update ectd readme instructions for app bundle #32
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| on: | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| - main | |
| paths: | |
| - 'app/**' | |
| - 'utils.R' | |
| - 'renv.lock' | |
| - 'ectd_readme/README.qmd' | |
| name: Publish ECTD bundle | |
| jobs: | |
| build-deploy: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: write | |
| pages: write | |
| id-token: write | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Quarto | |
| uses: quarto-dev/quarto-actions/setup@v2 | |
| with: | |
| tinytex: true | |
| - name: Install R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: '4.4.1' | |
| - name: Install R Dependencies | |
| uses: r-lib/actions/setup-renv@v2 | |
| with: | |
| cache-version: 1 | |
| - name: Render ADRG PDF (custom) | |
| env: | |
| QUARTO_PRINT_STACK: true | |
| run: | | |
| quarto render adrg/adrg-quarto-pdf.qmd --to pdf | |
| shell: bash | |
| - name: Render ECTD README (custom) | |
| env: | |
| QUARTO_PRINT_STACK: true | |
| run: | | |
| quarto render ectd_readme/README.qmd --to gfm | |
| - name: Render cover letter (custom) | |
| env: | |
| QUARTO PRINT STACK: true | |
| run: | | |
| quarto render cover-letter/cover-letter.qmd | |
| - name: Compile ECTD Bundle (custom) | |
| run: | | |
| source("utils.R"); create_app_bundle(); create_ectd_bundle() | |
| shell: Rscript {0} | |
| - name: Set up object storage s3cmd cli tool | |
| uses: s3-actions/s3cmd@v1.6.1 | |
| with: | |
| provider: linode | |
| region: 'us-east-1' | |
| access_key: ${{ secrets.S3_ACCESS_KEY }} | |
| secret_key: ${{ secrets.S3_SECRET_KEY }} | |
| - name: Publish ECTD App bundle to Linode Object Storage | |
| run: | | |
| s3cmd put ectd_bundle/r4app.zip --mime-type 'application/zip' --acl-public s3://rsubmission-draft/r4app.zip | |
| - name: Check out ECTD bundle destination repo | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: RConsortium/submissions-pilot4-webR-to-fda | |
| path: ./submissions-pilot4-webR-to-fda | |
| token: ${{ secrets.API_TOKEN_GITHUB }} | |
| - name: Copy ECTD bundle | |
| run: bash ./.github/scripts/copy-ectd-bundle.sh | |
| env: | |
| DESTINATION_DIR: submissions-pilot4-webR-to-fda/m5/datasets/rconsortiumpilot4/analysis/adam/programs | |
| ADRG_DESTINATION_DIR: submissions-pilot4-webR-to-fda/m5/datasets/rconsortiumpilot4/analysis/adam/datasets | |
| README_DESTINATION_DIR: submissions-pilot4-webR-to-fda | |
| LETTER_DESTINATION_DIR: submissions-pilot4-webR-to-fda/m1/us | |
| - name: Push ECTD bundle repository | |
| run: bash ./.github/scripts/push-ectd-bundle.sh |