params(dpi=40, color_map="viridis")
+RNG = np.random.default_rng(seed=42)
+# sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=DPI, color_map="viridis")
 matplotlib.use("agg")  # same as GitHub action runner
 _ = spatialdata_plot