Finishing a Research Project

The project is done only when the last checklist is green. This skill walks the final mile: rendering, archiving, DOI, submission, and optional grant follow-up.

Announce at start: "Using finishing-a-research-project to close out <slug>."

For unmet items: tell the user which, ask for a short reason per skipped item, write reasons into knowledge/_meta/gate-overrides.log, and mark the project in the log as either status: done (with documented omissions) or status: paused. Hidden partial completion is not closure — explicit justification is. </SOFT-GATE>

Closing Checklist

1. Manuscript renders cleanly — make render in output/<book|article>/ exits 0; PDF/HTML opens without warnings
2. Wiki lint green — python scripts/lint-wiki.py exits 0
3. BibTeX consistent — every citation key in the manuscript exists in references.bib; no unused keys (or unused are intentional)
4. Peer review done — both constructive and adversarial reviewer reports archived under output/<target>/reviews/; all Major issues resolved or explicitly deferred with rationale
5. Hypothesis addressed — pre-registered Hypothesis is explicitly confirmed, refuted, or marked "inconclusive — exploratory" in the manuscript
6. Data reproducibility — output/data-analysis/ has requirements.txt or environment.yml; a README says "run python main.py to reproduce"; seeds are fixed
7. Data archive — raw datasets in input/data/ are licensed; derivatives in output/data-analysis/results/ are documented
8. Synthesis stable — all knowledge/synthesis/*.md referenced by the manuscript have status: stable
9. Log closing entry in knowledge/_meta/log.md:

   - YYYY-MM-DD · finish · <slug> · output=<path>

10. Publication archive (DOI) — offer to deposit on Zenodo (or institution repository); update the log with DOI
11. Decision: submission / follow-up — journal / publisher / conference? grant renewal?
12. If follow-up grant: route to grant-finder
13. If done done: commit everything (git add . && git commit -m "finish: <slug>"), tag the release

Process Flow

digraph finishing {
    "Render check" [shape=box];
    "Wiki lint" [shape=box];
    "BibTeX consistency" [shape=box];
    "Peer review archived" [shape=box];
    "Hypothesis resolution" [shape=box];
    "Data reproducibility" [shape=box];
    "Data archive" [shape=box];
    "Synthesis stable" [shape=box];
    "Any check fail?" [shape=diamond];
    "Fix and re-check" [shape=box];
    "Log closing entry" [shape=box];
    "DOI / archive publication" [shape=box];
    "Follow-up grant?" [shape=diamond];
    "Invoke grant-finder" [shape=box];
    "Commit & tag" [shape=box];
    "Done" [shape=doublecircle];

    "Render check" -> "Wiki lint";
    "Wiki lint" -> "BibTeX consistency";
    "BibTeX consistency" -> "Peer review archived";
    "Peer review archived" -> "Hypothesis resolution";
    "Hypothesis resolution" -> "Data reproducibility";
    "Data reproducibility" -> "Data archive";
    "Data archive" -> "Synthesis stable";
    "Synthesis stable" -> "Any check fail?";
    "Any check fail?" -> "Fix and re-check" [label="yes"];
    "Fix and re-check" -> "Render check";
    "Any check fail?" -> "Log closing entry" [label="no"];
    "Log closing entry" -> "DOI / archive publication";
    "DOI / archive publication" -> "Follow-up grant?";
    "Follow-up grant?" -> "Invoke grant-finder" [label="yes"];
    "Follow-up grant?" -> "Commit & tag" [label="no"];
    "Invoke grant-finder" -> "Commit & tag";
    "Commit & tag" -> "Done";
}

Reproducibility Statement Template

Drop into the manuscript (or supplementary material):

## Reproducibility

All analyses are reproducible from `output/data-analysis/`:

- **Code:** <files>
- **Data inputs:** `input/data/<files>` (licenses: <list>)
- **Environment:** Python <version>, see `output/data-analysis/requirements.txt`
- **Entry point:** `python output/data-analysis/main.py`
- **Random seed:** <fixed value>
- **Repository:** <git URL or Zenodo DOI>

Archive / DOI

Options:

• Zenodo — free, accepts datasets + code + manuscripts; gives DOI immediately
• Institutional repository — university OA repository
• GitHub Release + Zenodo-GitHub integration — tag release, Zenodo creates DOI automatically

Pick one with user, update log entry with DOI.

Submission Handoff

If submission targeted:

• Identify journal / publisher / conference CfP
• Check author guidelines — may require format conversion (quarto render --to docx / --to latex, or pandoc)
• Produce cover letter draft
• Confirm corresponding author + ORCID
• Do NOT submit on the user's behalf — prepare and hand over

Red Flags

Key Principles

• The checklist is the closure — not "feels done"
• Hypothesis honesty — what was predicted, what came out, what's open
• Reproducibility — manuscript AND data AND code AND environment
• DOI before submission — an archived version exists before the publisher process
• Log entry is the final artefact — the project is closed in the log