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Polish release archive docs #36

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146 changes: 65 additions & 81 deletions docs/RELEASE_ARCHIVE_CARD.md
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---
title: GeneLab Benchmark Release Archive Card
page_type: release_archive_card
status: release_candidate_metadata_ready
last_reviewed: 2026-06-05
claim_boundary: archive_metadata_no_new_result_or_payload_claim
title: SpaceBio-Bench Release Archive Status
page_type: release_archive_status
status: public_ready
last_reviewed: 2026-06-16
---

# GeneLab Benchmark Release Archive Card
# SpaceBio-Bench Release Archive Status

## Card Purpose
## Purpose

This card defines what would be archived for a paper-supporting release of
GeneLab Benchmark, what is intentionally excluded, and which gates remain before
minting a final DOI or claiming a frozen research-object release.
This card summarizes the repository materials that support a paper or archive
release for SpaceBio-Bench / GeneLab Benchmark. It is a planning aid for
repository packaging, citation metadata, and dataset links.

It does not create a DOI, approve a new result release, or freeze v9 payloads.

## Archive Candidate Summary
## Current Archive Scope

| Field | Current value |
|---|---|
| Release candidate | `v7.1.2` documentation, public-card, and metadata patch on current `main` |
| Repository branch | `main` as public entry point with curated v9 metadata-alpha evidence subset |
| Current result boundary | v1-v7 canonical historical benchmark surface |
| Documentation patch | v7.1.2 metadata/card patch, no new result generation |
| Dataset payload boundary | HF feature-matrix package plus GitHub task/evaluation metadata |
| DOI status | Not minted in this card |
| Archive status | GitHub release-ready metadata; DOI deposition and source-archive checksum still pending |
| Public release line | `v7.1.2` documentation, public-card, citation, and metadata patch |
| Result surface | v7.1 canonical historical benchmark results |
| Repository entry point | `main` branch and `v7.1.2` tag |
| Dataset access | Hugging Face public fold package plus GitHub task metadata |
| v9 public bulk | Metadata catalog for task/source/fold/audit/baseline records |
| DOI status | Ready for final metadata review before archive deposition |

## Archive Contents

The archive candidate should include:

- Source code and evaluation scripts in `scripts/`.
- Public task metadata, labels, and fold definitions in `tasks/`.
- Public result JSON and summary artifacts in `evaluation/` and versioned
evaluation directories.
- Human-facing release documentation in `README.md`, `docs/`, and
`CITATION.cff`.
- Release metadata in `.zenodo.json`.
- Hugging Face dataset card text in `docs/hf_dataset_card.md`.
- SpaceBio-Bench transparency cards in `docs/SPACEBIOBENCH_*.md`.
- Curated v9 public bulk metadata-alpha evidence in `v9/` and
`docs/V9_PUBLIC_BULK_ALPHA_*.md`.

## Excluded From The Archive Claim

The archive candidate should not claim to include:

- Raw NASA OSDR source payloads.
- Controlled-access human sequence data.
- Frozen v9 public bulk payload files.
- Locally hash-verified v9 payload bundle.
- DOI-ready RO-Crate research object.
- Clinical, crew-health, countermeasure, intervention, or Mars-regime guidance.

## Required Before DOI Or Final Release Tag

Before a DOI-oriented release:

- Confirm the final manuscript author list, affiliations, and manuscript title
in `CITATION.cff` and `.zenodo.json`.
- Create or confirm an annotated GitHub release tag, `v7.1.2`, from a final
commit that includes the public card and release-archive metadata polish.
- Generate and store a checksum for the release source archive.
- Confirm the Hugging Face dataset card links to the intended canonical branch
and release tag.
- Record individual OSDR dataset citations for any analysis subset used in the
manuscript.
- Decide whether v9 metadata-alpha artifacts are cited as future work, a
supplemental surface, or excluded from the paper archive.
- If claiming research-object completeness, add RO-Crate or equivalent
provenance metadata.

## Current Readiness

| Gate | Status | Note |
The repository archive should include:

- source code and evaluation scripts in `scripts/`;
- public task metadata, labels, and fold definitions in `tasks/`;
- result JSON and summary artifacts in `evaluation/` and versioned evaluation
directories;
- public documentation in `README.md`, `docs/`, and `CITATION.cff`;
- release metadata in `.zenodo.json`;
- Hugging Face dataset card source in `docs/hf_dataset_card.md`;
- SpaceBio-Bench public cards in `docs/SPACEBIOBENCH_*.md`;
- v9 public bulk metadata catalog files under `v9/`.

