Write a closed reproducibility manifest into a Salmon Data Package — write_sdp_reproducibility

Binds an explicit inventory of reviewed semantic selections, workflow records, provenance, and source records to exact paths, media types, byte sizes, and SHA-256 hashes in reproducibility/manifest.json. The writer does not discover files. Validation requires the declarations to be closed over the actual reproducibility tree, which prevents accidental publication of local notes or editor backups.

Usage

write_sdp_reproducibility_manifest(path, artifacts, overwrite = FALSE)

Arguments

path: Existing Salmon Data Package directory.
artifacts: Non-empty data frame with exactly path, role, and media_type columns. Paths are package-relative. Roles are reviewed_semantic_selections, workflow, provenance, or source and must agree with the canonical directory layout.
overwrite: Logical; replace an existing managed manifest when TRUE.

Value

The manifest path, invisibly.

Examples

sdp_path <- tempfile("sdp-")
dir.create(file.path(sdp_path, "reproducibility", "workflow"),
           recursive = TRUE)
writeLines("message('prepare data')",
           file.path(sdp_path, "reproducibility", "workflow", "prepare.R"))
artifacts <- data.frame(
  path = "reproducibility/workflow/prepare.R",
  role = "workflow",
  media_type = "text/x-r-source"
)
write_sdp_reproducibility_manifest(sdp_path, artifacts)
validate_sdp_reproducibility_manifest(sdp_path)
unlink(sdp_path, recursive = TRUE)