updated workflow files

ersilia-os · Dec 16, 2024 · f13de84 · f13de84
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diff --git a/.github/scripts/verify_model_outcome.py b/.github/scripts/verify_model_outcome.py
@@ -6,7 +6,7 @@ def check_non_null_outcomes_in_output_csv(csv_file_path):
         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]:
+            if val not in ['', None]: # Returns if even one outcome is not null
                 return False
     return True
 

diff --git a/.github/workflows/post-model-upload.yml b/.github/workflows/post-model-upload.yml
@@ -47,7 +47,7 @@ jobs:
           data['DockerHub'] = 'https://hub.docker.com/r/ersiliaos/{0}'.format(data['Identifier'])
           data['Docker Architecture'] = arch
           with open('metadata.yml', 'w') as f:
-            yaml.dump(data, default_flow_style=False, sort_keys=False)
+            yaml.dump(data, f, default_flow_style=False, sort_keys=False)
           "
           rm arch.txt
 
@@ -105,20 +105,35 @@ jobs:
           REPO_NAME: ${{ github.event.repository.name }}
           AIRTABLE_API_KEY: ${{ secrets.AIRTABLE_API_KEY }}
         run: |
+          source activate
+          pip install requests pyairtable
           echo "Updating metadata to AirTable looking at owner: $USER_NAME"
-          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/update_metadata_to_airtable.py
-          python3 update_metadata_to_airtable.py $USER_NAME $REPO_NAME $BRANCH $AIRTABLE_API_KEY
-          rm update_metadata_to_airtable.py
+          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/airtableops.py
+          python3 airtableops.py airtable-update --user $USER_NAME --repo $REPO_NAME --branch $BRANCH --api-key $AIRTABLE_API_KEY
+          rm airtableops.py
   
+      - name: sync metadata to S3 JSON
+        id: sync-metadata-to-s3
+        env:
+          AIRTABLE_API_KEY: ${{ secrets.AIRTABLE_API_KEY }}
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+        run: |
+          source activate
+          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/convert_airtable_to_json.py
+          pip install boto3 requests pyairtable
+          python convert_airtable_to_json.py $AIRTABLE_API_KEY $AWS_ACCESS_KEY_ID $AWS_SECRET_ACCESS_KEY
+          rm convert_airtable_to_json.py
+
       - name: Update README file
         id: update-readme-file
         env:
           MODEL_ID: ${{ github.event.repository.name }}
         run: |
           echo "Updating README file with AirTable metadata for model: $MODEL_ID"
-          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/update_readme_from_airtable.py
-          python3 update_readme_from_airtable.py $MODEL_ID .
-          rm update_readme_from_airtable.py
+          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/airtableops.py
+          python3 airtableops.py readme-update --repo $MODEL_ID --path .
+          rm airtableops.py
           less README.md
 
       - name: Commit and push changes done to the README file
@@ -166,7 +181,14 @@ jobs:
           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!
+            This model is a new incorporation to the Ersilia Model Hub or it has been modified. If you are assigned to this issue, please try it out and ensure everything works!
+            To test a model, first clone it in your local system (ideally, from dockerhub) using the CLI commands:
+            ```
+            ersilia -v fetch eosxxxx --from_dockerhub
+            ersilia serve eosxxxx
+            ersilia test
+            ```
+            The test command will automatically check that the model can handle null outputs and whether it produces consistent results. Please copy here the result of the test command. If it passes, simply close the issue as completed. If it fails, please detail at which step and whether you have taken any steps to solve it. Please tag the original model contributor and one of Ersilia's maintainers for support.
           labels: |
             test
         if: steps.check_existing_test_issue.outputs.issue_number == ''
diff --git a/.github/workflows/test-model-pr.yml b/.github/workflows/test-model-pr.yml
@@ -54,21 +54,6 @@ jobs:
           conda init
           python -m pip install git+https://github.com/ersilia-os/ersilia.git
   
