updating readme [skip ci]

.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/test-model-pr.yml

@@ -11,7 +11,23 @@ jobs:
       - uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # pin@v3.5.2
         with:
           lfs: true
-
+
+# This might stop working in the future, so we need to keep an eye on it
+      - 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: Add conda to system path
         run: echo $CONDA/bin >> $GITHUB_PATH
 

.github/workflows/test-model.yml

@@ -16,7 +16,23 @@ 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'
-
+
+# This might stop working in the future, so we need to keep an eye on it
+      - 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: Add conda to system path
         run: echo $CONDA/bin >> $GITHUB_PATH
 
@@ -98,32 +114,4 @@ jobs:
           name: debug-logs
           retention-days: 1
           path: /home/runner/eos/console.log
-
-      - name: Shuffle assignees
-        id: shuffle
-        run: |
-          export assignees=$(echo "${{ vars.assignees }}" | awk 'BEGIN {FS=","}; {srand();split($0,a,FS); print a[int(rand()*NF+1)]}')
-          echo "$assignees" >> $GITHUB_STEP_SUMMARY
-          echo "shuffled_assignee=$assignees" >> $GITHUB_OUTPUT
-          echo "shuffled_assignee=$assignees" >> $GITHUB_ENV
 
-      - name: Check for existing issue
-        id: check_issue
-        run: |
-          gh auth login --with-token <<< ${{ secrets.GITHUB_TOKEN }}
-          issue_number=$(gh issue list --limit 100 --search "${{ vars.test_issue_title }}" --json number --jq '.[0].number')
-          echo "::set-output name=issue_number::$issue_number"
-   
-      - name: Create a Test issue
-        uses: actions-ecosystem/action-create-issue@b63bc2bbacb6a838dfe4a9f70da6665ae0962a49
-        id: create_issue 
-        with:
-          github_token: ${{ secrets.github_token }}
-          title: ${{ vars.test_issue_title }}
-          assignees: |
-            ${{ steps.shuffle.outputs.shuffled_assignee }}
-          body: |
-            This model is ready for testing. If you are assigned to this issue, please try it out using the CLI, Google Colab and DockerHub and let us know if it works!
-          labels: |
-            test
-        if: steps.check_issue.outputs.issue_number == ''

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

@@ -36,6 +36,7 @@ jobs:
           fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
           lfs: 'true'
 
+# This might stop working in the future, so we need to keep an eye on it
       - name: Free Disk Space (Ubuntu)
         uses: jlumbroso/free-disk-space@main
         with:
@@ -50,26 +51,8 @@ jobs:
           haskell: true
           large-packages: true
           swap-storage: true
-
-      - name: Generate the Dockerfile
-        id: generate-dockerfile
-        env:
-          REPO_NAME: ${{ github.event.repository.name }}
-        run: |
-          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
-
+
+# Install ersilia in the next few steps to test the built image with ersilia CLI
       - name: Add conda to system path
         run: echo $CONDA/bin >> $GITHUB_PATH
 
@@ -95,26 +78,116 @@ jobs:
           echo "After conda init"
           conda init
           python -m pip install git+https://github.com/ersilia-os/ersilia.git
+
+# Build a V2 image and test it with ersilia CLI
+
+      - name: Generate the V2 Dockerfile
+        id: generateDockerfileV2
+        env:
+          REPO_NAME: ${{ github.event.repository.name }}
+        run: |
+          wget -O place_a_dockerfile_in_current_eos_repo.py 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 $REPO_NAME
+          rm place_a_dockerfile_in_current_eos_repo.py
+
+      # We cannot tag it as anything other than latest because 
+      # ersilia cli only looks for the 'latest' tag
+      - name: Build only V2 AMD64 Image for Testing
+        id: buildForTestV2
+        continue-on-error: true  # Allow this to fail; this might fail bacause conda-pack would not work for this model
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          load: true
+          tags: ersiliaos/${{ github.event.repository.name }}:latest
 
       # 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
+      - name: Test built v2 image
+        id: testBuiltImageV2
+        continue-on-error: true  # Allow this to fail
         run: |
           ersilia -v fetch ${{ github.event.repository.name }} --from_dockerhub
           ersilia -v serve ${{ github.event.repository.name }}
-          ersilia -v run -i "CCCC" -o "output.json"
-          expected=$(jq '.[0].output.outcome[]' output.json | wc -l)
-          result=$(jq '.[0].output.outcome[] | select(. != null)' output.json | wc -l)
-          echo "Expected correct outcomes $expected"
-          echo "Returned correct outcomes $result"
-          if ! ([ $result -gt 0 ] && [ $result -le $expected ])
-            then
-              echo "Error in model output, aborting build and push"
-              exit 1
+          ersilia example -n 1 -f input.csv --predefined
+          ersilia -v run -i "input.csv" -o "output.csv"
+          ersilia close
+          output=$(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
+          rm output.csv
         env:
           PULL_IMAGE: n
+        if: steps.buildForTestV2.outcome == 'success'
 
