Packaging now works. Updated the DESCRIPTION #101
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| 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 |