Merge main into cran-submission #59
Workflow file for this run
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| # GitHub Copilot Setup Steps for serodynamics | |
| # | |
| # This workflow configures the GitHub Copilot coding agent's environment | |
| # by preinstalling R, JAGS, and all required dependencies. | |
| # | |
| # See: https://docs.github.com/en/copilot/how-tos/use-copilot-agents/coding-agent/customize-the-agent-environment | |
| # For detailed setup instructions, see .github/copilot-instructions.md | |
| # | |
| # This workflow aligns with the setup requirements documented in .github/copilot-instructions.md: | |
| # - R version >= 4.1.0 (as specified in DESCRIPTION) | |
| # - JAGS 4.3.1 system library and R interface | |
| # - All package dependencies (Imports, Suggests, and development needs) | |
| name: "Copilot Setup Steps" | |
| # Automatically run the setup steps when they are changed to allow for easy validation, | |
| # and allow manual testing through the repository's "Actions" tab | |
| on: | |
| workflow_dispatch: | |
| push: | |
| paths: | |
| - .github/workflows/copilot-setup-steps.yml | |
| pull_request: | |
| paths: | |
| - .github/workflows/copilot-setup-steps.yml | |
| jobs: | |
| # The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot. | |
| copilot-setup-steps: | |
| runs-on: ubuntu-latest | |
| # Set the permissions to the lowest permissions possible needed for your steps. | |
| # Copilot will be given its own token for its operations. | |
| permissions: | |
| contents: read | |
| # Timeout after 55 minutes (max is 59 for copilot-setup-steps) | |
| timeout-minutes: 55 | |
| steps: | |
| # Checkout code - Copilot will do this automatically if we don't, | |
| # but we need it to install dependencies from DESCRIPTION | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| # Install system dependencies required for R packages | |
| # See .github/copilot-instructions.md "Verify Development Environment" section | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y \ | |
| libcurl4-openssl-dev \ | |
| libssl-dev \ | |
| libxml2-dev \ | |
| libfontconfig1-dev \ | |
| libharfbuzz-dev \ | |
| libfribidi-dev \ | |
| libfreetype6-dev \ | |
| libpng-dev \ | |
| libtiff5-dev \ | |
| libjpeg-dev | |
| # Install JAGS (Just Another Gibbs Sampler) - REQUIRED for this package | |
| # Version 4.3.1 as documented in .github/copilot-instructions.md | |
| - name: Install JAGS | |
| run: | | |
| sudo apt-get install -y jags | |
| echo "JAGS installed successfully" | |
| # Set up pandoc for documentation | |
| - name: Set up Pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| # Set up R using the standard GitHub Actions setup | |
| # R version >= 4.1.0 required (see DESCRIPTION and .github/copilot-instructions.md) | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@HEAD | |
| with: | |
| r-version: 'release' | |
| use-public-rspm: true | |
| # Install R dependencies with caching for faster subsequent runs | |
| - name: Install R dependencies | |
| uses: r-lib/actions/setup-r-dependencies@HEAD | |
| with: | |
| extra-packages: | | |
| any::devtools | |
| any::rcmdcheck | |
| any::lintr | |
| any::spelling | |
| any::rmarkdown | |
| needs: check | |
| # Install rjags from source to ensure proper linking with JAGS | |
| # See .github/copilot-instructions.md "JAGS Installation" section | |
| - name: Install rjags | |
| run: | | |
| install.packages("rjags", | |
| repos = "https://cloud.r-project.org", | |
| type = "source", | |
| verbose = TRUE) | |
| withr::local_options(warn = 2) | |
| library(rjags) | |
| library(runjags) | |
| runjags::findjags() | |
| runjags::testjags() | |
| shell: Rscript {0} | |
| # Verify JAGS installation | |
| # See .github/copilot-instructions.md "JAGS Installation" section for details | |
| - name: Verify JAGS installation | |
| run: | | |
| echo "=== Verifying JAGS Installation ===" | |
| echo "System JAGS command:" | |
| which jags || echo "Warning: jags command not found in PATH" | |
| echo "" | |
| echo "R JAGS interface packages:" | |
| Rscript -e 'cat("rjags version:", as.character(packageVersion("rjags")), "\n")' | |
| Rscript -e 'cat("runjags version:", as.character(packageVersion("runjags")), "\n")' | |
| echo "" | |
| echo "JAGS location (from runjags):" | |
| Rscript -e 'print(runjags::findjags())' | |
| echo "" | |
| echo "Running JAGS test:" | |
| Rscript -e 'runjags::testjags()' | |
| # Verify R environment is properly configured | |
| # See .github/copilot-instructions.md "Verify Development Environment" section | |
| - name: Verify development environment | |
| run: | | |
| echo "=== R Development Environment Status ===" | |
| Rscript -e ' | |
| cat("R version:", R.version.string, "\n\n") | |
| # Check R version meets minimum requirement (>= 4.1.0) | |
| r_version <- paste(R.version$major, R.version$minor, sep = ".") | |
| cat("Checking R version >= 4.1.0... ") | |
| if (getRversion() >= "4.1.0") { | |
| cat("PASSED (", r_version, ")\n\n", sep = "") | |
| } else { | |
| cat("FAILED (", r_version, ")\n\n", sep = "") | |
| stop("R version must be >= 4.1.0") | |
| } | |
| # Display key installed packages | |
| cat("Key installed packages:\n") | |
| key_packages <- c("devtools", "rjags", "runjags", "rcmdcheck", "lintr", "spelling", "testthat") | |
| for (pkg in key_packages) { | |
| if (requireNamespace(pkg, quietly = TRUE)) { | |
| cat(" -", pkg, ":", as.character(packageVersion(pkg)), "\n") | |
| } else { | |
| cat(" -", pkg, ": NOT INSTALLED\n") | |
| } | |
| } | |
| cat("\nTotal packages installed:", nrow(installed.packages()), "\n") | |
| cat("\nDevelopment environment setup complete!\n") | |
| ' |