check.yml

## This is a simplified action for building and testing a Bioconductor package
## based on:
## * https://github.com/lcolladotor/biocthis/blob/master/actions/check-bioc.yml
## * https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
## * https://github.com/seandavi/BuildABiocWorkshop2020/blob/master/.github/workflows/basic_checks.yaml
name: R-CMD-check-bioc

permissions: read-all

## Specify which branches to run on
## The "devel" branch corresponds to Bioc-devel and "RELEASE_X" branches are
## Bioconductor releases. See http://bioconductor.org/developers/how-to/git/.
on:
  push:
    branches:
      - devel
      - 'RELEASE_*'
      - ci
  pull_request:
    branches:
      - devel
      - 'RELEASE_*'
      - ci

jobs:
  get-bioc-release:
    # Identify the Bioconductor release from the git branch. Also specifies a
    # Bioconductor Docker image to use.
    runs-on: ubuntu-latest
    outputs:
      biocimage: ${{ steps.get-release.outputs.biocimage }}
      biocrelease: ${{ steps.get-release.outputs.biocrelease }}

    steps:
      - id: get-release
        name: Get Bioconductor release
        run: |
          if echo "$GITHUB_REF" | grep -q "RELEASE_"; then
              biocrelease="$(basename -- $GITHUB_REF | tr '[:upper:]' '[:lower:]')"
          else
              biocrelease="devel"
          fi
          biocimage="bioconductor/bioconductor_docker:${biocrelease}"
          echo "Bioc release: ${biocrelease}"
          echo "Bioc docker image: {$biocimage}"
          ## Store the information
          echo "biocimage=${biocimage}" >> $GITHUB_OUTPUT
          echo "biocrelease=${biocrelease}" >> $GITHUB_OUTPUT

  get-bioc-version:
    # Identify the Bioconductor version number and R version to use. This is
    # done by checking the versions in the Bioconductor Docker container
    # selected by get-bioc-release.
    runs-on: ubuntu-latest
    needs: get-bioc-release
    container:
      image: ${{ needs.get-bioc-release.outputs.biocimage }}
    outputs:
      Rversion: ${{ steps.set-versions.outputs.rversion }}
      biocversion: ${{ steps.set-versions.outputs.biocversion }}

    steps:
      - id: get-versions
        name: Get Bioconductor/R versions
        run: |
          biocconfig <- "https://bioconductor.org/config.yaml"
          biocrelease <- "${{ needs.get-bioc-release.outputs.biocrelease }}"
          cat("Bioc release RAW: ", biocrelease, "\n")
          biocrelease <- ifelse(
            grepl(biocrelease, "release"),
            "release", "devel"
          )
          biocmap <- BiocManager:::.version_map_get_online(biocconfig)
          biocversion <- subset(biocmap, BiocStatus == biocrelease)[, 'Bioc']
          rversion <- subset(biocmap, BiocStatus == biocrelease)[, 'R']
          writeLines(as.character(c(biocversion, rversion)),
                     "versions.txt")
          cat("GET VERSIONS", "\n")
          cat("Bioc release: ", biocrelease, "\n")
          cat("Bioc version: ", as.character(biocversion), "\n")
          cat("R version: ", as.character(rversion), "\n")
        shell: Rscript {0}
      - id: set-versions
        name: Set Bioconductor/R versions
        run: |
          biocversion=$(head -n 1 versions.txt)
          rversion=$(tail -n 1 versions.txt)
          echo "SET VERSIONS"
          echo "Bioc version: ${biocversion}"
          echo "R version: ${rversion}"
          ## Store the information
          echo "biocversion=${biocversion}" >> $GITHUB_OUTPUT
          echo "rversion=${rversion}" >> $GITHUB_OUTPUT

  R-CMD-check-docker:
    ## Run checks in the Bioconductor Docker container
    name: ubuntu-latest (r-biocdocker bioc-${{ needs.get-bioc-version.outputs.biocversion }})
    needs: [get-bioc-release, get-bioc-version]
    runs-on: ubuntu-latest
    container:
      image: ${{ needs.get-bioc-release.outputs.biocimage }}
      volumes:
        - /home/runner/work/_temp/Library:/usr/local/lib/R/host-site-library
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_BIOC_VERSION: ${{ needs.get-bioc-version.outputs.biocversion }}

    steps:
      - name: Checkout
        uses: actions/checkout@v4

      - name: Install extra linux dependencies
        run: sudo apt-get update -y && sudo apt-get install -y libcurl4-openssl-dev devscripts qpdf

      - name: Setup R dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          cache-version: 3
          extra-packages: any::rcmdcheck
          needs: check

        # Fixes https://github.com/Bioconductor/bioconductor_docker/issues/22
      - name: Manually install preprocessCore
        run: |
          install.packages(
            "preprocessCore",
            repos = BiocManager::repositories(),
            type = "source",
            configure.args = "--disable-threading"
          )
        shell: Rscript {0}

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

      - name: Check R package
        uses: r-lib/actions/check-r-package@v2
        with:
          upload-snapshots: true
          upload-results: true

