Initialize a Shennong analysis project — sn_initialize

This helper bootstraps a clean analysis-project structure for end users who want to analyze their own data with Shennong. When with_agent = TRUE, it materializes the packaged project-governance template; otherwise it creates the same project skeleton without the governance layer.

Usage

sn_initialize_project(
  path = ".",
  project_name = NULL,
  objective =
    "Build a reproducible Shennong-based single-cell analysis workflow for this project.",
  with_agent = TRUE,
  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.
with_agent: Logical; if TRUE, materialize the full Codex-facing governance template. Defaults to TRUE.
overwrite: Whether to replace existing managed files copied from the template. Defaults to FALSE.

Value

Invisibly returns a named list containing the initialized project directory plus the main created directory and file paths.

Examples

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