+# If the test failed build a V1 image and test it with ersilia CLI
+
+      - name: Generate the V1 Dockerfile
+        id: generateDockerfileV1
+        if: steps.testBuiltImageV2.outcome == 'failure' || steps.testBuiltImageV2.outcome == 'skipped'
+        env:
+          REPO_NAME: ${{ github.event.repository.name }}
+        run: |
+          rm Dockerfile # Remove the V2 Dockerfile
+          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 $REPO_NAME v1
+          rm place_a_dockerfile_in_current_eos_repo.py
+
+      # We cannot tag it as anything other than latest because 
+      # ersilia cli only looks for the 'latest' tag
+      - name: Build only V1 AMD64 Image for Testing
+        id: buildForTestV1
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          load: true
+          tags: ersiliaos/${{ github.event.repository.name }}:latest
+
+      # TODO This is very hacky, maybe we want to use the ersilia test command in the future for this
+      - name: Test built v1 image
+        id: testBuiltImageV1
+        run: |
+          ersilia -v fetch ${{ github.event.repository.name }} --from_dockerhub
+          ersilia -v serve ${{ github.event.repository.name }}
+          ersilia example -n 1 -f input.csv --predefined
+          ersilia -v run -i "input.csv" -o "output.csv"
+          ersilia close
+          output=$(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
+          rm output.csv
+        env:
+          PULL_IMAGE: n
+
+# Create an issue to track that this model did not work with the V2 image
+
+      - name: Check for existing issue
+        id: check_existing_alert_issue
+        run: |
+          gh auth login --with-token <<< ${{ secrets.GITHUB_TOKEN }}
+          issue_number=$(gh issue list --limit 100 --search "${{ vars.DOCKER_BUILD_FAILURE_ISSUE_TITLE }}" --json number --jq '.[0].number')
+          echo "::set-output name=issue_number::$issue_number"
+        if: steps.testBuiltImageV1.conclusion != 'skipped'
+
+      - name: Create an alert issue
+        uses: actions-ecosystem/action-create-issue@b63bc2bbacb6a838dfe4a9f70da6665ae0962a49
+        id: create_alert_issue 
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          title: ${{ vars.DOCKER_BUILD_FAILURE_ISSUE_TITLE }}
+          body: |
+            This model failed to build with v2 image. Please investigate and fix the issue.
+          labels: |
+            bug
+        if: ${{ (steps.check_existing_alert_issue.conclusion != 'skipped') && (steps.check_existing_alert_issue.outputs.issue_number == '') }}
+
+# Finally build and push if everything is successful
+
       - name: Build and push
         id: buildMultiple
         continue-on-error: true
@@ -165,7 +238,6 @@ jobs:
              json.dump(data, f, indent=4)
           "
           rm arch.txt
-          rm place_a_dockerfile_in_current_eos_repo.py
           
       - name: Commit and push changes done to the Metadata JSON file
         uses: actions-js/push@156f2b10c3aa000c44dbe75ea7018f32ae999772 # pin@v1.4
@@ -222,3 +294,34 @@ jobs:
           password: ${{ secrets.DOCKERHUB_PASSWORD }}
           repository: ersiliaos/${{ github.event.repository.name }}
           short-description: "Ersilia Model Hub Identifier: ${{ github.event.repository.name }}"
+
+# Create an issue within the repository to track that this model is ready for testing
+
+      - name: Shuffle assignees
+        id: shuffle
+        run: |
+          export assignees=$(echo "${{ vars.assignees }}" | awk 'BEGIN {FS=","}; {srand();split($0,a,FS); print a[int(rand()*NF+1)]}')
+          echo "$assignees" >> $GITHUB_STEP_SUMMARY
+          echo "shuffled_assignee=$assignees" >> $GITHUB_OUTPUT
+          echo "shuffled_assignee=$assignees" >> $GITHUB_ENV
+
+      - name: Check for existing issue
+        id: check_existing_test_issue
+        run: |
+          gh auth login --with-token <<< ${{ secrets.GITHUB_TOKEN }}
+          issue_number=$(gh issue list --limit 100 --search "${{ vars.test_issue_title }}" --json number --jq '.[0].number')
+          echo "::set-output name=issue_number::$issue_number"
+   
+      - name: Create a Test issue
+        uses: actions-ecosystem/action-create-issue@b63bc2bbacb6a838dfe4a9f70da6665ae0962a49
+        id: create_test_issue 
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          title: ${{ vars.TEST_ISSUE_TITLE }}
+          assignees: |
+            ${{ steps.shuffle.outputs.shuffled_assignee }}
+          body: |
+            This model is ready for testing. If you are assigned to this issue, please try it out using the CLI, Google Colab and DockerHub and let us know if it works!
+          labels: |
+            test
+        if: steps.check_existing_test_issue.outputs.issue_number == ''