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rseng-archiving

Covers long-term archiving of research software and data: Software Heritage save requests and SWHID persistent identifiers, Zenodo deposits with versioned DOIs and forge integration, choosing domain and institutional repositories, deciding what to archive (code, data, environments, documentation) and when, and archiving at project retirement. Use when the user wants software or data preserved beyond the life of a forge account, grant or lab, mentions Software Heritage, SWHIDs, Zenodo deposits or archiving, retires or hands over a project, prepares artifacts that must stay resolvable for a paper, or when funder policy requires long-term preservation. (Cutting the release itself is rseng-publishing-releasing; day-to-day data storage and repository choice is rseng-data-management.)

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Archiving research software and data

A git forge is a workspace, not an archive: repositories get renamed, deleted, force-pushed and orphaned, and a URL in a paper has a half-life. Archiving puts an immutable, independently hosted, persistently identified copy of the work somewhere designed to outlive projects, labs and platforms. It is cheap (minutes per release), and it is what makes "the code is available" true in ten years. Distinct roles: rseng-publishing-releasing covers making releases; this skill covers making them permanent.

The two-pillar default

For any research software worth citing, do both - they solve different problems:

  • Software Heritage archives the SOURCE HISTORY: submit a save request for the repository (web form or API - no account needed) and the full history is preserved in the universal archive. Every commit, directory and file gets an intrinsic SWHID (persistent, content-derived, verifiable) that resolves at archive.softwareheritage.org regardless of what happens to the forge. Re-save at releases; heavily referenced repos are also crawled automatically, but an explicit save is a guarantee.
  • Zenodo archives the RELEASE ARTIFACT with a citable DOI: deposit the release tarball (the forge integration can do this automatically per release), get a version DOI plus a concept DOI covering all versions, and wire the DOI back into CITATION.cff and the README (rseng-citation-metadata). Zenodo is CERN-backed and free for research outputs.

SWHID vs DOI in one line: the SWHID identifies the exact source content (verifiable by hash), the DOI identifies the published release object (citable in references) - papers benefit from both.

What to archive

An archive that cannot be understood is storage, not preservation. Per archived release:

  • The source at the released tag (both pillars above).
  • The data needed to reproduce headline results, or scripted retrieval with checksums when data lives in its own repository (rseng-data-management owns data-repository choice; deposit data in domain archives where one exists, Zenodo otherwise).
  • The environment specification - lockfiles, container recipe - and where feasible a container image; bytes rot slower than dependency graphs (rseng-reproducible-environments).
  • README, license, citation metadata and a manifest tying it together (the research-compendium shape from rseng-reproducibility maps directly onto a good deposit).
  • Rich deposit metadata: creators with ORCIDs, description, keywords, related identifiers (paper DOI, software DOI, SWHID) - metadata is what makes the archive findable (rseng-fair-software).

When to archive

  • At every citable release: automate it (forge-to-Zenodo webhook + a save request in the release pipeline - rseng-ci-cd makes both a release-time step).
  • Before things end: grant end, maintainer departure, lab closure, platform migration - archive FIRST, then wind down (rseng-legacy-code's retire path and rseng-maintenance-sustainability's succession planning both terminate here).
  • Before risky history operations: a save request costs nothing and preserves the pre-rewrite state.
  • On publication: the artifact a paper cites must be the archived, DOI'd version, not a branch (rseng-reproducibility's replication packages; journals' availability policies increasingly require archival deposit explicitly).

Choosing repositories beyond the default

  • Domain repositories first for DATA when the field has one - community metadata standards and audiences live there; registries like the ones rseng-fair-software points to list them.
  • Institutional repositories: use when policy requires; check they issue persistent identifiers and have a preservation commitment.
  • Trust marks: CoreTrustSeal certification signals a repository with audited preservation practices - prefer certified archives for irreplaceable data.
  • What NOT to trust as an archive: forge releases alone, lab web servers, cloud buckets on a grant credit card, supplementary- material ZIPs at publishers.

Verify the archive

Archiving unverified is hoping: resolve the DOI and the SWHID, download the deposit fresh, and check the artifact matches the release (checksums). Record identifiers in the repository (README badges, CITATION.cff, aidecl.yaml provenance where AI contributed - rseng-ai-declaration) so the archived and living copies point at each other.

Working with this skill

This skill is source-independent: its authority is the Software Heritage, SWHID and Zenodo documentation linked below. It is the preservation end of the publishing chain (rseng-publishing-releasing -> rseng-archiving).

