spatialdata-io/.github/workflows/prepare_test_data.yaml at 433014e81d405ae80810f0eec68f79f56a3d43f4 · scverse/spatialdata-io · GitHub

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name: Prepare test data

on:
    schedule:
        - cron: "0 0 1 * *" # run once a month to prevent artifact expiration
    workflow_dispatch:
    # Uncomment and adjust the branch name if you need to add new datasets to the artifact.
    # It needs to be a branch in the spatialdata-io origin repository, not from a fork.
#    push:
#        branches:
#            - main

jobs:
    prepare-data:
        runs-on: ubuntu-latest

        steps:
            - uses: actions/checkout@v4

            - name: Download test datasets
              run: |
                  mkdir -p ./data
                  cd ./data

                  # -------
                  # the Xenium datasets are licensed as CC BY 4.0, as shown here
                  # https://www.10xgenomics.com/support/software/xenium-onboard-analysis/latest/resources/xenium-example-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
                  # this file seems to be corrupted; skipping it for now
                  # 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

                  # 10x Genomics Xenium 4.0.0 (v1) Human ovary, nuclear expansion
                  curl -O https://cf.10xgenomics.com/samples/xenium/4.0.0/Xenium_V1_Human_Ovary_tiny/Xenium_V1_Human_Ovary_tiny_outs.zip

                  # 10x Genomics Xenium 4.0.0 (v1) Human ovary, multimodal cell segmentation
                  curl -O https://cf.10xgenomics.com/samples/xenium/4.0.0/Xenium_V1_MultiCellSeg_Human_Ovary_tiny/Xenium_V1_MultiCellSeg_Human_Ovary_tiny_outs.zip

                  # 10x Genomics Xenium 4.0.0 (v1+Protein) Human kidney, multimodal cell segmentation
                  curl -O https://cf.10xgenomics.com/samples/xenium/4.0.0/Xenium_V1_Protein_Human_Kidney_tiny/Xenium_V1_Protein_Human_Kidney_tiny_outs.zip

                  # -------
                  # the Visium HD dataset is licensed as CC BY 4.0, as shown here
                  # https://www.10xgenomics.com/support/software/space-ranger/latest/resources/visium-hd-example-data

                  # 10x Genomics Visium HD 4.0.1 3' Mouse Brain Chunk
                  curl -O https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_Tiny_3prime_Dataset/Visium_HD_Tiny_3prime_Dataset_outs.zip

                  # -------
                  # we received written permission to make the following dataset public and integrate it in the CI system of spatialdata-io
                  # Spatial Genomics seqFISH v2
                  curl -O https://s3.embl.de/spatialdata/raw_data/seqfish-2-test-dataset.zip

                  # -------
                  # MACSima OMAP datasets are licensed as CC BY 4.0
                  # OMAP23 for format v1.x.x
                  curl -o OMAP23_small.zip "https://zenodo.org/api/records/18196452/files-archive"

                  # OMAP10 for format v0.x.x
                  curl -o OMAP10_small.zip "https://zenodo.org/api/records/18196366/files-archive"

            - name: Unzip files
              run: |
                  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@v4
              with:
                  name: data
                  path: ./data