main.yaml

on:
  schedule:
    - cron: "0 0 * * *"
  workflow_dispatch:
  workflow_call:

name: Main CI workflow

jobs:
  deploy:
    runs-on: ${{ matrix.config.os }}

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

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: windows-2022, r: 'release'}
          - {os: macOS-12, 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: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - name: Checkout pharmr
        uses: actions/checkout@v3
        with:
          path: pharmr_repo

      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}

      - uses: r-lib/actions/setup-pandoc@v2

      - name: Query dependencies
        working-directory: pharmr_repo
        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}

      - uses: actions/setup-python@v2
        with:
            python-version: "3.11"

      - name: Restore R package cache
        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
        working-directory: pharmr_repo
        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 png (temporary)
        working-directory: pharmr_repo
        if: runner.os == 'Windows'
        run: |
          install.packages('png', repos='https://mran.microsoft.com/snapshot/2022-11-27')
        shell: Rscript {0}

      - name: Install R dependencies
        working-directory: pharmr_repo
        run: |
          remotes::install_deps(dependencies = TRUE)
          remotes::install_cran("rcmdcheck")
          install.packages('reticulate')
        shell: Rscript {0}

      - name: Install pharmr
        working-directory: pharmr_repo
        run: |
          remotes::install_local(force=TRUE)
        shell: Rscript {0}

      - name: Checkout Pharmpy
        uses: actions/checkout@v3
        with:
          repository: pharmpy/pharmpy
          path: pharmpy_repo
          fetch-depth: 0

      - name: Install Pharmpy in venv
        working-directory: pharmpy_repo
        run: |
          python3.11 -m venv pharmpy_venv
          source pharmpy_venv/bin/activate
          pip install .

      - name: Test Pharmpy
        working-directory: pharmr_repo
        run: |
          reticulate::py_discover_config()
          reticulate::use_python('../pharmpy_repo/pharmpy_venv/bin')
          pharmr::print_pharmpy_version()
        shell: Rscript {0}

      - name: Install deploy dependencies
        run: |
          install.packages("devtools")
        shell: Rscript {0}

      - name: Update DESCRIPTION and documentation
        working-directory: pharmr_repo/deploy
        run: |
          reticulate::use_python('../../pharmpy_repo/pharmpy_venv/bin')          
          reticulate::py_run_file('build_functions.py')
          devtools::document()
        shell: Rscript {0}

      - name: Check
        working-directory: pharmr_repo
        env:
          _R_CHECK_CRAN_INCOMING_REMOTE_: false
        run: |
          reticulate::py_discover_config()
          reticulate::use_python('../pharmpy_repo/pharmpy_venv/bin')
          pharmr::print_pharmpy_version()
          options(crayon.enabled = TRUE)
          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
          rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "warning", check_dir = "check")
        shell: Rscript {0}

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@main
        with:
          name: results-cran
          path: check