(Active) Update hospitilization truth data weekly #178
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| name: (Active) Update hospitilization truth data weekly | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| skip_zoltar_upload: | |
| description: 'true/false indicating whether to skip Zoltar upload' | |
| required: false | |
| default: 'false' | |
| schedule: | |
| - cron: '0 16 * * 0' | |
| jobs: | |
| upload_zoltar: | |
| if: github.repository_owner == 'reichlab' | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| node-version: [10.2] | |
| steps: | |
| # - run: sudo apt-get remove ghc-** azure-cli firefox google-cloud-sdk google-chrome-stable hhvm dotnet-sdk-** dotnet-runtime-** moby-** adoptopenjdk-** mongodb-org-** mysql-** | |
| # - run: sudo apt-get autoremove | |
| - name: Free disk space | |
| run: | | |
| df --human-readable | |
| sudo apt clean | |
| docker rmi $(docker image ls --all --quiet) | |
| rm --recursive --force "$AGENT_TOOLSDIRECTORY" | |
| - name: Maximize build space | |
| uses: easimon/maximize-build-space@v4 | |
| with: | |
| root-reserve-mb: 4096 | |
| swap-size-mb: 4096 | |
| remove-dotnet: 'true' | |
| remove-android: 'true' | |
| remove-haskell: 'true' | |
| - name: Check space available | |
| run: df --human-readable | |
| - name: Checkout covid19-forecast-hub repo | |
| uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| path: covid19-forecast-hub | |
| - name: Checkout LFS objects | |
| run: git lfs checkout | |
| working-directory: ./covid19-forecast-hub | |
| - name: Setup GitHub Action for R language | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - name: Install system dependencies | |
| run: sudo apt-get install libudunits2-dev libcurl4-openssl-dev libgdal-dev | |
| - name: Checkout covidData | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: reichlab/covidData | |
| token: ${{secrets.GH_TOKEN}} | |
| path: covidData | |
| - name: Setup Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.x' # Version range or exact version of a Python version to use, using SemVer's version range syntax | |
| architecture: 'x64' # optional x64 or x86. Defaults to x64 if not specified | |
| - name: Install python dependencies | |
| run: pip3 install -r visualization/requirements.txt | |
| working-directory: ./covid19-forecast-hub | |
| - name: Install R dependencies (for covidData + covidHubUtils) | |
| working-directory: ./covid19-forecast-hub | |
| run: Rscript code/R_scripts/install_dependencies.R | |
| env: | |
| GITHUB_PAT: ${{ secrets.GH_TOKEN }} | |
| - run: mkdir ./covidData/data-raw/JHU/ | |
| - name: Install covidData | |
| run: make recent_data | |
| working-directory: ./covidData/code/data-processing | |
| - name: Generate truth csv files (Hospitalization) | |
| run: Rscript ./covid19-forecast-hub/code/R_scripts/generate_truth_csvs.R | |
| - name: Push generated files to GitHub | |
| run: bash ./travis/push-gh.sh | |
| working-directory: ./covid19-forecast-hub | |
| env: | |
| GH_TOKEN: ${{secrets.GH_TOKEN}} | |
| - name: Check space available after update | |
| run: df --human-readable |