R_CMD_check_main_weekly.yaml

on:
  schedule:
    - cron: '0 13 * * 6' # every Saturday at 13am UTC
  
  workflow_dispatch:
    
name: 'R check'

jobs:
  R-CMD-check-main:
    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.os }} (${{ matrix.config.r }})

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: macOS-latest, r: 'release'}

    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 }}
      CDM5_REDSHIFT_CDM_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM_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 }}
      WEBAPI_TEST_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_WEBAPI_URL }}
      WEBAPI_TEST_SECURE_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_SECURE_WEBAPI_URL }}
      WEBAPI_TEST_ADMIN_USER_NAME: ${{ secrets.WEBAPI_TEST_ADMIN_USER_NAME }}
      WEBAPI_TEST_ADMIN_USER_PASSWORD: ${{ secrets.WEBAPI_TEST_ADMIN_USER_PASSWORD }}
      TORCH_INSTALL: '1'

    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

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::rcmdcheck
          needs: check

      - name: setup r-reticulate venv
        shell: Rscript {0}
        run: |
          python_packages <- 
            c("polars", "tqdm", "connectorx", "pyarrow", "numpy==1.26.4")
          
          library(reticulate)
          virtualenv_create("r-reticulate", Sys.which("python"))
          virtualenv_install("r-reticulate", 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"'