WIP: Clean up the s3 upload workflow #151
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| # This workflow tests the model on the main branch | ||
| # TODO(@dhanshree): Test ersilia in all supported Python versions | ||
| 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: | ||
| # 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 | ||
| - uses: actions/[email protected] | ||
| with: | ||
| lfs: true | ||
| - uses: conda-incubator/setup-miniconda@v3 | ||
| with: | ||
| auto-update-conda: true | ||
| python-version: "3.10.10" | ||
| - name: Install dependencies | ||
| run: | | ||
| conda install git-lfs -c conda-forge | ||
| git-lfs install | ||
| conda install gh -c conda-forge | ||
| python -m pip install 'ersilia[test]' | ||
| - 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: ${{ secrets.GITHUB_TOKEN }} | ||
| amend: true | ||
| force: true | ||
| - name: Test output | ||
| run: | | ||
| output=$(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 | ||
| # TODO(@dhanshree) We can potentially restore the retries. | ||
| # TODO(@dhanshree) Correct the test command as needed | ||
| - name: Test model | ||
| env: | ||
| MODEL_ID: ${{ github.event.repository.name }} | ||
| run: | | ||
| ersilia -v test $MODEL_ID -d $MODEL_ID --inspect --remote -l deep > test.log | ||
| # Upload EOS logs and test logs | ||
| - 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 | ||
| ./*.log | ||
