actions.yml

on:
  push:
    branches-ignore: 
      - updateREADME
  pull_request:
    branches:
      - master
  workflow_dispatch:  # Allow manual triggers
  schedule:
    - cron: '0 8 * * 4'

name: R-CMD-check

jobs:
  ## pre-job to determine if a job has been run for the same SHA (e.g. on a different branch)
  gatekeeper:
    runs-on: ubuntu-latest
    outputs:
      should_skip: ${{ steps.skip_check.outputs.should_skip }}
    steps:
      - id: skip_check
        uses: fkirc/skip-duplicate-actions@master
        with:
          github_token: ${{ github.token }}

  versions:
    needs: gatekeeper
    if: (github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (github.event_name != 'schedule' && (needs.gatekeeper.outputs.should_skip == 'false') && !contains(github.event.head_commit.message, 'worksave') && !contains(github.event.head_commit.message, 'skip-ci'))
    runs-on: ubuntu-latest
    outputs:
      r: ${{ steps.setup.outputs.r }}
      bioc: ${{ steps.setup.outputs.bioc }}
      dockerise: ${{ steps.setup.outputs.dockerise }}
      docker_tag: ${{ steps.setup.outputs.docker_tag }}
    steps:
      - uses: rlespinasse/github-slug-action@v3.x
      - uses: r-lib/actions/setup-r@v2
      - name: Get R/Bioc versions
        id: setup
        run: |
          BRANCH_NAME="${{ env.GITHUB_REF_SLUG }}"
          ## R and Bioc versions
          Rscript -e "install.packages('BiocManager', Ncpus=2)"
          r_devel=$(Rscript -e "vm=BiocManager:::.version_map(); cat(as.character(vm[vm\$BiocStatus == 'devel',]\$R))")
          r_release=$(Rscript -e "vm=BiocManager:::.version_map(); cat(as.character(vm[vm\$BiocStatus == 'release',]\$R))")
          if [[ $BRANCH_NAME =~ "release_" ]]
          then
            bioc="latest"
            r="$r_release"
          else
            bioc="devel"
            r="$r_devel"
          fi
          echo "r=$r" >> $GITHUB_OUTPUT
          echo "bioc=$bioc" >> $GITHUB_OUTPUT

          ## Docker
          # Only Dockerise for 'master' or 'RELEASE_*' branches
          dockerise='false'
          [[ github.event_name != 'schedule' && ($BRANCH_NAME == "master" || $BRANCH_NAME =~ "release_") ]] && dockerise='true'
          echo "dockerise=$dockerise" >> $GITHUB_OUTPUT
          # Docker tag is 'github' for master and the branch name for release branches
          docker_tag="github"
          [[ $BRANCH_NAME =~ "release_" ]] && docker_tag=$BRANCH_NAME
          echo "docker_tag=$docker_tag" >> $GITHUB_OUTPUT

  R-CMD-check:
    needs: [gatekeeper, versions]
    ## run scheduled jobs only on main repo - do not run a duplicate job for merges etc. Do not run if commit messages include any of 'worksave' or 'skip-ci'
    if: (github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (github.event_name != 'schedule' && (needs.gatekeeper.outputs.should_skip == 'false') && !contains(github.event.head_commit.message, 'worksave') && !contains(github.event.head_commit.message, 'skip-ci'))
    runs-on: ${{ matrix.config.os }}
    container: ${{ matrix.config.image }}

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

    strategy:
      fail-fast: false
      matrix:
        config:
          - { os: windows-latest, r: '${{ needs.versions.outputs.r }}', bioc: '${{ needs.versions.outputs.bioc }}'}
          - { os: macOS-latest, r: '${{ needs.versions.outputs.r }}', bioc: '${{ needs.versions.outputs.bioc }}'}
          - { os: ubuntu-latest, r: '${{ needs.versions.outputs.r }}', bioc: '${{ needs.versions.outputs.bioc }}', image: 'bioconductor/bioconductor_docker:${{ needs.versions.outputs.bioc }}'}

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

    steps:
      - name: Check out repo ⬇️
        uses: actions/checkout@v2

      - name: Set up R ▶️
        uses: r-lib/actions/setup-r@v2
        if: matrix.config.image == null
        with:
          r-version: ${{ matrix.config.r }}

      - name: Create slug/short variables
        uses: rlespinasse/github-slug-action@v3.x

      - name: Install remotes 🔭
        run: |
          install.packages('remotes', Ncpus=2)
        shell: Rscript {0}

      - name: Set BiocManager version 📆
        if: matrix.config.image == null
        run: |
          install.packages('BiocManager', Ncpus=2)
          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, Ncpus=2)
        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@v1
        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 and package dependencies using github action 🔧
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-repositories: 'https://cloud.r-project.org'

      - name: Install extra dependencies for macOS
        if: runner.os == 'macOS'
        run: |
          brew install --cask xquartz
          brew install gcc

      - name: Install extra dependencies for linux
        if: runner.os == 'Linux'
        env:
          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
        run: |
          sudo apt-get update
          sudo apt-get install -y pandoc-citeproc
          sudo apt-get install -y qpdf

      - name: Install R dependencies 🔨
        run: |
          options(repos = c(CRAN = "https://cran.r-project.org"))
          remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories(), Ncpus=2)
          remotes::install_cran("rcmdcheck", Ncpus=2)
          remotes::install_cran("covr", Ncpus=2)
        shell: Rscript {0}

