updated workflow files #17
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| 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 # [email protected] | |
| 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 $MODEL_ID --path . | |
| rm airtableops.py | |
| less README.md | |
| - name: Commit and push changes done to the README file | |
| uses: actions-js/push@156f2b10c3aa000c44dbe75ea7018f32ae999772 # [email protected] | |
| with: | |
| author_name: "ersilia-bot" | |
| author_email: "[email protected]" | |
| message: "updating readme [skip ci]" | |
| repository: "ersilia-os/${{ 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 $MODEL_ID | |
| ersilia example -n 5 -f input.csv --predefined | |
| ersilia -v run -i "input.csv" -o "output.csv" | |
| ersilia close | |
| cat output.csv | |
| - name: Test output | |
| run: | | |
| output=$(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 |