Use CdmExecutionSettings to set the cohort schema and table for createCohortBasedCovariateSettings
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| # For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. | |
| # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions | |
| on: | |
| push: | |
| branches: | |
| - '**' | |
| pull_request: | |
| branches: | |
| - '**' | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: windows-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"} | |
| - {os: macOS-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"} | |
| - {os: ubuntu-20.04, r: 'release', rtools: '', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GH_TOKEN }} | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM54_SCHEMA }} | |
| CDM5_ORACLE_OHDSI_SCHEMA: ${{ secrets.CDM5_ORACLE_OHDSI_SCHEMA }} | |
| CDM5_ORACLE_PASSWORD: ${{ secrets.CDM5_ORACLE_PASSWORD }} | |
| CDM5_ORACLE_SERVER: ${{ secrets.CDM5_ORACLE_SERVER }} | |
| CDM5_ORACLE_USER: ${{ secrets.CDM5_ORACLE_USER }} | |
| CDM5_POSTGRESQL_CDM_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM54_SCHEMA }} | |
| CDM5_POSTGRESQL_OHDSI_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_OHDSI_SCHEMA }} | |
| CDM5_POSTGRESQL_PASSWORD: ${{ secrets.CDM5_POSTGRESQL_PASSWORD }} | |
| CDM5_POSTGRESQL_SERVER: ${{ secrets.CDM5_POSTGRESQL_SERVER }} | |
| CDM5_POSTGRESQL_USER: ${{ secrets.CDM5_POSTGRESQL_USER }} | |
| CDM5_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM54_SCHEMA }} | |
| CDM5_SQL_SERVER_OHDSI_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_OHDSI_SCHEMA }} | |
| CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }} | |
| CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }} | |
| CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }} | |
| CDM5_REDSHIFT_CDM_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM54_SCHEMA }} | |
| CDM5_REDSHIFT_OHDSI_SCHEMA: ${{ secrets.CDM5_REDSHIFT_OHDSI_SCHEMA }} | |
| CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }} | |
| CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }} | |
| CDM5_REDSHIFT_USER: ${{ secrets.CDM5_REDSHIFT_USER }} | |
| CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }} | |
| CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }} | |
| CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - uses: r-lib/actions/setup-tinytex@v2 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install system requirements | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get install -y libssh-dev | |
| Rscript -e 'install.packages("remotes")' | |
| while read -r cmd | |
| do | |
| eval sudo $cmd | |
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::rcmdcheck | |
| needs: check | |
| - uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| args: 'c("--no-manual", "--as-cran")' | |
| error-on: '"warning"' | |
| check-dir: '"check"' | |
| - name: Upload source package | |
| if: success() && runner.os == 'Windows' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: package_tarball | |
| path: check/*.tar.gz | |
| - name: Install covr | |
| if: runner.os == 'Linux' | |
| run: | | |
| remotes::install_cran("covr") | |
| remotes::install_cran("xml2") | |
| shell: Rscript {0} | |
| - name: Test coverage | |
| if: runner.os == 'Linux' | |
| run: | | |
| cov <- covr::package_coverage( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") | |
| ) | |
| covr::to_cobertura(cov) | |
| shell: Rscript {0} | |
| - uses: codecov/codecov-action@v4 | |
| if: runner.os == 'Linux' | |
| with: | |
| file: ./cobertura.xml | |
| plugin: noop | |
| disable_search: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| Release: | |
| needs: R-CMD-Check | |
| runs-on: macOS-latest | |
| env: | |
| GH_TOKEN: ${{ secrets.GH_TOKEN }} | |
| if: ${{ github.event_name != 'pull_request' && github.ref == 'refs/heads/main' }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Check if version has increased | |
| run: | | |
| echo "new_version="$(perl compare_versions --tag) >> $GITHUB_ENV | |
| - name: Display new version number | |
| if: ${{ env.new_version != '' }} | |
| run: | | |
| echo "${{ env.new_version }}" | |
| - name: Create release | |
| if: ${{ env.new_version != '' }} | |
| uses: actions/create-release@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GH_TOKEN }} | |
| with: | |
| tag_name: ${{ env.new_version }} | |
| release_name: Release ${{ env.new_version }} | |
| body: | | |
| See NEWS.md for release notes. | |
| draft: false | |
| prerelease: false | |
| # AGS: Commenting out until Strategus is in HADES | |
| # - uses: r-lib/actions/setup-r@v2 | |
| # if: ${{ env.new_version != '' }} | |
| # | |
| # - name: Install drat | |
| # if: ${{ env.new_version != '' }} | |
| # run: | | |
| # install.packages('drat') | |
| # shell: Rscript {0} | |
| # | |
| # - name: Remove any tarballs that already exists | |
| # if: ${{ env.new_version != '' }} | |
| # run: | | |
| # rm -f *.tar.gz | |
| # | |
| # - name: Download package tarball | |
| # if: ${{ env.new_version != '' }} | |
| # uses: actions/download-artifact@v4 | |
| # with: | |
| # name: package_tarball | |
| # | |
| # - name: Push to drat | |
| # if: ${{ env.new_version != '' }} | |
| # run: | | |
| # bash deploy.sh | |
| # | |
| # - name: Push to BroadSea | |
| # if: ${{ env.new_version != '' }} | |
| # run: | | |
| # curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/ | |
| # |