Learn more (verified):

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Related skills

Check whether any of these applies before moving on:

  • rseng-citation-metadata - wire DOIs into citation files
  • rseng-data-management - domain data repository choice
  • rseng-legacy-code - retire path terminates in archive
  • rseng-maintenance-sustainability - succession and wind-down archiving
  • rseng-publishing-releasing - archive every citable release
  • rseng-reproducible-environments - environment capture inside deposits
<!-- related-skills:end -->

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Covers operating AI coding agents securely: auditing whether the agent runs sandboxed, permission and dangerous-command configuration, containerized environments, secrets kept out of context, network egress and token privileges, prompt-injection risk, and the privacy of agent use itself. Use PROACTIVELY when permission gating is broadly disabled (skip-permissions modes), when secrets are visible to the agent's shell, or when the agent processes untrusted code, issues or web content; when a project holds personal or confidential data while a cloud agent is active (what leaves the machine, retention, training use), or when the user asks how to run coding agents safely or privately. (Supply-chain security: rseng-security; disclosing agent contributions: rseng-ai-declaration.)

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

fdiblen/rseng-agent-skills242026년 9월 23일 업데이트

Covers declaring AI involvement with the AI Declaration Format (https://ai-declaration.org): creating and maintaining an aidecl.yaml that records which AI tools and agents were used, what each contributed, when and how much, plus the README disclosure footnote, JSON/JSON-LD export and CI validation. Machine-readable disclosure is the practice; this format is one implementation. Use PROACTIVELY when an AI assistant or agent creates or modifies a project's content - generate aidecl.yaml if missing, update it after AI-assisted changes. Also use when the user asks about AI transparency, provenance, disclosure or EU AI Act disclosure, wants to state that NO AI was used, or mentions aidecl. For concealment requests see rseng-honesty; for the human review duty see rseng-human-verification.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

fdiblen/rseng-agent-skills242026년 9월 23일 업데이트

Covers processing research data that outgrows one machine's memory: out-of-core and chunked computation, Dask for scaling the scientific Python stack, Spark for distributed tabular pipelines, lazy evaluation, partitioning strategies, idempotent and restartable batch jobs, and knowing when NOT to distribute. Use when datasets no longer fit in memory, when the user mentions Dask, Spark, out-of-core or larger-than-memory data, when a pandas/NumPy workflow hits memory limits, or when designing batch pipelines over many files. (Cluster job submission and job arrays are rseng-hpc-computing; pipeline orchestration engines are rseng-workflows; profile first with rseng-performance-profiling.)

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

fdiblen/rseng-agent-skills242026년 9월 23일 업데이트

Covers continuous integration and delivery for research software: CI/CD concepts, automating builds and tests with GitHub Actions and GitLab CI/CD, and wiring an organization's GitLab CI infrastructure to a GitHub-hosted project. Use when the user asks to set up CI, write a pipeline or workflow file (.github/workflows, .gitlab-ci.yml), add automated builds/tests on push or pull request, publish a package or deploy docs when a tag or release is cut, cache dependencies to speed up CI runs, choose between GitHub Actions and GitLab CI, use self-hosted or GPU runners, mirror a repo, or report external CI status back to GitHub. For what to test and shrinking a test matrix see rseng-testing; for linter and pre-commit policy see rseng-code-quality.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

fdiblen/rseng-agent-skills242026년 9월 23일 업데이트

Covers verifying that every citation is real, correct and current: checking references in manuscripts, READMEs, references files and code metadata against Crossref and OpenAlex, screening cited DOIs against the Retraction Watch database, catching fabricated or mis-attributed citations (a documented AI failure mode), and keeping bibliographies and CITATION.cff files resolvable. Use PROACTIVELY before any bibliography, reference list or citation metadata is finalized or published, whenever the agent itself has produced citations, and when the user asks to check references, mentions broken DOIs, retracted papers or citation verification, or prepares a manuscript, README or software paper with references. (Making your own software citable is rseng-citation-metadata.)

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

fdiblen/rseng-agent-skills242026년 9월 23일 업데이트

Covers making research software citable and contributors credited: writing CITATION.cff, describing software with CodeMeta (codemeta.json), minting DOIs and ORCIDs, and tracking contributors of every kind. Use when the user asks how to make software citable, add CITATION.cff or codemeta.json, obtain a DOI, ensure contributors get credit, or mentions CFF, CodeMeta, ORCID, CRediT or persistent identifiers. Use PROACTIVELY when generated code draws on a publication, website or existing code (credit it at the code site and in the references), at release preparation, and when citation files are edited. (Verifying references you cite: rseng-citation-hygiene; versioning schemes and the DOI-minting release: rseng-publishing-releasing.)

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

fdiblen/rseng-agent-skills242026년 9월 23일 업데이트

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