sanity check #8
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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/44795785 | ||
| # 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/data | ||
| curl -o pipeline.yml https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/29daa86241829b362152785caf30ab61/pipeline.yml | ||
| - name: Replace template contents in configuration file | ||
| run: | | ||
| cd teaseq/vis/data | ||
| sed -i 's+paired_scatters: True+paired_scatters: False+g' pipeline.yml | ||
| -name: Check line was edited | ||
| run: | | ||
| cd teaseq/vis/data | ||
| grep paired_scatters 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 | ||
