Merge pull request #163 from CHOP-CGTInformatics/minor-updates #395
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| name: test-coverage | |
| jobs: | |
| test-coverage: | |
| runs-on: ubuntu-latest | |
| env: | |
| NOT_CRAN: true | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| REDCAP_URI: ${{ secrets.REDCAP_URI }} | |
| REDCAPTIDIER_CLASSIC_API: ${{ secrets.REDCAPTIDIER_CLASSIC_API }} | |
| REDCAPTIDIER_LONGITUDINAL_API: ${{ secrets.REDCAPTIDIER_LONGITUDINAL_API }} | |
| REDCAPTIDIER_LONGITUDINAL_NOARMS_API: ${{ secrets.REDCAPTIDIER_LONGITUDINAL_NOARMS_API }} | |
| SUPERHEROES_REDCAP_API: ${{ secrets.SUPERHEROES_REDCAP_API }} | |
| REDCAPTIDIER_RESTRICTED_ACCESS_API: ${{ secrets.REDCAPTIDIER_RESTRICTED_ACCESS_API }} | |
| REDCAPTIDIER_CLASSIC_NOREPEAT_API: ${{ secrets.REDCAPTIDIER_CLASSIC_NOREPEAT_API }} | |
| REDCAPTIDIER_LONGITUDINAL_NOREPEAT_API: ${{ secrets.REDCAPTIDIER_LONGITUDINAL_NOREPEAT_API }} | |
| REDCAPTIDIER_REPEAT_FIRST_INSTRUMENT_API: ${{ secrets.REDCAPTIDIER_REPEAT_FIRST_INSTRUMENT_API }} | |
| REDCAPTIDIER_DEEP_DIVE_VIGNETTE_API: ${{ secrets.REDCAPTIDIER_DEEP_DIVE_VIGNETTE_API }} | |
| REDCAPTIDIER_REPEATING_EVENT_API: ${{ secrets.REDCAPTIDIER_REPEATING_EVENT_API }} | |
| REDCAPTIDIER_LARGE_SPARSE_API: ${{ secrets.REDCAPTIDIER_LARGE_SPARSE_API }} | |
| REDCAPTIDIER_DAG_API: ${{ secrets.REDCAPTIDIER_DAG_API }} | |
| REDCAPTIDIER_LONGITUDINAL_DAG_API: ${{ secrets.REDCAPTIDIER_LONGITUDINAL_DAG_API }} | |
| steps: | |
| - name: Update Ubuntu, Install cURL Headers, add Libraries | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install libcurl4-openssl-dev libxml2-dev | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - name: Install pak dependency | |
| run: | | |
| install.packages("pak") | |
| shell: Rscript {0} | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::covr, any::xml2 | |
| needs: coverage | |
| - name: Test coverage | |
| run: covr::codecov(quiet = FALSE) | |
| shell: Rscript {0} |