R-CMD-check.yaml

on:
  push:
    branches:
      - master
  pull_request:
    branches:
      - master
  schedule:
    - cron: "1 7 11 * *"

name: OS-check

jobs:
  OS-check:
    runs-on: ${{ matrix.config.os }}

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

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

    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: ${{ matrix.config.rspm }}
      GITHUB_TOKEN: ${{ secrets.GHTOKEN2 }}
      GITHUB_PAT: ${{ secrets.GHTOKEN2 }}

    steps:
      - uses: actions/checkout@v2

      ## R is already included in the Bioconductor docker images
      - name: Setup R from r-lib
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}

      ## pandoc is already included in the Bioconductor docker images
      - name: Setup pandoc from r-lib
        uses: r-lib/actions/setup-pandoc@v2

      - name: Query dependencies
        run: |
          install.packages('remotes')
          saveRDS(remotes::dev_package_deps("Intro_To_Python/",dependencies = TRUE), ".github/depends.Rds", version = 2)
          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
          remotes::install_cran("BiocManager")
          remotes::install_cran("devtools")
        shell: Rscript {0}

      - name: Cache R packages
        if: runner.os != 'Windows'
        uses: actions/cache@v4
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-

      - name: Cache R packages
        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
        uses: actions/cache@v4
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_13-r-4.1-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_13-r-4.1-

      - name: Cache R packages on Linux
        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
        uses: actions/cache@v4
        with:
          path: /home/runner/work/_temp/Library
          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_13-r-4.1-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_13-r-4.1-

      - name: Install Linux system dependencies
        if: runner.os == 'Linux'
        run: |
          sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu-22.04", package=unlist(strsplit(read.dcf("ATACCutRunChIP/DESCRIPTION")[,"Depends"],", |\n")))), collapse = " "))')
          echo $sysreqs
          sudo -s eval "$sysreqs"
          sudo apt -y install libfontconfig1-dev
          sudo apt-get install libharfbuzz-dev libfribidi-dev
          sudo apt-get install libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev

      - name: Install macOS system dependencies
        if: matrix.config.os == 'macOS-latest'
        run: |
          ## Enable installing XML from source if needed
          brew install libxml2
          echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV

          ## Required to install magick as noted at
          ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
          brew install imagemagick@6

          ## For textshaping, required by ragg, and required by pkgdown
          brew install harfbuzz fribidi

          ## For installing usethis's dependency gert
          brew install libgit2

      - name: Install Windows system dependencies
        if: runner.os == 'Windows'
        run: |
          ## Edit below if you have any Windows system dependencies
        shell: Rscript {0}

      - name: Install dependencies 1
        run: |
          remotes::install_deps("Intro_To_Python/",dependencies = TRUE)
          remotes::install_cran("rcmdcheck")
          remotes::install_cran("BiocManager", force = TRUE)
        shell: Rscript {0}
        
      - name: Install dependencies 2
        if: matrix.config.r == 'devel'
        run: |
          BiocManager::install(version = "devel", ask=F)
          BiocManager::install("rmarkdown", version = "devel")
          BiocManager::install("devtools", version = "devel")
          BiocManager::install("RockefellerUniversity/compileCourses",subdir="compileCourses", version = "devel")
        shell: Rscript {0}
        
      - name: Install dependencies 3
        if: matrix.config.r != 'devel'
        run: |
          BiocManager::install("rmarkdown")
          BiocManager::install("devtools")
          BiocManager::install("RockefellerUniversity/compileCourses",subdir="compileCourses")  
        shell: Rscript {0}

      - name: Cache R packages
        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
        uses: actions/cache@v4
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_13-r-4.1-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_13-r-4.1-

      - name: Install System Dependencies
        if: runner.os == 'Linux'
        run: |
          sudo apt-get update -y
          sudo apt-get install -y glpk-utils
          sudo apt-get install -y libcurl4-openssl-dev
        shell: bash {0}

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

      - name: Install package
        if: github.ref == 'refs/heads/master'
        run: |
          devtools::install("Intro_To_Python/",dependencies = TRUE,quick = TRUE)
        shell: Rscript {0}

      - name: CompileCourse
        run: |
          require(compileCourses)
          compileCourses::compileSingleCourseMaterial(repo="RockefellerUniversity",subdir="Intro_To_Python",branch="master")
        shell: Rscript {0}