From 5491545abc4f914b778cdcf979ed6d77c7975531 Mon Sep 17 00:00:00 2001
From: Luca Marconato <m.lucalmer@gmail.com>
Date: Tue, 10 Dec 2024 16:22:09 +0100
Subject: [PATCH] new test datasets

---
 .github/workflows/prepare_test_data.yaml | 22 ++++++++++++++++++----
 tests/test_xenium.py                     |  3 +++
 2 files changed, 21 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/prepare_test_data.yaml b/.github/workflows/prepare_test_data.yaml
index 10d58c44..6c468b3a 100644
--- 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
index fedb824b..2fb35ce1 100644
--- 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