check.yaml

# Run CI for R using https://eddelbuettel.github.io/r-ci/

name: check

on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]

env:
  USE_BSPM: "true"
  _R_CHECK_FORCE_SUGGESTS_: "false"
  NO_BINARY_INSTALL_R_PACKAGES: 'c("madrat", "magclass", "citation", "gms", "goxygen", "GDPuc", "roxygen2")'

jobs:
  check:
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v3

      - name: Bootstrap
        run: |
          sudo chown runner -R .
          sudo locale-gen en_US.UTF-8
          sudo add-apt-repository -y ppa:ubuntugis/ppa
          curl -OLs https://eddelbuettel.github.io/r-ci/run.sh
          chmod 0755 run.sh
          ./run.sh bootstrap
          rm -f bspm_*.tar.gz

      - name: Enable r-universe repo, modify bspm integration
        run: |
          # install packages from https://pik-piam.r-universe.dev and CRAN
          echo '
          options(repos = c(universe = "https://pik-piam.r-universe.dev",
                            CRAN = "https://cloud.r-project.org"))
          ' >> .Rprofile
          cat .Rprofile
          # modify bspm integration to never install binary builds of PIK CRAN packages
          sudo sed -i '/bspm::enable()/d' /etc/R/Rprofile.site
          # need double % because of printf, %s is replaced with "$NO_BINARY_INSTALL_R_PACKAGES" (see "env:" above)
          printf '
          local({
            expr <- quote({
              if (!is.null(repos)) {
                noBinaryInstallRPackages <- %s
                pkgs <- c(bspm::install_sys(pkgs[!pkgs %%in%% noBinaryInstallRPackages]),
                          pkgs[pkgs %%in%% noBinaryInstallRPackages])
              }
              type <- "source"
            })
            trace(utils::install.packages, expr, print = FALSE)
          })
          ' "$NO_BINARY_INSTALL_R_PACKAGES" | sudo tee --append /etc/R/Rprofile.site >/dev/null
          cat /etc/R/Rprofile.site

      - name: Set up Pandoc
        uses: r-lib/actions/setup-pandoc@v2

      - name: Set up Python 3.9
        uses: actions/setup-python@v4
        with:
          python-version: 3.9

      - name: Cache R libraries
        if: ${{ !env.ACT }} # skip when running locally via nektos/act
        uses: pat-s/always-upload-cache@v3
        with:
          path: /usr/local/lib/R/
          key: 3-${{ runner.os }}-usr-local-lib-R-${{ hashFiles('DESCRIPTION') }}
          restore-keys: |
            3-${{ runner.os }}-usr-local-lib-R-

      - name: Restore R library permissions
        run: |
          sudo chmod 2777 /usr/local/lib/R /usr/local/lib/R/site-library

      - name: Install dependencies
        run: |
          ./run.sh install_aptget libhdf5-dev libharfbuzz-dev libfribidi-dev
          ./run.sh install_all
          ./run.sh install_r_binary covr rstudioapi
          ./run.sh install_r lucode2

      - name: Install python dependencies if applicable
        run: |
          [ -f requirements.txt ] && python -m pip install --upgrade pip wheel || true
          [ -f requirements.txt ] && pip install -r requirements.txt || true

      - name: Remove bspm integration # to get rid of error when running install.packages
        run: |
          sudo sed -i '/  trace(utils::install.packages, expr, print = FALSE)/d' /etc/R/Rprofile.site
          cat /etc/R/Rprofile.site

      - name: Verify validation key
        shell: Rscript {0}
        run: lucode2:::validkey(stopIfInvalid = TRUE)

      - name: Checks
        shell: Rscript {0}
        run: |
          options(crayon.enabled = TRUE)
          lucode2::check(runLinter = FALSE)

      - name: Test coverage
        shell: Rscript {0}
        run: covr::codecov(quiet = FALSE)
        env:
          NOT_CRAN: "true"