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
 

.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:
@@ -102,15 +103,12 @@ jobs:
         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 $expected ])
-            then
-              echo "Error in model output, aborting build and push"
-              exit 1
+          ersilia -v run -i "CCCC" -o "output.csv"
+          ersilia close
+          output=$(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