test_macos.yml

name: "Unit tests: macOS"

on:
  push:
    branches:
      - '**'
  pull_request:
    branches:
      - '**'

jobs:
  test:
    name: tests on macOS with R ${{ matrix.R }}
    runs-on: macos-latest
    strategy:
      fail-fast: false
      matrix:
        R: ['4.1.0']
        python-version: ['3.10']  # Explicitly define Python version in matrix

    steps:
      - name: Checkout repository
        uses: actions/checkout@v3

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.R }}
          Ncpus: 2
      
      - name: Setup Python
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
          cache: 'pip'
          
      - name: Query dependencies
        run: |
          install.packages('remotes')
          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
        shell: Rscript {0}
        
      - name: Cache R packages
        uses: actions/cache@v2
        id: cache
        with:
          path: |
            ${{ env.R_LIBS_USER }}
          key: ${{ runner.os }}-R${{ matrix.R }}-2-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ runner.os }}-R${{ matrix.R }}-2-
      
      - name: Install packages
        run: |
          install.packages(c("devtools"))
          remotes::install_deps(dependencies = TRUE)
          remotes::install_cran("rcmdcheck")
        shell: Rscript {0}

      - name: Setup Python environment
        shell: Rscript {0}
        run: |
          library(reticulate)
          
          # Use the GitHub Actions Python
          Sys.setenv(RETICULATE_PYTHON = Sys.which("python"))
          
          # Install pip packages
          system2("pip", c("install", "--upgrade", "pip"))
          system2("pip", c("install", "--upgrade", "numpy", "pandas", "matplotlib"))
          system2("pip", c("install", "--upgrade", "git+https://github.com/SABS-R3-Epidemiology/epiabm.git@main#egg=pyEpiabm&subdirectory=pyEpiabm"))
          
          # Verify Python configuration
          py_config <- reticulate::py_config()
          message("Python configuration:")
          message(paste("Python version:", py_config$version))
          message(paste("Python path:", py_config$python))
          
          # Test imports
          reticulate::py_run_string("
          import numpy
          import pandas
          import matplotlib
          import pyEpiabm
          print('All required Python packages successfully imported')
          ")

      - name: Check
        env:
          _R_CHECK_CRAN_INCOMING_REMOTE_: false
          RETICULATE_PYTHON: ${{ env.pythonLocation }}/python
        run: |
          options(crayon.enabled = TRUE)
          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
        shell: Rscript {0}

      - name: Show testthat output
        if: always()
        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true