diff --git a/.github/workflows/R_CMD_check_Hades.yaml b/.github/workflows/R_CMD_check_Hades.yaml index ee60624..550e187 100644 --- a/.github/workflows/R_CMD_check_Hades.yaml +++ b/.github/workflows/R_CMD_check_Hades.yaml @@ -20,29 +20,49 @@ jobs: fail-fast: false matrix: config: - - {os: windows-latest, r: 'release'} # Does not appear to have Java 32-bit, hence the --no-multiarch + - {os: windows-latest, r: 'release'} - {os: macOS-latest, r: 'release'} - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - #- {os: ubuntu-20.04, r: 'devel', 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_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_SCHEMA }} + 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_CDM_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM_SCHEMA }} + 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_CDM_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM_SCHEMA }} + 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: ${{ secrets.CDM_BIG_QUERY_OHDSI_SCHEMA }} steps: - uses: actions/checkout@v3 @@ -55,111 +75,109 @@ jobs: - uses: r-lib/actions/setup-pandoc@v2 - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Cache R packages - if: runner.os != 'Windows' - uses: actions/cache@v3 - with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- - - - name: Install system dependencies + - 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"))') - - - name: Install libssh - if: runner.os == 'Linux' - run: | - sudo apt-get install libssh-dev - - name: Install dependencies - run: | - remotes::install_deps(dependencies = TRUE, INSTALL_opts=c("--no-multiarch")) - remotes::install_cran("rcmdcheck") - shell: Rscript {0} - - - name: Install covr - if: runner.os == 'macOS' - run: | - remotes::install_cran("covr") - shell: Rscript {0} - - - name: Remove check folder if exists - if: runner.os == 'macOS' - run: unlink("check", recursive = TRUE) - shell: Rscript {0} - - - name: Check - env: - _R_CHECK_CRAN_INCOMING_REMOTE_: false - run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-multiarch"), error_on = "warning", check_dir = "check") - shell: Rscript {0} + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check - - name: Upload check results - if: failure() - uses: actions/upload-artifact@v3 + - uses: r-lib/actions/check-r-package@v2 with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check - + 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@v3 + 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} - - - uses: actions/checkout@v3 - with: - fetch-depth: 0 - name: Remove any tarballs that already exists + if: ${{ env.new_version != '' }} run: | rm -f *.tar.gz - + - name: Download package tarball - uses: actions/download-artifact@v3 + if: ${{ env.new_version != '' }} + uses: actions/download-artifact@v2 with: - name: package_tarball - - - name: Tag and push to drat and BroadSea + name: package_tarball + + - name: Push to drat + if: ${{ env.new_version != '' }} + run: | + bash deploy.sh + + - name: Push to BroadSea + if: ${{ env.new_version != '' }} run: | - perl compare_versions --tag && \ - bash deploy.sh && \ curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/ - \ No newline at end of file diff --git a/.github/workflows/nightly_cleanup_Hades.yml b/.github/workflows/nightly_cleanup_Hades.yml deleted file mode 100644 index 80af7c7..0000000 --- a/.github/workflows/nightly_cleanup_Hades.yml +++ /dev/null @@ -1,18 +0,0 @@ -name: 'nightly artifacts cleanup' -on: - schedule: - - cron: '0 1 * * *' # every night at 1 am UTC - -jobs: - remove-old-artifacts: - runs-on: ubuntu-latest - timeout-minutes: 10 - - steps: - - name: Remove old artifacts - uses: c-hive/gha-remove-artifacts@v1 - with: - age: '7 days' - # Optional inputs - # skip-tags: true - skip-recent: 1