Adding a few e2e tests (#99)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: timtreis

src/spatialdata_plot/pl/basic.py

@@ -692,8 +692,15 @@ def show(
                     cs_contents.query(f"cs == '{cs}'")["has_shapes"][0],
                 ]
             ):
-                ax.set_xlim(extent[cs][0], extent[cs][1])
-                ax.set_ylim(extent[cs][3], extent[cs][2])  # (0, 0) is top-left
+                # If the axis already has limits, only expand them but not overwrite
+                x_min, x_max = ax.get_xlim()
+                y_min, y_max = ax.get_ylim()
+                x_min = min(x_min, extent[cs][0])
+                x_max = max(x_max, extent[cs][1])
+                y_min = min(y_min, extent[cs][2])
+                y_max = max(y_max, extent[cs][3])
+                ax.set_xlim(x_min, x_max)
+                ax.set_ylim(y_max, y_min)  # (0, 0) is top-left
 
         if fig_params.fig is not None and save is not None:
             save_fig(fig_params.fig, path=save)

src/spatialdata_plot/pl/utils.py

@@ -9,6 +9,7 @@
 from types import MappingProxyType
 from typing import Any, Literal, Optional, Union
 
+import matplotlib
 import matplotlib.pyplot as plt
 import multiscale_spatial_image as msi
 import numpy as np
@@ -20,7 +21,6 @@
 from cycler import Cycler, cycler
 from matplotlib import colors, patheffects, rcParams
 from matplotlib.axes import Axes
-from matplotlib.cm import get_cmap
 from matplotlib.collections import PatchCollection
 from matplotlib.colors import Colormap, LinearSegmentedColormap, ListedColormap, Normalize, TwoSlopeNorm, to_rgba
 from matplotlib.figure import Figure
@@ -271,13 +271,19 @@ def _get_extent_after_transformations(element: Any, cs_name: str) -> Sequence[in
             for images_key in sdata.images:
                 for e_id in element_ids:
                     if images_key == e_id:
-                        extent[cs_name][e_id] = _get_extent_after_transformations(sdata.images[e_id], cs_name)
+                        if not isinstance(sdata.images[e_id], msi.multiscale_spatial_image.MultiscaleSpatialImage):
+                            extent[cs_name][e_id] = _get_extent_after_transformations(sdata.images[e_id], cs_name)
+                        else:
+                            pass
 
         if has_labels and cs_contents.query(f"cs == '{cs_name}'")["has_labels"][0]:
             for labels_key in sdata.labels:
                 for e_id in element_ids:
                     if labels_key == e_id:
-                        extent[cs_name][e_id] = _get_extent_after_transformations(sdata.labels[e_id], cs_name)
+                        if not isinstance(sdata.labels[e_id], msi.multiscale_spatial_image.MultiscaleSpatialImage):
+                            extent[cs_name][e_id] = _get_extent_after_transformations(sdata.labels[e_id], cs_name)
+                        else:
+                            pass
 
         if has_shapes and cs_contents.query(f"cs == '{cs_name}'")["has_shapes"][0]:
             for shapes_key in sdata.shapes:
@@ -303,7 +309,9 @@ def get_point_bb(
                             sdata.shapes[e_id]["geometry"].apply(lambda geom: geom.geom_type == "Point")
                         ]
                         tmp_polygons = sdata.shapes[e_id][
-                            sdata.shapes[e_id]["geometry"].apply(lambda geom: geom.geom_type == "Polygon")
+                            sdata.shapes[e_id]["geometry"].apply(
+                                lambda geom: geom.geom_type in ["Polygon", "MultiPolygon"]
+                            )
                         ]
 
                         if not tmp_points.empty:
@@ -448,7 +456,7 @@ def _prepare_cmap_norm(
     vcenter: float | None = None,
     **kwargs: Any,
 ) -> CmapParams:
-    cmap = copy(get_cmap(cmap))
+    cmap = copy(matplotlib.colormaps[rcParams["image.cmap"] if cmap is None else cmap])
     cmap.set_bad("lightgray" if na_color is None else na_color)
 
     if isinstance(norm, Normalize):

tests/_images/Images_can_render_image.png

@@ -18,14 +18,9 @@
 #    ".png" is appended to <your_filename>, no need to set it
 
