From MuData to SpatialData #353
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| name: Run tutorials (spatial preprocessing) | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| env: | |
| debug: 'true' | |
| jobs: | |
| spatial_preprocessing: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] # , "macos-latest", "windows-latest" | |
| python-version: ["3.10"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: File tree | |
| if: env.debug == 'true' | |
| run: tree | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| auto-activate-base: true | |
| auto-update-conda: true | |
| channels: conda-forge | |
| channel-priority: strict | |
| activate-environment: pipeline_env | |
| environment-file: pipeline_env.yaml | |
| - name: Install Panpipes | |
| shell: bash -el {0} | |
| run: | | |
| pip install .[spatial] | |
| conda list | |
| - name: Conda info | |
| if: env.debug == 'true' | |
| shell: bash -el {0} | |
| run: conda info | |
| - name: Conda list | |
| if: env.debug == 'true' | |
| shell: pwsh | |
| run: conda list | |
| - name: Preparing the data | |
| run: | | |
| mkdir spatial spatial/preprocess spatial/preprocess/data | |
| cd spatial/preprocess/data | |
| curl -L -o V1_Human_Heart_unfilt.zarr.zip https://figshare.com/ndownloader/files/52236521 | |
| unzip V1_Human_Heart_unfilt.zarr.zip | |
| rm V1_Human_Heart_unfilt.zarr.zip | |
| curl -L -o V1_Human_Lymph_Node_unfilt.zarr.zip https://figshare.com/ndownloader/files/52236575 | |
| unzip V1_Human_Lymph_Node_unfilt.zarr.zip | |
| rm V1_Human_Lymph_Node_unfilt.zarr.zip | |
| # Note: we run the following to test that the commands works | |
| - name: Preparing the configuration file | |
| shell: bash -el {0} | |
| run: | | |
| cd spatial/preprocess | |
| panpipes preprocess_spatial config | |
| - name: Edit the submission file | |
| run: | | |
| cd spatial/preprocess | |
| curl -o pipeline.yml https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/main/docs/preprocess_spatial_data/pipeline.yml | |
| - name: Replace template contents in configuration file | |
| run: | | |
| cd spatial/preprocess | |
| sed -i 's+../ingestion/qc.data/+./data/+g' pipeline.yml | |
| - name: File tree | |
| if: env.debug == 'true' | |
| run: tree spatial/preprocess | |
| - name: Review pipeline tasks | |
| shell: bash -el {0} | |
| run: | | |
| cd spatial/preprocess | |
| panpipes preprocess_spatial show full --local | |
| - name: Run pipeline tasks | |
| shell: bash -el {0} | |
| run: | | |
| cd spatial/preprocess | |
| panpipes preprocess_spatial make full --local | |
| - name: File tree | |
| if: env.debug == 'true' | |
| run: tree spatial/preprocess |