[TEST] refactor pytest fixtures to live in one file

Author: sophiamaedler

tests/conftest.py

@@ -0,0 +1,62 @@
+import shutil
+
+import numpy as np
+import pandas as pd
+import pytest
+from anndata import AnnData
+from spatialdata import SpatialData
+from spatialdata.datasets import blobs
+
+rng = np.random.default_rng()
+
+
+@pytest.fixture
+def h5sc_object() -> AnnData:
+    # Two cells, two channels, small images
+    cell_ids = [101, 102, 107, 109]
+    n_cells = 4
+    channel_names = np.array(["seg_all_nucleus", "ch0", "ch1"])
+    channel_mapping = np.array(["mask", "image", "image"])  # or whatever mapping your code expects
+    n_channels = len(channel_names)
+    H, W = 10, 10
+
+    # --- obs ---
+    obs = pd.DataFrame({"scportrait_cell_id": cell_ids}, index=np.arange(n_cells))
+
+    # --- var (channel metadata) ---
+    var = pd.DataFrame(index=np.arange(n_channels).astype("str"))
+    var["channels"] = channel_names
+    var["channel_mapping"] = channel_mapping
+
+    adata = AnnData(obs=obs, var=var)
+    adata.obsm["single_cell_images"] = rng.random((n_cells, n_channels, H, W))
+    adata.uns["single_cell_images"] = {
+        "channel_mapping": channel_mapping,
+        "channel_names": channel_names,
+        "compression": "lzf",
+        "image_size": np.int64(H),
+        "n_cells": np.int64(n_cells),
+        "n_channels": np.int64(n_channels),
+        "n_image_channels": np.int64(n_channels - 1),
+        "n_masks": np.int64(1),
+    }
+
+    yield adata
+
+
+@pytest.fixture()
+def sdata(tmp_path) -> SpatialData:
+    sdata = blobs()
+    # Write to temporary location
+    sdata_path = tmp_path / "sdata.zarr"
+    sdata.write(sdata_path)
+    yield sdata
+    shutil.rmtree(sdata_path)
+
+
+@pytest.fixture
+def sdata_with_labels() -> SpatialData:
+    sdata = blobs()
+    sdata["table"].obs["labelling_categorical"] = sdata["table"].obs["instance_id"].astype("category")
+    sdata["table"].obs["labelling_continous"] = (sdata["table"].obs["instance_id"] > 10).astype(float)
+    return sdata

tests/unit_tests/plotting/test_sdata.py

@@ -10,14 +10,6 @@
 from scportrait.plotting import sdata as plotting
 
 
-@pytest.fixture
-def sdata():
-    sdata = blobs()
-    sdata["table"].obs["labelling_categorical"] = sdata["table"].obs["instance_id"].astype("category")
-    sdata["table"].obs["labelling_continous"] = (sdata["table"].obs["instance_id"] > 10).astype(float)
-    return sdata  # provides images and labels used in tests
-
-
 @pytest.mark.parametrize(
     "channel_names, palette, return_fig, show_fig",
     [
@@ -26,9 +18,9 @@ def sdata():
         ([0, 1], None, False, False),
     ],
 )
-def test_plot_image(sdata, channel_names, palette, return_fig, show_fig):
+def test_plot_image(sdata_with_labels, channel_names, palette, return_fig, show_fig):
     fig = plotting.plot_image(
-        sdata=sdata,
+        sdata=sdata_with_labels,
         image_name="blobs_image",
         channel_names=channel_names,
         palette=palette,
@@ -51,9 +43,9 @@ def test_plot_image(sdata, channel_names, palette, return_fig, show_fig):
         (None, None),  # test only mask overlay without image
     ],
 )
-def test_plot_segmentation_mask(sdata, selected_channels, background_image):
+def test_plot_segmentation_mask(sdata_with_labels, selected_channels, background_image):
     fig = plotting.plot_segmentation_mask(
-        sdata=sdata,
+        sdata=sdata_with_labels,
         masks=["blobs_labels"],
         background_image=background_image,
         selected_channels=selected_channels,
@@ -73,9 +65,9 @@ def test_plot_segmentation_mask(sdata, selected_channels, background_image):
         (True, "labelling_continous"),
     ],
 )
-def test_plot_labels(sdata, vectorized, color):
+def test_plot_labels(sdata_with_labels, vectorized, color):
     fig = plotting.plot_labels(
-        sdata=sdata,
+        sdata=sdata_with_labels,
         label_layer="blobs_labels",
         vectorized=vectorized,
         color=color,

tests/unit_tests/tools/sdata/test_write.py

@@ -7,16 +7,6 @@
 from spatialdata.datasets import blobs
 
 
-@pytest.fixture()
-def sdata(tmp_path):
-    sdata = blobs()
-    # Write to temporary location
-    sdata_path = tmp_path / "sdata.zarr"
-    sdata.write(sdata_path)
-    yield sdata
-    shutil.rmtree(sdata_path)
-
-
 @pytest.fixture()
 def sdata_path(tmp_path):
     # Write to temporary location