 
-class TestLabels(PlotTester, metaclass=PlotTesterMeta):
-    def test_plot_labels(self, sdata_blobs: SpatialData):
-        # TODO: support multiscale labels
-        if "blobs_multiscale_labels" in sdata_blobs.labels:
-            del sdata_blobs.labels["blobs_multiscale_labels"]
-        sdata_blobs.pl.render_labels(color="channel_2_mean").pl.show()
-
-
 class TestImages(PlotTester, metaclass=PlotTesterMeta):
-    def test_plot_images(self, sdata_blobs: SpatialData):
+    def test_plot_can_render_image(self, sdata_blobs: SpatialData):
         sdata_blobs.pl.render_images(elements="blobs_image").pl.show()
+
+    # def test_plot_can_render_multiscale_image(self, sdata_blobs: SpatialData):
+    #     sdata_blobs.pl.render_images(elements="blobs_multiscale_image").pl.show()

tests/_images/Images_images.png

@@ -0,0 +1,23 @@
+import matplotlib
+import scanpy as sc
+import spatialdata_plot  # noqa: F401
+from spatialdata import SpatialData
+
+from tests.conftest import PlotTester, PlotTesterMeta
+
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=40, color_map="viridis")
+matplotlib.use("agg")  # same as GitHub action runner
+_ = spatialdata_plot
+
+# WARNING:
+# 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
+# 2. tests which produce a plot must be prefixed with `test_plot_`
+# 3. if the tolerance needs to be changed, don't prefix the function with `test_plot_`, but with something else
+#    the comp. function can be accessed as `self.compare(<your_filename>, tolerance=<your_tolerance>)`
+#    ".png" is appended to <your_filename>, no need to set it
+
+
+class TestLabels(PlotTester, metaclass=PlotTesterMeta):
+    def test_plot_labels(self, sdata_blobs: SpatialData):
+        sdata_blobs.pl.render_labels(elements="blobs_labels").pl.show()

tests/_images/Points_points.png

@@ -0,0 +1,23 @@
+import matplotlib
+import scanpy as sc
+import spatialdata_plot  # noqa: F401
+from spatialdata import SpatialData
+
+from tests.conftest import PlotTester, PlotTesterMeta
+
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=40, color_map="viridis")
+matplotlib.use("agg")  # same as GitHub action runner
+_ = spatialdata_plot
+
+# WARNING:
+# 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
+# 2. tests which produce a plot must be prefixed with `test_plot_`
+# 3. if the tolerance needs to be changed, don't prefix the function with `test_plot_`, but with something else
+#    the comp. function can be accessed as `self.compare(<your_filename>, tolerance=<your_tolerance>)`
+#    ".png" is appended to <your_filename>, no need to set it
+
+
+class TestPoints(PlotTester, metaclass=PlotTesterMeta):
+    def test_plot_points(self, sdata_blobs: SpatialData):
+        sdata_blobs.pl.render_points(elements="blobs_points").pl.show()

tests/_images/Shapes_can_render_circles.png

@@ -0,0 +1,26 @@
+import matplotlib
+import scanpy as sc
+import spatialdata_plot  # noqa: F401
+from spatialdata import SpatialData
+
+from tests.conftest import PlotTester, PlotTesterMeta
+
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=40, color_map="viridis")
+matplotlib.use("agg")  # same as GitHub action runner
+_ = spatialdata_plot
+
+# WARNING:
+# 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
+# 2. tests which produce a plot must be prefixed with `test_plot_`
+# 3. if the tolerance needs to be changed, don't prefix the function with `test_plot_`, but with something else
+#    the comp. function can be accessed as `self.compare(<your_filename>, tolerance=<your_tolerance>)`
+#    ".png" is appended to <your_filename>, no need to set it
+
+
+class TestShapes(PlotTester, metaclass=PlotTesterMeta):
+    def test_plot_can_render_circles(self, sdata_blobs: SpatialData):
+        sdata_blobs.pl.render_shapes(element="blobs_circles").pl.show()
+
+    def test_plot_can_render_polygons(self, sdata_blobs: SpatialData):
+        sdata_blobs.pl.render_shapes(element="blobs_polygons").pl.show()

tests/_images/Shapes_can_render_polygons.png

@@ -150,24 +150,3 @@ def test_get_bb_wrong_input_length(sdata, request):
 
     with pytest.raises(ValueError, match="Parameter 'y' must be of length 2."):
         sdata.pp.get_bb((0, 5), (0, 5, 2))
-
-
-# @pytest.mark.parametrize(
-#     "sdata, keys, nrows ",
-#     [
-#         ("full_sdata", "data1", 3),
-#         ("full_sdata", ["data1", "data3"], 23),
-#     ],
-# )
-# def test_table_gets_subset_when_images_are_subset(sdata, keys, nrows, request):
-#     """Tests wether the images inside sdata can be clipped to a bounding box."""
-
-#     sdata = request.getfixturevalue(sdata)
-
-#     assert sdata.table.n_obs == 30
-
-#     new_sdata = sdata.pp.get_elements(keys)
-
-#     print(new_sdata.table)
-
-#     assert len(new_sdata.table.obs) == nrows