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AGENTS.md

Notes for AI coding agents working on this repository.

Project

  • treescanr is an R package at the repository root (R/, inst/, vignettes/).
  • treescan_project/ holds the original epiENGAGE scripts. Keep them as they are: they are the reference for the port (see r-package-port.md).
  • Conventions: minimal dependencies (tinyverse), data.table for heavy processing, functions pipeable with |>, tinytest integration tests (inst/tinytest/), quarto for README.qmd and the vignettes, 2 cores by default, and NEWS.md updated with user-facing changes.

Use the devcontainer when podman or docker is available

If the environment has podman or docker, it is generally easier to run things inside the devcontainer image. It already has R, Quarto, the package dependencies, and the TreeScan(TM) binary (TREESCAN_BIN). This means the tests that call TreeScan run instead of being skipped:

# The TreeScan Linux binary is x86-64 only, hence --platform
podman run --rm --platform linux/amd64 -v "$PWD":/src:ro \
  ghcr.io/epiforesite/treescanr-dev:latest bash -c '
    cp -r /src /tmp/pkg && cd /tmp/pkg &&
    R CMD build . && R CMD check --no-manual treescanr_*.tar.gz'
  • The image is private: pull it after podman login ghcr.io with a token that has read:packages.
  • To rebuild it, run .devcontainer/build.sh <treescan-linux-tarball>. Never commit the TreeScan binary or tarball: its license requires every user to agree to it.

Without a container, the TreeScan tests are skipped unless TREESCAN_BIN points to a local binary.

Common tasks

  • Documentation: Rscript -e 'roxygen2::roxygenise()'
  • README: edit README.qmd, then run quarto render README.qmd
  • Tests: Rscript -e 'tinytest::test_package("treescanr")' (package installed)
  • Website: pkgdown::build_site() (needs the package installed, because the quarto vignette renders in a separate process). It is deployed by .github/workflows/pkgdown.yaml.