set up a self-contained folder for an agent to answer a v1qs question

Usage

cbb_setup_workspace(
  question_id,
  base_dir = tempdir(),
  timeout_minutes = 60,
  overwrite = FALSE,
  bfc = NULL
)

Arguments

question_id: character(1) value matched against `v1qs$question_id`
base_dir: path under which the question folder is created, default `tempdir()`
timeout_minutes: numeric(1) time budget stated in the prompt, default 60
overwrite: logical(1); if TRUE, remove and recreate an existing question folder
bfc: a `BiocFileCache` instance; if NULL, `cbb_filecache()` is used

Value

(invisibly) a list with elements `question_dir`, `workspace_dir`, `prompt_path`, `files`, and `prompt`

Note

mirrors the per-question `workspace/` + `prompt.md` layout produced by Genentech's `compbiobench-runner` before it invokes an LLM CLI; this function only stages the folder, it does not run any agent

Examples

if (FALSE) { # \dontrun{
  ws = cbb_setup_workspace("bam-infer-read-length-q1")
  ws$workspace_dir
  cat(ws$prompt)
} # }