Initialize Codex-style project guidance for a Shennong analysis

This helper scaffolds a governed analysis project from the packaged inst/codex/project-template/ assets.

Usage

sn_initialize_codex_project(
  path = ".",
  project_name = NULL,
  objective =
    "Build a reproducible Shennong-based single-cell analysis workflow for this project.",
  overwrite = FALSE
)

Arguments

path

Project directory to initialize. Defaults to the current working directory.

project_name

Optional human-readable project name. If NULL, the final path component of path is used.

objective

Short project objective written into the generated project README, memory, and config files.

overwrite

Whether to replace existing managed files copied from the template. Defaults to FALSE.

Value

Invisibly returns the same structure as sn_initialize_project().

Examples

project_dir <- file.path(tempdir(), "codex-analysis-project")
created <- sn_initialize_codex_project(
  path = project_dir,
  project_name = "PBMC pilot study",
  objective = "Build a reproducible Shennong-based PBMC analysis workflow.",
  overwrite = TRUE
)
file.exists(created$agents)
#> [1] TRUE
file.exists(created$prompt)
#> [1] TRUE