Packaging now works. Updated the DESCRIPTION #83
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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'] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - 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: "3.10" | |
| - 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 installed 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 r-reticulate venv | |
| shell: Rscript {0} | |
| run: | | |
| library(reticulate) | |
| reticulate::py_run_string(" | |
| import sys | |
| import subprocess | |
| subprocess.check_call([sys.executable, '-m', 'pip', 'install', '--upgrade', 'pip']) | |
| ") | |
| # Install required packages | |
| reticulate::py_run_string(" | |
| import sys | |
| import subprocess | |
| # Install basic packages | |
| packages = ['numpy', 'pandas', 'matplotlib'] | |
| for package in packages: | |
| subprocess.check_call([sys.executable, '-m', 'pip', 'install', '--upgrade', package]) | |
| # Install pyEpiabm from GitHub | |
| subprocess.check_call([ | |
| sys.executable, '-m', 'pip', 'install', '--upgrade', | |
| 'git+https://github.com/SABS-R3-Epidemiology/epiabm.git@main#egg=pyEpiabm&subdirectory=pyEpiabm' | |
| ]) | |
| ") | |
| env_name <- "r-py-env" | |
| python_version = "3.9" | |
| tryCatch({ | |
| # Check if virtualenv package is available | |
| if (!reticulate::virtualenv_exists(env_name)) { | |
| message(sprintf("Creating new Python virtual environment: %s", env_name)) | |
| # Create virtual environment with system site packages to help with SSL | |
| reticulate::virtualenv_create( | |
| envname = env_name, | |
| version = python_version, | |
| packages = "pip", | |
| system_site_packages = TRUE | |
| ) | |
| } | |
| # Activate the environment | |
| reticulate::use_virtualenv(env_name, required = TRUE) | |
| return(TRUE) | |
| }, error = function(e) { | |
| warning(sprintf("Failed to create/activate Python environment: %s", e$message)) | |
| return(FALSE) | |
| }) | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| 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 | |
| shell: bash |