From MuData to SpatialData #165
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| name: Run tutorials (visualization) | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| env: | |
| debug: 'true' | |
| jobs: | |
| visualization: | |
| 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 | |
| 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 -e . | |
| conda list | |
| - name: Conda info | |
| shell: bash -el {0} | |
| run: conda info | |
| - name: Conda list | |
| shell: pwsh | |
| run: conda list | |
| # Note: all three files are renamed during the download to trim the "subsample_" prefix | |
| - name: Preparing the data | |
| run: | | |
| mkdir -p teaseq/vis/data && cd teaseq/vis/data | |
| curl -L -o teaseq_clustered.h5mu https://figshare.com/ndownloader/files/43246446 | |
| - name: Preparing the data | |
| run: | | |
| mkdir -p teaseq/vis && cd teaseq/vis | |
| curl -o paired_scatters.csv https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/69bf8febdd6c95141c3e20de10f533c4/paired_scatters.csv | |
| curl -o custom_markers.csv https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/cd6f66ea922d4bd2b896050780f0d8dd/custom_markers.csv | |
| curl -o paired_scatters_markers.csv https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/68a767929ecdc47cf945f855f58e046a/paired_scatters_markers.csv | |
| # Note: we run the following to test that the commands works | |
| # However, the following task will replacing the file anyway | |
| - name: Preparing the configuration file | |
| shell: bash -el {0} | |
| run: | | |
| cd teaseq/vis/data | |
| panpipes vis config | |
| - name: Edit the submission file | |
| run: | | |
| cd teaseq/vis | |
| curl -o pipeline.yml https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/main/docs/visualization/pipeline.yml | |
| - name: File tree | |
| run: tree teaseq | |
| - name: Review pipeline tasks | |
| shell: bash -el {0} | |
| run: | | |
| cd teaseq/vis | |
| panpipes vis show full --local | |
| - name: Run pipeline tasks | |
| shell: bash -el {0} | |
| run: | | |
| cd teaseq/vis | |
| panpipes vis make full --local | |
| - name: File tree | |
| if: always() | |
| run: tree teaseq |