mlpack/.github/workflows/main.yml

on:
  workflow_dispatch:
  push:
    branches:
      - master
      - main
  pull_request:
    branches:
      - master
      - main
  release:
    types: [published, created, edited]
permissions:
  contents: read
name: mlpack.mlpack

jobs:
  jobR:
    name: mlpack R tarball
    if: ${{ github.repository == 'mlpack/mlpack' }}
    runs-on: ubuntu-latest

    outputs:
      r_bindings: ${{ steps.mlpack_version.outputs.mlpack_r_package }}

    steps:
      - uses: actions/checkout@v3

      - name: Extract mlpack version
        id: mlpack_version
        run: |
          MLPACK_VERSION_MAJOR=$(grep -i ".*#define MLPACK_VERSION_MAJOR.*" src/mlpack/core/util/version.hpp | grep -o "[0-9]*")
          MLPACK_VERSION_MINOR=$(grep -i ".*#define MLPACK_VERSION_MINOR.*" src/mlpack/core/util/version.hpp | grep -o "[0-9]*")
          MLPACK_VERSION_PATCH=$(grep -i ".*#define MLPACK_VERSION_PATCH.*" src/mlpack/core/util/version.hpp | grep -o "[0-9]*")
          MLPACK_VERSION_VALUE=${MLPACK_VERSION_MAJOR}.${MLPACK_VERSION_MINOR}.${MLPACK_VERSION_PATCH}
          echo "mlpack_r_package=$(echo mlpack_"$MLPACK_VERSION_VALUE".tar.gz)" >> $GITHUB_OUTPUT

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

      # Setup R actions
      - uses: r-lib/actions/setup-r@v2

      # Get and set up ccache
      - name: Get CCache
        uses: hendrikmuhs/ccache-action@v1.2
        with:
          # can also be eg ${{ matrix.os }} but just ubuntu-latest here
          key: ${{ runner.os }}
          # this is the default but 'sccache' can be selected here
          variant: ccache

      - name: Prepare R for Ccache 
        run: |
          mkdir -p ~/.R
          cp -vax .github/etc/R_Makevars_${{ runner.os }} ~/.R/Makevars
          
      - name: Configure Ccache for R
        run: |
          ccache --set-config "sloppiness=include_file_ctime"
          ccache --set-config "hash_dir=false" 
          ccache --show-config
          ccache --zero-stats

      - name: Query dependencies
        run: |
          cp src/mlpack/bindings/R/mlpack/DESCRIPTION.in DESCRIPTION
          Rscript -e "install.packages('remotes')" -e "saveRDS(remotes::dev_package_deps(dependencies = TRUE), 'depends.Rds')"

      - name: Cache R packages
        if: runner.os != 'Windows' && runner.os != 'macOS'
        uses: actions/cache@v3
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ runner.os }}-r-release-${{ hashFiles('depends.Rds') }}
          restore-keys: ${{ runner.os }}-r-release-

      - name: Install Build Dependencies
        run: |
          sudo apt-get update
          # We don't install cereal via apt, because the Debian packagers
          # split the rapidjson dependency into a separate package.  We will
          # bundle the cereal sources with the R package, so we want them to
          # be exactly the upstream sources (with rapidjson included).
          sudo apt-get install -y --allow-unauthenticated libopenblas-dev liblapack-dev g++ libensmallen-dev libhdf5-dev libarmadillo-dev libcurl4-openssl-dev
          wget https://github.com/USCiLab/cereal/archive/refs/tags/v1.3.2.tar.gz
          tar -xvzpf v1.3.2.tar.gz
          #
          # These directives cause warnings on CRAN:
          # https://github.com/USCiLab/cereal/blob/master/include/cereal/external/base64.hpp#L28-L31
          # The command below comments them out.
          sed -i 's|#pragma|// #pragma|' cereal-1.3.2/include/cereal/external/base64.hpp
          #
          # Fix cereal compilation on clang 19+; see
          # https://github.com/USCiLab/cereal/pull/835
          sed -i 's|::template apply|::apply|' cereal-1.3.2/include/cereal/types/tuple.hpp

      - name: Install R-bindings dependencies
        run: |
          remotes::install_deps(dependencies = TRUE)
          remotes::install_cran("roxygen2")
          remotes::install_cran("pkgbuild")
        shell: Rscript {0}

      - name: CMake
        run: |
          mkdir build
          cd build && cmake -DDEBUG=OFF -DPROFILE=OFF -DBUILD_CLI_EXECUTABLES=OFF -DBUILD_PYTHON_BINDINGS=OFF -DBUILD_JULIA_BINDINGS=OFF -DBUILD_GO_BINDINGS=OFF -DBUILD_R_BINDINGS=ON -DDOWNLOAD_DEPENDENCIES=ON -DBUILD_TESTS=ON -DCEREAL_INCLUDE_DIR=../cereal-1.3.2/include/ ..

      - name: Build
        run: |
          cd build && make -j4

      - name: Run tests via ctest
        run: |
          cd build && CTEST_OUTPUT_ON_FAILURE=1 ctest -T Test .

      - name: Upload R packages
        uses: actions/upload-artifact@v4.4.0
        with:
          name: mlpack_r_tarball
          path: build/src/mlpack/bindings/R/${{ steps.mlpack_version.outputs.mlpack_r_package }}

  R-CMD-check:
    needs: jobR
    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.name }}
    if: ${{ github.repository == 'mlpack/mlpack' }}

    strategy:
      fail-fast: false
      matrix:
        config:
          - { os: windows-latest, r: "release", name: "Windows R" }
          - { os: macOS-latest, r: "release", name: "macOS R" }
          - {
              os: ubuntu-latest,
              r: "devel",
              http-user-agent: "release",
              name: "Linux R",
            }

    env:
      MAKEFLAGS: "-j 2"
      R_BUILD_ARGS: "--no-build-vignettes"
      R_CHECK_ARGS: "--no-build-vignettes"
      _R_CHECK_FORCE_SUGGESTS: 0
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes

    steps:
      - uses: actions/download-artifact@v4.1.8
        with:
          name: mlpack_r_tarball

      - uses: r-lib/actions/setup-pandoc@v2

      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}
          http-user-agent: ${{ matrix.config.http-user-agent }}
          use-public-rspm: true

      - name: Query dependencies
        run: Rscript -e "install.packages('remotes')" -e "saveRDS(remotes::dev_package_deps('${{ needs.jobR.outputs.r_bindings }}', dependencies = TRUE), 'depends.Rds')"

      - name: Cache R packages
        if: runner.os != 'Windows' && runner.os != 'macOS'
        uses: actions/cache@v1
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('depends.Rds') }}
          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-

      - name: Install check dependencies
        if: runner.os != 'Windows' && runner.os != 'macOS'
        run: |
          sudo apt-get update
          sudo apt-get install -y --allow-unauthenticated libcurl4-openssl-dev

      - name: Install dependencies
        run: |
          install.packages('remotes')
          remotes::install_deps('${{ needs.jobR.outputs.r_bindings }}', dependencies = TRUE)
          remotes::install_cran("rcmdcheck")
          remotes::install_cran("curl")
        shell: Rscript {0}

      - name: Check
        # TODO: revert to error_on = 'warning'
        run: Rscript -e "rcmdcheck::rcmdcheck('${{ needs.jobR.outputs.r_bindings }}', args = c('--no-manual','--as-cran'), error_on = 'error', check_dir = 'check')"

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@v3
        with:
          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
          path: |
            check/mlpack.Rcheck/00check.log
            check/mlpack.Rcheck/00install.out