R-CMD-check.yaml

on:
  push:
  pull_request:
    branches:
      - main
  schedule:
    - cron: '0 8 1 * *'

name: R-CMD-check

permissions:
  contents: write

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

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

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

    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      CRAN: ${{ matrix.config.cran }}
      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

    steps:
      - name: Check out repo
        uses: actions/checkout@v3

      - name: Set up R
        uses: r-lib/actions/setup-r@HEAD
        if: matrix.config.image == null
        with:
          r-version: ${{ matrix.config.r }}

      - name: Set up pandoc
        uses: r-lib/actions/setup-pandoc@HEAD
        if: matrix.config.image == null

      - name: Install remotes
        run: |
          install.packages('remotes')
        shell: Rscript {0}

      - name: Set BiocManager version
        if: matrix.config.image == null
        run: |
          install.packages('BiocManager')
          BiocManager::install(ask = FALSE)
        shell: Rscript {0}

      - name: Query dependencies
        run: |
          saveRDS(remotes::dev_package_deps(dependencies = TRUE, repos = c(getOption('repos'), BiocManager::repositories())), 'depends.Rds', version = 2)
        shell: Rscript {0}

      - name: Cache R packages
        if: runner.os != 'Windows' && matrix.config.image == null
        uses: actions/cache@v4
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ runner.os }}-r-${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-${{ hashFiles('depends.Rds') }}
          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-

      - name: Install system dependencies
        if: runner.os == 'Linux'
        env:
          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
        run: |
          sudo apt-get update && sudo apt-get -y install libcurl4-openssl-dev

      - name: Install dependencies
        run: |
          local_deps <- remotes::local_package_deps(dependencies = TRUE)
          deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
          BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]], Ncpu = 2L)
          remotes::install_cran('rcmdcheck', Ncpu = 2L)
        shell: Rscript {0}

      - name: Session info
        run: |
          options(width = 100)
          pkgs <- installed.packages()[, "Package"]
          sessioninfo::session_info(pkgs, include_base = TRUE)
        shell: Rscript {0}

      - name: Check
        run: rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'warning', check_dir = 'check')
        shell: Rscript {0}

      - name: BiocCheck
        run: |
          BiocManager::install("BiocCheck")
          BiocCheck::BiocCheck(".")
        shell: Rscript {0}

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@HEAD
        with:
          name: ${{ runner.os }}-r${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-results
          path: check

      - name: pkgdown dependencies
        if: github.event_name == 'push' && matrix.config.os == 'ubuntu-latest'
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::pkgdown, local::., any::covr, any::xml2
          needs: website, coverage

      - name: Test coverage
        if: github.event_name == 'push' && matrix.config.os == 'ubuntu-latest'
        run: |
          cov <- covr::package_coverage(
            quiet = FALSE,
            clean = FALSE,
            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
          )
          print(cov)
          covr::to_cobertura(cov)
        shell: Rscript {0}

      - uses: codecov/codecov-action@v5
        if: github.event_name == 'push' && matrix.config.os == 'ubuntu-latest'
        with:
          # Fail if error if not on PR, or if on PR and token is given
          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
          files: ./cobertura.xml
          plugins: noop
          disable_search: true
          token: ${{ secrets.CODECOV_TOKEN }}

      - name: Show testthat output
        if: always()
        run: |
          ## --------------------------------------------------------------------
          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
        shell: bash

      - name: Upload test results
        if: failure()
        uses: actions/upload-artifact@v4
        with:
          name: coverage-test-failures
          path: ${{ runner.temp }}/package

      - name: Build site
        if: github.event_name == 'push' && matrix.config.os == 'ubuntu-latest'
        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
        shell: Rscript {0}

      - name: Deploy to GitHub pages 🚀
        if: github.event_name == 'push' && github.ref == 'refs/heads/main' && matrix.config.os == 'ubuntu-latest'
        uses: JamesIves/github-pages-deploy-action@v4.4.1
        with:
          clean: false
          branch: gh-pages
          folder: docs