test-model.yml

name: Model test on push

on:
  push: 
    branches: ['main']
  workflow_dispatch:

jobs:
  test:
    if: github.repository != 'ersilia-os/eos-template'
    runs-on: ubuntu-latest
    steps:
      - name: Checkout persist credentials
        uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # pin@v3.5.2
        with:
          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
      
      - 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
        env:
          USER_NAME: ${{ github.repository_owner }}
          BRANCH: "main"
          REPO_NAME: ${{ github.event.repository.name }}
          AIRTABLE_API_KEY: ${{ secrets.AIRTABLE_API_KEY }}
        uses: nick-fields/retry@v3
        with:
          timeout_minutes: 10
          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/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: |
          source activate
          echo "Updating README file with AirTable metadata for model: $MODEL_ID"
          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
        uses: actions-js/push@156f2b10c3aa000c44dbe75ea7018f32ae999772 # pin@v1.4
        with:
          author_name: "ersilia-bot"
          author_email: "ersilia-bot@users.noreply.github.com"
          message: "updating readme [skip ci]"
          repository: "ersilia-os/${{ github.event.repository.name }}"
          github_token: ${{ secrets.GITHUB_TOKEN }}
          amend: true
          force: true
      
      - name: Fetch model
        env:
          MODEL_ID: ${{ github.event.repository.name }}
        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
            ersilia -v serve $MODEL_ID
            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
        with:
          name: debug-logs
          retention-days: 14
          path: /home/runner/eos/*.log