      - name: BiocCheck
        run: |
          BiocManager::install("BiocCheck")
          BiocCheck::BiocCheck(
            dir('check', 'tar.gz$', full.names = TRUE),
            `no-check-R-ver` = TRUE,
            `no-check-bioc-help` = TRUE
          )
        shell: Rscript {0}

  R-CMD-check:
    ## Run checks on other platforms.
    name: ${{ matrix.config.os }} (r-${{ needs.get-bioc-version.outputs.rversion }} bioc-${{ needs.get-bioc-version.outputs.biocversion }})
    needs: [get-bioc-release, get-bioc-version]
    runs-on: ${{ matrix.config.os }}
    strategy:
      fail-fast: false
      matrix:
        experimental: [true]
        config:
          - {os: windows-latest}
          - {os: macOS-latest}
          - {os: ubuntu-20.04, rspm: "https://packagemanager.posit.co/cran/__linux__/focal/latest"}
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: ${{ matrix.config.rspm }}
      R_BIOC_VERSION: ${{ needs.get-bioc-version.outputs.biocversion }}
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - name: Checkout
        uses: actions/checkout@v4

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

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ needs.get-bioc-version.outputs.rversion }}
          use-public-rspm: true

      - name: Setup R dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          cache-version: 3
          extra-packages: any::rcmdcheck
          needs: check

      # Fixes https://github.com/Bioconductor/bioconductor_docker/issues/22
      - name: Manually install preprocessCore on Linux
        if: runner.os == 'Linux'
        run: |
          install.packages(
            "preprocessCore",
            repos = BiocManager::repositories(),
            type = "source",
            configure.args = "--disable-threading"
          )
        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 R package
        uses: r-lib/actions/check-r-package@v2
        with:
          upload-snapshots: true
          upload-results: true

  test-coverage:
    ## Calculate package test coverage. Only runs if R-CMD-check-docker has
    ## completed successfully. Uses the Bioconductor Docker image.
    if: github.ref == 'refs/heads/devel'
    needs: [get-bioc-release, get-bioc-version, R-CMD-check-docker]
    runs-on: ubuntu-latest
    container:
      image: ${{ needs.get-bioc-release.outputs.biocimage }}
      volumes:
        - /home/runner/work/_temp/Library:/usr/local/lib/R/host-site-library
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_BIOC_VERSION: ${{ needs.get-bioc-version.outputs.biocversion }}

    steps:
      - name: Checkout
        uses: actions/checkout@v4

      - name: Install extra linux dependencies
        run: sudo apt-get update -y && sudo apt-get install -y libcurl4-openssl-dev devscripts qpdf

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::covr, any::xml2
          needs: coverage

      # Fixes https://github.com/Bioconductor/bioconductor_docker/issues/22
      - name: Manually install preprocessCore
        run: |
          install.packages(
            "preprocessCore",
            repos = BiocManager::repositories(),
            type = "source",
            configure.args = "--disable-threading"
          )
        shell: Rscript {0}

      - name: Test coverage
        run: |
          cov <- covr::package_coverage(
            quiet = FALSE,
            clean = FALSE,
            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
          )
          covr::to_cobertura(cov)
        shell: Rscript {0}

      - uses: codecov/codecov-action@v4
        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 }}
          file: ./cobertura.xml
          plugin: 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

  pkgdown:
    ## Build pkgdown site and push to gh-pages branch. Only runs if on the
    ## devel branch and R-CMD-check-docker has completed successfully. Uses the
    ## Bioconductor Docker image.
    if: github.ref == 'refs/heads/devel' || github.base_ref == 'devel'
    needs: [get-bioc-release, get-bioc-version, R-CMD-check-docker]
    runs-on: ubuntu-latest
    container:
      image: ${{ needs.get-bioc-release.outputs.biocimage }}
      volumes:
        - /home/runner/work/_temp/Library:/usr/local/lib/R/host-site-library
    concurrency:
      # Only restrict concurrency for non-PR jobs
      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_BIOC_VERSION: ${{ needs.get-bioc-version.outputs.biocversion }}

    steps:

      - name: Checkout
        uses: actions/checkout@v4

      - name: Install extra linux dependencies
        run: sudo apt-get update -y && sudo apt-get install -y libcurl4-openssl-dev devscripts qpdf

      - name: Setup R dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          cache-version: 3
          extra-packages: any::pkgdown, local::.
          needs: website

      # Fixes https://github.com/Bioconductor/bioconductor_docker/issues/22
      - name: Manually install preprocessCore
        run: |
          install.packages(
            "preprocessCore",
            repos = BiocManager::repositories(),
            type = "source",
            configure.args = "--disable-threading"
          )
        shell: Rscript {0}

      - name: Build pkgdown site
        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
        shell: Rscript {0}

      - name: Deploy to GitHub pages 🚀
        if: github.event_name != 'pull_request'
        uses: JamesIves/github-pages-deploy-action@v4.6.8
        with:
          clean: false
          branch: gh-pages
          folder: docs