R.yml

name: R

on:
  push:
    branches: [main]
    tags-ignore: ["**"]
    paths:
      - ".github/workflows/rchk.yml"
      - ".github/workflows/R.yml"
      - "r/**"
      - "!r/README.md"
      - 'c/Make*'
      - 'c/*.mk'
      - 'c/**/*.[ch]p?p?'
  pull_request:
    branches-ignore: [gh-pages]
    paths:
      - ".github/workflows/rchk.yml"
      - ".github/workflows/R.yml"
      - "r/**"
      - "!r/README.md"
      - 'c/Make*'
      - 'c/*.mk'
      - 'c/**/*.[ch]p?p?'
  # Manual run
  workflow_dispatch:

env:
  R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
  _R_CHECK_FORCE_SUGGESTS_: false
  _R_CHECK_CRAN_INCOMING_REMOTE_: false

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

jobs:
  R-CMD-check:
    if: "! contains(github.event.head_commit.message, '[skip ci]')"
    runs-on: ${{ matrix.os }}
    name: Check ${{ matrix.os }} (${{ matrix.r }})
    strategy:
      # When set to true, GitHub cancels all in-progress jobs if any matrix job fails.
      fail-fast: true
      matrix:
        # macos-15-intel is an intel runner, macos-14 is apple silicon
        os: [ ubuntu-22.04, windows-latest, macos-15-intel, macos-14 ]
        r: [ release ]
        include:
          - { os: windows-latest, r: '4.1' }
          # Use latest ubuntu to make it easier to install dependencies
          - { os: ubuntu-24.04, r: 'devel', http-user-agent: 'release' }
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      MAKEFLAGS: "-j 2"

    steps:
      - name: Disable autocrlf
        if: runner.os == 'Windows'
        run: git config --global core.autocrlf false

      - uses: actions/checkout@v6

      - name: Fix permissions
        if: runner.os == 'Windows'
        run: chmod +x r/cleanup

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

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          install-pandoc: true
          extra-packages: any::purrr@1.0.4, any::remotes, any::rcmdcheck, any::spelling
          needs: check
          working-directory: r

      - name: Check (NOT CRAN)
        env:
          NOT_CRAN: true
        uses: r-lib/actions/check-r-package@v2
        with:
          args: 'c("--no-manual", "--run-donttest", "--run-dontrun", "--timings")'
          working-directory: r

      - name: Check (as CRAN)
        if: matrix.os != 'ubuntu-24.04'
        env:
          NOT_CRAN: false
        uses: r-lib/actions/check-r-package@v2
        with:
          args: 'c("--no-manual", "--as-cran")'
          working-directory: r

      - name: Stricter CFLAGS
        if: matrix.os == 'ubuntu-24.04'
        run: |
          mkdir -p ~/.R
          echo 'CFLAGS=-g -O2  -Wall -Wstrict-prototypes -pedantic -fstack-protector-strong -DUSE_TYPE_CHECKING_STRICT  -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -Werror' > ~/.R/Makevars
        shell: bash
        working-directory: r

      - name: Check (as CRAN) with stricter CFLAGS and GCC 14
        if: matrix.os == 'ubuntu-24.04'
        env:
          NOT_CRAN: false
          CC: gcc-14
        uses: r-lib/actions/check-r-package@v2
        with:
          args: 'c("--no-manual", "--as-cran")'
          working-directory: r

      - name: Show testthat output
        if: failure()
        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
        shell: bash
        working-directory: r

      - name: Install package
        run: |
          remotes::install_local(".", force = TRUE, upgrade = "never", build_manual = TRUE, build_vignettes = TRUE)
        shell: Rscript {0}
        working-directory: r

  coverage:
    needs: R-CMD-check
    name: Coverage ${{ matrix.os }} (${{ matrix.r }})
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest]
        r: [release]
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - uses: actions/checkout@v6

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

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          install-pandoc: true
          extra-packages: any::covr any::xml2 any::rex
          needs: coverage
          working-directory: r

      - name: Test coverage
        env:
          NOT_CRAN: true
        run: |
          exclude_pattern = rex::rex(or(group(or("#", "//"), any_spaces, "nocov"),
                                        group(or("ASSUME", "unreachable", "assert"), maybe(" "), "("),
                                        group(or("DEBUG1", "DEBUG2", "DEBUG3"), maybe("_PRINT")),
                                        group(or("GCOV", "GCOVR", "LCOV"), "_EXCL_LINE")))
          options(covr.gcov_additional_paths="c",
                  covr.filter_non_package=FALSE,
                  covr.exclude_pattern=exclude_pattern)
          coverage <- withr::with_makevars(c(MOOCORE_DEBUG="1", LTO_OPT="-fno-lto"),
            covr::package_coverage(type="all", quiet=FALSE, clean=FALSE,
              commentDonttest = FALSE, commentDontrun = FALSE, flags="R",
              relative_path=normalizePath(file.path(getwd(), "..")),
              install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
            ))
          print(coverage)
          covr::to_cobertura(coverage)
          list.files("../", pattern="*.xml", recursive=TRUE)
        shell: Rscript {0}
        working-directory: r

      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v6
        with:
          fail_ci_if_error: true
          files: ./r/cobertura.xml
          verbose: true
          flags: R
          plugins: noop
          disable_search: true
          token: ${{secrets.CODECOV_TOKEN}}

  pkgdown:
    name: pkgdown ${{ matrix.os }} (${{ matrix.r }})
    needs: R-CMD-check
    permissions:
      contents: write # github-pages-deploy-action
    concurrency: # Recommended if you intend to make multiple deployments in quick succession.
      group: web-${{ github.workflow }}-${{ github.ref }}
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest]
        r: [release]
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - uses: actions/checkout@v6

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

      - name: Install optipng
        run: sudo apt-get install -y optipng

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          install-pandoc: true
          extra-packages: any::pkgdown, local::.
          needs: website
          working-directory: r

      - name: Build website
        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE, run_dont_run = TRUE)
        shell: Rscript {0}
        working-directory: r

      - name: Deploy 🚀
        if: success() && github.event_name == 'push' && github.ref == 'refs/heads/main'
        uses: JamesIves/github-pages-deploy-action@v4
        with:
          folder: r/docs # The folder the action should deploy.
          target-folder: r
          single-commit: true
          clean: true

  rchk:
    needs: pkgdown
    uses: multi-objective/moocore/.github/workflows/rchk.yml@main