updated workflow files

.github/scripts/verify_model_outcome.py

@@ -0,0 +1,27 @@
+import csv
+
+def check_non_null_outcomes_in_output_csv(csv_file_path):
+    with open(csv_file_path, 'r') as csv_file:
+        csv_reader = csv.reader(csv_file)
+        header = next(csv_reader)
+        row = next(csv_reader)
+        for val in row[2:]: # Skip the first two columns (Inchikey and input)
+            if val not in ['', None]:
+                return False
+    return True
+
+if __name__ == '__main__':
+    # Read file path from command line
+    import sys
+    if len(sys.argv) < 2:
+        print('Usage: python verify_model_output.py <output_csv_file>')
+        exit(1)
+
+    output_csv_file = sys.argv[1]
+
+    if check_non_null_outcomes_in_output_csv(output_csv_file):
+        # If there are null outcomes, exit with status code 1
+        print('All outcomes are null')
+    else:
+        print('Some outcomes are not null')
+

.github/workflows/upload-model-to-dockerhub.yml

@@ -14,12 +14,12 @@ jobs:
     steps:
       # https://github.com/docker/setup-qemu-action
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3
 
       # https://github.com/docker/setup-buildx-action
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
 
       # log in to dockerhub
       - name: Login to Docker Hub
@@ -35,7 +35,22 @@ jobs:
           persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
           fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
           lfs: 'true'
+
+      - name: Free Disk Space (Ubuntu)
+        uses: jlumbroso/free-disk-space@main
+        with:
+          # this might remove tools that are actually needed,
+          # if set to "true" but frees about 6 GB
+          tool-cache: true
 
+          # all of these default to true, but feel free to set to
+          # "false" if necessary for your workflow
+          android: true
+          dotnet: true
+          haskell: true
+          large-packages: true
+          swap-storage: true
+
       - name: Generate the Dockerfile
         id: generate-dockerfile
         env:
@@ -44,11 +59,64 @@ jobs:
           wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/place_a_dockerfile_in_current_eos_repo.py
           python -m pip install requests
           python place_a_dockerfile_in_current_eos_repo.py $REPO_NAME
-                                          
+
+      # We cannot tag it as anything other than latest because 
+      # ersilia cli only looks for the 'latest' tag
+      - name: Build only AMD64 Image for Testing
+        id: buildForTest
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          load: true
+          tags: ersiliaos/${{ github.event.repository.name }}:latest
+
+      - name: Add conda to system path
+        run: echo $CONDA/bin >> $GITHUB_PATH
+
+      - name: Source conda
+        run: source $CONDA/etc/profile.d/conda.sh
+
+      - name: Set Python to 3.10.10
+        run:
+         conda install -y python=3.10.10 
+
+      - name: Install dependencies
+        run: |
+          source activate
+          conda init
+          conda install git-lfs -c conda-forge
+          git-lfs install
+          conda install gh -c conda-forge
+
+      - name: Install ersilia
+        run: |
+          source activate
+          python --version
+          echo "After conda init"
+          conda init
+          python -m pip install git+https://github.com/ersilia-os/ersilia.git
+          
+      # TODO This is very hacky, maybe we want to use the ersilia test command in the future for this
+      - name: Test Built Image
+        id: testBuiltImage
+        run: |
+          ersilia -v fetch ${{ github.event.repository.name }} --from_dockerhub
+          ersilia -v serve ${{ github.event.repository.name }}
+          ersilia -v run -i "CCCC" -o "output.csv"
+          ersilia close
+          output=$(python .github/scripts/verify_model_outcome.py output.csv)
+          if echo "$output" | grep -q "All outcomes are null"; then
+            echo "Error in model outcome, aborting build"
+            exit 1
+          fi
+        env:
+          PULL_IMAGE: n
+
       - name: Build and push
         id: buildMultiple
         continue-on-error: true
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
+        timeout-minutes: 45
         with:
           context: .
           platforms: linux/amd64,linux/arm64
@@ -69,15 +137,15 @@ jobs:
       - name: Build only for Linux/amd64
         id: buildSingle
         if: steps.buildCheck.outputs.failed == 'true'
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           context: .
           platforms: linux/amd64
           push: ${{ github.event_name != 'pull_request' }}
           tags: ersiliaos/${{ github.event.repository.name }}:latest
 
       - name: Update Metadata JSON file with DockerHub info
-        id: UpdateMetadata
+        id: updateMetadata
         run: |
           mv Dockerfile_legacy Dockerfile
           python3 -c "
@@ -106,32 +174,6 @@ jobs:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           amend: true
           force: true
-
-      - name: Add conda to system path
-        run: echo $CONDA/bin >> $GITHUB_PATH
-
-      - name: Source conda
-        run: source $CONDA/etc/profile.d/conda.sh
-
-      - name: Set Python to 3.10.10
-        run:
-         conda install -y python=3.10.10 
-
-      - name: Install dependencies
-        run: |
-          source activate
-          conda init
-          conda install git-lfs -c conda-forge
-          git-lfs install
-          conda install gh -c conda-forge
-
-      - name: Install ersilia
-        run: |
-          source activate
-          python --version
-          echo "After conda init"
-          conda init
-          python -m pip install git+https://github.com/ersilia-os/ersilia.git
 
       - name: Update metadata to AirTable
         id: update-metadata-to-airtable