Setup codex-universal (Codex Cloud) for R package development

setup-codex-universal.sh

# This setup script prepares a Codex Cloud environment for developing and testing R packages.
# It installs the rig, R, an R toolchain, configures CRAN and parallel-testing defaults,
# It installs all package dependencies listed in the project’s DESCRIPTION file.
# It then installs the local package itself.
# If the package uses reticulate, it also materializes a package python venv

# install rig
curl -L https://rig.r-pkg.org/deb/rig.gpg -o /etc/apt/trusted.gpg.d/rig.gpg
echo "deb http://rig.r-pkg.org/deb rig main" > /etc/apt/sources.list.d/rig.list
apt-get update
apt-get install -y r-rig

# install R
rig add release

# Set some R env variables for R for better devtools/testthat behavior
# (I interactively asked codex cloud how many cores are available,
#  it ran nproc and got back 5)
cat >> ~/.Renviron <<'EOF'
NOT_CRAN=true
TESTTHAT_CPUS=5
R_CLI_DYNAMIC=false,
R_CLI_NUM_COLORS=1,
NO_COLOR=1,
TESTTHAT_PARALLEL=false
EOF

# Set up some R options to
# - configure a CRAN with Posit Package Manager, which
#   offers pre-built binaries.
# - improve testthat output for codex
cat >> ~/.Rprofile <<'EOF'
options(
  repos = c(CRAN = sprintf(
    "https://packagemanager.posit.co/cran/latest/bin/linux/noble-%s/%s",
    R.version["arch"], substr(getRversion(), 1, 3)
  )),
  Ncpus = 4L,
  testthat.use_colours = FALSE,
  testthat.summary.omit_dots = TRUE,
  pager = 'cat',
  cli.dynamic = FALSE,
  cli.num_colors = 1L,
  testthat.default_reporter = "summary"
)
EOF

# - parse the package DESCRIPTION file and install all package dependencies
# - then install the package itself and try to load it.
# - then, if the package has python/reticulate requirements,
#   force reticulate to download all python packages
# (Note, we don't use pak for R package install because it errors on codex cloud due to internet proxy settings)
Rscript - <<'EOF'
desc <- as.list(as.data.frame(read.dcf("DESCRIPTION")))
pkgs <- c(
  desc$Depends,
  desc$Imports,
  desc$Suggests
) |>
  strsplit(",", fixed = TRUE) |>
  unlist(use.names = FALSE) |>
  trimws() |>
  sub("\\s*\\(.*\\)", "", x = _) |>
  c("remotes", "devtools") |>
  setdiff(unname(c(
    "R",
    installed.packages(priority = c("base", "recommended"))[, "Package"]
  )))
install.packages(pkgs)
remotes::install_local()
try({
  # try to load the package
  library(desc$Package, character.only = TRUE)

  # if the package has python requirements,
  # force reticulate to materialize a venv (i.e., download python, python packages)
  if (!"keras3" %in% loadedNamespaces()) {
    if ("keras" %in% loadedNamespaces()) keras::py_require_legacy_keras()
    if ("tensorflow" %in% loadedNamespaces()) tensorflow::py_require_tensorflow()
  }
  if ("reticulate" %in% loadedNamespaces()) {
    reticulate::py_config()
    cat("\nUV_OFFLINE=1\n", file = "~/.Renviron", append = TRUE)
  }
})
EOF

curl -LsSf https://github.com/posit-dev/air/releases/latest/download/air-installer.sh | sh