add tangram github action

.github/workflows/spatial_deconvolution-ci.yml → .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

.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