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

      #   # runs rmdcheck, first runs 'devtools::install to make sure there is a copy of mixOmics the parallel workers can access'
      # - name: Check ✅ 
      #   if: (!contains(github.event.head_commit.message, 'skip-check'))
      #   run: |
      #     remotes::install_cran("devtools", Ncpus=2)
      #     devtools::install()
      #     devtools::check(args = c("--no-manual"), error_on = "warning", check_dir = "check")
      #   shell: Rscript {0}

      # - name: BiocCheck 🧬 ✅
      #   if: (!contains(github.event.head_commit.message, 'skip-check'))
      #   run: |
      #     BiocManager::install("BiocCheck", Ncpus=2)
      #     BiocCheck::BiocCheck(".")
      #   shell: Rscript {0}

      # - name: Check --as-cran ✅ ✅ 
      #   if: (github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (github.event_name == 'workflow_dispatch' && github.repository == 'mixOmicsTeam/mixOmics')
      #   env:
      #     _R_CHECK_CRAN_INCOMING_: false
      #   run: |
      #     options(devtools.check.dir = "check/asCRAN", devtools.check.warning = "never")
      #     devtools::check(args = c("--no-manual", "--as-cran", "--ignore-vignettes", "--run-dontrun"), build_args = c("--no-build-vignettes"))
      #   shell: Rscript {0}

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

      # - name: Show testthat output 📖
      #   if: always()
      #   run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
      #   shell: bash

      # - name: Push to DockerHub 📦
      #   if: runner.os == 'Linux' && needs.versions.outputs.dockerise == 'true' && !contains(github.event.head_commit.message, 'skip-docker')
      #   uses: docker/build-push-action@v1
      #   with:
      #     username: ${{ secrets.DOCKER_USERNAME }}
      #     password: ${{ secrets.DOCKER_PASSWORD }}
      #     repository: mixomicsteam/mixomics
      #     tags: ${{ needs.versions.outputs.docker_tag }}
      #     build_args: BIOC_VERSION=${{ needs.versions.outputs.bioc }} 

      - name: Create coverage report 🔍
        if: (runner.os == 'Linux' && github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (runner.os == 'Linux' && github.event_name == 'workflow_dispatch' && github.repository == 'mixOmicsTeam/mixOmics')
        run: |
          set +e
          echo "Checking if covr is installed..."
          Rscript -e "if (!requireNamespace('covr', quietly = TRUE)) install.packages('covr')"

          echo "Generating and saving coverage report..."
          # Print RUNNER_TEMP path for debugging
          echo "RUNNER_TEMP path: $RUNNER_TEMP"

          # Generate coverage object, print temp installation path, and save it
          Rscript -e "
            install_path <- file.path(normalizePath(Sys.getenv('RUNNER_TEMP'), winslash = '/'), 'package')
            print(paste('Installation path:', install_path))
            cov <- covr::package_coverage(
              quiet = FALSE,
              clean = FALSE,
              install_path = install_path
            )
            print('Coverage calculated!')
            saveRDS(cov, 'coverage.rds')
            print(cov)"
          set -e

      - name: Upload coverage report to Codecov
        if: (runner.os == 'Linux' && github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (runner.os == 'Linux' && github.event_name == 'workflow_dispatch' && github.repository == 'mixOmicsTeam/mixOmics')
        run: |
          set +e
          echo "Uploading coverage report to Codecov..."
          # Load coverage object from saved file and upload to Codecov
          Rscript -e "cov <- readRDS('coverage.rds'); covr::codecov(coverage = cov)"
          set -e
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}


      # - name: Test coverage
      #   if: (runner.os == 'Linux' && github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (runner.os == 'Linux' && github.event_name == 'workflow_dispatch' && github.repository == 'mixOmicsTeam/mixOmics')
      #   run: |
      #     cov <- covr::package_coverage(
      #       quiet = FALSE,
      #       clean = FALSE,
      #       install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
      #     )
      #     print("Coverage calculated!")
      #     print(cov)
      #     covr::to_cobertura(cov)
      #   shell: Rscript {0}
  
      # - uses: codecov/codecov-action@v4
      #   if: (runner.os == 'Linux' && github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (runner.os == 'Linux' && github.event_name == 'workflow_dispatch' && github.repository == 'mixOmicsTeam/mixOmics')
      #   with:
      #     file: ./cobertura.xml
      #     plugin: noop
      #     disable_search: true
      #     token: ${{ secrets.CODECOV_TOKEN }}

      # - name: Create coverage report 🔍
      #   if: (runner.os == 'Linux' && github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (runner.os == 'Linux' && github.event_name == 'workflow_dispatch' && github.repository == 'mixOmicsTeam/mixOmics')
      #   # the commands between 'set +e' and 'set -e' are run without throwing any error
      #   run: |
      #     set +e
      #     echo "Checking if covr is installed..."
      #     Rscript -e "if (!requireNamespace('covr', quietly = TRUE)) install.packages('covr')"
      #     echo "Generating coverage report..."
      #     Rscript -e "cov <- covr::package_coverage(type = c('tests', 'examples')); print(cov)"
      #     echo "Uploading coverage report..."
      #     Rscript -e "covr::codecov(coverage = cov)"
      #     set -e
      #   env:
      #     CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

      # - name: Notify Slack 📣
      #   uses: 8398a7/action-slack@v3
      #   with:
      #     status: ${{ job.status }}
      #     fields: repo,message,commit,author,action,eventName,ref,workflow,job,took # selectable (default: repo,message)
      #   env:
      #     SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }} # set in rep's setting >> secrets