diff --git a/.github/workflows/spatial_deconvolution-ci.yml b/.github/workflows/spatial_deconvolution_cell2location-ci.yml similarity index 96% rename from .github/workflows/spatial_deconvolution-ci.yml rename to .github/workflows/spatial_deconvolution_cell2location-ci.yml index ac964e32..b43215bb 100644 --- a/.github/workflows/spatial_deconvolution-ci.yml +++ b/.github/workflows/spatial_deconvolution_cell2location-ci.yml @@ -1,4 +1,4 @@ -name: Run tutorials (spatial deconvolution) +name: Run tutorials (spatial deconvolution cell2location) on: push: @@ -12,7 +12,7 @@ env: debug: 'true' jobs: - spatial_deconvolution: + spatial_deconvolution_cell2location: runs-on: ubuntu-latest strategy: fail-fast: false diff --git a/.github/workflows/spatial_deconvolution_tangram-ci.yml b/.github/workflows/spatial_deconvolution_tangram-ci.yml new file mode 100644 index 00000000..c06d8b75 --- /dev/null +++ b/.github/workflows/spatial_deconvolution_tangram-ci.yml @@ -0,0 +1,98 @@ +name: Run tutorials (spatial deconvolution tangram) + +on: + push: + branches: + - main + pull_request: + branches: + - main + +env: + debug: 'true' + +jobs: + spatial_deconvolution_tangram: + 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 deconvolution_tangram deconvolution_tangram/data deconvolution_tangram/data/spatial_data + cd deconvolution_tangram/data + curl -L -o Human_Heart_reference.h5mu https://figshare.com/ndownloader/files/44969677 + cd spatial_data + curl -L -o Human_Heart.zarr.zip https://figshare.com/ndownloader/files/51667673 + unzip Human_Heart.zarr.zip + rm Human_Heart.zarr.zip + + + # Note: we run the following to test that the commands works + - name: Preparing the configuration file + shell: bash -el {0} + run: | + cd deconvolution_tangram + panpipes deconvolution_spatial config + + - name: Edit the submission file + run: | + cd deconvolution_tangram + curl -o pipeline.yml https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/sarah_spatialData/docs/deconvolution_tangram/pipeline.yml + + - name: File tree + if: env.debug == 'true' + run: tree deconvolution_tangram + + - name: Review pipeline tasks + shell: bash -el {0} + run: | + cd deconvolution_tangram + panpipes deconvolution_spatial show full --local + + - name: Run pipeline tasks + shell: bash -el {0} + run: | + cd deconvolution_tangram + panpipes deconvolution_spatial make full --local + + - name: File tree + if: env.debug == 'true' + run: tree deconvolution_tangram