## Scope Notes

The repository archive does not bundle raw NASA OSDR source payloads or
controlled-access human sequence data. Source biological data remain governed
by NASA OSDR and the individual OSDR study pages.

The v9 public bulk surface is documented as a metadata catalog. Larger payload
bundles, DOI-specific archive records, or research-object packaging can be
added as separate release work when the relevant metadata and checks are ready.

## Before DOI Deposition

- Confirm manuscript title, author list, affiliations, and release date.
- Review `CITATION.cff` and `.zenodo.json` against the final manuscript.
- Confirm the intended GitHub tag and release URL.
- Confirm the Hugging Face dataset card links to the intended repository tag.
- Record dataset-specific OSDR citations for the manuscript subset.
- Generate a source archive checksum after selecting the final release archive.

## Current Status

| Area | Status | Public file |
|---|---|---|
| Public README entry point | Pass | Links card pack and portfolio brief |
| Citation metadata | Pass for current public identity | `CITATION.cff` exists; final manuscript author list/title review still needed |
| Zenodo metadata | Candidate ready | `.zenodo.json` added for DOI deposition |
| License | Pass for code | MIT license present |
| HF dataset card | Pass | Links transparency cards on current public `main` |
| Claim-boundary cards | Pass | System, evaluation, readiness, and claim cards are public-review ready |
| Release archive manifest | Pass | `docs/RELEASE_ARCHIVE_MANIFEST.md` added |
| Source archive checksum | Pending DOI archive | Generate after final GitHub release archive is selected |
| DOI | Pending | Mint through Zenodo or equivalent archive after metadata review |
| v9 frozen payload | Blocked | Payload-level hash verification remains pending |

## External Standards Used
| README entry point | Ready | `README.md` |
| Citation metadata | Ready for final manuscript review | `CITATION.cff` |
| Zenodo metadata | Ready for final manuscript review | `.zenodo.json` |
| Code license | Ready | `LICENSE` |
| HF dataset card | Ready | `docs/hf_dataset_card.md` |
| Public documentation map | Ready | `docs/SPACEBIOBENCH_TRANSPARENCY_CARD_PACK.md` |
| Release manifest | Ready | `release/release_manifest.json` |
| Archive manifest | Ready | `docs/RELEASE_ARCHIVE_MANIFEST.md` |
| Source archive checksum | To be generated after archive selection | release-specific checksum record |
| DOI | To be minted by Zenodo or the selected archive service | archive record |

## References

- GitHub citation files:
https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files
- Citation File Format:
https://citation-file-format.github.io/
- Zenodo GitHub integration:
https://help.zenodo.org/docs/deposit/github/
- DataCite Metadata Schema 4.7:
https://schema.datacite.org/meta/kernel-4.7/
- DataCite Metadata Schema:
https://schema.datacite.org/
- RO-Crate:
https://www.researchobject.org/ro-crate/1.2/
https://www.researchobject.org/ro-crate/
78 changes: 36 additions & 42 deletions docs/RELEASE_ARCHIVE_CHECKLIST.md
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---
title: GeneLab Benchmark Release Archive Checklist
title: SpaceBio-Bench Release Archive Checklist
page_type: release_archive_checklist
status: release_candidate_checklist
last_reviewed: 2026-06-05
claim_boundary: checklist_no_new_release_or_doi_claim
status: public_ready
last_reviewed: 2026-06-16
---

# GeneLab Benchmark Release Archive Checklist
# SpaceBio-Bench Release Archive Checklist

## Current Status

This checklist separates what is ready for a paper-supporting archive from what
must wait until the final manuscript, tag, and DOI are available.
This checklist separates repository materials that are ready now from final
metadata actions that should happen near DOI or archive deposition.

