testing github actions

PMBio · Sep 19, 2024 · 63d3c03 · 63d3c03
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diff --git a/.github/workflows/pipeline-tests.yml b/.github/workflows/pipeline-tests.yml
@@ -42,7 +42,7 @@ jobs:
       environment_file: ./deeprvat_env_no_gpu.yml
       prerun_cmd: cp ./tests/deeprvat/training_association_testing/deeprvat_config.yaml ./example/
       dry_run: false
-      postrun_cmd: python $GITHUB_WORKSPACE/tests/deeprvat/compare_reference.py compare-training ./example/ $GITHUB_WORKSPACE/tests/deeprvat/test_data/training/ "Cholesterol" "Platelet_crit"
+      #postrun_cmd: python $GITHUB_WORKSPACE/tests/deeprvat/compare_reference.py compare-training ./example/ $GITHUB_WORKSPACE/tests/deeprvat/test_data/training/ "Cholesterol" "Platelet_crit"
 
   # Association Testing Pretrained Pipeline
   Smoke-Association-Testing-Pretrained:

diff --git a/.github/workflows/run-pipeline.yml b/.github/workflows/run-pipeline.yml
@@ -46,6 +46,8 @@ jobs:
       runs-on: ubuntu-latest
       env:
         CUDA_VISIBLE_DEVICES: -1
+      outputs:
+        output1: ${{ steps.pipeline_run.outputs }}
       steps:
         - name: Check out repository code
           uses: actions/checkout@v4
@@ -81,7 +83,23 @@ jobs:
             ${{ (endsWith(inputs.pipeline_config, 'ml') && '--configfile')  || '' }}  ${{ inputs.pipeline_config }} \
             --snakefile ${{inputs.pipeline_file}} --show-failed-logs -F -p ${{ inputs.pipeline_extra_flags }}
           shell: micromamba-shell {0}
+          id: pipeline_run
         - name: Run post pipeline cmd
           if: inputs.postrun_cmd
           run: ${{inputs.postrun_cmd}}
           shell: micromamba-shell {0}
+        # - name: Run post pipeline cmd
+        #   if: inputs.postrun_cmd
+        #   needs: steps.run_pipeline.outputs
+        #   run: echo "$OUTPUT1" #${{inputs.postrun_cmd}}
+        #   shell: micromamba-shell {0}
+  Compare-Pipeline-Output:
+    runs-on: unbuntu-latest
+    needs: Pipeline-Tests-RunTraining.Run-Pipeline
+    #if: github.ref == 'refs/heads/master'
+    steps:
+      - env:
+        OUTPUT1: ${{needs.Pipeline-Tests-RunTraining.Run-Pipeline.outputs.output1}}
+      run: echo "$OUTPUT1"
+
+