R_CDM_check_hades.yaml

# 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'}
          - {os: macOS-latest, r: 'release'}
          - {os: ubuntu-22.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/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_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@v3
      
      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}

      - uses: actions/setup-python@v4
        with:
          python-version: '3.10' 
      
      - 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", "22.04"))')
          
      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          cache: always
          extra-packages: any::rcmdcheck
          needs: check
          
      - name: setup r-reticulate venv
        shell: Rscript {0}
        run: |
          python_packages <- 
            c("polars", "tqdm", "connectorx", "pyarrow", "pynvml", "numpy==1.26.4")
          
          library(reticulate)
          virtualenv_create("r-reticulate", Sys.which("python"), packages=python_packages)
          virtualenv_install("r-reticulate", "torch", pip_options = c("--index-url https://download.pytorch.org/whl/cpu"))
          
          path_to_python <- virtualenv_python("r-reticulate")
          writeLines(sprintf("RETICULATE_PYTHON=%s", path_to_python),
                     Sys.getenv("GITHUB_ENV"))
      
      - uses: r-lib/actions/check-r-package@v2
        with:
          args: 'c("--no-manual", "--as-cran")'
          error-on: '"warning"'
          check-dir: '"check"'

      - name: Install covr
        if: runner.os == 'ubuntu-22.04'
        run: |
          remotes::install_cran("covr")
        shell: Rscript {0}

      - name: Test coverage
        if: runner.os == 'ubuntu-22.04'
        run: covr::codecov(token = "${{ secrets.CODECOV_TOKEN }}")
        shell: Rscript {0}

      - 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

  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
          
      - 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/