-      - name: Check metadata before updating to AirTable
-        id: check-metadata
-        env:
-          USER_NAME: ${{ github.event.pull_request.head.repo.owner.login }}
-          BRANCH: "main"
-          REPO_NAME: ${{ github.event.repository.name }}
-        uses: nick-fields/retry@v3
-        with:
-          timeout_minutes: 10
-          max_attempts: 3
-          command: |
-            source activate
-            wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/update_metadata_to_airtable.py
-            python3 update_metadata_to_airtable.py $USER_NAME $REPO_NAME $BRANCH
-
       - name: Predict output
         env:
           MODEL_ID: ${{ github.event.repository.name }}
@@ -79,9 +64,9 @@ jobs:
           command: |
             source activate
             echo "Sample model id selected: $MODEL_ID"
-            ersilia -v fetch $MODEL_ID --repo_path .
+            ersilia -v fetch $MODEL_ID --from_dir .
             ersilia -v serve $MODEL_ID
-            ersilia sample -n 5 -f input.csv
+            ersilia example inputs -n 5 -f input.csv --predefined
             ersilia -v api -i input.csv
             ersilia close
           

diff --git a/.github/workflows/test-model.yml b/.github/workflows/test-model.yml
@@ -1,4 +1,4 @@
-name: Model Test on push
+name: Model test on push
 
 on:
   push: 
@@ -72,10 +72,24 @@ jobs:
           max_attempts: 3
           command: |
             source activate
+            pip install requests pyairtable
             echo "Updating metadata to AirTable looking at owner: $USER_NAME"
-            wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/update_metadata_to_airtable.py
-            python3 update_metadata_to_airtable.py $USER_NAME $REPO_NAME $BRANCH $AIRTABLE_API_KEY
-            rm update_metadata_to_airtable.py
+            wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/airtableops.py
+            python3 airtableops.py airtable-update --user $USER_NAME --repo $REPO_NAME --branch $BRANCH --api-key $AIRTABLE_API_KEY
+            rm airtableops.py
+
+      - name: sync metadata to S3 JSON
+        id: sync-metadata-to-s3
+        env:
+          AIRTABLE_API_KEY: ${{ secrets.AIRTABLE_API_KEY }}
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+        run: |
+          source activate
+          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/convert_airtable_to_json.py
+          pip install boto3 requests pyairtable
+          python convert_airtable_to_json.py $AIRTABLE_API_KEY $AWS_ACCESS_KEY_ID $AWS_SECRET_ACCESS_KEY
+          rm convert_airtable_to_json.py
 
       - name: Update README file
         id: update-readme-file
@@ -84,9 +98,9 @@ jobs:
         run: |
           source activate
           echo "Updating README file with AirTable metadata for model: $MODEL_ID"
-          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/update_readme_from_airtable.py
-          python3 update_readme_from_airtable.py $MODEL_ID .
-          rm update_readme_from_airtable.py
+          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/airtableops.py
+          python3 airtableops.py readme-update --repo $MODEL_ID --path .
+          rm airtableops.py
           less README.md
 
       - name: Commit and push changes done to the README file
@@ -100,22 +114,38 @@ jobs:
           amend: true
           force: true
 
-      - name: Predict output
+      - name: Fetch model
         env:
           MODEL_ID: ${{ github.event.repository.name }}
-        uses: nick-fields/retry@v3
-        with:
-          timeout_minutes: 10
-          max_attempts: 3
-          command: |
+        run: |
+            source activate
+            ersilia -v fetch $MODEL_ID --from_dir .
+            FOLDER="$HOME/eos/repository/$MODEL_ID"
+            if [ ! -d "$FOLDER" ]; then
+              echo "Error: Folder '$FOLDER' does not exist." >&2
+              exit 1
+            fi
+
+      - name: Generate input and run model
+        env:
+          MODEL_ID: ${{ github.event.repository.name }}
+        run: |
             source activate
-            echo "Sample model id selected: $MODEL_ID"
-            ersilia -v fetch $MODEL_ID --repo_path .
             ersilia -v serve $MODEL_ID
-            ersilia sample -n 5 -f input.csv
-            ersilia -v run -i input.csv
+            ersilia example inputs -n 5 -f input.csv --predefined
+            ersilia -v run -i "input.csv" -o "output.csv"
             ersilia close
-          
+            cat output.csv
+      
+      - name: Test output
+        run: |
+            output=$(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 test"
+              exit 1
+            fi
+            rm output.csv
+
       - name: Upload log output
         if: always()
         uses: actions/upload-artifact@83fd05a356d7e2593de66fc9913b3002723633cb #pin v3.1.1

