R-CMD-check.yaml

# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]

name: R-CMD-check

jobs:
  R-CMD-check:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GJPAT2 }}
      # GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RGL_USE_NULL: TRUE
      _R_CHECK_DONTTEST_EXAMPLES_: FALSE
      _R_CHECK_TESTS_NLINES_: 0
      NEUPRINT_TOKEN: ${{ secrets.NEUPRINT_TOKEN }}
      CLIO_TOKEN: ${{ secrets.CLIO_TOKEN }}
      FLYWIRE_PRINCIPLES: IAGREETOTHEFLYWIREPRINCIPLES

    steps:
      - uses: actions/checkout@v2

      - uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - 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: 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 dependencies
        run: |
          remotes::install_deps(dependencies = TRUE)
          remotes::install_cran("rcmdcheck")
          remotes::install_cran("covr")
          remotes::install_cran("pkgdown")
          remotes::install_cran("devtools")
        shell: Rscript {0}

      - name: Add some R options for later steps
        run: |
          cat("\noptions(fafbseg.use_static_celltypes=TRUE)\n", file = "~/.Rprofile", append = TRUE)
        shell: Rscript {0}

      - name: Download flywire data
        run: |
          fafbseg::download_flywire_release_data()
        shell: Rscript {0}

      - uses: r-lib/actions/check-r-package@v2

      - name: Deploy package
        run: |
          git config --local user.name "$GITHUB_ACTOR"
          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
          Rscript -e 'devtools::install(); pkgdown::deploy_to_branch(new_process = FALSE)'