v1.0.0 to v1.0.0

---

name: template-reproducibility-audit

description: |

Deterministic reproducibility audit — fixed seeds, regenerate-from-clean, double-run

diff before Zenodo/arXiv/release. USE WHEN outputs drift between runs, "worked on my

machine", need regenerate-from-clean proof, or pre-release reproducibility check — even

without naming docs/prompts.

metadata:

version: "1.0.0"

last_updated: "2026-05-25"

status: active

data_access_level: verified_only

task_type: open-ended

modes:

- double-run

- release-readiness

related_skills:

- template-manuscript-claim-verification

- template-validation-quality

---

# Reproducibility audit

Complements [manuscript-claim-verification](../manuscript-claim-verification/SKILL.md) (claim truth) by focusing on **stability of artifacts**.

## Natural invoke

- "Prove template_code_project is reproducible before Zenodo"

- "Numbers in the PDF don't match after a clean rebuild"

- "Double-run the pipeline and diff outputs"

## Inputs to confirm

- **Project** — from [`docs/_generated/active_projects.md`](../../_generated/active_projects.md).

## Workflow

1. **Determinism** — fixed RNG seeds, `MPLBACKEND=Agg`; no wall-clock/hostname/path leaks. List nondeterministic sources.

2. **Regenerate from clean** — wipe working outputs, run core pipeline, regenerate manuscript variables. Capture exit status per stage.

3. **Diff** — compare regenerated `output/<name>/` and manuscript variables vs prose assertions. Hand-typed numbers not from generated variables are findings even if equal.

4. **Double-run stability** — regenerate twice with clean tree between; any run-1 vs run-2 diff is hard failure.

5. **Fix** — seed injection, variable-ize hard-typed numbers, remove timestamp leakage. Update `projects/<n>/AGENTS.md` and README.md with regeneration command. Never hand-edit `output/`.

## Deliverables

- Drift table: artifact | committed | regenerated | action.

- Commands + raw output; no invented coverage numbers.

## Verification commands

```bash

uv sync

uv run python projects/<project>/scripts/z_generate_manuscript_variables.py

git stash --include-untracked -- output/<project> 2>/dev/null || true

git status --porcelain output/<project>

uv run python scripts/pipeline/stage_01_test.py --project <project>

uv run python -m infrastructure.validation.cli prerender projects/<project>/manuscript --repo-root .

uv run python -m infrastructure.validation.cli pdf output/<project>/pdf/

uv run python -m infrastructure.validation.cli integrity output/<project>/

```

## When NOT to use

- **Stage fails during regeneration** → [pipeline-debugging](../pipeline-debugging/SKILL.md)

- **Per-sentence claim audit** → [manuscript-claim-verification](../manuscript-claim-verification/SKILL.md)