PSI-PROF COVID rnd 18 submission #238
Workflow file for this run
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| name: Validate and Visualize Submission | |
| on: | |
| pull_request_target: | |
| types: [synchronize, opened, reopened] | |
| branches: | |
| - master | |
| paths: | |
| - 'data-processed/**.parquet' | |
| jobs: | |
| validates-files: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| sparse-checkout: | | |
| .github | |
| code | |
| hub-config | |
| data-locations | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Install system dependencies | |
| run: sudo apt-get install libcurl4-openssl-dev libudunits2-dev libgdal-dev | |
| - name: Cache R packages | |
| id: cache | |
| uses: actions/cache@v2 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-${{ hashFiles('.github/requirements.txt') }}-1 | |
| - name: Install dependencies | |
| if: ( steps.cache.outputs.cache-hit != 'true' ) | |
| run: | | |
| R -e 'Sys.setenv("NOT_CRAN" = TRUE) | |
| install.packages(c("arrow", "gh", "remotes")) | |
| Sys.unsetenv("NOT_CRAN") | |
| remotes::install_url("https://github.com/midas-network/SMHvalidation/archive/refs/heads/main.zip") | |
| remotes::install_url("https://github.com/Infectious-Disease-Modeling-Hubs/hubUtils/archive/refs/heads/main.zip")' | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Run Validation - Open/reopen | |
| if: ( github.event.action != 'synchronize' ) | |
| run: | | |
| Rscript code/validation/validation.R | |
| env: | |
| GH_PR_NUMBER: ${{ github.event.pull_request.number }} | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Run Validation - Synchronize | |
| if: ( github.event.action == 'synchronize' ) | |
| run: | | |
| Rscript code/validation/validation.R | |
| env: | |
| GH_PR_NUMBER: ${{ github.event.pull_request.number }} | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GH_COMMIT_SHA: ${{ github.event.pull_request.head.sha }} | |
| - name: Upload Projection Plot as Artifact | |
| uses: actions/upload-artifact@v3 | |
| if: always() | |
| with: | |
| name: validation_plot_${{ github.event.pull_request.number }} | |
| path: ./proj_plot/* | |
| if-no-files-found: ignore | |