added stockholm key; fixed width fasta; updated warning for calc button #3
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| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| name: ci-cd | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.python }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: "ubuntu-20.04", python: "3.9.17"} | |
| env: | |
| APP: bridge-rna-designer | |
| PORT: 8080 | |
| steps: | |
| - id: "Checkout" | |
| name: "Checkout code" | |
| uses: actions/checkout@v3 | |
| - id: "Python" | |
| name: "Set up Python" | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.config.python }} | |
| - id: "Python-deps" | |
| name: "Install app dependencies" | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| - id: "pytest-install" | |
| name: "Install pytest" | |
| run: | | |
| pip install pytest | |
| - id: "pytest-run" | |
| name: "Run pytest" | |
| shell: bash -l {0} | |
| run: | | |
| pytest -s tests | |
| - id: "Google-Auth" | |
| name: "Authenticate to Google Cloud" | |
| uses: "google-github-actions/auth@v1" | |
| with: | |
| credentials_json: "${{ secrets.GOOGLE_CREDENTIALS }}" | |
| - id: "gcloud-setup" | |
| name: "Set up GCP Cloud SDK" | |
| uses: google-github-actions/setup-gcloud@v1 | |
| with: | |
| project_id: "${{ secrets.GCP_PROJECT_ID }}" | |
| - id: "Docker-Auth" | |
| name: "Docker authentication" | |
| run: | | |
| gcloud auth configure-docker us-west1-docker.pkg.dev --project ${{ secrets.GCP_PROJECT_ID }} | |
| - id: "Docker-Build" | |
| name: "Build and push container" | |
| run: | | |
| docker build -t "us-west1-docker.pkg.dev/${{ secrets.GCP_PROJECT_ID }}/${{ env.APP }}/${{ env.APP }}:${{ github.sha }}" . \ | |
| && docker push "us-west1-docker.pkg.dev/${{ secrets.GCP_PROJECT_ID }}/${{ env.APP }}/${{ env.APP }}:${{ github.sha }}" | |
| - id: "Deploy" | |
| name: "Deploy to Cloud Run" | |
| uses: google-github-actions/deploy-cloudrun@v1 | |
| with: | |
| service: "${{ env.APP }}" | |
| image: "us-west1-docker.pkg.dev/${{ secrets.GCP_PROJECT_ID }}/${{ env.APP }}/${{ env.APP }}:${{ github.sha }}" | |
| region: "us-west1" | |
| flags: > | |
| --service-account=${{ secrets.GCP_SERVICE_ACCOUNT }} | |
| --port=${{ env.PORT }} | |
| --cpu=2 | |
| --memory=2Gi | |
| --max-instances=1 | |
| --concurrency=80 | |