From f66e75ea4170bc1ef83a3a01ff3577ee67c7ee28 Mon Sep 17 00:00:00 2001 From: Schuemie Date: Wed, 10 Feb 2021 15:29:25 +0100 Subject: [PATCH] Adding back rest of script --- .github/workflows/R_CMD_check_Hades.yaml | 151 ++++++++++++++++++++++- 1 file changed, 150 insertions(+), 1 deletion(-) diff --git a/.github/workflows/R_CMD_check_Hades.yaml b/.github/workflows/R_CMD_check_Hades.yaml index d759004..72db945 100644 --- a/.github/workflows/R_CMD_check_Hades.yaml +++ b/.github/workflows/R_CMD_check_Hades.yaml @@ -11,6 +11,120 @@ on: 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'} # Does not appear to have Java 32-bit, hence the --no-multiarch + - {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: + R_REMOTES_NO_ERRORS_FROM_WARNINGS: true + RSPM: ${{ matrix.config.rspm }} + CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_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_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_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 }} + + steps: + - uses: actions/checkout@v2 + + - uses: r-lib/actions/setup-r@v1 + with: + r-version: ${{ matrix.config.r }} + + - uses: r-lib/actions/setup-tinytex@v1 + + - uses: r-lib/actions/setup-pandoc@v1 + + - name: Query dependencies + run: | + install.packages('remotes') + saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) + writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") + shell: Rscript {0} + + - name: Cache R packages + if: runner.os != 'Windows' + uses: actions/cache@v2 + 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 + if: runner.os == 'Linux' + run: | + 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} + + - name: Upload check results + if: failure() + uses: actions/upload-artifact@v2 + with: + name: ${{ runner.os }}-r${{ matrix.config.r }}-results + path: check + + - name: Upload source package + if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/master' + uses: actions/upload-artifact@v2 + with: + name: package_tarball + path: check/*.tar.gz + + - name: Test coverage + if: runner.os == 'macOS' + run: covr::codecov() + shell: Rscript {0} + Release: runs-on: macOS-latest @@ -28,7 +142,12 @@ jobs: - 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 @@ -41,4 +160,34 @@ jobs: Automatically generated release draft: false prerelease: false + + - uses: r-lib/actions/setup-r@v1 + 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/ \ No newline at end of file