new test datasets

scverse · Dec 10, 2024 · 5491545 · 5491545
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commit 5491545
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Showing 2 changed files with 21 additions and 4 deletions.
diff --git a/.github/workflows/prepare_test_data.yaml b/.github/workflows/prepare_test_data.yaml
@@ -18,15 +18,29 @@ jobs:
               run: |
                   mkdir -p ./data
                   cd ./data
+
+                  # 10x Genomics Xenium 2.0.0
                   curl -O https://cf.10xgenomics.com/samples/xenium/2.0.0/Xenium_V1_human_Breast_2fov/Xenium_V1_human_Breast_2fov_outs.zip
                   curl -O https://cf.10xgenomics.com/samples/xenium/2.0.0/Xenium_V1_human_Lung_2fov/Xenium_V1_human_Lung_2fov_outs.zip
 
+                  # 10x Genomics Xenium 3.0.0 (5K) Mouse ileum, multimodal cell segmentation
+                  curl -O https://cf.10xgenomics.com/samples/xenium/3.0.0/Xenium_Prime_MultiCellSeg_Mouse_Ileum_tiny/Xenium_Prime_MultiCellSeg_Mouse_Ileum_tiny.zip
+
+                  # 10x Genomics Xenium 3.0.0 (5K) Mouse ileum, nuclear expansion
+                  curl -O https://cf.10xgenomics.com/samples/xenium/3.0.0/Xenium_Prime_Mouse_Ileum_tiny/Xenium_Prime_Mouse_Ileum_tiny_outs.zip
+
+                  # Spatial Genomics seqFISH v2
+                  curl -O https://s3.embl.de/spatialdata/raw_data/seqfish-2-test-dataset.zip
+
             - name: Unzip files
               run: |
-                  unzip ./data/Xenium_V1_human_Breast_2fov_outs.zip -d ./data/Xenium_V1_human_Breast_2fov_outs
-                  unzip ./data/Xenium_V1_human_Lung_2fov_outs.zip -d ./data/Xenium_V1_human_Lung_2fov_outs
-                  rm ./data/Xenium_V1_human_Breast_2fov_outs.zip
-                  rm ./data/Xenium_V1_human_Lung_2fov_outs.zip
+                  cd ./data
+                  for file in *.zip; do
+                      dir="${file%.zip}"
+                      mkdir -p "$dir"
+                      unzip "$file" -d "$dir"
+                      rm "$file"
+                  done
 
             - name: Upload artifacts
               uses: actions/upload-artifact@v3

diff --git a/tests/test_xenium.py b/tests/test_xenium.py
@@ -63,3 +63,6 @@ def test_example_data(dataset: str, expected: str) -> None:
     extent = get_extent(sdata, exact=False)
     extent = {ax: (math.floor(extent[ax][0]), math.ceil(extent[ax][1])) for ax in extent}
     assert str(extent) == expected
+
+
+# TODO: add tests for Xenium 3.0.0