deploy.yml

name: R

on: [push, pull_request]

permissions:
  contents: read
  pages: write
  id-token: write

jobs:
  build:
    runs-on: ubuntu-22.04
    env:
      cache-version: 8
    steps:
      - uses: actions/checkout@v3
      - name: Set up libraries for Ubuntu
        run: |
          sudo apt-get update
          sudo apt-get install -y libsodium-dev libharfbuzz-dev libfribidi-dev libcurl4-openssl-dev texlive-latex-base texlive-fonts-extra pandoc libmagick++-dev libhdf5-dev

      - name: Set up R 4.0
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: 4.0
      - name: Get R and OS version
        id: get-version
        run: |
          cat("::set-output name=os-version::", sessionInfo()$running, "\n", sep = "")
          cat("::set-output name=r-version::", R.Version()$version.string, "\n", sep = "")
          cat("::endgroup::\n")
        shell: Rscript {0}
      - name: Cache dependencies
        id: cache-deps
        uses: actions/cache@v2
        with:
          path: ${{ env.R_LIBS_USER }}/*
          key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{ env.cache-version }}-deps
      - name: Install dependencies
        if: steps.cache-deps.outputs.cache-hit != 'true'
        run: |
          install.packages(c("remotes", "rcmdcheck", "BiocManager", "Seurat", "covr"))
          BiocManager::install("BiocCheck")
          remotes::install_github(c("RubD/Giotto", "mojaveazure/seurat-disk"))
          remotes::install_deps(dependencies = TRUE)
        shell: Rscript {0}
        env:
          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      - name: rcmdcheck
        run: |
          rcmdcheck::rcmdcheck(
            error_on = "warning",
            check_dir = "check"
          )
        shell: Rscript {0}
        env:
          _R_CHECK_FORCE_SUGGESTS_: false
      - name: BiocCheck
        run: |
          BiocCheck::BiocCheck(
            dir('check', 'tar.gz$', full.names = TRUE),
            `no-check-R-ver` = TRUE,
            `no-check-pkg-size` = TRUE,
            `no-check-vignettes` = TRUE
          )
        shell: Rscript {0}
        env:
          _R_CHECK_FORCE_SUGGESTS_: false
      - name: Run covr
        run: |
          covr::package_coverage()
        shell: Rscript {0}
      - name: Downgrade pkgdown
        run: |
          remotes::install_version("pkgdown", "2.0.3")
        shell: Rscript {0}
      - name: Build docs
        run: |
          Rscript -e 'pkgdown::build_site(new_process = FALSE)'
          touch docs/.nojekyll
      - uses: actions/upload-pages-artifact@v1
        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
        with:
          path: ./docs
  deploy:
    runs-on: ubuntu-22.04
    needs: build
    environment:
      name: github-pages
      url: ${{ steps.deployment.outputs.page_url }}
    steps:
      - name: Deploy to GitHub Pages
        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
        id: deployment
        uses: actions/deploy-pages@v1