## Ready Now

- Root `README.md` presents the project, canonical result doc, transparency
card pack, portfolio brief, and HF dataset link.
- `CITATION.cff` exists and is machine-readable citation metadata using the
current public repository identity.
- `.zenodo.json` exists as candidate Zenodo metadata using the current public
- Root `README.md` presents the project, canonical result document, public
documentation map, and HF dataset link.
- `CITATION.cff` is machine-readable citation metadata using the current public
repository identity.
- `LICENSE` is present and declares MIT for code.
- `.zenodo.json` provides archive metadata using the current public repository
identity.
- `LICENSE` declares MIT for code.
- `docs/hf_dataset_card.md` is synchronized with the public HF card surface.
- SpaceBio-Bench system, evaluation, readiness, claim, and transparency cards
are `public_review_ready`.
- `docs/RELEASE_ARCHIVE_CARD.md` documents archive scope and exclusions.
- `docs/RELEASE_ARCHIVE_MANIFEST.md` documents archive contents and final tag
- SpaceBio-Bench public cards are marked `public_ready`.
- `docs/RELEASE_ARCHIVE_CARD.md` summarizes archive scope.
- `docs/RELEASE_ARCHIVE_MANIFEST.md` lists archive file groups and final tag
procedure.
- CI has passed for the recent public-card merge PRs.
- CI and public release QA pass for the current public docs.

## Needs Final Author Or Manuscript Review
## Final Metadata Review

- Confirm final manuscript author list and affiliations in `CITATION.cff`.
- Confirm final creator metadata in `.zenodo.json`.
- Confirm final paper title and whether the archive title should match exactly.
- Confirm manuscript author list and affiliations in `CITATION.cff`.
- Confirm creator metadata in `.zenodo.json`.
- Confirm final paper title and archive title.
- Confirm final version string and release date.
- Add DOI after Zenodo or the selected archive mints it.
- Add DOI after Zenodo or the selected archive service mints it.
- Add dataset-specific OSDR citations for the manuscript subset.

## Needs Final Release Action
## Final Release Actions

- Create or confirm annotated Git tag `v7.1.2` from the final
public-card/archive-metadata commit.
- Create GitHub release from the tag.
- Confirm Git tag `v7.1.2` or a successor tag from the intended public commit.
- Create or update the GitHub release from the tag.
- Verify Zenodo deposition metadata.
- Download source archive and record SHA-256 checksum.
- Store release DOI, tag, release URL, and checksum in a release-specific
manifest.
- Update README, HF card, and citation metadata with DOI if appropriate.

## Still Blocked For Stronger Claims
## Public QA Commands

- Frozen v9 public bulk payload release.
- DOI/archive-ready v9 metadata-alpha release.
- Complete RO-Crate research-object release.
- Clinical, crew-health, intervention, countermeasure, or Mars-regime claims.
- Foundation-model leaderboard claims without matched adapter/run manifests.
```bash
git diff --check
make release-qa
make hpc-public-qa
```

## Red-Flag Checks To Re-Run
Optional archive hygiene checks:

```bash
git diff --check
git ls-files | rg '(^output/|^outputs/|__pycache__|\\.DS_Store$|\\.log$|\\.tmp$|\\.bak$|~$|\\.zip$|\\.tar$|\\.tar\\.gz$|\\.gz$|\\.pdf$|\\.pptx$|\\.png$|\\.jpg$|\\.jpeg$|\\.gif$)'
rg --glob '!docs/RELEASE_ARCHIVE_CHECKLIST.md' -n '(gh[pousr]_[A-Za-z0-9_]{20,}|sk-[A-Za-z0-9]{20,}|hf_[A-Za-z0-9]{20,}|/Users/jak4013|~/.claude)' README.md docs scripts tests .github
rg --glob '!docs/RELEASE_ARCHIVE_CHECKLIST.md' -n 'status: draft|draft_public_ready|blob/codex|codex/spacebiobench' README.md docs
git ls-files | rg '(^output/|^outputs/|__pycache__|\\.DS_Store$|\\.log$|\\.tmp$|\\.bak$|~$|\\.zip$|\\.tar$|\\.tar\\.gz$|\\.gz$|\\.pdf$|\\.pptx$|\\.jpg$|\\.jpeg$|\\.gif$)'
rg -n '(gh[pousr]_[A-Za-z0-9_]{20,}|sk-[A-Za-z0-9]{20,}|hf_[A-Za-z0-9]{20,})' README.md docs scripts tests .github
```

Expected interpretation:

- Generated or binary artifacts should not appear unless intentionally archived.
- Secret scans should not show literal credentials.
- Local personal paths should appear only in tests that explicitly forbid them.
- Public cards should remain `public_review_ready`.
- Generated or binary artifacts should appear only when intentionally tracked.
- Secret scans are expected to show no literal credentials.
- Public cards should remain `public_ready`.
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