diff --git a/.github/workflows/upload-bentoml.yml b/.github/workflows/upload-bentoml.yml
@@ -40,21 +40,21 @@ jobs:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_PASSWORD }}
 
-      # # 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
+      # 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
+          # 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: Setup conda
         id: setupConda
@@ -97,10 +97,13 @@ jobs:
         id: testBuiltImage
         env:
           PULL_IMAGE: n
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          AWS_DEFAULT_REGION: us-east-1
         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 serve ${{ github.event.repository.name }} --track #Added --track here
+          ersilia example inputs -n 1 -f input.csv --predefined
           ersilia -v run -i "input.csv" -o "output.csv"
           ersilia close
           output=$(python .github/scripts/verify_model_outcome.py output.csv)

diff --git a/.github/workflows/upload-ersilia-pack.yml b/.github/workflows/upload-ersilia-pack.yml
@@ -11,14 +11,10 @@ jobs:
 
       - name: Checkout repository
         uses: actions/checkout@v4
+        with:
+          lfs: true
 
-      - name: Check if we can use this workflow
-        run: |
-          if [[ -f install.yml ]]; then
-            echo "This workflow is not supported for this repository"
-            exit 1
-          fi
-      
+      - run: git lfs pull
       # https://github.com/docker/setup-qemu-action
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v3
@@ -36,21 +32,21 @@ jobs:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_PASSWORD }}
 
-      # # 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
+      # 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
+          # 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
 
       # Install ersilia-pack, requests, and ersilia to test the built image with ersilia CLI
       - name: Setup Python for Ersilia Pack
@@ -70,7 +66,6 @@ jobs:
 
       - name: Build only AMD64 Image for Testing
         id: buildForTestErsiliaPack
-        continue-on-error: true  # Allow this to fail;
         uses: docker/build-push-action@v6.7.0
         with:
           context: ../ # We need to go back to the root directory to find the Dockerfile and copy the model repository
@@ -81,13 +76,15 @@ jobs:
         id: testBuiltImageErsiliaPack
         env:
           PULL_IMAGE: n
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          AWS_DEFAULT_REGION: us-east-1
         if: steps.buildForTestErsiliaPack.outcome == 'success'
-        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 example -n 1 -f input.csv --predefined
-          ersilia -v run -i "input.csv" -o "output.csv"
+          ersilia -v serve ${{ github.event.repository.name }} --track #Added --track here
+          ersilia example inputs -n 1 -f input.csv --predefined
+          ersilia -v run -i "input.csv" -o "output.csv" 
           ersilia close
           output=$(python .github/scripts/verify_model_outcome.py output.csv)
           if echo "$output" | grep -q "All outcomes are null"; then

diff --git a/.github/workflows/upload-model-to-dockerhub.yml b/.github/workflows/upload-model-to-dockerhub.yml
@@ -1,10 +1,11 @@
 name: Upload model to DockerHub
 on:
   workflow_dispatch:
-  # workflow_run:
-  #   workflows: ["Upload model to S3"]
-  #   types:
-  #     - completed
+
+  workflow_run:
+    workflows: ["Upload model to S3"]
+    types:
+      - completed
 
 jobs:
   upload-ersilia-pack:
@@ -25,4 +26,4 @@ jobs:
     uses: ./.github/workflows/upload-bentoml.yml
     secrets: inherit
     with:
-      version: legacy-bentoml
+      version: legacy-bentoml