Create, bundle, reopen, and compare reproducible popgenVCF projects

Reproducible projects preserve canonical scientific results, software and RNG identity, input checksums, parameters, module records, artifacts, reports, and provenance in a portable checksummed bundle that can be reopened without recomputation.

Usage

new_project_rng(seed = NA_integer_, kind = RNGkind(), streams = list())

new_popgenvcf_project(
  name,
  results = list(),
  inputs = data.table::data.table(),
  parameters = list(),
  modules = list(),
  artifacts = list(),
  reports = list(),
  provenance = list(),
  rng = new_project_rng(),
  project_id = project_uuid(),
  created_at = format(Sys.time(), tz = "UTC", usetz = TRUE),
  package_version = tryCatch(as.character(utils::packageVersion("popgenVCF")),
    error = function(e) NA_character_),
  git_sha = Sys.getenv("GITHUB_SHA", unset = NA_character_)
)

validate_popgenvcf_project(x)

project_table(x)

write_popgenvcf_project(project, path, overwrite = FALSE)

verify_popgenvcf_project(path)

read_popgenvcf_project(path, verify = TRUE)

compare_popgenvcf_projects(current, baseline)

Arguments

seed: Optional integer random seed.
kind: R random-number generator settings.
streams: Named module or worker seed records.
name: Human-readable project name.
results: Named canonical analysis results.
inputs: Input identity table or named character vector of paths.
parameters, modules, artifacts, reports, provenance: Named project components.
rng: Project RNG metadata.
project_id: Stable project UUID.
created_at: UTC creation timestamp.
package_version, git_sha: Software identity.
x: A project or project comparison.
project: A validated project.
path: A destination or existing .popgenvcf bundle.
overwrite: Permit replacement of an existing bundle.
verify: Verify internal SHA256 checksums while reading.
current, baseline: Projects or bundle paths to compare.

Value

Constructors return canonical project metadata. Writing returns the normalized bundle path invisibly. Reading returns a validated PopgenVCFProject. Comparison returns a PopgenVCFProjectComparison; table conversion returns a data table.