r-dependencies-tests.yml

name: r-dependencies-tests
permissions:
  contents: read

on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]
  workflow_dispatch:

jobs:
  test:
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, macos-latest, windows-latest]
    runs-on: ${{ matrix.os }}

    steps:
      - name: Checkout
        uses: actions/checkout@v4

      # --- Python 3.12 on all OSes ---
      - name: Set up Python 3.12
        uses: actions/setup-python@v5
        with:
          python-version: "3.12"

      # --- R on all OSes ---
      - name: Set up R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: "release"
      
      - name: Fix paths for rpy2 ABI mode
        shell: bash
        run: |
          # Find where R is
          # 1. Capture and set R_HOME explicitly
          R_HOME_DIR=$(R RHOME)
          echo "Detected R_HOME: $R_HOME_DIR"
          echo "R_HOME=$R_HOME_DIR" >> $GITHUB_ENV


          # 2. Platform-specific dynamic library config
          if [ "$RUNNER_OS" = "Windows" ]; then
            # On Windows, DLLs are located under bin/x64 and found via PATH
            R_BIN_DIR="${R_HOME_DIR}/bin/x64"
            echo "Adding $R_BIN_DIR to PATH"
            echo "PATH=$R_BIN_DIR${PATH:+:$PATH}" >> "$GITHUB_ENV"
          else
            # On Unix, libR.so lives under $R_HOME/lib and is found via LD_LIBRARY_PATH
            R_LIB_DIR="${R_HOME_DIR}/lib"
            echo "Adding $R_LIB_DIR to LD_LIBRARY_PATH"
            echo "LD_LIBRARY_PATH=$R_LIB_DIR${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}" >> "$GITHUB_ENV"
          fi

          # 3. Use a writable location for R_LIBS_USER (per-job)
          R_USERLIBS="${RUNNER_TEMP}/r-lib"
          echo "Setting R_LIBS_USER to $R_USERLIBS"
          mkdir -p "$R_USERLIBS"
          echo "R_LIBS_USER=$R_USERLIBS" >> $GITHUB_ENV

          

      - name: Cache Rtools 4.5 installer
        if: runner.os == 'Windows'
        id: cache-rtools
        uses: actions/cache@v4
        with:
          path: rtools-cache
          key: rtools45-6768-6492

      - name: Download Rtools 4.5 installer
        if: runner.os == 'Windows' && steps.cache-rtools.outputs.cache-hit != 'true'
        shell: pwsh
        run: |
          New-Item -ItemType Directory -Force -Path "$env:GITHUB_WORKSPACE\rtools-cache" | Out-Null
          Invoke-WebRequest `
            -Uri "https://cran.r-project.org/bin/windows/Rtools/rtools45/files/rtools45-6768-6492.exe" `
            -OutFile "$env:GITHUB_WORKSPACE\rtools-cache\rtools45-6768-6492.exe"

      - name: Export RTOOLS_INSTALLER_EXE env var
        if: runner.os == 'Windows'
        shell: pwsh
        run: |
          $installer = "$env:GITHUB_WORKSPACE\rtools-cache\rtools45-6768-6492.exe"
          if (-not (Test-Path $installer)) {
            Write-Error "Rtools installer not found at $installer"
          }
          "RTOOLS_INSTALLER_EXE=$installer" >> $env:GITHUB_ENV

      - name: Install Python package
        run: |
          python -m pip install --upgrade pip
          python -m pip install pytest pytest-cov pytest-xdist arviz tqdm
          python -m pip install -e ".[dev]"
        shell: bash

      - name: Test with pytest
        env:
          BRMSPY_DESTRUCTIVE_RDEPS_TESTS: "1"
          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
          COVERAGE_FILE: .coverage.${{ matrix.os }}
          BRMSPY_RTOOLS_INSTALLER_EXE: ${{ env.RTOOLS_INSTALLER_EXE }}
          RPY2_CFFI_MODE: "ABI"
        shell: bash
        run: set -xeuo pipefail && ./run_tests_rdeps.sh

      # Upload per-OS coverage artifacts
      - name: Upload coverage artifacts
        if: ${{ always() }}
        uses: actions/upload-artifact@v4
        with:
          name: coverage-${{ matrix.os }}
          path: .coverage*
          include-hidden-files: true
          if-no-files-found: ignore

  merge-coverage:
    runs-on: ubuntu-latest
    needs: test
    if: github.event_name == 'push' && github.ref == 'refs/heads/master'

    permissions:
      contents: write

    steps:
      - name: Checkout
        uses: actions/checkout@v4

      - name: Set up Python 3.12
        uses: actions/setup-python@v5
        with:
          python-version: "3.12"

      - name: Download coverage artifacts
        uses: actions/download-artifact@v4
        with:
          # pull all coverage-* artifacts from this workflow run
          pattern: coverage-*
          merge-multiple: true

      - name: Sanity-check downloaded coverage files
        run: |
          echo "Workspace contents after download:"
          ls -la
          echo
          echo "Coverage data files:"
          ls -la .coverage* || echo "No .coverage* files found"

      - name: Combine coverage and generate reports
        env:
          COVERAGE_RCFILE: .coveragerc-r-dependencies
        run: |
          python -m pip install --upgrade pip
          python -m pip install coverage

          # Combine all .coverage.* into a single .coverage
          coverage combine

          # Machine-readable reports
          coverage json -o coverage.json
          coverage xml -o coverage.xml

          # Human-readable summary (similar to pytest-cov's table)
          echo "==== Combined coverage report ===="
          coverage report -m
          echo "=================================="

      - name: Upload merged coverage artifact
        uses: actions/upload-artifact@v4
        with:
          name: coverage-rdeps-merged
          path: |
            .coverage
            coverage.json
            coverage.xml

      - name: Update coverage badge
        uses: ./.github/actions/cover-badge
        with:
          filename: coverage-rdeps.svg
          label: coverage-rdeps