CODECOV-all-OS.yaml

on:
  push:
    branches:
      - master
  pull_request:
    branches:
      - master

name: CODECOV

jobs:
  R-CMD-check:
    runs-on: ${{ matrix.config.os }}
    name: ${{ matrix.config.os }} (${{ matrix.config.r }})

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: macOS-latest,   r: 'release'}
          - {os: windows-latest, r: 'release'}
          - {os: ubuntu-20.04,   r: 'release'}

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

    steps:
      - uses: actions/checkout@v2

      # macOS-specific steps
      - name: Fix Homebrew Issues
        if: runner.os == 'macOS'
        run: |
          if [ -d "/opt/homebrew/Library/Taps/homebrew/homebrew-core" ]; then
              cd /opt/homebrew/Library/Taps/homebrew/homebrew-core
              git stash -u || echo "No changes to stash"
              git clean -d -f || echo "No files to clean"
          fi
          brew uninstall openssl@1.1 ruby@3.0 || echo "Deprecated formulae not found"
          brew install openssl@3 ruby || echo "Failed to install replacements"
          brew doctor || echo "brew doctor warnings"
          brew config || echo "brew config warnings"
          brew update || echo "Failed to update Homebrew"
          brew install libomp qpdf || echo "Failed to install utilities"
          export DYLD_LIBRARY_PATH=$(brew --prefix libomp)/lib
          echo "DYLD_LIBRARY_PATH=$(brew --prefix libomp)/lib" >> $GITHUB_ENV

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

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

      - uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: true
          python-version: 3.9
          miniconda-version: "latest"

      - name: Query dependencies
        run: |
          install.packages('remotes')
          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
        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: Install system dependencies
        if: runner.os == 'Linux'
        run: |
          while read -r cmd
          do
            eval sudo $cmd
          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
          sudo apt install libharfbuzz-dev
          sudo apt install libfribidi-dev

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

      - name: Fix Conda permissions on macOS
        if: runner.os == 'macOS'
        run: sudo chown -R $UID $CONDA

      - name: Installing text and testing it
        run:  |
          install.packages("devtools")
          library(devtools)
          devtools::install_github("theharmonylab/topics")
          devtools::install_github("oscarkjell/text")
          text::textrpp_install(prompt = FALSE)
          text::textrpp_initialize(textEmbed_test = TRUE)
        shell: Rscript {0}

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

      # Test coverage
      - name: Test coverage
        env:
          OMP_MAX_ACTIVE_LEVELS: 2
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
        run: covr::codecov(token = Sys.getenv("CODECOV_TOKEN"))
        shell: Rscript {0}

      # Debugging step to confirm coverage files are generated
      - name: List files for debugging
        run: ls -R

      # Wait to ensure all coverage data is saved
      - name: Wait for coverage files to be ready
        run: sleep 5

      # Upload coverage to Codecov
      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v3
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          flags: ${{ matrix.config.os }}
          verbose: true
          files: "path/to/coverage/file"  # Replace with actual coverage file path