Merge pull request #286 from darwin-eu-dev/dbplyr2 #443
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GH_TOKEN }} | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| CDM5_ORACLE_CDM54_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_CDM54_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_CDM54_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_CDM54_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 }} | |
| CDM_SNOWFLAKE_CDM53_SCHEMA: ${{ secrets.CDM_SNOWFLAKE_CDM53_SCHEMA }} | |
| CDM_SNOWFLAKE_OHDSI_SCHEMA: ${{ secrets.CDM_SNOWFLAKE_OHDSI_SCHEMA }} | |
| CDM_SNOWFLAKE_PASSWORD: ${{ secrets.CDM_SNOWFLAKE_PASSWORD }} | |
| CDM_SNOWFLAKE_CONNECTION_STRING: ${{ secrets.CDM_SNOWFLAKE_CONNECTION_STRING }} | |
| CDM_SNOWFLAKE_USER: ${{ secrets.CDM_SNOWFLAKE_USER }} | |
| CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }} | |
| CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }} | |
| CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }} | |
| CDM5_SPARK_CDM_SCHEMA: ${{ secrets.CDM5_SPARK_CDM_SCHEMA }} | |
| CDM5_SPARK_OHDSI_SCHEMA: ${{ secrets.CDM5_SPARK_OHDSI_SCHEMA }} | |
| CDM_BIG_QUERY_CONNECTION_STRING: ${{ secrets.CDM_BIG_QUERY_CONNECTION_STRING }} | |
| CDM_BIG_QUERY_KEY_FILE: ${{ secrets.CDM_BIG_QUERY_KEY_FILE }} | |
| CDM_BIG_QUERY_CDM_SCHEMA: ${{ secrets.CDM_BIG_QUERY_CDM_SCHEMA }} | |
| CDM_BIG_QUERY_OHDSI_SCHEMA: ${{ secrets.CDM_BIG_QUERY_OHDSI_SCHEMA }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup Java | |
| if: runner.os != 'Linux' | |
| uses: actions/setup-java@v4 | |
| with: | |
| distribution: 'corretto' | |
| java-version: '8' | |
| - 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 == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main' | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: package_tarball | |
| path: check/*.tar.gz | |
| - name: Install covr | |
| if: runner.os == 'macOS' | |
| run: | | |
| install.packages("covr") | |
| shell: Rscript {0} | |
| - name: Test coverage | |
| if: runner.os == 'macOS' | |
| run: covr::codecov() | |
| shell: Rscript {0} | |
| Release: | |
| needs: R-CMD-Check | |
| runs-on: macOS-latest | |
| env: | |
| GH_TOKEN: ${{ secrets.GH_TOKEN }} | |
| if: ${{ github.event_name != 'pull_request' && github.ref == 'refs/heads/main' }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Check if version has increased | |
| run: | | |
| echo "new_version="$(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 | |
| - 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@v2 | |
| 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/ |