Deterministic publication submission packages — publication-submission-packages • popgenVCF

Creates and validates journal-ready package specifications, supplementary indexes, and package manifests with deterministic ordering, checksums, publication-contract bindings, and fail-closed mutation detection.

Usage

new_publication_submission_package_spec(
  id,
  journal_profile,
  layout_profile,
  figure_style,
  report_spec,
  archive_format = c("zip", "tar.gz"),
  root_directory = "submission",
  required_roles = c("manuscript", "metadata", "provenance"),
  version = "1.0.0"
)

validate_publication_submission_package_spec(
  spec,
  journal_profile,
  layout_profile,
  figure_style,
  report_spec
)

new_publication_supplementary_index(supplements = list())

validate_publication_supplementary_index(index)

new_publication_submission_package_manifest(
  spec,
  files,
  supplementary_index = new_publication_supplementary_index(),
  output_manifest_fingerprint,
  execution_fingerprint
)

validate_publication_submission_package_manifest(
  manifest,
  spec,
  supplementary_index
)

publication_submission_package_report(manifest)

Arguments

id: Stable package identifier.
journal_profile: Validated journal profile.
layout_profile: Validated publication layout profile.
figure_style: Validated publication figure-style profile.
report_spec: Validated publication report specification.
archive_format: Archive format, either zip or tar.gz.
root_directory: Stable archive root directory.
required_roles: Required logical file roles.
version: Specification version.
spec: A submission-package specification.
supplements: Supplementary entries with package and manuscript metadata.
index: A supplementary-material index.
files: Package file entries.
supplementary_index: Validated supplementary-material index.
output_manifest_fingerprint: Fingerprint of the originating report output manifest.
execution_fingerprint: Fingerprint of the originating report execution.
manifest: A package manifest.

Value

Constructors return deterministic fingerprinted records. Validators return TRUE invisibly. publication_submission_package_report() returns Markdown report lines.